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  • 201.
    Blom, Henning
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    Jerve, Anna
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    Qu, Qinming
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    Chen, Dong Lei
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    Märss, Tiiu
    Tallinn University of Technology.
    Dupret, Vincent
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    Sanchez, Sophie
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    Ahlberg, Per
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    The affinity of Lophosteus  and the evolution of osteichthyan characters2011Conference paper (Refereed)
  • 202.
    Bodare, Sofia
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Functional Genomics. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Stocks, Michael
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Yang, J-C
    Taiwan Forestry Research Institute.
    Lascoux, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Origin and demographic history of the endemic Taiwan spruce (Picea morrisonicola)2013In: Ecology and Evolution, ISSN 2045-7758, E-ISSN 2045-7758, Vol. 3, no 10, p. 3320-3333Article in journal (Refereed)
    Abstract [en]

    Taiwan spruce (Picea morrisonicola) is a vulnerable conifer species endemic to the island of Taiwan. A warming climate and competition from subtropical tree species has limited the range of Taiwan spruce to the higher altitudes of the island. Using seeds sampled from an area in the central mountain range of Taiwan, 15 nuclear loci were sequenced in order to measure genetic variation and to assess the long-term genetic stability of the species. Genetic diversity is low and comparable to other spruce species with limited ranges such as Picea breweriana, Picea chihuahuana, and Picea schrenkiana. Importantly, analysis using approximate Bayesian computation (ABC) provides evidence for a drastic decline in the effective population size approximately 0.3–0.5 million years ago (mya). We used simulations to show that this is unlikely to be a false-positive result due to the limited sample used here. To investigate the phylogenetic origin of Taiwan spruce, additional sequencing was performed in the Chinese spruce Picea wilsonii and combined with previously published data for three other mainland China species, Picea purpurea, Picea likiangensis, and P. schrenkiana. Analysis of population structure revealed that P. morrisonicola clusters most closely with P. wilsonii, and coalescent analyses using the program MIMAR dated the split to 4–8 mya, coincidental to the formation of Taiwan. Considering the population decrease that occurred after the split, however, led to a much more recent origin.

  • 203.
    Bogusz, Marcin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Evolutionary Approaches to Sequence Alignment2018Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Molecular evolutionary biology allows us to look into the past by analyzing sequences of amino acids or nucleotides. These analyses can be very complex, often involving advanced statistical models of sequence evolution to construct phylogenetic trees, study the patterns of natural selection and perform a number of other evolutionary studies. In many cases, these evolutionary studies require a prerequisite of multiple sequence alignment (MSA) - a technique, which aims at grouping the characters that share a common ancestor, or homology, into columns. This information regarding shared homology is needed by statistical models to describe the process of substitutions in order to perform evolutionary inference. Sequence alignment, however, is difficult and MSAs often contain whole regions of wrongly aligned characters, which impact downstream analyses.

    In this thesis I use two broad groups of approaches to avoid errors in the alignment. The first group addresses the analysis methods without sequence alignment by explicitly modelling the processes of substitutions, and insertions and deletions (indels) between pairs of sequences using pair hidden Markov models. I describe an accurate tree inference method that uses a neighbor joining clustering approach to construct a tree from a matrix of model-based evolutionary distances.

    Next, I develop a pairwise method of modelling how natural selection acts on substitutions and indels. I further show the relationship between the constraints acting on these two evolutionary forces to show that natural selection affects them in a similar way.

    The second group of approaches deals with errors in existing alignments. I use a statistical model-based approach to evaluate the quality of multiple sequence alignments.

    First, I provide a graph-based tool for removing wrongly aligned pairs of residues by splitting them apart. This approach tends to produce better results when compared to standard column-based filtering.

    Second, I provide a way to compare MSAs using a probabilistic framework. I propose new ways of scoring of sequence alignments and show that popular methods produce similar results.

    The overall purpose of this work is to facilitate more accurate evolutionary analyses by addressing the problem of sequence alignment in a statistically rigorous manner.

    List of papers
    1. Phylogenetic Tree Estimation With and Without Alignment: New Distance Methods and Benchmarking
    Open this publication in new window or tab >>Phylogenetic Tree Estimation With and Without Alignment: New Distance Methods and Benchmarking
    2017 (English)In: Systematic Biology, ISSN 1063-5157, E-ISSN 1076-836X, Vol. 66, no 2, p. 218-231Article in journal (Refereed) Published
    Abstract [en]

    Phylogenetic tree inference is a critical component of many systematic and evolutionary studies. The majority of these studies are based on the two-step process of multiple sequence alignment followed by tree inference, despite persistent evidence that the alignment step can lead to biased results. Here we present a two-part study that first presents PaHMM-Tree, a novel neighbor joining-based method that estimates pairwise distances without assuming a single alignment. We then use simulations to benchmark its performance against a wide-range of other phylogenetic tree inference methods, including the first comparison of alignment-free distance-based methods against more conventional tree estimation methods. Our new method for calculating pairwise distances based on statistical alignment provides distance estimates that are as accurate as those obtained using standard methods based on the true alignment. Pairwise distance estimates based on the two-step process tend to be substantially less accurate. This improved performance carries through to tree inference, where PaHMM-Tree provides more accurate tree estimates than all of the pairwise distance methods assessed. For close to moderately divergent sequence data we find that the two-step methods using statistical inference, where information from all sequences is included in the estimation procedure, tend to perform better than PaHMM-Tree, particularly full statistical alignment, which simultaneously estimates both the tree and the alignment. For deep divergences we find the alignment step becomes so prone to error that our distance-based PaHMM-Tree outperforms all other methods of tree inference. Finally, we find that the accuracy of alignment-free methods tends to decline faster than standard two-step methods in the presence of alignment uncertainty, and identify no conditions where alignment-free methods are equal to or more accurate than standard phylogenetic methods even in the presence of substantial alignment error.

    Keywords
    Alignment-free, distance-based phylogenetics, pair Hidden Markov Models, phylogenetic inference, statistical alignment
    National Category
    Evolutionary Biology
    Identifiers
    urn:nbn:se:uu:diva-316533 (URN)10.1093/sysbio/syw074 (DOI)000397703800009 ()27633353 (PubMedID)
    Available from: 2017-03-02 Created: 2017-03-02 Last updated: 2018-09-19Bibliographically approved
    2. Selection acting on indels and substitutions in protein coding sequences
    Open this publication in new window or tab >>Selection acting on indels and substitutions in protein coding sequences
    (English)Manuscript (preprint) (Other academic)
    Abstract [en]

    Patterns of selection acting on an expressed protein act to maintain or adapt its structure and function over time. The most widely used method for studying these selective forces is the ratio of synonymous to non-synonymous substitutions (dN/dS), which helps distinguish between neutral, purifying (negative), and adaptive (positive) selection. This ratio, however, examines only amino acid substitutions and ignores other evolutionary forces like small-scale insertions and deletions (indels) that may affect protein evolution. There are currently no statistically robust methods for studying the forces acting on protein sequence indels, with the few ad hoc solutions highly dependent on the gap patterns produced by alignment and filtering steps. This study broadens our understanding of how selection acts on indels in proteins by explicitly examining the relationship between selective constraint acting on substitutions and indels. We present a probabilistic model that jointly estimates dN/dS and the indel rate through statistical alignment, which removes biases in both parameter estimates caused by alignment error. We apply our method to thousands of genes from human-mouse and human-chicken pairwise analyses, revealing that the indel rate and selection (dN/dS) tends to be related, demonstrating that purifying selection acting in proteins tends to affect non-synonymous mutations and indels in a quantifiably similar way. We also investigate how the selective forces acting on substitutions and indels vary along genes. Our findings and methods offer the opportunity to begin studying the interaction between substitutions and indels, and the first widely applicable tools for understanding how they impact protein evolution.

    Keywords
    Natural Selection, Protein Evolution, Pair hidden Markov models
    National Category
    Evolutionary Biology
    Identifiers
    urn:nbn:se:uu:diva-360838 (URN)
    Available from: 2018-09-18 Created: 2018-09-18 Last updated: 2018-09-19
    3. A graph-based approach for improving the homologyinference in multiple sequence alignments
    Open this publication in new window or tab >>A graph-based approach for improving the homologyinference in multiple sequence alignments
    (English)Manuscript (preprint) (Other academic)
    Abstract [en]

    Multiple sequence alignment (MSA) is ubiquitous in evolutionary studies and other areas ofbioinformatics. In nearly all cases MSAs are taken to be a known and xed quantity on which toperform downstream analysis despite extensive evidence that MSA accuracy and uncertainty aectsresults. Mistakes in the MSA are known to cause a wide range of problems for downstream evolutionaryinference, ranging from false inference of positive selection to long branch attraction artifacts. The mostpopular approach to dealing with this problem is to remove (lter) specic columns in the MSA thatare thought to be prone to error, either through proximity to gaps or through some scoring function.Although popular, this approach has had mixed success and several studies have even suggested thatltering might be detrimental to phylogenetic studies. Here we present a dierent approach to dealingwith MSA accuracy and uncertainty through a graph-based approach implemented in the freely availablesoftware Divvier. The aim of Divvier is to identify clusters of characters that have strong statisticalevidence of shared homology, based on the output of a pair hidden Markov model. These clusters canthen be used to either lter characters out the MSA, through a process we call partial ltering, or torepresent each of the clusters in a new column, through a process we call divvying up. We validateour approach through its performance on real and simulated benchmarks, nding Divvier substantiallyoutperforms all other ltering software for treating MSAs by retaining more true positive homology callsand removing more false positive homology calls. We also nd that Divvier, in contrast to other lteringtools, can alleviate long branch attraction artifacts induced by MSA and reduces the variation in treeestimates caused by MSA uncertainty.

    National Category
    Evolutionary Biology
    Identifiers
    urn:nbn:se:uu:diva-360839 (URN)
    Available from: 2018-09-18 Created: 2018-09-18 Last updated: 2018-09-21
    4. Examining sequence alignments using a model-based approach
    Open this publication in new window or tab >>Examining sequence alignments using a model-based approach
    (English)Manuscript (preprint) (Other academic)
    Abstract [en]

    Multiple sequence alignment (MSA) is a commonly performed procedure required for a number of evolutionary and comparative analyses. The common two-step process of sequence alignment followed by statistical phylogenetic inference depends on MSA quality. MSA is computationally difficult and as a result in many cases sequence alignments contain regions of spurious homologies. These errors in the alignment affect downstream results, so choosing an accurate MSA is critical.  Researchers often face the problem of choosing an aligner out of many multiple sequence alignment methods (MSAMs). This choice is often based on the results of benchmarks with various popular methods claiming high accuracy scores. These methods compete to obtain the highest scores in the commonly used sum-of-pairs benchmark—which accounts for a fraction of the true homologies recovered—ignoring the fraction of introduced false positive homologies. Furthermore, these benchmarks do not account for the fact that some homologies are more difficult to recover than the others. We take a probabilistic model-based approach to examine the quality of pairwise homologies returned by four popular MSAMs. We use pair-hidden Markov models to break down alignment columns into pairs and obtain distributions of pairwise posterior scores for these aligners. Basing our results on a structural benchmark and a simulation study, we find that MSAMs appear to return a sample from a confidence set defined by high posterior probabilities. Furthermore, we find that the reference alignment contains low pairwise posterior portions of pairwise homologies which cannot be expected to be recovered by any MSAM. Finally, we look at several possible test statistics, with and without the need for reference alignments, and ultimately suggest using positive predictive value (PPV) and mean posterior probability for MSA evaluation.

    Keywords
    Sequence alignment, alignment accuracy, alignment uncertainty, pair hidden Markov models
    National Category
    Evolutionary Biology
    Identifiers
    urn:nbn:se:uu:diva-360840 (URN)
    Available from: 2018-09-19 Created: 2018-09-19 Last updated: 2018-09-21
  • 204.
    Bogusz, Marcin
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Ali, Raja Hashim
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Whelan, Simon
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Examining sequence alignments using a model-based approachManuscript (preprint) (Other academic)
    Abstract [en]

    Multiple sequence alignment (MSA) is a commonly performed procedure required for a number of evolutionary and comparative analyses. The common two-step process of sequence alignment followed by statistical phylogenetic inference depends on MSA quality. MSA is computationally difficult and as a result in many cases sequence alignments contain regions of spurious homologies. These errors in the alignment affect downstream results, so choosing an accurate MSA is critical.  Researchers often face the problem of choosing an aligner out of many multiple sequence alignment methods (MSAMs). This choice is often based on the results of benchmarks with various popular methods claiming high accuracy scores. These methods compete to obtain the highest scores in the commonly used sum-of-pairs benchmark—which accounts for a fraction of the true homologies recovered—ignoring the fraction of introduced false positive homologies. Furthermore, these benchmarks do not account for the fact that some homologies are more difficult to recover than the others. We take a probabilistic model-based approach to examine the quality of pairwise homologies returned by four popular MSAMs. We use pair-hidden Markov models to break down alignment columns into pairs and obtain distributions of pairwise posterior scores for these aligners. Basing our results on a structural benchmark and a simulation study, we find that MSAMs appear to return a sample from a confidence set defined by high posterior probabilities. Furthermore, we find that the reference alignment contains low pairwise posterior portions of pairwise homologies which cannot be expected to be recovered by any MSAM. Finally, we look at several possible test statistics, with and without the need for reference alignments, and ultimately suggest using positive predictive value (PPV) and mean posterior probability for MSA evaluation.

  • 205.
    Bogusz, Marcin
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Whelan, Simon
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Phylogenetic Tree Estimation With and Without Alignment: New Distance Methods and Benchmarking2017In: Systematic Biology, ISSN 1063-5157, E-ISSN 1076-836X, Vol. 66, no 2, p. 218-231Article in journal (Refereed)
    Abstract [en]

    Phylogenetic tree inference is a critical component of many systematic and evolutionary studies. The majority of these studies are based on the two-step process of multiple sequence alignment followed by tree inference, despite persistent evidence that the alignment step can lead to biased results. Here we present a two-part study that first presents PaHMM-Tree, a novel neighbor joining-based method that estimates pairwise distances without assuming a single alignment. We then use simulations to benchmark its performance against a wide-range of other phylogenetic tree inference methods, including the first comparison of alignment-free distance-based methods against more conventional tree estimation methods. Our new method for calculating pairwise distances based on statistical alignment provides distance estimates that are as accurate as those obtained using standard methods based on the true alignment. Pairwise distance estimates based on the two-step process tend to be substantially less accurate. This improved performance carries through to tree inference, where PaHMM-Tree provides more accurate tree estimates than all of the pairwise distance methods assessed. For close to moderately divergent sequence data we find that the two-step methods using statistical inference, where information from all sequences is included in the estimation procedure, tend to perform better than PaHMM-Tree, particularly full statistical alignment, which simultaneously estimates both the tree and the alignment. For deep divergences we find the alignment step becomes so prone to error that our distance-based PaHMM-Tree outperforms all other methods of tree inference. Finally, we find that the accuracy of alignment-free methods tends to decline faster than standard two-step methods in the presence of alignment uncertainty, and identify no conditions where alignment-free methods are equal to or more accurate than standard phylogenetic methods even in the presence of substantial alignment error.

  • 206.
    Bogusz, Marcin
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Whelan, Simon
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Selection acting on indels and substitutions in protein coding sequencesManuscript (preprint) (Other academic)
    Abstract [en]

    Patterns of selection acting on an expressed protein act to maintain or adapt its structure and function over time. The most widely used method for studying these selective forces is the ratio of synonymous to non-synonymous substitutions (dN/dS), which helps distinguish between neutral, purifying (negative), and adaptive (positive) selection. This ratio, however, examines only amino acid substitutions and ignores other evolutionary forces like small-scale insertions and deletions (indels) that may affect protein evolution. There are currently no statistically robust methods for studying the forces acting on protein sequence indels, with the few ad hoc solutions highly dependent on the gap patterns produced by alignment and filtering steps. This study broadens our understanding of how selection acts on indels in proteins by explicitly examining the relationship between selective constraint acting on substitutions and indels. We present a probabilistic model that jointly estimates dN/dS and the indel rate through statistical alignment, which removes biases in both parameter estimates caused by alignment error. We apply our method to thousands of genes from human-mouse and human-chicken pairwise analyses, revealing that the indel rate and selection (dN/dS) tends to be related, demonstrating that purifying selection acting in proteins tends to affect non-synonymous mutations and indels in a quantifiably similar way. We also investigate how the selective forces acting on substitutions and indels vary along genes. Our findings and methods offer the opportunity to begin studying the interaction between substitutions and indels, and the first widely applicable tools for understanding how they impact protein evolution.

  • 207.
    Bohlin, Jon
    et al.
    Norwegian Inst Publ Hlth, Dept Infect Dis Epidemiol & Modelling, Div Infect Control & Environm Hlth, Lovisenberggata 8, N-0456 Oslo, Norway;Norwegian Inst Publ Hlth, Ctr Fertil & Hlth, POB 222 Skoyen, N-0213 Oslo, Norway;Norwegian Univ Life Sci, Fac Vet Sci, Prod Anim Clin Sci, Ullevalsveien 72, N-0454 Oslo, Norway.
    Pettersson, John
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology. Univ Sydney, Sch Life & Environm Sci, Charles Perkins Ctr, Marie Bashir Inst Infect Dis & Biosecur, Sydney, NSW 2006, Australia;Univ Sydney, Sydney Med Sch, Sydney, NSW 2006, Australia;Publ Hlth Agcy Sweden, Nobels Vg 18, SE-17182 Solna, Sweden.
    Evolution of Genomic Base Composition: From Single Cell Microbes to Multicellular Animals2019In: COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL, ISSN 2001-0370, Vol. 17, p. 362-370Article, review/survey (Refereed)
    Abstract [en]

    Whole genome sequencing (WGS) of thousands of microbial genomes has provided considerable insight into evolutionary mechanisms in the microbial world. While substantially fewer eukaryotic genomes are available for analyses the number is rapidly increasing. This mini-review summarizes broadly evolutionary dynamics of base composition in the different domains of life from the perspective of prokaryotes. Common and different evolutionary mechanisms influencing genomic base composition in eukaryotes and prokaryotes are discussed. The conclusion from the data currently available suggests that while there are similarities there are also striking differences in how genomic base composition has evolved within prokaryotes and eukaryotes. For instance, homologous recombination appears to increase GC content locally in eukaryotes due to a non-selective process termed GC-biased gene conversion (gBGC). For prokaryotes on the other hand, increase in genomic GC content seems to be driven by the environment and selection. We find that similar phenomena observed for some organisms in each respective domain may be caused by very different mechanisms: while gBGC and recombination rates appear to explain the negative correlation between GC3 (GC content based on the third codon nudeotides) and genome size in some eukaryotes uptake of AT rich DNA sequences is the main reason for a similar negative correlation observed in prokaryotes. We provide further examples that indicate that base composition in prokaryotes and eukaryotes have evolved under very different constraints. 

  • 208.
    Bolivar, Paulina
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Gueguen, Laurent
    Univ Claude Bernard Lyon 1, CNRS, UMR 5558, Lab Biol & Biometrie Evolut, Lyon, France.
    Duret, Laurent
    Univ Claude Bernard Lyon 1, CNRS, UMR 5558, Lab Biol & Biometrie Evolut, Lyon, France.
    Ellegren, Hans
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Mugal, Carina
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    GC-biased gene conversion conceals the prediction of the nearly neutral theory in avian genomes2019In: Genome Biology, ISSN 1465-6906, E-ISSN 1474-760X, Vol. 20, article id 5Article in journal (Refereed)
    Abstract [en]

    Background: The nearly neutral theory of molecular evolution predicts that the efficacy of natural selection increases with the effective population size. This prediction has been verified by independent observations in diverse taxa, which show that life-history traits are strongly correlated with measures of the efficacy of selection, such as the d(N)/d(S) ratio. Surprisingly, avian taxa are an exception to this theory because correlations between life-history traits and d(N)/d(S) are apparently absent. Here we explore the role of GC-biased gene conversion on estimates of substitution rates as a potential driver of these unexpected observations.

    Results: We analyze the relationship between d(N)/d(S) estimated from alignments of 47 avian genomes and several proxies for effective population size. To distinguish the impact of GC-biased gene conversion from selection, we use an approach that accounts for non-stationary base composition and estimate d(N)/d(S) separately for changes affected or unaffected by GC-biased gene conversion. This analysis shows that the impact of GC-biased gene conversion on substitution rates can explain the lack of correlations between life-history traits and d(N)/d(S). Strong correlations between life-history traits and d(N)/d(S) are recovered after accounting for GC-biased gene conversion. The correlations are robust to variation in base composition and genomic location.

    Conclusions: Our study shows that gene sequence evolution across a wide range of avian lineages meets the prediction of the nearly neutral theory,the efficacy of selection increases with effective population size. Moreover, our study illustrates that accounting for GC-biased gene conversion is important to correctly estimate the strength of selection.

  • 209.
    Bolivar, Paulina
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Mugal, Carina
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Sebastiano, Matteo Rossi
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology. Ludwig Maximilians Univ Munchen, Fac Biol, Dept Biol 2, Planegg Martinsried, Germany.
    Nater, Alexander
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology. Univ Konstanz, Dept Biol, Chair Zool & Evolutionary Biol, Constance, Germany.
    Wang, Mi
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Dutoit, Ludovic
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Ellegren, Hans
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Biased Inference of Selection Due to GC-Biased Gene Conversion and the Rate of Protein Evolution in Flycatchers When Accounting for It2018In: Molecular biology and evolution, ISSN 0737-4038, E-ISSN 1537-1719, Vol. 35, no 10, p. 2475-2486Article in journal (Refereed)
    Abstract [en]

    The rate of recombination impacts on rates of protein evolution for at least two reasons: it affects the efficacy of selection due to linkage and influences sequence evolution through the process of GC-biased gene conversion (gBGC). We studied how recombination, via gBGC, affects inferences of selection in gene sequences using comparative genomic and population genomic data from the collared flycatcher (Ficedula albicollis). We separately analyzed different mutation categories ("strong"-to-"weak" "weak-to-strong," and GC-conservative changes) and found that gBGC impacts on the distribution of fitness effects of new mutations, and leads to that the rate of adaptive evolution and the proportion of adaptive mutations among nonsynonymous substitutions are underestimated by 22-33%. It also biases inferences of demographic history based on the site frequency spectrum. In light of this impact, we suggest that inferences of selection (and demography) in lineages with pronounced gBGC should be based on GC-conservative changes only. Doing so, we estimate that 10% of nonsynonymous mutations are effectively neutral and that 27% of nonsynonymous substitutions have been fixed by positive selection in the flycatcher lineage. We also find that gene expression level, sex-bias in expression, and the number of protein-protein interactions, but not Hill-Robertson interference (HRI), are strong determinants of selective constraint and rate of adaptation of collared flycatcher genes. This study therefore illustrates the importance of disentangling the effects of different evolutionary forces and genetic factors in interpretation of sequence data, and from that infer the role of natural selection in DNA sequence evolution.

  • 210.
    Bolund, Elisabeth
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Hayward, Adam
    Pettay, Jenni E.
    Lummaa, Virpi
    Effects of the demographic transition on the genetic variances and covariances of human life-history traits2015In: Evolution, ISSN 0014-3820, E-ISSN 1558-5646, Vol. 69, no 3, p. 747-755Article in journal (Refereed)
    Abstract [en]

    The recent demographic transitions to lower mortality and fertility rates in most human societies have led to changes and even quick reversals in phenotypic selection pressures. This can only result in evolutionary change if the affected traits are heritable, but changes in environmental conditions may also lead to subsequent changes in the genetic variance and covariance (the G matrix) of traits. It currently remains unclear if there have been concomitant changes in the G matrix of life-history traits following the demographic transition. Using 300 years of genealogical data from Finland, we found that four key life-history traits were heritable both before and after the demographic transition. The estimated heritabilities allow a quantifiable genetic response to selection during both time periods, thus facilitating continued evolutionary change. Further, the G matrices remained largely stable but revealed a trend for an increased additive genetic variance and thus evolutionary potential of the population after the transition. Our results demonstrate the validity of predictions of evolutionary change in human populations even after the recent dramatic environmental change, and facilitate predictions of how our biology interacts with changing environments, with implications for global public health and demography.

  • 211.
    Bolund, Elisabeth
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Lummaa, V.
    Univ Turku, Dept Biol, Turku, Finland..
    The effects of resource availability and the demographic transition on the genetic correlation between number of children and grandchildren in humans2017In: Heredity, ISSN 0018-067X, E-ISSN 1365-2540, Vol. 118, no 2, p. 186-192Article in journal (Refereed)
    Abstract [en]

    Studies of evolutionary change require an estimate of fitness, and lifetime reproductive success is widely used for this purpose. However, many species face a trade-off between the number and quality of offspring and in such cases number of grandoffspring may better represent the genetic contribution to future generations. Here, we apply quantitative genetic methods to a genealogical data set on humans from Finland to address how the genetic correlation between number of children and grandchildren is influenced by the severity of the trade-off between offspring quality and quantity, as estimated by different levels of resource access among individuals in the population. Further, we compare the genetic correlation before and after the demographic transition to low mortality and fertility rates. The genetic correlation was consistently high (0.79-0.92) with the strongest correlations occurring in individuals with higher access to resources and before the demographic transition, and a tendency for lower correlations in resource poor individuals and after the transition. These results indicate that number of grandoffspring is a slightly better predictor of long-term genetic fitness than number of offspring in a human population across a range of environmental conditions, and more generally, that patterns of resource availability need to be taken into account when estimating genetic covariances with fitness.

  • 212.
    Bolívar, Paulina
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Rates and patterns of molecular evolution in avian genomes2019Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Evolution is the change in inherited characteristics of a population through subsequent generations. The interplay of several evolutionary mechanisms determines the rate at which this change occurs. In short, genetic variation is generated though mutation, and the fate of these mutations in a population is determined mainly by the combined effect of genetic drift, natural selection and recombination. Elucidating the relative impact of these mechanisms is complex; making it a long-standing question in evolutionary biology. In this thesis, I focus on disentangling the relative roles of these evolutionary mechanisms and genetic factors in determining rates and patterns of evolution at the molecular level, by studying variation in the DNA sequence of multiple avian species, and in particular the collared flycatcher (Ficedula albicollis). Specifically, I aim to further our understanding regarding the impact of recombination rate on genome evolution, through its interaction with the efficacy of selection and through the process of GC-biased gene conversion (gBGC), which has been poorly characterized in birds. I demonstrate that gBGC has a pervasive effect on the genome of the collared flycatcher and other avian species, as it increases the substitution rate and affects interpretations of the impact of natural selection and adaptation. Interestingly, its effect is even stronger in neutrally evolving sites compared to sites evolving under selection. After accounting for gBGC, I disentangle the true impact of natural selection versus non-adaptive processes in determining rates of molecular evolution in the collared flycatcher genome, shedding light on the process of adaptation. Finally, I demonstrate the significant role of recombination through its impact on linked selection, along with mutation rate differences, in determining relative levels of genetic diversity and their relationship to the fast-Z effect across the avian phylogeny. This thesis urges future studies to account for the effect of recombination before interpreting patterns of selection in sequence evolution.

    List of papers
    1. Recombination Rate Variation Modulates Gene Sequence Evolution Mainly via GC-Biased Gene Conversion, Not Hill-Robertson Interference, in an Avian System
    Open this publication in new window or tab >>Recombination Rate Variation Modulates Gene Sequence Evolution Mainly via GC-Biased Gene Conversion, Not Hill-Robertson Interference, in an Avian System
    2016 (English)In: Molecular biology and evolution, ISSN 0737-4038, E-ISSN 1537-1719, Vol. 33, no 1, p. 216-227Article in journal (Refereed) Published
    Abstract [en]

    The ratio of nonsynonymous to synonymous substitution rates (ω) is often used to measure the strength of natural selection. However, ω may be influenced by linkage among different targets of selection, that is, Hill-Robertson interference (HRI), which reduces the efficacy of selection. Recombination modulates the extent of HRI but may also affect ω by means of GC-biased gene conversion (gBGC), a process leading to a preferential fixation of G:C ("strong," S) over A:T ("weak," W) alleles. As HRI and gBGC can have opposing effects on ω, it is essential to understand their relative impact to make proper inferences of ω. We used a model that separately estimated S-to-S, S-to-W, W-to-S, and W-to-W substitution rates in 8,423 avian genes in the Ficedula flycatcher lineage. We found that the W-to-S substitution rate was positively, and the S-to-W rate negatively, correlated with recombination rate, in accordance with gBGC but not predicted by HRI. The W-to-S rate further showed the strongest impact on both dN and dS. However, since the effects were stronger at 4-fold than at 0-fold degenerated sites, likely because the GC content of these sites is farther away from its equilibrium, ω slightly decreases with increasing recombination rate, which could falsely be interpreted as a consequence of HRI. We corroborated this hypothesis analytically and demonstrate that under particular conditions, ω can decrease with increasing recombination rate. Analyses of the site-frequency spectrum showed that W-to-S mutations were skewed toward high, and S-to-W mutations toward low, frequencies, consistent with a prevalent gBGC-driven fixation bias.

    Keywords
    gBGC; Hill-Robertson interference; d(N)/d(S); divergence; diversity; rate of molecular evolution
    National Category
    Evolutionary Biology Biochemistry and Molecular Biology
    Identifiers
    urn:nbn:se:uu:diva-280275 (URN)10.1093/molbev/msv214 (DOI)000369992600017 ()26446902 (PubMedID)
    Funder
    Swedish Research Council, 2010-5650Swedish Research Council, 2013-8271EU, European Research Council, AdG 249976Knut and Alice Wallenberg Foundation
    Available from: 2016-03-09 Created: 2016-03-09 Last updated: 2019-04-09Bibliographically approved
    2. Biased Inference of Selection Due to GC-Biased Gene Conversion and the Rate of Protein Evolution in Flycatchers When Accounting for It
    Open this publication in new window or tab >>Biased Inference of Selection Due to GC-Biased Gene Conversion and the Rate of Protein Evolution in Flycatchers When Accounting for It
    Show others...
    2018 (English)In: Molecular biology and evolution, ISSN 0737-4038, E-ISSN 1537-1719, Vol. 35, no 10, p. 2475-2486Article in journal (Refereed) Published
    Abstract [en]

    The rate of recombination impacts on rates of protein evolution for at least two reasons: it affects the efficacy of selection due to linkage and influences sequence evolution through the process of GC-biased gene conversion (gBGC). We studied how recombination, via gBGC, affects inferences of selection in gene sequences using comparative genomic and population genomic data from the collared flycatcher (Ficedula albicollis). We separately analyzed different mutation categories ("strong"-to-"weak" "weak-to-strong," and GC-conservative changes) and found that gBGC impacts on the distribution of fitness effects of new mutations, and leads to that the rate of adaptive evolution and the proportion of adaptive mutations among nonsynonymous substitutions are underestimated by 22-33%. It also biases inferences of demographic history based on the site frequency spectrum. In light of this impact, we suggest that inferences of selection (and demography) in lineages with pronounced gBGC should be based on GC-conservative changes only. Doing so, we estimate that 10% of nonsynonymous mutations are effectively neutral and that 27% of nonsynonymous substitutions have been fixed by positive selection in the flycatcher lineage. We also find that gene expression level, sex-bias in expression, and the number of protein-protein interactions, but not Hill-Robertson interference (HRI), are strong determinants of selective constraint and rate of adaptation of collared flycatcher genes. This study therefore illustrates the importance of disentangling the effects of different evolutionary forces and genetic factors in interpretation of sequence data, and from that infer the role of natural selection in DNA sequence evolution.

    Place, publisher, year, edition, pages
    OXFORD UNIV PRESS, 2018
    Keywords
    d(N)/d(S), distribution of fitness effects, GC-biased gene conversion, gene expression, Hill-Robertson interference
    National Category
    Evolutionary Biology Genetics
    Identifiers
    urn:nbn:se:uu:diva-372675 (URN)10.1093/molbev/msy149 (DOI)000452566800011 ()30085180 (PubMedID)
    Available from: 2019-01-09 Created: 2019-01-09 Last updated: 2019-04-09Bibliographically approved
    3. GC-biased gene conversion conceals the prediction of the nearly neutral theory in avian genomes
    Open this publication in new window or tab >>GC-biased gene conversion conceals the prediction of the nearly neutral theory in avian genomes
    Show others...
    2019 (English)In: Genome Biology, ISSN 1465-6906, E-ISSN 1474-760X, Vol. 20, article id 5Article in journal (Refereed) Published
    Abstract [en]

    Background: The nearly neutral theory of molecular evolution predicts that the efficacy of natural selection increases with the effective population size. This prediction has been verified by independent observations in diverse taxa, which show that life-history traits are strongly correlated with measures of the efficacy of selection, such as the d(N)/d(S) ratio. Surprisingly, avian taxa are an exception to this theory because correlations between life-history traits and d(N)/d(S) are apparently absent. Here we explore the role of GC-biased gene conversion on estimates of substitution rates as a potential driver of these unexpected observations.

    Results: We analyze the relationship between d(N)/d(S) estimated from alignments of 47 avian genomes and several proxies for effective population size. To distinguish the impact of GC-biased gene conversion from selection, we use an approach that accounts for non-stationary base composition and estimate d(N)/d(S) separately for changes affected or unaffected by GC-biased gene conversion. This analysis shows that the impact of GC-biased gene conversion on substitution rates can explain the lack of correlations between life-history traits and d(N)/d(S). Strong correlations between life-history traits and d(N)/d(S) are recovered after accounting for GC-biased gene conversion. The correlations are robust to variation in base composition and genomic location.

    Conclusions: Our study shows that gene sequence evolution across a wide range of avian lineages meets the prediction of the nearly neutral theory,the efficacy of selection increases with effective population size. Moreover, our study illustrates that accounting for GC-biased gene conversion is important to correctly estimate the strength of selection.

    Place, publisher, year, edition, pages
    BMC, 2019
    Keywords
    Nearly neutral theory, Life-history traits, d(N), d(S), GC-biased gene conversion, Base composition, Avian genomes
    National Category
    Evolutionary Biology
    Identifiers
    urn:nbn:se:uu:diva-375222 (URN)10.1186/s13059-018-1613-z (DOI)000455139400002 ()30616647 (PubMedID)
    Funder
    Swedish Research Council, 2013-8271Knut and Alice Wallenberg Foundation, 2014/0044
    Available from: 2019-01-30 Created: 2019-01-30 Last updated: 2019-04-09Bibliographically approved
    4. Variation in the Z Chromosome to Autosomes Ratio of Genetic Diversity across Birds and its Relationship to the Fast-Z effect
    Open this publication in new window or tab >>Variation in the Z Chromosome to Autosomes Ratio of Genetic Diversity across Birds and its Relationship to the Fast-Z effect
    (English)Manuscript (preprint) (Other academic)
    Keywords
    sex chromosomes, genetic diversity, Fast-Z evolution, genetic drift, selection
    National Category
    Evolutionary Biology
    Research subject
    Biology with specialization in Evolutionary Genetics
    Identifiers
    urn:nbn:se:uu:diva-380263 (URN)
    Available from: 2019-03-25 Created: 2019-03-25 Last updated: 2019-04-09
  • 213.
    Bolívar, Paulina
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Mugal, Carina F
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Nater, Alexander
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Ellegren, Hans
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Recombination Rate Variation Modulates Gene Sequence Evolution Mainly via GC-Biased Gene Conversion, Not Hill-Robertson Interference, in an Avian System2016In: Molecular biology and evolution, ISSN 0737-4038, E-ISSN 1537-1719, Vol. 33, no 1, p. 216-227Article in journal (Refereed)
    Abstract [en]

    The ratio of nonsynonymous to synonymous substitution rates (ω) is often used to measure the strength of natural selection. However, ω may be influenced by linkage among different targets of selection, that is, Hill-Robertson interference (HRI), which reduces the efficacy of selection. Recombination modulates the extent of HRI but may also affect ω by means of GC-biased gene conversion (gBGC), a process leading to a preferential fixation of G:C ("strong," S) over A:T ("weak," W) alleles. As HRI and gBGC can have opposing effects on ω, it is essential to understand their relative impact to make proper inferences of ω. We used a model that separately estimated S-to-S, S-to-W, W-to-S, and W-to-W substitution rates in 8,423 avian genes in the Ficedula flycatcher lineage. We found that the W-to-S substitution rate was positively, and the S-to-W rate negatively, correlated with recombination rate, in accordance with gBGC but not predicted by HRI. The W-to-S rate further showed the strongest impact on both dN and dS. However, since the effects were stronger at 4-fold than at 0-fold degenerated sites, likely because the GC content of these sites is farther away from its equilibrium, ω slightly decreases with increasing recombination rate, which could falsely be interpreted as a consequence of HRI. We corroborated this hypothesis analytically and demonstrate that under particular conditions, ω can decrease with increasing recombination rate. Analyses of the site-frequency spectrum showed that W-to-S mutations were skewed toward high, and S-to-W mutations toward low, frequencies, consistent with a prevalent gBGC-driven fixation bias.

  • 214.
    Borinder, Niclas H.
    et al.
    Uppsala University, Music and Museums, Museum of Evolution.
    Poropat, Stephen F.
    Australian Age Dinosaurs Nat Hist Museum, Winton, Qld 4735, Australia.;Monash Univ, Wellington Rd, Clayton, Vic 3800, Australia..
    Kear, Benjamin P.
    Uppsala University, Music and Museums, Museum of Evolution.
    Reassessment of the earliest documented stegosaurian fossils from Asia2016In: Cretaceous research (Print), ISSN 0195-6671, E-ISSN 1095-998X, Vol. 68, p. 61-69Article in journal (Refereed)
    Abstract [en]

    In 1929, the famous Swedish palaeontologist Carl Wiman documented the first unequivocal stegosaurian dinosaur fossils from Asia. His material comprised an isolated dermal spine, together with a dorsal vertebra that was briefly described but never figured. Since then these remains have languished in obscurity, being noted in some stegosaur review articles but often ignored altogether. However, recent auditing of the Museum of Evolution palaeontological collection at Uppsala University in Sweden has led to the rediscovery of Wiman's original specimens, as well as two additional previously unrecognised stegosaurian dorsal vertebrae. All of these bones derive from the Lower Cretaceous (Berriasian-Valanginian) Mengyin Formation of Shandong Province in eastern China, and are morphologically compatible with the stratigraphically proximal stegosaurian taxon Wuerhosaurus from the Valanginian-Albian Tugulu Group in the Xinjiang Uyghur Autonomous Region of Western China. Wirnan's seminal stegosaurian fossils thus expand current palaeobiogeographical distributions, and contribute to the otherwise enigmatic record of Early Cretaceous stegosaurian occurrences.

  • 215.
    Boughman, Janette W.
    et al.
    Michigan State Univ, Dept Integrat Biol, E Lansing, MI 48824 USA..
    Svanbäck, Richard
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Synergistic selection between ecological niche and mate preference primes diversification2017In: Evolution, ISSN 0014-3820, E-ISSN 1558-5646, Vol. 71, no 1, p. 6-22Article in journal (Refereed)
    Abstract [en]

    The ecological niche and mate preferences have independently been shown to be important for the process of speciation. Here, we articulate a novel mechanism by which ecological niche use and mate preference can be linked to promote speciation. The degree to which individual niches are narrow and clustered affects the strength of divergent natural selection and population splitting. Similarly, the degree to which individual mate preferences are narrow and clustered affects the strength of divergent sexual selection and assortative mating between diverging forms. This novel perspective is inspired by the literature on ecological niches; it also explores mate preferences and how they may contribute to speciation. Unlike much comparative work, we do not search for evolutionary patterns using proxies for adaptation and sexual selection, but rather we elucidate how ideas from niche theory relate to mate preference, and how this relationship can foster speciation. Recognizing that individual and population niches are conceptually and ecologically linked to individual and population mate preference functions will significantly increase our understanding of rapid evolutionary diversification in nature. It has potential to help solve the difficult challenge of testing the role of sexual selection in the speciation process. We also identify ecological factors that are likely to affect individual niche and individual mate preference in synergistic ways and as a consequence to promote speciation. The ecological niche an individual occupies can directly affect its mate preference. Clusters of individuals with narrow, differentiated niches are likely to have narrow, differentiated mate preference functions. Our approach integrates ecological and sexual selection research to further our understanding of diversification processes. Such integration may be necessary for progress because these processes seem inextricably linked in the natural world.

  • 216. Bowman, John L
    et al.
    Kohchi, Takayuki
    Yamato, Katsuyuki T
    Jenkins, Jerry
    Shu, Shengqiang
    Ishizaki, Kimitsune
    Yamaoka, Shohei
    Nishihama, Ryuichi
    Nakamura, Yasukazu
    Berger, Frédéric
    Adam, Catherine
    Aki, Shiori Sugamata
    Althoff, Felix
    Araki, Takashi
    Arteaga-Vazquez, Mario A
    Balasubrmanian, Sureshkumar
    Barry, Kerrie
    Bauer, Diane
    Boehm, Christian R
    Briginshaw, Liam
    Caballero-Perez, Juan
    Catarino, Bruno
    Chen, Feng
    Chiyoda, Shota
    Chovatia, Mansi
    Davies, Kevin M
    Delmans, Mihails
    Demura, Taku
    Dierschke, Tom
    Dolan, Liam
    Dorantes-Acosta, Ana E
    Eklund, D. Magnus
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution. Monash Univ, Sch Biol Sci, Melbourne, Vic 3800, Australia.
    Florent, Stevie N
    Flores-Sandoval, Eduardo
    Fujiyama, Asao
    Fukuzawa, Hideya
    Galik, Bence
    Grimanelli, Daniel
    Grimwood, Jane
    Grossniklaus, Ueli
    Hamada, Takahiro
    Haseloff, Jim
    Hetherington, Alexander J
    Higo, Asuka
    Hirakawa, Yuki
    Hundley, Hope N
    Ikeda, Yoko
    Inoue, Keisuke
    Inoue, Shin-Ichiro
    Ishida, Sakiko
    Jia, Qidong
    Kakita, Mitsuru
    Kanazawa, Takehiko
    Kawai, Yosuke
    Kawashima, Tomokazu
    Kennedy, Megan
    Kinose, Keita
    Kinoshita, Toshinori
    Kohara, Yuji
    Koide, Eri
    Komatsu, Kenji
    Kopischke, Sarah
    Kubo, Minoru
    Kyozuka, Junko
    Lagercrantz, Ulf
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Lin, Shih-Shun
    Lindquist, Erika
    Lipzen, Anna M
    Lu, Chia-Wei
    De Luna, Efraín
    Martienssen, Robert A
    Minamino, Naoki
    Mizutani, Masaharu
    Mizutani, Miya
    Mochizuki, Nobuyoshi
    Monte, Isabel
    Mosher, Rebecca
    Nagasaki, Hideki
    Nakagami, Hirofumi
    Naramoto, Satoshi
    Nishitani, Kazuhiko
    Ohtani, Misato
    Okamoto, Takashi
    Okumura, Masaki
    Phillips, Jeremy
    Pollak, Bernardo
    Reinders, Anke
    Rövekamp, Moritz
    Sano, Ryosuke
    Sawa, Shinichiro
    Schmid, Marc W
    Shirakawa, Makoto
    Solano, Roberto
    Spunde, Alexander
    Suetsugu, Noriyuki
    Sugano, Sumio
    Sugiyama, Akifumi
    Sun, Rui
    Suzuki, Yutaka
    Takenaka, Mizuki
    Takezawa, Daisuke
    Tomogane, Hirokazu
    Tsuzuki, Masayuki
    Ueda, Takashi
    Umeda, Masaaki
    Ward, John M
    Watanabe, Yuichiro
    Yazaki, Kazufumi
    Yokoyama, Ryusuke
    Yoshitake, Yoshihiro
    Yotsui, Izumi
    Zachgo, Sabine
    Schmutz, Jeremy
    Insights into Land Plant Evolution Garnered from the Marchantia polymorpha Genome2017In: Cell, ISSN 0092-8674, E-ISSN 1097-4172, Vol. 171, no 2, p. 287-304.15Article in journal (Refereed)
    Abstract [en]

    The evolution of land flora transformed the terrestrial environment. Land plants evolved from an ancestral charophycean alga from which they inherited developmental, biochemical, and cell biological attributes. Additional biochemical and physiological adaptations to land, and a life cycle with an alternation between multicellular haploid and diploid generations that facilitated efficient dispersal of desiccation tolerant spores, evolved in the ancestral land plant. We analyzed the genome of the liverwort Marchantia polymorpha, a member of a basal land plant lineage. Relative to charophycean algae, land plant genomes are characterized by genes encoding novel biochemical pathways, new phytohormone signaling pathways (notably auxin), expanded repertoires of signaling pathways, and increased diversity in some transcription factor families. Compared with other sequenced land plants, M. polymorpha exhibits low genetic redundancy in most regulatory pathways, with this portion of its genome resembling that predicted for the ancestral land plant. PAPERCLIP.

  • 217.
    Brandis, Gerrit
    et al.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
    Hughes, Diarmaid
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
    A large chromosomal inversion causes the formation of an unstable tufA/B hybrid operonManuscript (preprint) (Other academic)
  • 218.
    Brandis, Gerrit
    et al.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
    Hughes, Diarmaid
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
    Co-evolution protects the tuf genes from inactivation by mobile genetic elementsManuscript (preprint) (Other academic)
  • 219.
    Brandis, Gerrit
    et al.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
    Hughes, Diarmaid
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
    The Selective Advantage of Synonymous Codon Usage Bias in Salmonella2016In: PLoS Genetics, ISSN 1553-7390, E-ISSN 1553-7404, Vol. 12, no 3, article id e1005926Article in journal (Refereed)
    Abstract [en]

    The genetic code in mRNA is redundant, with 61 sense codons translated into 20 different amino acids. Individual amino acids are encoded by up to six different codons but within codon families some are used more frequently than others. This phenomenon is referred to as synonymous codon usage bias. The genomes of free-living unicellular organisms such as bacteria have an extreme codon usage bias and the degree of bias differs between genes within the same genome. The strong positive correlation between codon usage bias and gene expression levels in many microorganisms is attributed to selection for translational efficiency. However, this putative selective advantage has never been measured in bacteria and theoretical estimates vary widely. By systematically exchanging optimal codons for synonymous codons in the tuf genes we quantified the selective advantage of biased codon usage in highly expressed genes to be in the range 0.2–4.2 x 10−4 per codon per generation. These data quantify for the first time the potential for selection on synonymous codon choice to drive genome-wide sequence evolution in bacteria, and in particular to optimize the sequences of highly expressed genes. This quantification may have predictive applications in the design of synthetic genes and for heterologous gene expression in biotechnology.

  • 220. Brattås, Per Ludvik
    et al.
    Jönsson, Marie E.
    Fasching, Liana
    Nelander Wahlestedt, Jenny
    Shahsavani, Mansoureh
    Falk, Ronny
    Falk, Anna
    Jern, Patric
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Parmar, Malin
    Jakobsson, Johan
    TRIM28 Controls a Gene Regulatory Network Based on Endogenous Retroviruses in Human Neural Progenitor Cells2017In: Cell reports, ISSN 2211-1247, E-ISSN 2211-1247, Vol. 18, no 1, p. 1-11Article in journal (Refereed)
    Abstract [en]

    Endogenous retroviruses (ERVs), which make up 8% of the human genome, have been proposed to participate in the control of gene regulatory networks. In this study, we find a region- and developmental stage-specific expression pattern of ERVs in the developing human brain, which is linked to a transcriptional network based on ERVs. We demonstrate that almost 10,000, primarily primate-specific, ERVs act as docking platforms for the co-repressor protein TRIM28 in human neural progenitor cells, which results in the establishment of local heterochromatin. Thereby, TRIM28 represses ERVs and consequently regulates the expression of neighboring genes. These results uncover a gene regulatory network based on ERVs that participates in control of gene expression of protein-coding transcripts important for brain development.

  • 221. Brawand, David
    et al.
    Wagner, Catherine E.
    Li, Yang I.
    Malinsky, Milan
    Keller, Irene
    Fan, Shaohua
    Simakov, Oleg
    Ng, Alvin Y.
    Lim, Zhi Wei
    Bezault, Etienne
    Turner-Maier, Jason
    Johnson, Jeremy
    Alcazar, Rosa
    Noh, Hyun Ji
    Russell, Pamela
    Aken, Bronwen
    Alfoeldi, Jessica
    Amemiya, Chris
    Azzouzi, Naoual
    Baroiller, Jean-Francois
    Barloy-Hubler, Frederique
    Berlin, Aaron
    Bloomquist, Ryan
    Carleton, Karen L.
    Conte, Matthew A.
    D'Cotta, Helena
    Eshel, Orly
    Gaffney, Leslie
    Galibert, Francis
    Gante, Hugo F.
    Gnerre, Sante
    Greuter, Lucie
    Guyon, Richard
    Haddad, Natalie S.
    Haerty, Wilfried
    Harris, Rayna M.
    Hofmann, Hans A.
    Hourlier, Thibaut
    Hulata, Gideon
    Jaffe, David B.
    Lara, Marcia
    Lee, Alison P.
    MacCallum, Iain
    Mwaiko, Salome
    Nikaido, Masato
    Nishihara, Hidenori
    Ozouf-Costaz, Catherine
    Penman, David J.
    Przybylski, Dariusz
    Rakotomanga, Michaelle
    Renn, Suzy C. P.
    Ribeiro, Filipe J.
    Ron, Micha
    Salzburger, Walter
    Sanchez-Pulido, Luis
    Santos, M. Emilia
    Searle, Steve
    Sharpe, Ted
    Swofford, Ross
    Tan, Frederick J.
    Williams, Louise
    Young, Sarah
    Yin, Shuangye
    Okada, Norihiro
    Kocher, Thomas D.
    Miska, Eric A.
    Lander, Eric S.
    Venkatesh, Byrappa
    Fernald, Russell D.
    Meyer, Axel
    Ponting, Chris P.
    Streelman, J. Todd
    Lindblad-Toh, Kerstin
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Seehausen, Ole
    Di Palma, Federica
    The genomic substrate for adaptive radiation in African cichlid fish2014In: Nature, ISSN 0028-0836, E-ISSN 1476-4687, Vol. 513, no 7518, p. 375-381Article in journal (Refereed)
    Abstract [en]

    Cichlid fishes are famous for large, diverse and replicated adaptive radiations in the Great Lakes of East Africa. To understand themolecular mechanisms underlying cichlid phenotypic diversity, we sequenced the genomes and transcriptomes of five lineages of African cichlids: the Nile tilapia (Oreochromis niloticus), an ancestral lineage with low diversity; and four members of the East African lineage: Neolamprologus brichardi/pulcher (older radiation, Lake Tanganyika), Metriaclima zebra (recent radiation, Lake Malawi), Pundamilia nyererei (very recent radiation, Lake Victoria), and Astatotilapia burtoni (riverine species around Lake Tanganyika). We found an excess of gene duplications in the East African lineage compared to tilapia and other teleosts, an abundance of non-coding element divergence, accelerated coding sequence evolution, expression divergence associated with transposable element insertions, and regulation by novel microRNAs. In addition, we analysed sequence data from sixty individuals representing six closely related species from Lake Victoria, and show genome-wide diversifying selection on coding and regulatory variants, some of which were recruited from ancient polymorphisms. We conclude that a number of molecular mechanisms shaped East African cichlid genomes, and that amassing of standing variation during periods of relaxed purifying selection may have been important in facilitating subsequent evolutionary diversification.

  • 222.
    Brechlin, Birte Hildegard Elisabeth
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Bridges for the wolverine (Gulo gulo): Spatial and non-spatial population genetic analysis in STRUCTURE and BAPS and implications for decision makers2015Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    The conservation of large predators is among the most challenging tasks facing conservation biologists and the protection of the wolverine (Gulo gulo) is no exception. Studying and monitoring these vastly roaming carnivores is only possible due to the collective effort from the Norwegian Nature and Swedish Environmental protection agencies and the group for Monitoring of Large Carnivores at Uppsala University. Wolverines are as so many large predators beloved from the ones and hatefully persecuted from the others. After facing a dramatic bottleneck in the 1970s, the wolverines have been given protective status in Norway and Sweden and could increase their numbers again until licensed hunting was allowed in 1993. Today legal and illegal hunting as well as other anthropogenic factors work against that trend. To observe population trends genetic monitoring of the wolverine has been pursued over a number of years. Data has been collected in Norway and Sweden from sampling of tissue, hair and faeces. This study explores SNP data from tissue samples in the statistical programs R and STRUCTURE for analysing multi-locus genotype data to investigate population structure and the program BAPS for spatial genetic clustering. All analyses agreed on the clustering of the wolverine population into two distinct populations. In Scandinavia there are, besides the Sarek area in northern Sweden, very little truly wild and undisturbed territories left. Human impact plays a well-known, but little studied role in mammal population analyses. Conclusively, the spatial clustering results are projected onto maps displaying anthropogenic development. It shows that the fast growing human population and consecutive urban development around Trondheim in Norway might cause a major obstacle to gene flow between the populations south and north of that belt of urbanization. In order to allow gene flow and thus saving the genetic variety and long-term survival of the Scandinavian wolverine population, the investigation and construction of Wildlife crossings or incorporating other measures to include wildlife into our ever changing landscapes is called into focus for decision makers in city and road development.

  • 223.
    Breed, Martin F.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Ottewell, K. M.
    Gardner, M. G.
    Marklund, Maria H. K.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Dormontt, E. E.
    Lowe, A. J.
    Mating patterns and pollinator mobility are critical traits in forest fragmentation genetics2015In: Heredity, ISSN 0018-067X, E-ISSN 1365-2540, Vol. 115, no 2, p. 108-114Article in journal (Refereed)
    Abstract [en]

    Most woody plants are animal-pollinated, but the global problem of habitat fragmentation is changing the pollination dynamics. Consequently, the genetic diversity and fitness of the progeny of animal-pollinated woody plants sired in fragmented landscapes tend to decline due to shifts in plant-mating patterns (for example, reduced outcrossing rate, pollen diversity). However, the magnitude of this mating-pattern shift should theoretically be a function of pollinator mobility. We first test this hypothesis by exploring the mating patterns of three ecologically divergent eucalypts sampled across a habitat fragmentation gradient in southern Australia. We demonstrate increased selfing and decreased pollen diversity with increased fragmentation for two small-insect-pollinated eucalypts, but no such relationship for the mobile-bird-pollinated eucalypt. In a meta-analysis, we then show that fragmentation generally does increase selfing rates and decrease pollen diversity, and that more mobile pollinators tended to dampen these mating-pattern shifts. Together, our findings support the premise that variation in pollinator form contributes to the diversity of mating-pattern responses to habitat fragmentation.

  • 224.
    Breed, Martin F.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Ottewell, K. M.
    Gardner, M. G.
    Marklund, Maria H. K.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Stead, M. G.
    Harris, J. B. C.
    Lowe, A. J.
    Mating system and early viability resistance to habitat fragmentation in a bird-pollinated eucalypt2015In: Heredity, ISSN 0018-067X, E-ISSN 1365-2540, Vol. 115, no 2, p. 100-107Article in journal (Refereed)
    Abstract [en]

    Habitat fragmentation has been shown to disrupt ecosystem processes such as plant-pollinator mutualisms. Consequently, mating patterns in remnant tree populations are expected to shift towards increased inbreeding and reduced pollen diversity, with fitness consequences for future generations. However, mating patterns and phenotypic assessments of open-pollinated progeny have rarely been combined in a single study. Here, we collected seeds from 37 Eucalyptus incrassata trees from contrasting stand densities following recent clearance in a single South Australian population (intact woodland = 12.6 trees ha(-1); isolated pasture = 1.7 trees ha(-1); population area = 10 km(2)). 649 progeny from these trees were genotyped at eight microsatellite loci. We estimated genetic diversity, spatial genetic structure, indirect contemporary pollen flow and mating patterns for adults older than the clearance events and open-pollinated progeny sired post-clearance. A proxy of early stage progeny viability was assessed in a common garden experiment. Density had no impact on mating patterns, adult and progeny genetic diversity or progeny growth, but was associated with increased mean pollen dispersal. Weak spatial genetic structure among adults suggests high historical gene flow. We observed preliminary evidence for inbreeding depression related to stress caused by fungal infection, but which was not associated with density. Higher observed heterozygosities in adults compared with progeny may relate to weak selection on progeny and lifetime-accumulated mortality of inbred adults. E. incrassata appears to be resistant to the negative mating pattern and fitness changes expected within fragmented landscapes. This pattern is likely explained by strong outcrossing and regular long-distance pollen flow.

  • 225.
    Breed, Martin F.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Stead, Michael G.
    Australian Centre for Evolutionary Biology and Biodiversity (ACEBB) and School of Earth and Environmental Sciences, University of Adelaide.
    Ottewell, Kym M.
    Australian Centre for Evolutionary Biology and Biodiversity (ACEBB) and School of Earth and Environmental Sciences, University of Adelaide.
    Gardner, Michael G.
    Australian Centre for Evolutionary Biology and Biodiversity (ACEBB) and School of Earth and Environmental Sciences, University of Adelaide.
    Lowe, Andrew J.
    Australian Centre for Evolutionary Biology and Biodiversity (ACEBB) and School of Earth and Environmental Sciences, University of Adelaide.
    Which provenance and where?: Seed sourcing strategies for revegetation in a changing environment2013In: Conservation Genetics, ISSN 1566-0621, E-ISSN 1572-9737, Vol. 14, no 1, p. 1-10Article, review/survey (Refereed)
    Abstract [en]

    Revegetation is one practical application of science that should ideally aim to combine ecology with evolution to maximise biodiversity and ecosystem outcomes. The strict use of locally sourced seed in revegetation programs is widespread and is based on the expectation that populations are locally adapted. This practice does not fully integrate two global drivers of ecosystem change and biodiversity loss: habitat fragmentation and climate change. Here, we suggest amendments to existing strategies combined with a review of alternative seed-sourcing strategies that propose to mitigate against these drivers. We present a provenancing selection guide based on confidence surrounding climate change distribution modelling and data on population genetic and/or environmental differences between populations. Revegetation practices will benefit from greater integration of current scientific developments and establishment of more long-term experiments is key to improving the long-term success. The rapid growth in carbon and biodiversity markets creates a favourable economic climate to achieve these outcomes.

  • 226.
    Breed, Martin
    et al.
    Australian Centre for Evolutionary Biology and Biodiversity (ACEBB) and School of Earth and Environmental Sciences, University of Adelaide.
    Gardner, Michael G.
    Ottewell, Kym M.
    Navarro, Carlos M.
    Lowe, Andrew J.
    Shifts in reproductive assurance strategies and inbreeding costs associated with habitat fragmentation in Central American mahogany2012In: Ecology Letters, ISSN 1461-023X, E-ISSN 1461-0248, Vol. 15, no 5, p. 444-452Article in journal (Refereed)
    Abstract [en]

    The influence of habitat fragmentation on mating patterns and progeny fitness in trees is critical for understanding the long-term impact of contemporary landscape change on the sustainability of biodiversity. We examined the relationship between mating patterns, using microsatellites, and fitness of progeny, in a common garden trial, for the insect-pollinated big-leaf mahogany, Swietenia macrophylla King, sourced from forests and isolated trees in 16 populations across Central America. As expected, isolated trees had disrupted mating patterns and reduced fitness. However, for dry provenances, fitness was negatively related to correlated paternity, while for mesic provenances, fitness was correlated positively with outcrossing rate and negatively with correlated paternity. Poorer performance of mesic provenances is likely because of reduced effective pollen donor density due to poorer environmental suitability and greater disturbance history. Our results demonstrate a differential shift in reproductive assurance and inbreeding costs in mahogany, driven by exploitation history and contemporary landscape context.

  • 227.
    Breed, Martin
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Marklund, Maria H. K.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Ottewell, Kym M.
    Gardner, Michael G.
    Harris, J. Berton C.
    Lowe, Andrew J.
    Pollen diversity matters: revealing the neglected effect of pollen diversity on fitness in fragmented landscapes2012In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 21, no 24, p. 5955-5968Article in journal (Refereed)
    Abstract [en]

    Few studies have documented the impacts of habitat fragmentation on plant mating patterns together with fitness. Yet, these processes require urgent attention to better understand the impact of contemporary landscape change on biodiversity and for guiding native plant genetic resource management. We examined these relationships using the predominantly insect-pollinated Eucalyptus socialis. Progeny were collected from trees located in three increasingly disturbed landscapes in southern Australia and were planted out in common garden experiments. We show that individual mating patterns were increasingly impacted by lower conspecific density caused by habitat fragmentation. We determined that reduced pollen diversity probably has effects over and above those of inbreeding on progeny fitness. This provides an alternative mechanistic explanation for the indirect density dependence often inferred between conspecific density and offspring fitness.

  • 228.
    Bremer, Oskar
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    Silurian vertebrates of Gotland (Sweden) and the Baltic Basin2017Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    During the Silurian, the Swedish island Gotland was positioned close to the equator and covered by a shallow sea called the Baltic Basin. The sedimentary rocks (predominantly carbonates) comprising most of the island today were initially formed in this warm sea, and the relatively complete succession of rocks often contains fossil fragments and scales from early vertebrates, including heterostracans, anaspids, thelodonts, osteostracans, acanthodians, and a stem-osteichthyan. Fossils of early vertebrates become increasingly more common in younger Silurian rocks, but are mostly represented by fragmentary remains and rarer occurrences of articulated jawless vertebrates (agnathans). However, the record of articulated specimens and jawed vertebrates (gnathostomes) are more numerous in rocks of the following Devonian Period. Isolated peaks of agnathan diversity during the Silurian and disarticulated remains of gnathostomes from this period hint at a cryptic evolutionary history. A micropaleontological approach with broader sampling may provide a better understanding of early vertebrate distribution patterns and hopefully give some insights into this history. The objective of this study was to build upon previous sampling on Gotland and to use established frameworks for disarticulated remains with the aim of making comparisons with similar studies performed in the East Baltic. However, difficulties locating the collections from these previous works necessitated a different focus. Undescribed museum collections and newly sampled material enabled some taxonomical revisions and greatly improved the understanding of vertebrate distribution in the youngest part of the Gotland sequence. It also indicated that this interval may represent the early stages of the diversification of gnathostomes that become increasingly dominant toward the end of the Silurian. Furthermore, the description of samples from partly coeval sections in Poland enabled some preliminary comparisons outside of Gotland, and presented a striking example of restricted environmental occurrences for a thelodont taxon. This is encouraging for future sampling and investigations on Gotland. Together with the establishment of a facies-framework comparable to that developed in the East Baltic and correlations to other areas, this may prove fruitful for an increased understanding of early vertebrate distribution and evolution during the Silurian.

    List of papers
    1. An updated stratigraphic and environmental framework for the distribution of Silurian vertebrates on Gotland
    Open this publication in new window or tab >>An updated stratigraphic and environmental framework for the distribution of Silurian vertebrates on Gotland
    2015 (English)In: Estonian journal of earth sciences, ISSN 1736-4728, E-ISSN 1736-7557, Vol. 64, no 1, p. 13-18Article in journal (Refereed) Published
    Keywords
    vertebrate distribution, stratigraphy, facies, Silurian events, Gotland, Sweden
    National Category
    Developmental Biology Earth and Related Environmental Sciences
    Identifiers
    urn:nbn:se:uu:diva-251824 (URN)10.3176/earth.2015.03 (DOI)000351327700004 ()
    Available from: 2015-04-27 Created: 2015-04-24 Last updated: 2017-08-21
    2. End-Wenlock terminal Mulde carbon isotope excursion in Gotland, Sweden: Integration of stratigraphy and taphonomy for correlations across restricted facies and specialized faunas
    Open this publication in new window or tab >>End-Wenlock terminal Mulde carbon isotope excursion in Gotland, Sweden: Integration of stratigraphy and taphonomy for correlations across restricted facies and specialized faunas
    Show others...
    2016 (English)In: Palaeogeography, Palaeoclimatology, Palaeoecology, ISSN 0031-0182, E-ISSN 1872-616X, Vol. 457, p. 304-322Article in journal (Refereed) Published
    National Category
    Earth and Related Environmental Sciences
    Research subject
    Earth Science with specialization in Historical Geology and Palaeontology
    Identifiers
    urn:nbn:se:uu:diva-299498 (URN)10.1016/j.palaeo.2016.06.031 (DOI)000380598800025 ()
    Available from: 2016-07-21 Created: 2016-07-21 Last updated: 2017-08-21
    3. Vertebrate remains and conodont biostratigraphy in the Ludlow Burgsvik Formation of Gotland, Sweden
    Open this publication in new window or tab >>Vertebrate remains and conodont biostratigraphy in the Ludlow Burgsvik Formation of Gotland, Sweden
    (English)Manuscript (preprint) (Other academic)
    National Category
    Earth and Related Environmental Sciences
    Identifiers
    urn:nbn:se:uu:diva-328226 (URN)
    Available from: 2017-08-20 Created: 2017-08-20 Last updated: 2017-08-25
    4. Vertebrate dermal remains and conodont distribution in the upper Silurian Hamra and Sundre formations of Gotland, Sweden
    Open this publication in new window or tab >>Vertebrate dermal remains and conodont distribution in the upper Silurian Hamra and Sundre formations of Gotland, Sweden
    (English)Manuscript (preprint) (Other academic)
    National Category
    Earth and Related Environmental Sciences
    Identifiers
    urn:nbn:se:uu:diva-328227 (URN)
    Available from: 2017-08-20 Created: 2017-08-20 Last updated: 2017-08-21
    5. Vertebrate microremains from the upper Silurian Winnica Formation of the Holy Cross Mountains, Poland
    Open this publication in new window or tab >>Vertebrate microremains from the upper Silurian Winnica Formation of the Holy Cross Mountains, Poland
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    2018 (English)In: Geological Magazine, ISSN 0016-7568, E-ISSN 1469-5081, Vol. 155, no 7, p. 1523-1541Article in journal (Refereed) Published
    Abstract [en]

    Vertebrate microremains from the upper Silurian Winnica Formation in the Holy Cross Mountains, Poland are described from the Winnica and Rzepin sections. Both sites record the uppermost part of the Supianka Member, but represent different depositional environments. The Winnica samples come from a low-energy environment, while the Rzepin sample was taken from a high-energy, oolitic facies. Both sites contain thelodonts Thelodus parvidens, Thelodus trilobatus, an anaspid cf. Liivilepis and a number of acanthodian scales of 'nostolepid', poracanthodid and 'gomphonchid' types. Notable differences between the sites are the addition of the osteostracan Tahulaspis cf. ordinata, the thelodont Paralogania ludlowiensis and acanthodian scales identified as Nostolepis gracilis in the Rzepin section. Placing the vertebrate faunas within the vertebrate biozonation established for the Silurian proved difficult. The suggested late Ludlow age for the Supianka Member based on sequence stratigraphical and chemostratigraphical correlations cannot be definitely confirmed or refuted, but a late Ludfordian age seems the most plausible based on invertebrate and vertebrate faunas. The much lower abundance of poracanthodid acanthodians in the Rzepin sample supports the notion of Poracanthodes porosus Zone as a deep-water equivalent to a number of vertebrate biozones. The presence of P. ludlowiensis only in the oolitic sample confirms a long temporal range, but restricted environmental distribution for this taxon.

    National Category
    Other Earth and Related Environmental Sciences
    Identifiers
    urn:nbn:se:uu:diva-281657 (URN)10.1017/S0016756817000681 (DOI)000443814900008 ()
    Available from: 2016-03-29 Created: 2016-03-29 Last updated: 2018-11-06Bibliographically approved
  • 229.
    Bremer, Oskar
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    Blom, Henning
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    Three-dimensional virtual histology of the osteostracan Dartmuthia revealed by synchrotron radiation microtomography2018Conference paper (Other academic)
  • 230.
    Brink, Kirstin S.
    et al.
    University of Toronto.
    Campione, Nicolas E.
    Uppsala University, Disciplinary Domain of Science and Technology, Earth Sciences, Department of Earth Sciences.
    Hawthorn, Jessica R.
    University of Toronto.
    Amniote faunal revision of the Pictou Group (Permo-Carboniferous), Prince Edward Island, Canada2013In: Comptes rendus. Palevol, ISSN 1631-0683, E-ISSN 1777-571X, Vol. 12, no 7–8, p. 473-485Article in journal (Refereed)
    Abstract [en]

    The amniote faunal assemblages from the Pictou Group (Prince Edward Island, Canada) are re-evaluated for the first time in 50 years. Fossils recovered from formations within this group (Orby Head, Hillsborough River, and Kildare Capes) indicate the presence of a parareptile, representing the first occurrence of a non-synapsid amniote from the PEI redbeds. The amniote taxa from PEI are re-described within the context of current research, providing the basis for an updated faunal list for the vertebrate-bearing formations within the Pictou Group. The presence of a parareptile, diadectid, and possibly two synapsids (caseid and/or varanopid), together with the absence of edaphosaurids and definitive ophiacodontids, suggests similarities with the upland Bromacker and Richards Spur localities of Germany and Oklahoma, respectively. However, more research and new fossil discoveries are needed to confidently resolve the systematics and palaeoecology of amniotes from the Lower Permian of Atlantic Canada.

  • 231.
    Brousseau, Louise
    et al.
    INRA, Domaine St Paul, URFM Ecol Forets Mediterraneennes UR629, Site Agroparc CS,Site Agroparc CS 40509, F-84914 Avignon 9, France.;Natl Res Council IBBR CNR, Div Florence, Inst Biosci & BioResources, Via Madonna Piano 10, I-50019 Sesto Fiorentino, FI, France..
    Postolache, Dragos
    Natl Res Council IBBR CNR, Div Florence, Inst Biosci & BioResources, Via Madonna Piano 10, I-50019 Sesto Fiorentino, FI, France.;Scuola Super Sant Anna, Piazza Martiri Liberta 33, I-56127 Pisa, Italy.;Natl Inst Forest Res & Dev INCDS, Res Stn Simeria, Str Biscaria 1, Simeria 335900, Romania..
    Lascoux, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Drouzas, Andreas D.
    Aristotle Univ Thessaloniki, Sch Biol, GR-54124 Thessaloniki, Greece..
    Källman, Thomas
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
    Leonarduzzi, Cristina
    Natl Res Council IBBR CNR, Div Florence, Inst Biosci & BioResources, Via Madonna Piano 10, I-50019 Sesto Fiorentino, FI, France.;Natl 3 Res Council Corso Calatafimi, Div Palermo, Inst Biosci & BioResources, Natl Res Council IBBR CNR, I-90129 Palermo, PA, Italy..
    Liepelt, Sascha
    Univ Marburg, Fac Biol, Conservat Biol, Karl von Frisch Str, D-35032 Marburg, Germany..
    Piotti, Andrea
    Natl Res Council IBBR CNR, Div Florence, Inst Biosci & BioResources, Via Madonna Piano 10, I-50019 Sesto Fiorentino, FI, France..
    Popescu, Flaviu
    Natl Inst Forest Res & Dev INCDS, Res Stn Simeria, Str Biscaria 1, Simeria 335900, Romania..
    Roschanski, Anna M.
    Univ Marburg, Fac Biol, Conservat Biol, Karl von Frisch Str, D-35032 Marburg, Germany.;Leibniz Inst Plant Genet & Crop Plant Res IPK, Genebank Collect North, Inselstr 9, D-23999 Malchow Poel, Germany..
    Zhelev, Peter
    Univ Forestry, 10 Kl Ohridsky Blvd, Sofia 1797, Bulgaria..
    Fady, Bruno
    INRA, Domaine St Paul, URFM Ecol Forets Mediterraneennes UR629, Site Agroparc CS,Site Agroparc CS 40509, F-84914 Avignon 9, France..
    Vendramin, Giovanni Giuseppe
    Natl Res Council IBBR CNR, Div Florence, Inst Biosci & BioResources, Via Madonna Piano 10, I-50019 Sesto Fiorentino, FI, France..
    Local Adaptation in European Firs Assessed through Extensive Sampling across Altitudinal Gradients in Southern Europe2016In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 11, no 7, article id e0158216Article in journal (Refereed)
    Abstract [en]

    Background Local adaptation is a key driver of phenotypic and genetic divergence at loci responsible for adaptive traits variations in forest tree populations. Its experimental assessment requires rigorous sampling strategies such as those involving population pairs replicated across broad spatial scales. Methods A hierarchical Bayesian model of selection (HBM) that explicitly considers both the replication of the environmental contrast and the hierarchical genetic structure among replicated study sites is introduced. Its power was assessed through simulations and compared to classical 'within-site' approaches (FDIST, BAYESCAN) and a simplified, within-site, version of the model introduced here (SBM). Results HBM demonstrates that hierarchical approaches are very powerful to detect replicated patterns of adaptive divergence with low false-discovery (FDR) and false-non-discovery (FNR) rates compared to the analysis of different sites separately through within-site approaches. The hypothesis of local adaptation to altitude was further addressed by analyzing replicated Abies alba population pairs (low and high elevations) across the species' southern distribution range, where the effects of climatic selection are expected to be the strongest. For comparison, a single population pair from the closely related species A. cephalonica was also analyzed. The hierarchical model did not detect any pattern of adaptive divergence to altitude replicated in the different study sites. Instead, idiosyncratic patterns of local adaptation among sites were detected by within-site approaches. Conclusion Hierarchical approaches may miss idiosyncratic patterns of adaptation among sites, and we strongly recommend the use of both hierarchical (multi-site) and classical (within-site) approaches when addressing the question of adaptation across broad spatial scales.

  • 232.
    Brown, Caleb M.
    et al.
    Tyrrell Museum of Paleontology.
    Campione, Nicolas E.
    Department of Ecology and Evolutionary Biology, University of Toronto, Ontario, Canada.
    Giacomini, Henrique C.
    University of Toronto.
    O'Brien, Lorna J.
    University of Toronto.
    Vavrek, Matthew J.
    Philip J. Currie Dinosaur Museum.
    Evans, David C.
    Royal Ontario Museum.
    Ecological modelling, size distributions and taphonomic size bias in dinosaur faunas: a comment on Codron et al. (2012)2013In: Biology Letters, ISSN 1744-9561, E-ISSN 1744-957X, Vol. 9, no 1, p. 20120582-Article in journal (Refereed)
  • 233.
    Brown, Caleb M.
    et al.
    Tyrrell Museum of Paleontology.
    Evans, David C.
    Royal Museum of Nature.
    Campione, Nicolas E.
    Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Canada.
    O'Brien, Lorna J.
    University of Toronto.
    Eberth, David A.
    Tyrrell Museum of Paleontology.
    Evidence for taphonomic size bias in the Dinosaur Park Formation (Campanian, Alberta), a model Mesozoic terrestrial alluvial‐paralic system2013In: Palaeogeography, Palaeoclimatology, Palaeoecology, ISSN 0031-0182, E-ISSN 1872-616X, Vol. 372, no SI, p. 108-122Article in journal (Refereed)
    Abstract [en]

    A study of the distribution of dinosaurian body masses in the Dinosaur Park Formation (DPF; Campanian; southern Alberta), reveals a prominent negative skew; a pattern distinct from those of modern terrestrial faunas. We find a direct and robust correlation between taxon size (estimated live body mass) and known completeness. There is a clear dichotomy between large and small-bodied taxa at around 60 kg, in which taxa less than 60 kg are significantly less complete (mean completeness = 7.6%) than those with an estimated mass of 60 kg or greater (mean = 78.2%). Along with completeness, there is also a strong association of body size and taphonomic mode, with small taxa known largely from isolated and occasionally associated remains, and large taxa known from articulated skeletons. In addition, there is a significant correlation between taxon body mass and both date of discovery and of description, with taxa < 60 kg taking an average of 65.9 and 75.6 years to discover and describe, respectively, compared to 33.6 and 34.1 years for taxa > 60 kg. The rates of both cumulative discovery and description for large taxa are best described by a logarithmic curve nearing an asymptote, whereas small taxa show either a linear or power increase through time. This suggests that our current knowledge of the large-bodied dinosaur assemblage is reasonably representative of the true biological fauna with few discoveries likely to be made in the future. However, small taxa are greatly underestimated in both their diversity and abundance, with many more potential discoveries to be made. Given that (1) the sedimentary deposits and fossil assemblages in the DPF together represent one of the best studied examples of a Mesozoic alluvial‐paralic (terrestrial) ‘palaeoecosystem,’ and (2) similar patterns have been suggested (but not documented) for other Mesozoic terrestrial ecosystems in the Western Interior of North America, we suggest that this pattern of size bias may typify vertebrate fossil assemblages in terrestrial Mesozoic systems. If so, such biases must be considered before patterns of diversity in dinosaur communities through time can be considered accurate, or used to compare and interpret Mesozoic palaeoecosystems.

  • 234. Brown, Caleb Marshall
    et al.
    VanBuren, Collin S.
    Larson, Derek W.
    Brink, Kirstin S.
    Campione, Nicolas E.
    Uppsala University, Disciplinary Domain of Science and Technology, Earth Sciences, Department of Earth Sciences, Palaeobiology. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    Vavrek, Matthew J.
    Evans, David C.
    Tooth counts through growth in diapsid reptiles: implications for interpreting individual and size-related variation in the fossil record2015In: Journal of Anatomy, ISSN 0021-8782, E-ISSN 1469-7580, Vol. 226, no 4, p. 322-333Article in journal (Refereed)
    Abstract [en]

    Tooth counts are commonly recorded in fossil diapsid reptiles and have been used for taxonomic and phylogenetic purposes under the assumption that differences in the number of teeth are largely explained by interspecific variation. Although phylogeny is almost certainly one of the greatest factors influencing tooth count, the relative role of intraspecific variation is difficult, and often impossible, to test in the fossil record given the sample sizes available to palaeontologists and, as such, is best investigated using extant models. Intraspecific variation (largely manifested as size-related or ontogenetic variation) in tooth counts has been examined in extant squamates (lizards and snakes) but is poorly understood in archosaurs (crocodylians and dinosaurs). Here, we document tooth count variation in two species of extant crocodylians (Alligator mississippiensis and Crocodylus porosus) as well as a large varanid lizard (Varanus komodoensis). We test the hypothesis that variation in tooth count is driven primarily by growth and thus predict significant correlations between tooth count and size, as well as differences in the frequency of deviation from the modal tooth count in the premaxilla, maxilla, and dentary. In addition to tooth counts, we also document tooth allometry in each species and compare these results with tooth count change through growth. Results reveal no correlation of tooth count with size in any element of any species examined here, with the exception of the premaxilla of C.porosus, which shows the loss of one tooth position. Based on the taxa examined here, we reject the hypothesis, as it is evident that variation in tooth count is not always significantly correlated with growth. However, growth trajectories of smaller reptilian taxa show increases in tooth counts and, although current samples are small, suggest potential correlates between tooth count trajectories and adult size. Nevertheless, interspecific variation in growth patterns underscores the importance of considering and understanding growth when constructing taxonomic and phylogenetic characters, in particular for fossil taxa where ontogenetic patterns are difficult to reconstruct.

  • 235. Bruckner, Tim A.
    et al.
    Helle, Samuli
    Bolund, Elisabeth
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Lummaa, Virpi
    Culled males, infant mortality and reproductive success in a pre-industrial Finnish population2015In: Proceedings of the Royal Society of London. Biological Sciences, ISSN 0962-8452, E-ISSN 1471-2954, Vol. 282, no 1799Article in journal (Refereed)
    Abstract [en]

    Theoretical and empirical literature asserts that the sex ratio (i.e. M/F) at birth gauges the strength of selection in utero and cohort quality of males that survive to birth. We report the first individual-level test in humans, using detailed life-history data, of the 'culled cohort' hypothesis that males born to low annual sex ratio cohorts show lower than expected infant mortality and greater than expected lifetime reproductive success. We applied time-series and structural equation methods to a unique multi-generational dataset of a natural fertility population in nineteenth century Finland. We find that, consistent with culled cohorts, a 1 s.d. decline in the annual cohort sex ratio precedes an 8% decrease in the risk of male infant mortality. Males born to lower cohort sex ratios also successfully raised 4% more offspring to reproductive age than did males born to higher cohort sex ratios. The offspring result, however, falls just outside conventional levels of statistical significance. In historical Finland, the cohort sex ratio gauges selection against males in utero and predicts male infant mortality. The reproductive success findings, however, provide weak support for an evolutionarily adaptive explanation of male culling in utero.

  • 236.
    Budd, Graham E.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Earth Sciences, Department of Earth Sciences, Palaeobiology.
    Mann, Richard P.
    Univ Leeds, Sch Math, Dept Stat, Leeds LS2 9JT, W Yorkshire, England;Alan Turing Inst, London NW1 2DB, England.
    Modeling durophagous predation and mortality rates from the fossil record of gastropods2019In: Paleobiology, ISSN 0094-8373, E-ISSN 1938-5331, Vol. 45, no 2, p. 246-264Article in journal (Refereed)
    Abstract [en]

    Gastropods often show signs of unsuccessful attacks by durophagous predators in the form of healed scars in their shells. As such, fossil gastropods can be taken as providing a record of predation through geological time. However, interpreting the number of such scars has proved to be problematic-Would a low number of scars mean a low rate of attack or a high rate of success, for example? Here we develop a model of population dynamics among individuals exposed to predation, including both lethal and nonlethal attacks. Using this model, we calculate the equilibrium distributions of ages and healed scars in the population and among fossilized specimens, based on the assumption that predation is independent of age or scar number. Based on these results, we formally show that the rates of attack and success cannot be disambiguated without further information about population structure. Nevertheless, by making the assumptions that the non-durophagous predatory death rate is both constant and low, we show that it is possible to use relatively small assemblages of gastropods to produce accurate estimates of both attack and success rates, if the overall death rate can be estimated. We consider likely violations of the assumptions in our model and what sort of information would be required to solve this problem in these more general cases. However, it is not easy to extract the relevant information from the fossil record: a variety of important biases are likely to intervene to obscure the data that gastropod assemblages may yield. Nonetheless, the model provides a theoretical framework for interpreting summary data, including for comparison between different assemblages.

  • 237.
    Budd, Graham
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Earth Sciences, Department of Earth Sciences.
    Jensen, Sören
    Univ Extremadura, Fac Ciencias, Area Paleontol, Badajoz 06006, Spain.
    The origin of the animals and a ‘Savannah’ hypothesis for early bilaterian evolution2017In: Biological Reviews, ISSN 1464-7931, E-ISSN 1469-185X, Vol. 92, no 1, p. 446-473Article in journal (Refereed)
    Abstract [en]

    The earliest evolution of the animals remains a taxing biological problem, as all extant clades are highly derived and the fossil record is not usually considered to be helpful. The rise of the bilaterian animals recorded in the fossil record, commonly known as the ‘Cambrian explosion’, is one of the most significant moments in evolutionary history, and was an event that transformed first marine and then terrestrial environments. We review the phylogeny of early animals and other opisthokonts, and the affinities of the earliest large complex fossils, the so-called ‘Ediacaran’ taxa. We conclude, based on a variety of lines of evidence, that their affinities most likely lie in various stem groups to large metazoan groupings; a new grouping, the Apoikozoa, is erected to encompass Metazoa and Choanoflagellata. The earliest reasonable fossil evidence for total-group bilaterians comes from undisputed complex trace fossils that are younger than about 560 Ma, and these diversify greatly as the Ediacaran–Cambrian boundary is crossed a few million years later. It is generally considered that as the bilaterians diversified after this time, their burrowing behaviour destroyed the cyanobacterial mat-dominated substrates that the enigmatic Ediacaran taxa were associated with, the so-called ‘Cambrian substrate revolution’, leading to the loss of almost all Ediacara-aspect diversity in the Cambrian. Why, though, did the energetically expensive and functionally complex burrowing mode of life so typical of later bilaterians arise? Here we propose a much more positive relationship between late-Ediacaran ecologies and the rise of the bilaterians, with the largely static Ediacaran taxa acting as points of concentration of organic matter both above and below the sediment surface. The breaking of the uniformity of organic carbon availability would have signalled a decisive shift away from the essentially static and monotonous earlier Ediacaran world into the dynamic and burrowing world of the Cambrian. The Ediacaran biota thus played an enabling role in bilaterian evolution similar to that proposed for the Savannah environment for human evolution and bipedality. Rather than being obliterated by the rise of the bilaterians, the subtle remnants of Ediacara-style taxa within the Cambrian suggest that they remained significant components of Phanerozoic communities, even though at some point their enabling role for bilaterian evolution was presumably taken over by bilaterians or other metazoans. Bilaterian evolution was thus an essentially benthic event that only later impacted the planktonic environment and the style of organic export to the sea floor.

  • 238.
    Budd, Graham
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Earth Sciences, Department of Earth Sciences, Palaeobiology.
    Mann, Richard P.
    Univ Leeds, Sch Math, Dept Stat, Leeds LS2 9JT, W Yorkshire, England.
    History is written by the victors: The effect of the push of the past on the fossil record2018In: Evolution, ISSN 0014-3820, E-ISSN 1558-5646, Vol. 72, no 11, p. 2276-2291Article in journal (Refereed)
    Abstract [en]

    Survivorship biases can generate remarkable apparent rate heterogeneities through time in otherwise homogeneous birth-death models of phylogenies. They are a potential explanation for many striking patterns seen in the fossil record and molecular phylogenies. One such bias is the "push of the past": clades that survived a substantial length of time are likely to have experienced a high rate of early diversification. This creates the illusion of a secular rate slow-down through time that is, rather, a reversion to the mean. An extra effect increasing early rates of lineage generation is also seen in large clades. These biases are important but relatively neglected influences on many aspects of diversification patterns in the fossil record and elsewhere, such as diversification spikes after mass extinctions and at the origins of clades; they also influence rates of fossilization, changes in rates of phenotypic evolution and even molecular clocks. These inevitable features of surviving and/or large clades should thus not be generalized to the diversification process as a whole without additional study of small and extinct clades, and raise questions about many of the traditional explanations of the patterns seen in the fossil record.

  • 239.
    Bundsen, Andreas
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Artificial selection for large and small relative brain size in guppies (Poecilia reticulata) results in differences in cognitive ability2012Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
    Abstract [en]

    Vertebrate brain size is remarkably variable at all taxonomic levels. Brains of mammals forexample, range from 0.1 gram in small bats (Chiroptera) to about 8-9 kilos in Sperm whales(Physeter macrocephalus). But what does this variation in size really mean? The link between brainsize and cognition is debated due to, for instance the difficulties of comparing cognitive ability indifferent species. A large number of comparative studies continue to provide information aboutcorrelations found both within and between species. The relative size of the brain is an example of apopular measurement that correlates with cognitive ability. But to date, no experimental studieshave yielded any proof causality between relative brain size and cognitive ability. Here I usedguppies selected for either large or small relative brain size to investigate differences in cognitiveperformance of a quantity discrimination task. The results from this experiment provideexperimental evidence that relative brain size is important for cognitive ability, and that a differencein cognitive ability could be obtained already after two generations of selection experiments onrelative brain size in a vertebrate.

  • 240.
    Burki, Fabien
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    A new Lineage of Eukaryotes Illuminates Eraly Mitochondrial Genome Reduction2017In: Current Biology, ISSN 0960-9822, E-ISSN 1879-0445Article in journal (Refereed)
  • 241.
    Burki, Fabien
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Roger, Andrew J.
    Dalhousie Univ, Dept Biochem & Mol Biol, Halifax, NS, Canada;Dalhousie Univ, Ctr Comparat Genom & Evolutionary Bioinformat, Halifax, NS, Canada.
    Brown, Matthew W.
    Mississippi State Univ, Dept Biol Sci, Mississippi State, MS 39762 USA;Mississippi State Univ, Inst Genom Biocomp & Biotechnol, Mississippi State, MS 39762 USA.
    Simpson, Alastair G. B.
    Dalhousie Univ, Ctr Comparat Genom & Evolutionary Bioinformat, Halifax, NS, Canada;Dalhousie Univ, Dept Biol, Halifax, NS, Canada.
    The New Tree of Eukaryotes2020In: Trends in Ecology & Evolution, ISSN 0169-5347, E-ISSN 1872-8383, Vol. 35, no 1, p. 43-55Article, review/survey (Refereed)
    Abstract [en]

    For 15 years, the eukaryote Tree of Life (eToL) has been divided into five to eight major groupings, known as 'supergroups'. However, the tree has been profoundly rearranged during this time. The new eToL results from the widespread application of phylogenomics and numerous discoveries of major lineages of eukaryotes, mostly free-living heterotrophic protists. The evidence that supports the tree has transitioned from a synthesis of molecular phylogenetics and biological characters to purely molecular phylogenetics. Most current supergroups lack defining morphological or cell-biological characteristics, making the supergroup label even more arbitrary than before. Going forward, the combination of traditional culturing with maturing culture-free approaches and phylogenomics should accelerate the process of completing and resolving the eToL at its deepest levels.

  • 242.
    Burri, Reto
    et al.
    Laboratory for Conservation Biology, Department of Ecology and Evolution, Biophore, University of Lausanne, Lausanne, Switzerland, .
    Antoniazza, S
    Siverio, F
    Klein, A
    Roulin, A
    Fumagalli, L
    Isolation and characterization of 21 microsatellite markers in the barn owl (Tyto alba)2008In: Molecular Ecology Resources, ISSN 1755-098X, E-ISSN 1755-0998, Vol. 8, no 5, p. 977-979Article in journal (Refereed)
    Abstract [en]

    We report 21 new polymorphic microsatellite markers in the European barn owl (Tyto alba). The polymorphism of the reported markers was evaluated in a population situated in western Switzerland and in another from Tenerife, Canary Islands. The number of alleles per locus varies between two and 31, and expected heterozygosity per population ranges from 0.16 to 0.95. All loci are in Hardy-Weinberg equilibrium and no linkage disequilibrium was detected. Two loci exhibit a null allele in the Tenerife population.

  • 243.
    Burri, Reto
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Antoniazza, Sylvain
    Univ Lausanne, Biophore, Dept Ecol & Evolut, CH-1015 Lausanne, Switzerland.;Swiss Ornithol Inst, CH-6204 Sempach, Switzerland..
    Gaigher, Arnaud
    Univ Lausanne, Biophore, Dept Ecol & Evolut, Lab Conservat Biol, CH-1015 Lausanne, Switzerland..
    Ducrest, Anne-Lyse
    Univ Lausanne, Biophore, Dept Ecol & Evolut, CH-1015 Lausanne, Switzerland..
    Simon, Celine
    Univ Lausanne, Biophore, Dept Ecol & Evolut, CH-1015 Lausanne, Switzerland..
    Fumagalli, Luca
    Univ Lausanne, Biophore, Dept Ecol & Evolut, Lab Conservat Biol, CH-1015 Lausanne, Switzerland..
    Goudet, Jerome
    Univ Lausanne, Biophore, Dept Ecol & Evolut, CH-1015 Lausanne, Switzerland..
    Roulin, Alexandre
    Univ Lausanne, Biophore, Dept Ecol & Evolut, CH-1015 Lausanne, Switzerland..
    The genetic basis of color-related local adaptation in a ring-like colonization around the Mediterranean2016In: Evolution, ISSN 0014-3820, E-ISSN 1558-5646, Vol. 70, no 1, p. 140-153Article in journal (Refereed)
    Abstract [en]

    Uncovering the genetic basis of phenotypic variation and the population history under which it established is key to understand the trajectories along which local adaptation evolves. Here, we investigated the genetic basis and evolutionary history of a clinal plumage color polymorphism in European barn owls (Tyto alba). Our results suggest that barn owls colonized the Western Palearctic in a ring-like manner around the Mediterranean and meet in secondary contact in Greece. Rufous coloration appears to be linked to a recently evolved nonsynonymous-derived variant of the melanocortin 1 receptor (MC1R) gene, which according to quantitative genetic analyses evolved under local adaptation during or following the colonization of Central Europe. Admixture patterns and linkage disequilibrium between the neutral genetic background and color found exclusively within the secondary contact zone suggest limited introgression at secondary contact. These results from a system reminiscent of ring species provide a striking example of how local adaptation can evolve from derived genetic variation.

  • 244.
    Burri, Reto
    et al.
    Laboratory for Conservation Biology, Department of Ecology and Evolution, Biophore, University of Lausanne, Lausanne, Switzerland .
    Hirzel, Hélène Niculita
    Salamin, Nicolas
    Roulin, Alexandre
    Fumagalli, Luca
    Evolutionary patterns of MHC class II B in owls and their implications for the understanding of avian MHC evolution2008In: Molecular biology and evolution, ISSN 0737-4038, E-ISSN 1537-1719, Vol. 25, no 6, p. 1180-1191Article in journal (Refereed)
    Abstract [en]

    Owing to its special mode of evolution and central role in the adaptive immune system, the major histocompatibility complex (MHC) has become the focus of diverse disciplines such as immunology, evolutionary ecology, and molecular evolution. MHC evolution has been studied extensively in diverse vertebrate lineages over the last few decades, and it has been suggested that birds differ from the established mammalian norm. Mammalian MHC genes evolve independently, and duplication history (i.e., orthology) can usually be traced back within lineages. In birds, this has been observed in only 3 pairs of closely related species. Here we report strong evidence for the persistence of orthology of MHC genes throughout an entire avian order. Phylogenetic reconstructions of MHC class II B genes in 14 species of owls trace back orthology over tens of thousands of years in exon 3. Moreover, exon 2 sequences from several species show closer relationships than sequences within species, resembling transspecies evolution typically observed in mammals. Thus, although previous studies suggested that long-term evolutionary dynamics of the avian MHC was characterized by high rates of concerted evolution, resulting in rapid masking of orthology, our results question the generality of this conclusion. The owl MHC thus opens new perspectives for a more comprehensive understanding of avian MHC evolution.

  • 245.
    Burri, Reto
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Nater, Alexander
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Kawakami, Takeshi
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Mugal, Carina F.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Ólason, Páll I.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution.
    Smeds, Linnea
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Suh, Alexander
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Dutoit, Ludovic
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Bures, Stanislav
    Palacky Univ, Dept Zool, Lab Ornithol, Olomouc 77146, Czech Republic..
    Garamszegi, Laszlo Z.
    CSIC, Dept Evolutionary Ecol, Estn Biol Donana, Seville 41092, Spain..
    Hogner, Silje
    Univ Oslo, Ctr Ecol & Evolutionary Synth, Dept Biosci, N-0316 Oslo, Norway.;Univ Oslo, Nat Hist Museum, N-0318 Oslo, Norway..
    Moreno, Juan
    CSIC, Museo Nacl Ciencias Nat, E-28006 Madrid, Spain..
    Qvarnström, Anna
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Ruzic, Milan
    Bird Protect & Study Soc Serbia, Novi Sad 21000, Serbia..
    Saether, Stein-Are
    Univ Oslo, Ctr Ecol & Evolutionary Synth, Dept Biosci, N-0316 Oslo, Norway.;Norwegian Inst Nat Res NINA, N-7034 Trondheim, Norway..
    Saetre, Glenn-Peter
    Univ Oslo, Ctr Ecol & Evolutionary Synth, Dept Biosci, N-0316 Oslo, Norway..
    Toeroek, Janos
    Eotvos Lorand Univ, Dept Systemat Zool & Ecol, Behav Ecol Grp, H-1117 Budapest, Hungary..
    Ellegren, Hans
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Linked selection and recombination rate variation drive the evolution of the genomic landscape of differentiation across the speciation continuum of Ficedula flycatchers2015In: Genome Research, ISSN 1088-9051, E-ISSN 1549-5469, Vol. 25, no 11, p. 1656-1665Article in journal (Refereed)
    Abstract [en]

    Speciation is a continuous process during which genetic changes gradually accumulate in the genomes of diverging species. Recent studies have documented highly heterogeneous differentiation landscapes, with distinct regions of elevated differentiation ("differentiation islands") widespread across genomes. However, it remains unclear which processes drive the evolution of differentiation islands; how the differentiation landscape evolves as speciation advances; and ultimately, how differentiation islands are related to speciation. Here, we addressed these questions based on population genetic analyses of 200 resequenced genomes from 10 populations of four Ficedula flycatcher sister species. We show that a heterogeneous differentiation landscape starts emerging among populations within species, and differentiation islands evolve recurrently in the very same genomic regions among independent lineages. Contrary to expectations from models that interpret differentiation islands as genomic regions involved in reproductive isolation that are shielded from gene flow, patterns of sequence divergence (d(XY) relative node depth) do not support a major role of gene flow in the evolution of the differentiation landscape in these species. Instead, as predicted by models of linked selection, genome-wide variation in diversity and differentiation can be explained by variation in recombination rate and the density of targets for selection. We thus conclude that the heterogeneous landscape of differentiation in Ficedula flycatchers evolves mainly as the result of background selection and selective sweeps in genomic regions of low recombination. Our results emphasize the necessity of incorporating linked selection as a null model to identify genome regions involved in adaptation and speciation.

  • 246.
    Burri, Reto
    et al.
    Laboratory for Conservation Biology, Department of Ecology and Evolution, Biophore, University of Lausanne, Lausanne, Switzerland.
    Niculita-Hirzel, Hélène
    Roulin, Alexandre
    Fumagalli, Luca
    Isolation and characterization of major histocompatibility complex (MHC) class II B genes in the Barn owl (Aves: Tyto alba)2008In: Immunogenetics, ISSN 0093-7711, E-ISSN 1432-1211, Vol. 60, no 9, p. 543-550Article in journal (Refereed)
    Abstract [en]

    We isolated major histocompatibility complex class II B (MHCIIB) genes in the Barn owl (Tyto alba). A PCR-based approach combined with primer walking on genomic and complementary DNA as well as Southern blot analyses revealed the presence of two MHCIIB genes, both being expressed in spleen, liver, and blood. Characteristic structural features of MHCIIB genes as well as their expression and high non-synonymous substitution rates in the region involved in antigen binding suggest that both genes are functional. MHC organization in the Barn owl is simple compared to passerine species that show multiple duplications, and resembles the minimal essential MHC of chicken.

  • 247.
    Burri, Reto
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Promerová, Marta
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Goebel, J
    Fumagalli, L
    PCR-based isolation of multigene families: Lessons from the avian MHC class IIB.2014In: Molecular Ecology Resources, ISSN 1755-098X, E-ISSN 1755-0998, Vol. 14, no 4, p. 778-788Article in journal (Refereed)
    Abstract [en]

    The amount of sequence data available today highly facilitates the access to genes from many gene families. Primers amplifying the desired genes over a range of species are readily obtained by aligning conserved gene regions, and laborious gene isolation procedures can often be replaced by quicker PCR-based approaches. However, in the case of multigene families, PCR-based approaches bear the often ignored risk of incomplete isolation of family members. This problem is most prominent in gene families with highly variable and thus unpredictable number of gene copies among species, such as in the major histocompatibility complex (MHC). In the present study we (i) report new primers for the isolation of the MHC class IIB (MHCIIB) gene family in birds, and (ii) share our experience with isolating MHCIIB genes from an unprecedented number of avian species from all over the avian phylogeny. We report important and usually underappreciated problems encountered during PCR-based multigene family isolation, and provide a collection of measures to help significantly improving the chance of successfully isolating complete multigene families using PCR-based approaches.

  • 248.
    Burri, Reto
    et al.
    Laboratory for Conservation Biology, Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland .
    Salamin, Nicolas
    Studer, Romain A
    Roulin, Alexandre
    Fumagalli, Luca
    Adaptive divergence of ancient gene duplicates in the avian MHC class II beta2010In: Molecular biology and evolution, ISSN 0737-4038, E-ISSN 1537-1719, Vol. 27, no 10, p. 2360-2374Article in journal (Refereed)
    Abstract [en]

    Gene duplication and neofunctionalization are known to be important processes in the evolution of phenotypic complexity. They account for important evolutionary novelties that confer ecological adaptation, such as the major histocompatibility complex (MHC), a multigene family crucial to the vertebrate immune system. In birds, two MHC class II β (MHCIIβ) exon 3 lineages have been recently characterized, and two hypotheses for the evolutionary history of MHCIIβ lineages were proposed. These lineages could have arisen either by 1) an ancient duplication and subsequent divergence of one paralog or by 2) recent parallel duplications followed by functional convergence. Here, we compiled a data set consisting of 63 MHCIIβ exon 3 sequences from six avian orders to distinguish between these hypotheses and to understand the role of selection in the divergent evolution of the two avian MHCIIβ lineages. Based on phylogenetic reconstructions and simulations, we show that a unique duplication event preceding the major avian radiations gave rise to two ancestral MHCIIβ lineages that were each likely lost once later during avian evolution. Maximum likelihood estimation shows that following the ancestral duplication, positive selection drove a radical shift from basic to acidic amino acid composition of a protein domain facing the α-chain in the MHCII α β-heterodimer. Structural analyses of the MHCII α β-heterodimer highlight that three of these residues are potentially involved in direct interactions with the α-chain, suggesting that the shift following duplication may have been accompanied by coevolution of the interacting α- and β-chains. These results provide new insights into the long-term evolutionary relationships among avian MHC genes and open interesting perspectives for comparative and population genomic studies of avian MHC evolution.

  • 249.
    Butler, Aodhán D.
    Uppsala University, Disciplinary Domain of Science and Technology, Earth Sciences, Department of Earth Sciences, Palaeobiology.
    Exceptionally Preserved Cambrian Lophotrochozoa: Taxonomy, Systematics and Taphonomy of Chengjiang and Indian Springs Lophophorates2014Licentiate thesis, comprehensive summary (Other academic)
    Abstract [en]

    The origin and evolution of Lophotrochozoa can be traced to the plethora of lower Cambrian scleritome taxa.  We aim to determine the character suites linking these stem-Lophotrochozoa to their extant crown relatives, in particular the small shelly tommotiids and the stem-group brachiopods. Tracing the origin of morphological characters from these fossils informs the evolution and construction of lophotrochozoan body plans associated with the Cambrian Explosion. This is achieved by comparing records of exceptional preservation, most conspicuously Burgess Shale type Lagerstätten with more widespread Cambrian stem-brachiopods and small shelly fossils with their purported extant relatives, for example. Determining morphological character homologies is crucial to reconstructing the brachiopod stem-group and in polarising character changes associated with the putative transition from scleritome organisms to crown-group brachiopods. In this thesis arguments for a common origin of specific shell structures and exceptionally preserved soft-tissues are investigated. New records of enigmatic stem-group lophotrochozoans are described from two localities, the Indian Springs and Chengjiang Lagerstätte. Comprising the stem-brachiopod Mickwitzia cf. occidens, a putative stem-group entoproct Cotyledion tylodes and an enigmatic agglutinated tubular lophophorate possessing an unusual combination of phoronid, brachiopod and tommotiid characters, Yuganotheca elegans gen. et sp. nov. The interplay of bauplan, microbial activity and environmental factors resulting in such incidences of exceptional soft tissue preservation is also examined critically. Consequently, the evolution of through-gut bearing bilaterians is suggested as the reason for why the Cambrian hosts such a plethora of Lagerstätten. The closure of this taphonomic window is then associated with increased bioturbation following the Cambrian substrate revolution.

    List of papers
    1. Exceptionally-preserved Mickwitzia from the Indian Springs Lagerstätte.
    Open this publication in new window or tab >>Exceptionally-preserved Mickwitzia from the Indian Springs Lagerstätte.
    (English)In: Journal of Paleontology, ISSN 0022-3360, E-ISSN 1937-2337Article in journal (Other academic) Accepted
    Abstract [en]

    A new assemblage of the early Cambrian stem group brachiopod Mickwitzia is described from the Indian Springs Lagerstätte possessing exceptionally preserved mantle setae. Critical analysis of shell structure and mantle setae from these specimens with those from additional sites with variable diagenetic history reveals the extent of taphonomic alteration and further sheds light on the phylogenetic position of the mickwitziids. A morphometric approach to shell outline and growth landmarks within these specimens reveals a clear species level discriminant signal of Nevada Mickwitzia in comparison to M. monlifera from Sweden. Detailed electron micrographs allow revision of the genus diagnosis for Mickwitzia based on presence of inward pointing phosphatic cones and tangential setae bearing tubes. We also conclude the inward pointing cone structures are not consistent with setal bearing structures as previously thought, but rather represent an endopunctae-like structure. A tommotiid-like shell architecture and presence of acrotretid columns in the dorsal juvenile shell of M. cf. occidens further strengthens the proposed close relationship between stem-group brachiopods and tommotiids.

    Keywords
    Brachiopoda, Mickwitzia, shell penetrating setae, lower Cambrian, Indian Springs
    National Category
    Other Earth and Related Environmental Sciences Geology Evolutionary Biology
    Research subject
    Earth Science with specialization in Historical Geology and Palaeontology
    Identifiers
    urn:nbn:se:uu:diva-216149 (URN)
    Funder
    Swedish Research Council, 2009-4395, 2012-1658
    Available from: 2014-01-21 Created: 2014-01-19 Last updated: 2017-12-06
    2. The role of microbes in decay and preservation: a Cambrian Explosion of animals and Lagerstätten.
    Open this publication in new window or tab >>The role of microbes in decay and preservation: a Cambrian Explosion of animals and Lagerstätten.
    (English)Manuscript (preprint) (Other academic)
    Abstract [en]

    The abrupt appearance of animals in the early Cambrian has been interpreted either as an explosive biological diversification or, alternatively, as an artefact resulting from a sudden increase in the probability of animal remains becoming fossilised. We attempt to reconcile these competing interpretations in exceptionally-preserved biota, which provide a vital part of our knowledge of the disparity and diversity of the Cambrian fauna. We assess the factors influencing the potential for exceptional fossil preservation using the brine shrimp Artemia salina as our experimental model. Following gut wall rupture, but prior to cuticle failure, internal, gut-derived microbes spread into the body cavity and formed pseudomorphs of tissues. Gut-derived microbes were shown to be the main factor mediating both decay and biofilm replacement and tissue stabilisation. This pattern of preservation is consistent with results from other experimental studies and with the nature of Burgess Shale type fossil remains. Thus, the evolution of a through-gut may have not only underpinned the ecological revolution that bilaterian diversification represents, but also catalysed the exceptional preservation of early bilaterian fossils.

    Keywords
    Cambrian Explosion, palaeobiology, taphonomy, bilateria, metazoa
    National Category
    Other Earth and Related Environmental Sciences Evolutionary Biology Geology
    Research subject
    Earth Science with specialization in Historical Geology and Palaeontology
    Identifiers
    urn:nbn:se:uu:diva-216151 (URN)
    Available from: 2014-01-21 Created: 2014-01-19 Last updated: 2014-02-06
    3. A sclerite-bearing stem group entoproct from the early Cambrian and its implications
    Open this publication in new window or tab >>A sclerite-bearing stem group entoproct from the early Cambrian and its implications
    Show others...
    2013 (English)In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 3, p. 1066-Article in journal (Refereed) Published
    Abstract [en]

    The Lophotrochozoa includes disparate tentacle-bearing sessile protostome animals, which apparently appeared in the Cambrian explosion, but lack an uncontested fossil record. Here we describe abundant well preserved material of Cotyledion tylodes Luo et Hu, 1999, from the Cambrian (Series 2) Chengjiang deposits, reinterpreted here as a stem-group entoproct. The entoproct affinity is supported by the sessile body plan and interior soft anatomy. The body consists of an upper calyx and a lower elongate stalk with a distal holdfast. The soft anatomy includes a U-shaped gut with a mouth and aboral anus ringed by retractable marginal tentacles. Cotyledion differs from extant entoprocts in being larger, and having the calyx and the stalk covered by numerous loosely-spaced external sclerites. The description of entoprocts from the Chengjiang biota traces the ancestry of yet another lophotrochozoan phylum back to the Cambrian radiation, and has important implications for the earliest evolution of lophotrochozoans.

    National Category
    Natural Sciences
    Research subject
    Earth Science with specialization in Historical Geology and Palaeontology
    Identifiers
    urn:nbn:se:uu:diva-194748 (URN)10.1038/srep01066 (DOI)000313650900001 ()
    Funder
    Swedish Research Council, 2012–1658
    Available from: 2013-03-13 Created: 2013-02-19 Last updated: 2017-12-06Bibliographically approved
    4. An early Cambrian agglutinated tubular lophophorate with brachiopod characters
    Open this publication in new window or tab >>An early Cambrian agglutinated tubular lophophorate with brachiopod characters
    2014 (English)In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 4, p. 4682-Article in journal (Refereed) Published
    Abstract [en]

    The morphological disparity of lophotrochozoan phyla makes it difficult to predict the morphology of the last common ancestor. Only fossils of stem groups can help discover the morphological transitions that occurred along the roots of these phyla. Here, we describe a tubular fossil Yuganotheca elegans gen.et sp. nov. from the Cambrian (Stage 3) Chengjiang Lagerstätte (Yunnan, China) that exhibits an unusual combination of phoronid, brachiopod and tommotiid (Cambrian problematica) characters, notably a pair of agglutinated valves, enclosing a horseshoe-shaped lophophore, supported by a lower bipartite tubular attachment structure with a long coelomic pedicle providing anchorage. The discovery has important implications for the early evolution of lophotrochozoans, suggesting rooting of brachiopods into the sessile lophotrochozoans and the origination of their bivalved bauplan preceding the biomineralization of shell valves in crown brachiopods.

    National Category
    Geology Other Earth and Related Environmental Sciences Evolutionary Biology
    Research subject
    Earth Science with specialization in Historical Geology and Palaeontology
    Identifiers
    urn:nbn:se:uu:diva-216152 (URN)10.1038/srep04682 (DOI)000335885800001 ()
    Funder
    Swedish Research Council, 2009-4395, 2012-1658
    Available from: 2014-01-21 Created: 2014-01-19 Last updated: 2017-12-06Bibliographically approved
  • 250.
    Butler, Aodhán D.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Earth Sciences, Department of Earth Sciences, Palaeobiology.
    Cunningham, John A.
    University of Bristol.
    Donoghue, Philip C. J.
    University of Bristol.
    The role of microbes in decay and preservation: a Cambrian Explosion of animals and Lagerstätten.Manuscript (preprint) (Other academic)
    Abstract [en]

    The abrupt appearance of animals in the early Cambrian has been interpreted either as an explosive biological diversification or, alternatively, as an artefact resulting from a sudden increase in the probability of animal remains becoming fossilised. We attempt to reconcile these competing interpretations in exceptionally-preserved biota, which provide a vital part of our knowledge of the disparity and diversity of the Cambrian fauna. We assess the factors influencing the potential for exceptional fossil preservation using the brine shrimp Artemia salina as our experimental model. Following gut wall rupture, but prior to cuticle failure, internal, gut-derived microbes spread into the body cavity and formed pseudomorphs of tissues. Gut-derived microbes were shown to be the main factor mediating both decay and biofilm replacement and tissue stabilisation. This pattern of preservation is consistent with results from other experimental studies and with the nature of Burgess Shale type fossil remains. Thus, the evolution of a through-gut may have not only underpinned the ecological revolution that bilaterian diversification represents, but also catalysed the exceptional preservation of early bilaterian fossils.

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