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  • 1.
    Andersson, Jan O
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology. Mikrobiologi.
    A review of "Microbial Phylogeny and Evolution: Concepts and Controversies"2006In: Systematic Biology, ISSN 1063-5157, E-ISSN 1076-836X, Vol. 55, no 2, p. 359-361Article, book review (Other (popular science, discussion, etc.))
  • 2.
    Andersson, Jan O.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution.
    The New Foundations of Evolution: On the Tree of Life2011In: Systematic Biology, ISSN 1063-5157, E-ISSN 1076-836X, Vol. 60, no 1, p. 114-115Article, book review (Other (popular science, discussion, etc.))
  • 3.
    Björklund, Mats
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Merilä, Juha
    Fluctuating asymmetry and measurement error1995In: Systematic Biology, ISSN 1063-5157, E-ISSN 1076-836X, Vol. 44, p. 97-101Article in journal (Refereed)
  • 4.
    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.

  • 5. Britton, Tom
    et al.
    Anderson, Cajsa Lisa
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Botany.
    Jaquet, David
    Lundqvist, Samuel
    Bremer, Kåre
    Estimating divergence times in large phylogenetic trees2007In: Systematic Biology, ISSN 1063-5157, E-ISSN 1076-836X, Vol. 56, no 5, p. 741-752Article in journal (Refereed)
    Abstract [en]

    A new method, PATHd8, for estimating ultrametric trees from trees with edge (branch) lengths proportional to the number of substitutions is proposed. The method allows for an arbitrary number of reference nodes for time calibration, each defined either as absolute age, minimum age, or maximum age, and the tree need not be fully resolved. The method is based on estimating node ages by mean path lengths from the node to the leaves but correcting for deviations from a molecular clock suggested by reference nodes. As opposed to most existing methods allowing substitution rate variation, the new method smoothes substitution rates locally, rather than simultaneously over the whole tree, thus allowing for analysis of very large trees. The performance of PATHd8 is compared with other frequently used methods for estimating divergence times. In analyses of three separate data sets, PATHd8 gives similar divergence times to other methods, the largest difference being between crown group ages, where unconstrained nodes get younger ages when analyzed with PATHd8. Overall, chronograms obtained from other methods appear smoother, whereas PATHd8 preserves more of the heterogeneity seen in the original edge lengths. Divergence times are most evenly spread over the chronograms obtained from the Bayesian implementation and the clock-based Langley-Fitch method, and these two methods produce very similar ages for most nodes. Evaluations of PATHd8 using simulated data suggest that PATHd8 is slightly less precise compared with penalized likelihood, but it gives more sensible answers for extreme data sets. A clear advantage with PATHd8 is that it is more or less instantaneous even with trees having several thousand leaves, whereas other programs often run into problems when analyzing trees with hundreds of leaves. PATHd8 is implemented in freely available software.

  • 6. Brysting, Anne K.
    et al.
    Oxelman, Bengt
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Botany.
    Huber, Katharina T.
    Moulton, Vincent
    Brochmann, Christian
    Untangling complex histories of genome mergings in high polyploids2007In: Systematic Biology, ISSN 1063-5157, E-ISSN 1076-836X, Vol. 56, no 3, p. 467-476Article in journal (Refereed)
    Abstract [en]

    Polyploidy, the duplication of entire genomes, plays a major role in plant evolution. In allopolyploids, genome duplication is associated with hybridization between two or more divergent genomes. Successive hybridization and polyploidization events can build up species complexes of allopolyploids with complicated network-like histories, and the evolutionary history of many plant groups cannot be adequately represented by phylogenetic trees because of such reticulate events. The history of complex genome mergings within a high-polyploid species complex in the genus Cerastium (Caryophyllaceae) is here untangled by the use of a network algorithm and noncoding sequences of a low-copy number gene. The resulting network illustrates how hybridization and polyploidization have acted as key evolutionary processes in creating a plant group where high-level allopolyploids clearly outnumber extant parental genomes.

  • 7.
    Ekman, Stefan
    et al.
    Uppsala University, Music and Museums, Museum of Evolution.
    Andersen, Heidi Lie
    Universitetet i Bergen.
    Wedin, Mats
    Naturhistoriska riksmuseet.
    The Limitations of Ancestral State Reconstruction and the Evolution of the Ascus in the Lecanorales (Lichenized Ascomycota)2008In: Systematic Biology, ISSN 1063-5157, E-ISSN 1076-836X, Vol. 57, no 1, p. 141-156Article, review/survey (Refereed)
    Abstract [en]

    Ancestral state reconstructions of morphological or ecological traits on molecular phylogenies are becoming increasinglyfrequent. They rely on constancy of character state change rates over trees, a correlation between neutral geneticchange and phenotypic change, as well as on adequate likelihood models and (for Bayesian methods) prior distributions.This investigation explored the outcomes of a variety of methods for reconstructing discrete ancestral state in the ascus apexof the Lecanorales, a group containing the majority of lichen-forming ascomycetes. Evolution of this character complex hasbeen highly controversial in lichen systematics for more than two decades. The phylogeny was estimated using BayesianMarkov chain Monte Carlo inference on DNA sequence alignments of three genes (small subunit of the mitochondrialrDNA, large subunit of the nuclear rDNA, and largest subunit of RNA polymerase II). We designed a novel method forassessing the suitable number of discrete gamma categories, which relies on the effect on phylogeny estimates rather thanon likelihoods. Ancestral state reconstructions were performed using maximum parsimony and maximum likelihood ona posterior tree sample as well as two fully Bayesian methods. Resulting reconstructions were often strikingly differentdepending on the method used; different methods often assign high confidence to different states at a given node. Thetwo fully Bayesian methods disagree about the most probable reconstruction in about half of the nodes, even when similarlikelihood models and similar priors are used. We suggest that similar studies should use several methods, awaiting animproved understanding of the statistical properties of the methods. A Lecanora-type ascus may have been ancestral in theLecanorales. State transformations counts, obtained using stochastic mapping, indicate that the number of state changes is12 to 24, which is considerably greater than the minimum three changes needed to explain the four observed ascus apextypes. Apparently, the ascus in the Lecanorales is far more apt to change than has been recognized. Phylogeny correspondswell with morphology, although it partly contradicts currently used delimitations of the Crocyniaceae, Haematommataceae,Lecanoraceae, Megalariaceae, Mycoblastaceae, Pilocarpaceae, Psoraceae, Ramalinaceae, Scoliciosporaceae, and Squamarinaceae.

  • 8.
    Ekman, Stefan
    et al.
    Uppsala University, Music and Museums, Museum of Evolution.
    Blaalid, Rakel
    The Devil in the Details: Interactions between the Branch-Length Prior and Likelihood Model Affect Node Support and Branch Lengths in the Phylogeny of the Psoraceae2011In: Systematic Biology, ISSN 1063-5157, E-ISSN 1076-836X, Vol. 60, no 4, p. 541-561Article in journal (Refereed)
    Abstract [en]

    In popular use of Bayesian phylogenetics, a default branch-length prior is almost universally applied without knowing how a different prior would have affected the outcome. We performed Bayesian and maximum likelihood (ML) inference of phylogeny based on empirical nucleotide sequence data from a family of lichenized ascomycetes, the Psoraceae, the morphological delimitation of which has been controversial. We specifically assessed the influence of the combination of Bayesian branch-length prior and likelihood model on the properties of the Markov chain Monte Carlo tree sample, including node support, branch lengths, and taxon stability. Data included two regions of the mitochondrial ribosomal RNA gene, the internal transcribed spacer region of the nuclear ribosomal RNA gene, and the protein-coding largest subunit of RNA polymerase II. Data partitioning was performed using Bayes' factors, whereas the best-fitting model of each partition was selected using the Bayesian information criterion (BIC). Given the data and model, short Bayesian branch-length priors generate higher numbers of strongly supported nodes as well as short and topologically similar trees sampled from parts of tree space that are largely unexplored by the ML bootstrap. Long branch-length priors generate fewer strongly supported nodes and longer and more dissimilar trees that are sampled mostly from inside the range of tree space sampled by the ML bootstrap. Priors near the ML distribution of branch lengths generate the best marginal likelihood and the highest frequency of "rogue" (unstable) taxa. The branch-length prior was shown to interact with the likelihood model. Trees inferred under complex partitioned models are more affected by the stretching effect of the branch-length prior. Fewer nodes are strongly supported under a complex model given the same branch-length prior. Irrespective of model, internal branches make up a larger proportion of total tree length under the shortest branch-length priors compared with longer priors. Relative effects on branch lengths caused by the branch-length prior can be problematic to downstream phylogenetic comparative methods making use of the branch lengths. Furthermore, given the same branch-length prior, trees are on average more dissimilar under a simple unpartitioned model compared with a more complex partitioned models. The distribution of ML branch lengths was shown to better fit a gamma or Pareto distribution than an exponential one. Model adequacy tests indicate that the best-fitting model selected by the BIC is insufficient for describing data patterns in 5 of 8 partitions. More general substitution models are required to explain the data in three of these partitions, one of which also requires nonstationarity. The two mitochondrial ribosomal RNA gene partitions need heterotachous models. We found no significant correlations between, on the one hand, the amount of ambiguous data or the smallest branch-length distance to another taxon and, on the other hand, the topological stability of individual taxa. Integrating over several exponentially distributed means under the best-fitting model, node support for the family Psoraceae, including Psora, Protoblastenia, and the Micarea sylvicola group, is approximately 0.96. Support for the genus Psora is distinctly lower, but we found no evidence to contradict the current classification.

  • 9.
    Erixon, Per
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolutionary Biology, Systematic Botany.
    Svennblad, Bodil
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Mathematics, Mathematical Statistics.
    Britton, Tom
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Mathematics, Mathematical Statistics.
    Oxelman, Bengt
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolutionary Biology, Systematic Botany.
    Reliability of Bayesian Posterior Probabilities and Bootstrap Frequencies in Phylogenetics2003In: Systematic Biology, ISSN 1063-5157, E-ISSN 1076-836X, Vol. 52, no 5, p. 665-673Article in journal (Refereed)
    Abstract [en]

    Many empirical studies have revealed considerable differences between nonparametric bootstrapping and Bayesian posterior probabilities in terms of the support values for branches, despite claimed predictions about their approximate equivalence. We investigated this problem by simulating data, which were then analyzed by maximum likelihood bootstrapping and Bayesian phylogenetic analysis using identical models and reoptimization of parameter values. We show that Bayesian posterior probabilities are significantly higher than corresponding nonparametric bootstrap frequencies for true clades, but also that erroneous conclusions will be made more often. These errors are strongly accentuated when the models used for analyses are underparameterized. When data are analyzed under the correct model, nonparametric bootstrapping is conservative. Bayesian posterior probabilities are also conservative in this respect, but less so.

  • 10.
    Frajman, Bozo
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Biology.
    Eggens, Frida
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Botany.
    Oxelman, Bengt
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Biology.
    Hybrid origins and homoploid reticulate evolution within Heliosperma (Sileneae, Caryophyllaceae) – a multigene phylogenetic approach  with  Relative Dating2009In: Systematic Biology, ISSN 1063-5157, E-ISSN 1076-836X, Vol. 58, no 3, p. 328-345Article in journal (Refereed)
    Abstract [en]

    We used four potentially unlinked nuclear DNA regions from the gene   family encoding the second largest subunit of the RNA polymerases, as   well as the psbE-petG spacer and the rps16 intron from the chloroplast   genome, to evaluate the origin of and relationships within Heliosperma   (Sileneae, Caryophyllaceae). Relative dates of divergence times are   used to discriminate between hybridization and gene duplication/loss as   alternative explanations for topological conflicts between gene trees.   The observed incongruent relationships among the three major lineages   of Heliosperma are better explained by homoploid hybridization than by   gene duplication/losses because species branching events exceed gene   coalescence times under biologically reasonable population sizes and   generation times, making lineage sorting an unlikely explanation. The  origin of Heliosperma is complex and the gene trees likely reflect both reticulate evolution and sorting events. At least two lineages have   been involved in the origin of Heliosperma, one most closely related to   the ancestor of Viscaria and Atocion and the other to Eudianthe and/or Petrocoptis.

  • 11.
    Guschanski, Katerina
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Krause, Johannes
    Sawyer, Susanna
    Valente, Luis M.
    Bailey, Sebastian
    Finstermeier, Knut
    Sabin, Richard
    Gilissen, Emmanuel
    Sonet, Gontran
    Nagy, Zoltan T.
    Lenglet, Georges
    Mayer, Frieder
    Savolainen, Vincent
    Next-Generation Museomics Disentangles One of the Largest Primate Radiations2013In: Systematic Biology, ISSN 1063-5157, E-ISSN 1076-836X, Vol. 62, no 4, p. 539-554Article in journal (Refereed)
    Abstract [en]

    Guenons (tribe Cercopithecini) are one of the most diverse groups of primates. They occupy all of sub-Saharan Africa and show great variation in ecology, behavior, and morphology. This variation led to the description of over 60 species and subspecies. Here, using next-generation DNA sequencing (NGS) in combination with targeted DNA capture, we sequenced 92 mitochondrial genomes from museum-preserved specimens as old as 117 years. We infer evolutionary relationships and estimate divergence times of almost all guenon taxa based on mitochondrial genome sequences. Using this phylogenetic framework, we infer divergence dates and reconstruct ancestral geographic ranges. We conclude that the extraordinary radiation of guenons has been a complex process driven by, among other factors, localized fluctuations of African forest cover. We find incongruences between phylogenetic trees reconstructed from mitochondrial and nuclear DNA sequences, which can be explained by either incomplete lineage sorting or hybridization. Furthermore, having produced the largest mitochondrial DNA data set from museum specimens, we document how NGS technologies can “unlock” museum collections, thereby helping to unravel the tree-of-life. [Museum collection; next-generation DNA sequencing; primate radiation; speciation; target capture.]

  • 12.
    Hansen, T. F.
    et al.
    Oslo University.
    Bartoszek, Krzysztof
    Mathematical Sciences, Chalmers University of Technology and the University of Gothenburg.
    Interpreting the evolutionary regression: The interplay between observational and biological errors in phylogenetic comparative studies2012In: Systematic Biology, ISSN 1063-5157, E-ISSN 1076-836X, Vol. 61, no 3, p. 413-425Article in journal (Refereed)
    Abstract [en]

    Regressions of biological variables across species are rarely perfect. Usually, there are residual deviations fromthe estimated model relationship, and such deviations commonly show a pattern of phylogenetic correlations indicatingthat they have biological causes. We discuss the origins and effects of phylogenetically correlated biological variation inregression studies. In particular, we discuss the interplay of biological deviations with deviations due to observationalor measurement errors, which are also important in comparative studies based on estimated species means. We showhow bias in estimated evolutionary regressions can arise from several sources, including phylogenetic inertia and eitherobservational or biological error in the predictor variables. We show how all these biases can be estimated and correctedfor in the presence of phylogenetic correlations.We present general formulas for incorporating measurement error in linearmodels with correlated data. We also show how alternative regression models, such as major axis and reduced major axisregression, which are often recommended when there is error in predictor variables, are strongly biased when there isbiological variation in any part of the model.We argue that such methods should never be used to estimate evolutionary orallometric regression slopes.

  • 13. Jondelius, Ulf
    et al.
    Wallberg, Andreas
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Hooge, Matthew
    Raikova, Olga I.
    How the Worm Got its Pharynx: Phylogeny, Classification and Bayesian Assessment of Character Evolution in Acoela2011In: Systematic Biology, ISSN 1063-5157, E-ISSN 1076-836X, Vol. 60, no 6, p. 845-871Article in journal (Refereed)
    Abstract [en]

    Acoela are marine microscopic worms currently thought to be the sister taxon of all other bilaterians. Acoels have long been used as models in evolutionary scenarios, and generalized conclusions about acoel and bilaterian ancestral features are frequently drawn from studies of single acoel species. There is no extensive phylogenetic study of Acoela and the taxonomy of the 380 species is chaotic. Here we use two nuclear ribosomal genes and one mitochondrial gene in combination with 37 morphological characters in an analysis of 126 acoel terminals (about one-third of the described species) to estimate the phylogeny and character evolution of Acoela. We present an estimate of posterior probabilities for ancestral character states at 31 control nodes in the phylogeny. The overall reconstruction signal based on the shape of the posterior distribution of character states was computed for all morphological characters and control nodes to assess how well these were reconstructed. The body-wall musculature appears more clearly reconstructed than the reproductive organs. Posterior similarity to the root was calculated by averaging the divergence between the posterior distributions at the nodes and the root over all morphological characters. Diopisthoporidae is the sister group to all other acoels and has the highest posterior similarity to the root. Convolutidae, including several "model" acoels, is most divergent. Finally, we present a phylogenetic classification of Acoela down to the family level where six previous family level taxa are synonymized.

  • 14.
    Linder, Martin
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Mathematics, Mathematical Statistics.
    Britton, Tom
    Sennblad, Bengt
    Evaluation of Bayesian Models of Substitution Rate Evolution-Parental Guidance versus Mutual Independence2011In: Systematic Biology, ISSN 1063-5157, E-ISSN 1076-836X, Vol. 60, no 3, p. 329-342Article in journal (Refereed)
    Abstract [en]

    We have evaluated the performance of two classes of probabilistic models for substitution rate variation over phylogenetic trees. In the first class, branch rates are considered to be independent and identically distributed (i.i.d.) stochastic variables. Three versions with respect to the underlying distribution (Gamma, Inverse Gaussian, and LogNormal) are considered. The i.i.d. models are compared with the autocorrelated (AC) model, where rates of adjacent nodes in the tree are AC, so that a node rate is LogNormal distributed around the rate of the parent node. The performance of different models is evaluated using three empirical data sets. For all data sets, it was clear that all tested models extracted substantial knowledge from data when posterior divergence time distributions were compared with the prior distributions and, furthermore, that they clearly outperformed a molecular clock. Moreover, the descriptive power of the i.i.d. models, as evaluated by Bayes factors, was either equal to or clearly better than that of the AC model. The latter effect increased with extended taxon sampling. Likewise, under none of the models could we find compelling evidence, in any of the data sets, for rate correlation between adjacent branches/nodes. These findings challenge previous suggestions of universality of autocorrelation in sequence evolution. We also performed an additional comparison with a divergence time prior including calibration information from fossil evidence. Adding fossil information to the prior had negligible effect on Bayes factors and mainly affected the width of the posterior distribution of the divergence times, whereas the relative position of the mean divergence times were largely unaffected.

  • 15.
    Mindell, David P
    et al.
    University of Michigan, Museum of Zoology and Department of Ecology and Evolutionary Biology.
    Sorenson, Michael D
    University of Michigan, Museum of Zoology and Department of Ecology and Evolutionary Biology.
    Dimcheff, Derek E
    University of Michigan, Museum of Zoology and Department of Ecology and Evolutionary Biology.
    Hasegawa, M
    Ast, Jennifer C
    University of Michigan, Museum of Zoology and Department of Ecology and Evolutionary Biology.
    Yuri, Tamaki
    University of Michigan, Museum of Zoology and Department of Ecology and Evolutionary Biology.
    Interordinal relationships of birds and other reptiles based on whole mitochondrial genomes1999In: Systematic Biology, ISSN 1063-5157, E-ISSN 1076-836X, Vol. 48, p. 138-152Article in journal (Refereed)
  • 16.
    Morrison, David A.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Aristotle’s Ladder, Darwin’s Tree: The Evolution of Visual Metaphors for Biological Order. — By J. David Archibald2015In: Systematic Biology, ISSN 1063-5157, E-ISSN 1076-836X, Vol. 64, no 5, p. 892-895Article, book review (Other academic)
  • 17.
    Morrison, David A.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Biology of Evolution and Systematics: Cohesive, Concise, yet Comprehensive Introduction for Students and Professionals2016In: Systematic Biology, ISSN 1063-5157, E-ISSN 1076-836X, Vol. 65, no 1, p. 177-178Article, book review (Other academic)
  • 18.
    Morrison, David A.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Biology of Evolution and Systematics: Cohesive, Concise, yet Comprehensive Introduction for Students and Professionals. By Paul Sanghera2016In: Systematic Biology, ISSN 1063-5157, E-ISSN 1076-836X, Vol. 65, no 1, p. 177-178Article, book review (Other academic)
  • 19.
    Morrison, David A.
    Section for Parasitology, Swedish University of Agricultural Sciences.
    Is the tree of life the best metaphor, model, or heuristic for phylogenetics?2014In: Systematic Biology, ISSN 1063-5157, E-ISSN 1076-836X, Vol. 63, no 4, p. 628-638Article in journal (Refereed)
  • 20.
    Morrison, David A.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Multiple Sequence Alignment Methods — Edited by David J. Russell2015In: Systematic Biology, ISSN 1063-5157, E-ISSN 1076-836X, Vol. 64, no 4, p. 690-692Article, book review (Other academic)
  • 21.
    Morrison, David A.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Taxonomy of Australian Mammals. By Stephen Jackson and Colin Groves2016In: Systematic Biology, ISSN 1063-5157, E-ISSN 1076-836X, Vol. 65, no 2, p. 346-348Article, book review (Other academic)
  • 22.
    Morrison, David A.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    The Biology and Identification of the Coccidia (Apicomplexa) of Marsupials of the World. Donald W. Duszynski.2016In: Systematic Biology, ISSN 1063-5157, E-ISSN 1076-836X, Vol. 65, no 4, p. 722-724Article, book review (Other academic)
  • 23.
    Morrison, David A.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    The Book of Trees: Visualizing Branches of Knowledge — By Manuel Lima. Design for Information: an Introduction to the Histories, Theories, and Best Practices Behind Effective Information Visualizations. — By Isabel Meirelles.2015In: Systematic Biology, ISSN 1063-5157, E-ISSN 1076-836X, Vol. 64, no 3, p. 363-365Article, book review (Other academic)
  • 24.
    Morrison, David A.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    The Invention of Nature: The Adventures of Alexander von Humboldt, the Lost Hero of Science (UK). The Invention of Nature: Alexander von Humboldt’s New World (USA). By Andrea Wulf2016In: Systematic Biology, ISSN 1063-5157, E-ISSN 1076-836X, Vol. 65, no 6, p. 1117-1119Article, book review (Other academic)
  • 25.
    Morrison, David A.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    The Monkey’s voyage: how improbable journeys shaped the history of life. €”by Alan de Queiroz.2014In: Systematic Biology, ISSN 1063-5157, E-ISSN 1076-836X, Vol. 63, no 5, p. 847-849Article in journal (Other academic)
  • 26.
    Morrison, David A.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    The Tree of Life: Evolution and Classification of Living Organisms .—Edited by Pablo Vargas and Rafael Zardoya; translated by Anne Louise2015In: Systematic Biology, ISSN 1063-5157, E-ISSN 1076-836X, Vol. 64, no 3, p. 546-548Article, book review (Other academic)
  • 27.
    Morrison, David A.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Understanding Evolution .— By Kostas Kampourakis2015In: Systematic Biology, ISSN 1063-5157, E-ISSN 1076-836X, Vol. 64, no 6, p. 1121-1122Article, book review (Other academic)
  • 28.
    Nater, Alexander
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Burri, Reto
    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.
    Smeds, Linnea
    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.
    Resolving Evolutionary Relationships in Closely Related Species with Whole-Genome Sequencing Data2015In: Systematic Biology, ISSN 1063-5157, E-ISSN 1076-836X, Vol. 64, no 6, p. 1000-1017Article in journal (Refereed)
    Abstract [en]

    Using genetic data to resolve the evolutionary relationships of species is of major interest in evolutionary and systematic biology. However, reconstructing the sequence of speciation events, the so-called species tree, in closely related and potentially hybridizing species is very challenging. Processes such as incomplete lineage sorting and interspecific gene flow result in local gene genealogies that differ in their topology from the species tree, and analyses of few loci with a single sequence per species are likely to produce conflicting or even misleading results. To study these phenomena on a full phylogenomic scale, we use whole-genome sequence data from 200 individuals of four black-and-white flycatcher species with so far unresolved phylogenetic relationships to infer gene tree topologies and visualize genome-wide patterns of gene tree incongruence. Using phylogenetic analysis in nonoverlapping 10-kb windows, we show that gene tree topologies are extremely diverse and change on a very small physical scale. Moreover, we find strong evidence for gene flow among flycatcher species, with distinct patterns of reduced introgression on the Z chromosome. To resolve species relationships on the background of widespread gene tree incongruence, we used four complementary coalescent-based methods for species tree reconstruction, including complex modeling approaches that incorporate post-divergence gene flow among species. This allowed us to infer the most likely species tree with high confidence. Based on this finding, we show that regions of reduced effective population size, which have been suggested as particularly useful for species tree inference, can produce positively misleading species tree topologies. Our findings disclose the pitfalls of using loci potentially under selection as phylogenetic markers and highlight the potential of modeling approaches to disentangle species relationships in systems with large effective population sizes and post-divergence gene flow.

  • 29.
    Nylander, Johan A. A.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Zoology.
    Olsson, Urban
    Alström, Per
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Zoology.
    Sanmartin, Isabel
    Accounting for phylogenetic uncertainty in biogeography: A Bayesian approach to dispersal-vicariance analysis of the thrushes (Aves2008In: Systematic Biology, ISSN 1063-5157, E-ISSN 1076-836X, Vol. 57, no 2, p. 257-268Article in journal (Refereed)
    Abstract [en]

    The phylogeny of the thrushes (Aves: Turdus) has been difficult to reconstruct due to short internal branches and lack of node support for certain parts of the tree. Reconstructing the biogeographic history of this group is further complicated by the fact that current implementations of biogeographic methods, such as dispersal-vicariance analysis (DIVA; Ronquist, 1997), require a fully resolved tree. Here, we apply a Bayesian approach to dispersal-vicariance analysis that accounts for phylogenetic uncertainty and allows a more accurate analysis of the biogeographic history of lineages. Specifically, ancestral area reconstructions can be presented as marginal distributions, thus displaying the underlying topological uncertainty. Moreover, if there are multiple optimal solutions for a single node on a certain tree, integrating over the posterior distribution of trees often reveals a preference for a narrower set of solutions. We find that despite the uncertainty in tree topology, ancestral area reconstructions indicate that the Turdus clade originated in the eastern Palearctic during the Late Miocene. This was followed by an early dispersal to Africa from where a worldwide radiation took place. The uncertainty in tree topology and short branch lengths seems to indicate that this radiation took place within a limited time span during the Late Pliocene. The results support the role of Africa as a probable source area for intercontinental dispersals as suggested for other passerine groups, including basal diversification within the songbird tree.

  • 30.
    Nylander, Johan A. A.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Zoology.
    Ronquist, Fredrik
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Zoology.
    Huelsenbeck, John P.
    Nieves-Aldrey, José Luis
    Bayesian phylogenetic analysis of combined data2004In: Systematic Biology, ISSN 1063-5157, E-ISSN 1076-836X, Vol. 53, no 1, p. 47-67Article in journal (Other (popular science, discussion, etc.))
    Abstract [en]

    The recent development of Bayesian phylogenetic inference using Markov chain Monte Carlo (MCMC) techniques has facilitated the exploration of parameter-rich evolutionary models. At the same time, stochastic models have become more realistic (and complex) and have been extended to new types of data, such as morphology. Based on this foundation, we developed a Bayesian MCMC approach to the analysis of combined data sets and explored its utility in inferring relationships among gall wasps based on data from morphology and four genes (nuclear and mitochondrial, ribosomal and protein coding). Examined models range in complexity from those recognizing only a morphological and a molecular partition to those having complex substitution models with independent parameters for each gene. Bayesian MCMC analysis deals efficiently with complex models: convergence occurs faster and more predictably for complex models, mixing is adequate for all parameters even under very complex models, and the parameter update cycle is virtually unaffected by model partitioning across sites. Morphology contributed only 5% of the characters in the data set but nevertheless influenced the combined-data tree, supporting the utility of morphological data in multigene analyses. We used Bayesian criteria (Bayes factors) to show that process heterogeneity across data partitions is a significant model component, although not as important as among-site rate variation. More complex evolutionary models are associated with more topological uncertainty and less conflict between morphology and molecules. Bayes factors sometimes favor simpler models over considerably more parameter-rich models, but the best model overall is also the most complex and Bayes factors do not support exclusion of apparently weak parameters from this model. Thus, Bayes factors appear to be useful for selecting among complex models, but it is still unclear whether their use strikes a reasonable balance between model complexity and error in parameter estimates.

  • 31.
    Popp, Magnus
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolutionary Biology, Systematic Botany.
    Oxelman, Bengt
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolutionary Biology, Systematic Botany.
    Evolution of a RNA polymerase gene family in Silene (Caryophyllaceae) - incomplete concerted evolution and topological congruence among paralogues2004In: Systematic Biology, ISSN 1063-5157, E-ISSN 1076-836X, Vol. 53, no 6, p. 914-932Article in journal (Refereed)
    Abstract [sv]

    Four low-copy nuclear DNA intron regions from the second largest subunits of the RNA polymerase gene family (RPA2, RPB2, RPD2a, and RPD2b), the internal transcribed spacers (ITSs) from the nuclear ribosomal regions, and the rps16 intron from the chloroplast were sequenced and used in a phylogenetic analysis of 29 species from the tribe Sileneae (Caryophyllaceae). We used a low stringency nested polymerase chain reaction (PCR) approach to overcome the difficulties of constructing specific primers for amplification of the low copy nuclear DNA regions. Maximum parsimony analyses resulted in largely congruent phylogenetic trees for all regions. We tested overall model congruence in a likelihood context using the software PLATO and found that ITSs, RPA2, and RPB2 deviated from the maximum likelihood model for the combined data. The topology parameter was then isolated and topological congruence assessed by nonparametric bootstrapping. No strong topological incongruence was found. The analysis of the combined data sets resolves previously poorly known major relationships within Sileneae. Two paralogues of RPD2 were found, and several independent losses and incomplete concerted evolution were inferred. The among-site rate variation was significantly lower in the RNA polymerase introns than in the rps16 intron and ITSs, a property that is attractive in phylogenetic analyses.

  • 32.
    Rojas, Danny
    et al.
    Univ Aveiro, Dept Biol, P-3810193 Aveiro, Portugal.;Univ Aveiro, Ctr Environm & Marine Studies, P-3810193 Aveiro, Portugal.;SUNY Stony Brook, Dept Ecol & Evolut, 650 Life Sci Bldg, Stony Brook, NY 11794 USA..
    Warsi, Omar M.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology. SUNY Stony Brook, Dept Ecol & Evolut, 650 Life Sci Bldg, Stony Brook, NY 11794 USA..
    Davalos, Liliana M.
    SUNY Stony Brook, Dept Ecol & Evolut, 650 Life Sci Bldg, Stony Brook, NY 11794 USA.;SUNY Stony Brook, Sch Marine & Atmospher Sci, Consortium Interdisciplinary Environm Res, 129 Dana Hall, Stony Brook, NY 11794 USA..
    Bats (Chiroptera:Noctilionoidea) Challenge a Recent Origin of Extant Neotropical Diversity2016In: Systematic Biology, ISSN 1063-5157, E-ISSN 1076-836X, Vol. 65, no 3, p. 432-448Article in journal (Refereed)
    Abstract [en]

    The mechanisms underlying the high extant biodiversity in the Neotropics have been controversial since the 19th century. Support for the influence of period-specific changes on diversification often rests on detecting more speciation events during a particular period. The timing of speciation events may reflect the influence of incomplete taxon sampling, protracted speciation, and null processes of lineage accumulation. Here we assess the influence of these factors on the timing of speciation with new multilocus data for New World noctilionoid bats (Chiroptera: Noctilionoidea). Biogeographic analyses revealed the importance of the Neotropics in noctilionoid diversification, and the critical role of dispersal. We detected no shift in speciation rate associated with the Quaternary or pre-Quaternary periods, and instead found an increase in speciation linked to the evolution of the subfamily Stenodermatinae (similar to 18 Ma). Simulations modeling constant speciation and extinction rates for the phylogeny systematically showed more speciation events in the Quaternary. Since recording more divergence events in the Quaternary can result from lineage accumulation, the age of extant sister species cannot be interpreted as supporting higher speciation rates during this period. Instead, analyzing the factors that influence speciation requires modeling lineage-specific traits and environmental, spatial, and ecological drivers of speciation.

  • 33. Rothfels, Carl J.
    et al.
    Larsson, Anders
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Kuo, Li-Yaung
    Korall, Petra
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Chiou, Wen-Liang
    Pryer, Kathleen M.
    Overcoming Deep Roots, Fast Rates, and Short Internodes to Resolve the Ancient Rapid Radiation of Eupolypod II Ferns2012In: Systematic Biology, ISSN 1063-5157, E-ISSN 1076-836X, Vol. 61, no 3, p. 490-509Article in journal (Refereed)
    Abstract [en]

    Backbone relationships within the large eupolypod II clade, which includes nearly a third of extant fern species, have resisted elucidation by both molecular and morphological data. Earlier studies suggest that much of the phylogenetic intractability of this group is due to three factors: (i) a long root that reduces apparent levels of support in the ingroup; (ii) long ingroup branches subtended by a series of very short backbone internodes (the "ancient rapid radiation" model); and (iii) significantly heterogeneous lineage-specific rates of substitution. To resolve the eupolypod II phylogeny, with a particular emphasis on the backbone internodes, we assembled a data set of five plastid loci (atpA, atpB, matK, rbcL, and trnG-R) from a sample of 81 accessions selected to capture the deepest divergences in the clade. We then evaluated our phylogenetic hypothesis against potential confounding factors, including those induced by rooting, ancient rapid radiation, rate heterogeneity, and the Bayesian star-tree paradox artifact. While the strong support we inferred for the backbone relationships proved robust to these potential problems, their investigation revealed unexpected model-mediated impacts of outgroup composition, divergent effects of methods for countering the star-tree paradox artifact, and gave no support to concerns about the applicability of the unrooted model to data sets with heterogeneous lineage-specific rates of substitution. This study is among few to investigate these factors with empirical data, and the first to compare the performance of the two primary methods for overcoming the Bayesian star-tree paradox artifact. Among the significant phylogenetic results is the near-complete support along the eupolypod II backbone, the demonstrated paraphyly of Woodsiaceae as currently circumscribed, and the well-supported placement of the enigmatic genera Homalosorus, Diplaziopsis, and Woodsia.

  • 34.
    Svennblad, Bodil
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Mathematics, Mathematical Statistics.
    Consistent estimation of divergence times in phylogenetic trees with local molecular clocks2008In: Systematic Biology, ISSN 1063-5157, E-ISSN 1076-836X, Vol. 57, no 6, p. 947-954Article in journal (Refereed)
  • 35.
    Svennblad, Bodil
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Mathematics, Mathematical Statistics.
    Erixon, Per
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Botany.
    Oxelman, Bengt
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Botany.
    Britton, Tom
    Fundamental differences between the methods of maximum likelihood and maximum posterior probability in phylogenetics2006In: Systematic Biology, ISSN 1063-5157, E-ISSN 1076-836X, Vol. 55, no 1, p. 116-121Article in journal (Refereed)
  • 36.
    Whelan, Simon
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Allen, James E.
    Blackburne, Benjamin P.
    Talavera, David
    ModelOMatic: Fast and Automated Model Selection between RY, Nucleotide, Amino Acid, and Codon Substitution Models2015In: Systematic Biology, ISSN 1063-5157, E-ISSN 1076-836X, Vol. 64, no 1, p. 42-55Article in journal (Refereed)
    Abstract [en]

    Molecular phylogenetics is a powerful tool for inferring both the process and pattern of evolution from genomic sequence data. Statistical approaches, such as maximum likelihood and Bayesian inference, are now established as the preferred methods of inference. The choice of models that a researcher uses for inference is of critical importance, and there are established methods for model selection conditioned on a particular type of data, such as nucleotides, amino acids, or codons. A major limitation of existing model selection approaches is that they can only compare models acting upon a single type of data. Here, we extend model selection to allow comparisons between models describing different types of data by introducing the idea of adapter functions, which project aggregated models onto the originally observed sequence data. These projections are implemented in the program ModelOMatic and used to perform model selection on 3722 families from the PANDIT database, 68 genes from an arthropod phylogenomic data set, and 248 genes from a vertebrate phylogenomic data set. For the PANDIT and arthropod data, we find that amino acid models are selected for the overwhelming majority of alignments; with progressively smaller numbers of alignments selecting codon and nucleotide models, and no families selecting RY-based models. In contrast, nearly all alignments from the vertebrate data set select codon-based models. The sequence divergence, the number of sequences, and the degree of selection acting upon the protein sequences may contribute to explaining this variation in model selection. Our ModelOMatic program is fast, with most families from PANDIT taking fewer than 150 s to complete, and should therefore be easily incorporated into existing phylogenetic pipelines. ModelOMatic is available at https://code.google.com/p/modelomatic/.

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