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  • 1. Abbott, R.
    et al.
    Albach, D.
    Ansell, S.
    Arntzen, J. W.
    Baird, S. J. E.
    Bierne, N.
    Boughman, J.
    Brelsford, A.
    Buerkle, C. A.
    Buggs, R.
    Butlin, R. K.
    Dieckmann, U.
    Eroukhmanoff, F.
    Grill, A.
    Cahan, S. H.
    Hermansen, J. S.
    Hewitt, G.
    Hudson, A. G.
    Jiggins, C.
    Jones, J.
    Keller, B.
    Marczewski, T.
    Mallet, J.
    Martinez-Rodriguez, P.
    Möst, M.
    Mullen, S.
    Nichols, R.
    Nolte, A. W.
    Parisod, C.
    Pfennig, K.
    Rice, A. M.
    Ritchie, M. G.
    Seifert, B.
    Smadja, C. M.
    Stelkens, R.
    Szymura, J. M.
    Väinölä, R.
    Wolf, Jochen B. W.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Zinner, D.
    Hybridization and speciation2013In: Journal of Evolutionary Biology, ISSN 1010-061X, E-ISSN 1420-9101, Vol. 26, no 2, p. 229-246Article, review/survey (Refereed)
    Abstract [en]

    Hybridization has many and varied impacts on the process of speciation. Hybridization may slow or reverse differentiation by allowing gene flow and recombination. It may accelerate speciation via adaptive introgression or cause near-instantaneous speciation by allopolyploidization. It may have multiple effects at different stages and in different spatial contexts within a single speciation event. We offer a perspective on the context and evolutionary significance of hybridization during speciation, highlighting issues of current interest and debate. In secondary contact zones, it is uncertain if barriers to gene flow will be strengthened or broken down due to recombination and gene flow. Theory and empirical evidence suggest the latter is more likely, except within and around strongly selected genomic regions. Hybridization may contribute to speciation through the formation of new hybrid taxa, whereas introgression of a few loci may promote adaptive divergence and so facilitate speciation. Gene regulatory networks, epigenetic effects and the evolution of selfish genetic material in the genome suggest that the Dobzhansky-Muller model of hybrid incompatibilities requires a broader interpretation. Finally, although the incidence of reinforcement remains uncertain, this and other interactions in areas of sympatry may have knock-on effects on speciation both within and outside regions of hybridization.

  • 2.
    Adolfsson, Sofia
    et al.
    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.
    Lack of Dosage Compensation Accompanies the Arrested Stage of Sex Chromosome Evolution in Ostriches2013In: Molecular biology and evolution, ISSN 0737-4038, E-ISSN 1537-1719, Vol. 30, no 4, p. 806-810Article in journal (Refereed)
    Abstract [en]

    Sex chromosome evolution is usually seen as a process that, once initiated, will inevitably progress toward an advanced stage of degeneration of the nonrecombining chromosome. However, despite evidence that avian sex chromosome evolution was initiated > 100 Ma, ratite birds have been trapped in an arrested stage of sex chromosome divergence. We performed RNA sequencing of several tissues from male and female ostriches and assembled the transcriptome de novo. A total of 315 Z-linked genes fell into two categories: those that have equal expression level in the two sexes (for which Z-W recombination still occurs) and those that have a 2-fold excess of male expression (for which Z-W recombination has ceased). We suggest that failure to evolve dosage compensation has constrained sex chromosome divergence in this basal avian lineage. Our results indicate that dosage compensation is a prerequisite for, not only a consequence of, sex chromosome evolution.

  • 3.
    Adrian-Kalchhauser, Irene
    et al.
    Univ Basel, Program Man Soc Environm, Dept Environm Sci, Vesalgasse 1, CH-4051 Basel, Switzerland..
    Svensson, Ola
    Univ Gothenburg, Dept Biol & Environm Sci, Medicinaregatan 18A, S-41390 Gothenburg, Sweden.;Univ Gothenburg, Linnaeus Ctr Marine Evolutionary Biol, POB 46040530, Gothenburg, Sweden..
    Kutschera, Verena E.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Rosenblad, Magnus Alm
    Univ Gothenburg, Linnaeus Ctr Marine Evolutionary Biol, POB 46040530, Gothenburg, Sweden.;Univ Gothenburg, Dept Marine Sci, NBIS Bioinformat Infrastruct Life Sci, Medicinaregatan 9C, S-41390 Gothenburg, Sweden..
    Pippel, Martin
    Heidelberg Inst Theoret Studies, Schloss Wolfsbrunnenweg 35, D-69118 Heidelberg, Germany..
    Winkler, Sylke
    Max Planck Inst Mol Cell Biol & Genet, Pfotenhauerstr 108, D-01307 Dresden, Germany..
    Schloissnig, Siegfried
    Heidelberg Inst Theoret Studies, Schloss Wolfsbrunnenweg 35, D-69118 Heidelberg, Germany..
    Blomberg, Anders
    Univ Gothenburg, Linnaeus Ctr Marine Evolutionary Biol, POB 46040530, Gothenburg, Sweden.;Univ Gothenburg, Dept Marine Sci, Medicinaregatan 9C, S-41390 Gothenburg, Sweden..
    Burkhardt-Holm, Patricia
    Univ Basel, Program Man Soc Environm, Dept Environm Sci, Vesalgasse 1, CH-4051 Basel, Switzerland.;Univ Alberta, Dept Biol Sci, 11455 Saskatchewan Dr, Edmonton, AB, Canada..
    The mitochondrial genome sequences of the round goby and the sand goby reveal patterns of recent evolution in gobiid fish2017In: BMC Genomics, ISSN 1471-2164, E-ISSN 1471-2164, Vol. 18, article id 177Article in journal (Refereed)
    Abstract [en]

    Background: Vertebrate mitochondrial genomes are optimized for fast replication and low cost of RNA expression. Accordingly, they are devoid of introns, are transcribed as polycistrons and contain very little intergenic sequences. Usually, vertebrate mitochondrial genomes measure between 16.5 and 17 kilobases ( kb). Results: During genome sequencing projects for two novel vertebrate models, the invasive round goby and the sand goby, we found that the sand goby genome is exceptionally small (16.4 kb), while the mitochondrial genome of the round goby is much larger than expected for a vertebrate. It is 19 kb in size and is thus one of the largest fish and even vertebrate mitochondrial genomes known to date. The expansion is attributable to a sequence insertion downstream of the putative transcriptional start site. This insertion carries traces of repeats from the control region, but is mostly novel. To get more information about this phenomenon, we gathered all available mitochondrial genomes of Gobiidae and of nine gobioid species, performed phylogenetic analyses, analysed gene arrangements, and compared gobiid mitochondrial genome sizes, ecological information and other species characteristics with respect to the mitochondrial phylogeny. This allowed us amongst others to identify a unique arrangement of tRNAs among Ponto-Caspian gobies. Conclusions: Our results indicate that the round goby mitochondrial genome may contain novel features. Since mitochondrial genome organisation is tightly linked to energy metabolism, these features may be linked to its invasion success. Also, the unique tRNA arrangement among Ponto- Caspian gobies may be helpful in studying the evolution of this highly adaptive and invasive species group. Finally, we find that the phylogeny of gobiids can be further refined by the use of longer stretches of linked DNA sequence.

  • 4.
    Alavioon, Ghazal
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Hotzy, Cosima
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Nakhro, Khriezhanuo
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Rudolf, Sandra
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Scofield, Douglas
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Zajitschek, Susanne
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology. Spanish Natl Res Council, Donana Biol Stn, Seville 41092, Spain.
    Maklakov, Alex A
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology. Univ East Anglia, Sch Biol Sci, Norwich NR4 7TJ, Norfolk, England.
    Immler, Simone
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology. Univ East Anglia, Sch Biol Sci, Norwich NR4 7TJ, Norfolk, England.
    Haploid selection within a single ejaculate increases offspring fitness2017In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, no 30, p. 8053-8058Article in journal (Refereed)
    Abstract [en]

    An inescapable consequence of sex in eukaryotes is the evolution of a biphasic life cycle with alternating diploid and haploid phases. The occurrence of selection during the haploid phase can have far-reaching consequences for fundamental evolutionary processes including the rate of adaptation, the extent of inbreeding depression, and the load of deleterious mutations, as well as for applied research into fertilization technology. Although haploid selection is well established in plants, current dogma assumes that in animals, intact fertile sperm within a single ejaculate are equivalent at siring viable offspring. Using the zebrafish Danio rerio, we show that selection on phenotypic variation among intact fertile sperm within an ejaculate affects offspring fitness. Longer-lived sperm sired embryos with increased survival and a reduced number of apoptotic cells, and adult male offspring exhibited higher fitness. The effect on embryo viability was carried over into the second generation without further selection and was equally strong in both sexes. Sperm pools selected by motile phenotypes differed genetically at numerous sites throughout the genome. Our findings clearly link within-ejaculate variation in sperm phenotype to offspring fitness and sperm genotype in a vertebrate and have major implications for adaptive evolution.

  • 5.
    Ali, Raja Hashim
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Bogusz, Marcin
    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.
    A graph-based approach for improving the homologyinference in multiple sequence alignmentsManuscript (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.

  • 6. Allen, James E.
    et al.
    Whelan, Simon
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Assessing the State of Substitution Models Describing Noncoding RNA Evolution2014In: Genome Biology and Evolution, ISSN 1759-6653, E-ISSN 1759-6653, Vol. 6, no 1, p. 65-75Article in journal (Refereed)
    Abstract [en]

    Phylogenetic inference is widely used to investigate the relationships between homologous sequences. RNA molecules have played a key role in these studies because they are present throughout life and tend to evolve slowly. Phylogenetic inference has been shown to be dependent on the substitution model used. A wide range of models have been developed to describe RNA evolution, either with 16 states describing all possible canonical base pairs or with 7 states where the 10 mismatched nucleotides are reduced to a single state. Formal model selection has become a standard practice for choosing an inferential model and works well for comparing models of a specific type, such as comparisons within nucleotide models or within amino acid models. Model selection cannot function across different sized state spaces because the likelihoods are conditioned on different data. Here, we introduce statistical state-space projection methods that allow the direct comparison of likelihoods between nucleotide models and 7-state and 16-state RNA models. To demonstrate the general applicability of our new methods, we extract 287 RNA families from genomic alignments and perform model selection. We find that in 281/287 families, RNA models are selected in preference to nucleotide models, with simple 7-state RNA models selected for more conserved families with shorter stems and more complex 16-state RNA models selected for more divergent families with longer stems. Other factors, such as the function of the RNA molecule or the GC-content, have limited impact on model selection. Our models and model selection methods are freely available in the open-source software.

  • 7.
    Alström, Per
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology. Chinese Acad Sci, Inst Zool, Key Lab Zool Systemat & Evolut, Beijing 100101, Peoples R China.; Swedish Univ Agr Sci, Swedish Species Informat Ctr, Box 7007, S-75007 Uppsala, Sweden.
    Rasmussen, Pamela C
    Michigan State Univ, Dept Integrat Biol, E Lansing, MI 48864 USA.; Michigan State Univ, MSU Museum, E Lansing, MI 48864 USA.; Nat Hist Museum Tring, Bird Grp, Akeman St, Tring HP23 6AP, England.
    Zhao, Chao
    Cloud Mt Conservat, Dali 671003, Peoples R China.
    Xu, Jingzi
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Dalvi, Shashank
    GKVK, Natl Ctr Biol Sci, Researchers Wildlife Conservat, F-21,Bellary Rd, Bengaluru 560065, Karnataka, India.
    Cai, Tianlong
    Chinese Acad Sci, Inst Zool, Key Lab Zool Systemat & Evolut, Beijing 100101, Peoples R China.; Univ Chinese Acad Sci, Coll Life Sci, Beijing 100049, Peoples R China.
    Guan, Yuyan
    Univ Chinese Acad Sci, Coll Life Sci, Beijing 100049, Peoples R China.; Univ Chinese Acad Sci, Coll Life Sci, Beijing 100049, Peoples R China.
    Zhang, Ruiying
    Chinese Acad Sci, Inst Zool, Key Lab Zool Systemat & Evolut, Beijing 100101, Peoples R China.
    Kalyakin, Mikhail V.
    Lomonosov Moscow State Univ, Zool Museum, Bolshaya Nikitskaya Str 2, Moscow 125009, Russia.
    Lei, Fumin
    Chinese Acad Sci, Inst Zool, Key Lab Zool Systemat & Evolut, Beijing 100101, Peoples R China.
    Olsson, Urban
    Univ Gothenburg, Dept Biol & Environm Sci, Systemat & Biodivers, Box 463, S-40530 Gothenburg, Sweden.
    Integrative taxonomy of the Plain-backed Thrush (Zoothera mollissima) complex (Aves, Turdidae) reveals cryptic species, including a new species2016In: Avian Research, ISSN 0005-2175, E-ISSN 2053-7166, Vol. 7, article id 1Article in journal (Refereed)
    Abstract [en]

    Background: The Plain-backed Thrush Zoothera mollissima breeds in the Himalayas and mountains of central China. It was long considered conspecific with the Long-tailed Thrush Zoothera dixoni, until these were shown to be broadly sympatric.

    Methods: We revise the Z. mollissimaZ. dixoni complex by integrating morphological, acoustic, genetic (two mitochondrial and two nuclear markers), ecological and distributional datasets.

    Results: In earlier field observations, we noted two very different song types of “Plain-backed” Thrush segregated by breeding habitat and elevation. Further integrative analyses congruently identify three groups: an alpine breeder in the Himalayas and Sichuan, China (“Alpine Thrush”); a forest breeder in the eastern Himalayas and northwest Yunnan (at least), China (“Himalayan Forest Thrush”); and a forest breeder in central Sichuan (“Sichuan Forest Thrush”). Alpine and Himalayan Forest Thrushes are broadly sympatric, but segregated by habitat and altitude, and the same is probably true also for Alpine and Sichuan Forest Thrushes. These three groups differ markedly in morphology and songs. In addition, DNA sequence data from three non-breeding specimens from Yunnan indicate that yet another lineage exists (“Yunnan Thrush”). However, we find no consistent morphological differences from Alpine Thrush, and its breeding range is unknown. Molecular phylogenetic analyses suggest that all four groups diverged at least a few million years ago, and identify Alpine Thrush and the putative “Yunnan Thrush” as sisters, and the two forest taxa as sisters. Cytochrome b divergences among the four Z. mollissima sensu lato (s.l.) clades are similar to those between any of them and Z. dixoni, and exceed that between the two congeneric outgroup species. We lectotypify the name Oreocincla rostrata Hodgson, 1845 with the Z. mollissima sensu stricto (s.s.) specimen long considered its type. No available name unambiguously pertains to the Himalayan Forest Thrush.

    Conclusions: The Plain-backed Thrush Z. mollissima s.l. comprises at least three species: Alpine Thrush Z. mollissima s.s., with a widespread alpine breeding distribution; Sichuan Forest Thrush Z. griseiceps, breeding in central Sichuan forests; and Himalayan Forest Thrush, breeding in the eastern Himalayas and northwest Yunnan (at least), which is described herein as a new species. “Yunnan Thrush” requires further study.

  • 8.
    Amininasab, Seyed Mehdi
    et al.
    Univ Groningen, Behav & Physiol Ecol, Groningen Inst Evolutionary Life Sci, POB 11103, NL-9700 CC Groningen, Netherlands.;Behbahan Khatam Alanbia Univ Technol, Dept Environm Sci, Behbahan, Iran..
    Xu, Charles C. Y.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology. Univ Groningen, Behav & Physiol Ecol, Groningen Inst Evolutionary Life Sci, POB 11103, NL-9700 CC Groningen, Netherlands..
    Kingma, Sjouke A.
    Univ Groningen, Behav & Physiol Ecol, Groningen Inst Evolutionary Life Sci, POB 11103, NL-9700 CC Groningen, Netherlands..
    Komdeur, Jan
    Univ Groningen, Behav & Physiol Ecol, Groningen Inst Evolutionary Life Sci, POB 11103, NL-9700 CC Groningen, Netherlands..
    Effect of tree logging on reproductive performance in Blue Tits (Cyanistes caeruleus)2017In: Journal of Ornithology = Journal fur Ornithologie, ISSN 0021-8375, E-ISSN 1439-0361, Vol. 158, no 1, p. 339-344Article in journal (Refereed)
    Abstract [en]

    For birds, habitat quality is largely determined by local vegetation, and reproductive performance can therefore be negatively influenced by anthropogenic activities. A tree logging event enabled us to examine the effect of removing trees of different maturities and types on the reproductive performance of Blue Tits (Cyanistes caeruleus). Against expectations, only the logging of small coniferous trees, but not larger and deciduous trees, was associated with a reduction in the number of eggs laid, whereas logging had no significant effect on lay date. Therefore, we conclude that modest logging activity has no or limited negative influence on Blue Tit reproductive performance.

  • 9. Anderson, Tovi M.
    et al.
    vonHoldt, Bridgett M.
    Candille, Sophie I.
    Musiani, Marco
    Greco, Claudia
    Stahler, Daniel R.
    Smith, Douglas W.
    Padhukasahasram, Badri
    Randi, Ettore
    Leonard, Jennifer A.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolutionary Biology. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Bustamante, Carlos D.
    Ostrander, Elaine A.
    Tang, Hua
    Wayne, Robert K.
    Barsh, Gregory S.
    Molecular and Evolutionary History of Melanism in North American Gray Wolves2009In: Science, ISSN 0036-8075, E-ISSN 1095-9203, Vol. 323, no 5919, p. 1339-1343Article in journal (Refereed)
    Abstract [en]

    Morphological diversity within closely related species is an essential aspect of evolution and adaptation. Mutations in the Melanocortin 1 receptor (Mc1r) gene contribute to pigmentary diversity in natural populations of fish, birds, and many mammals. However, melanism in the gray wolf, Canis lupus, is caused by a different melanocortin pathway component, the K locus, that encodes a beta-defensin protein that acts as an alternative ligand for Mc1r. We show that the melanistic K locus mutation in North American wolves derives from past hybridization with domestic dogs, has risen to high frequency in forested habitats, and exhibits a molecular signature of positive selection. The same mutation also causes melanism in the coyote, Canis latrans, and in Italian gray wolves, and hence our results demonstrate how traits selected in domesticated species can influence the morphological diversity of their wild relatives.

  • 10. Antoniazza, Sylvain
    et al.
    Kanitz, Ricardo
    Neuenschwander, Samuel
    Burri, Reto
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Gaigher, Arnaud
    Roulin, Alexandre
    Goudet, Jerome
    Natural selection in a postglacial range expansion: the case of the colour cline in the European barn owl2014In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 23, no 22, p. 5508-5523Article, review/survey (Refereed)
    Abstract [en]

    Gradients of variationor clineshave always intrigued biologists. Classically, they have been interpreted as the outcomes of antagonistic interactions between selection and gene flow. Alternatively, clines may also establish neutrally with isolation by distance (IBD) or secondary contact between previously isolated populations. The relative importance of natural selection and these two neutral processes in the establishment of clinal variation can be tested by comparing genetic differentiation at neutral genetic markers and at the studied trait. A third neutral process, surfing of a newly arisen mutation during the colonization of a new habitat, is more difficult to test. Here, we designed a spatially explicit approximate Bayesian computation (ABC) simulation framework to evaluate whether the strong cline in the genetically based reddish coloration observed in the European barn owl (Tyto alba) arose as a by-product of a range expansion or whether selection has to be invoked to explain this colour cline, for which we have previously ruled out the actions of IBD or secondary contact. Using ABC simulations and genetic data on 390 individuals from 20 locations genotyped at 22 microsatellites loci, we first determined how barn owls colonized Europe after the last glaciation. Using these results in new simulations on the evolution of the colour phenotype, and assuming various genetic architectures for the colour trait, we demonstrate that the observed colour cline cannot be due to the surfing of a neutral mutation. Taking advantage of spatially explicit ABC, which proved to be a powerful method to disentangle the respective roles of selection and drift in range expansions, we conclude that the formation of the colour cline observed in the barn owl must be due to natural selection.

  • 11.
    Arnqvist, Göran
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Sayadi, Ahmed
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Immonen, Elina
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Hotzy, Cosima
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Rankin, Daniel
    Univ Zurich, Inst Evolutionary Biol & Environm Studies, Zurich, Switzerland..
    Tuda, Midori
    Kyushu Univ, Dept Bioresource Sci, Lab Insect Nat Enemies, Fukuoka 8128581, Japan.;Kyushu Univ, Inst Biol Control, Fac Agr, Fukuoka 8128581, Japan..
    Hjelmen, Carl E.
    Texas A&M Univ, Dept Entomol, College Stn, TX 77843 USA..
    Johnston, J. Spencer
    Texas A&M Univ, Dept Entomol, College Stn, TX 77843 USA..
    Genome size correlates with reproductive fitness in seed beetles2015In: Proceedings of the Royal Society of London. Biological Sciences, ISSN 0962-8452, E-ISSN 1471-2954, Vol. 282, no 1815, article id 20151421Article in journal (Refereed)
    Abstract [en]

    The ultimate cause of genome size (GS) evolution in eukaryotes remains a major and unresolved puzzle in evolutionary biology. Large-scale comparative studies have failed to find consistent correlations between GS and organismal properties, resulting in the 'C-value paradox'. Current hypotheses for the evolution of GS are based either on the balance between mutational events and drift or on natural selection acting upon standing genetic variation in GS. It is, however, currently very difficult to evaluate the role of selection because within-species studies that relate variation in life-history traits to variation in GS are very rare. Here, we report phylogenetic comparative analyses of GS evolution in seed beetles at two distinct taxonomic scales, which combines replicated estimation of GS with experimental assays of life-history traits and reproductive fitness. GS showed rapid and bidirectional evolution across species, but did not show correlated evolution with any of several indices of the relative importance of genetic drift. Within a single species, GS varied by 4-5% across populations and showed positive correlated evolution with independent estimates of male and female reproductive fitness. Collectively, the phylogenetic pattern of GS diversification across and within species in conjunction with the pattern of correlated evolution between GS and fitness provide novel support for the tenet that natural selection plays a key role in shaping GS evolution.

  • 12.
    Axelsson, Erik
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolutionary Biology. 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 Evolutionary Biology. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Quantification of Adaptive Evolution of Genes Expressed in Avian Brain and the Population Size Effect on the Efficacy of Selection2009In: Molecular biology and evolution, ISSN 0737-4038, E-ISSN 1537-1719, Vol. 26, no 5, p. 1073-1079Article in journal (Refereed)
    Abstract [en]

    Whether protein evolution is mainly due to fixation of beneficial alleles by positive selection or to random genetic drift has remained a contentious issue over the years. Here, we use two genomewide polymorphism data sets collected from chicken populations, together with divergence data from >5,000 chicken-zebra finch gene orthologs expressed in brain, to assess the amount of adaptive evolution in protein-coding genes of birds. First, we show that estimates of the fixation index (FI, the ratio of fixed nonsynonymous-to-synonymous changes over the ratio of the corresponding polymorphisms) are highly dependent on the character of the underlying data sets. Second, by using polymorphism data from high-frequency alleles, to avoid the confounding effect of slightly deleterious mutations segregating at low frequency, we estimate that about 20% of amino acid changes have been brought to fixation through positive selection during avian evolution. This estimate is intermediate to that obtained in humans (lower) and flies as well as bacteria (higher), and is consistent with population genetics theory that stipulates a positive relationship between the efficiency of selection and the effective population size. Further, by comparing the FIs for common and all alleles, we estimate that approximate to 20% of nonsynonymous variation segregating in chicken populations represent slightly deleterious mutations, which is less than in Drosophila. Overall, these results highlight the link between the effective population size and positive as well as negative selection.

  • 13.
    Babiker, Hiba
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Schlebusch, Carina M
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Hassan, Hisham Y
    Jakobsson, Mattias
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Genetic variation and population structure of Sudanese populations as indicated by 15 Identifiler sequence-tagged repeat (STR) loci.2011In: Investigative Genetics, ISSN 2041-2223, E-ISSN 2041-2223, Vol. 2, no 1Article in journal (Refereed)
    Abstract [en]

    BACKGROUND: There is substantial ethnic, cultural and linguistic diversity among the people living in east Africa, Sudan and the Nile Valley. The region around the Nile Valley has a long history of succession of different groups, coupled with demographic and migration events, potentially leading to genetic structure among humans in the region.

    RESULT: We report the genotypes of the 15 Identifiler microsatellite markers for 498 individuals from 18 Sudanese populations representing different ethnic and linguistic groups. The combined power of exclusion (PE) was 0.9999981, and the combined match probability was 1 in 7.4 × 1017. The genotype data from the Sudanese populations was combined with previously published genotype data from Egypt, Somalia and the Karamoja population from Uganda. The Somali population was found to be genetically distinct from the other northeast African populations. Individuals from northern Sudan clustered together with those from Egypt, and individuals from southern Sudan clustered with those from the Karamoja population. The similarity of the Nubian and Egyptian populations suggest that migration, potentially bidirectional, occurred along the Nile river Valley, which is consistent with the historical evidence for long-term interactions between Egypt and Nubia.

    CONCLUSION: We show that despite the levels of population structure in Sudan, standard forensic summary statistics are robust tools for personal identification and parentage analysis in Sudan. Although some patterns of population structure can be revealed with 15 microsatellites, a much larger set of genetic markers is needed to detect fine-scale population structure in east Africa and the Nile Valley.

  • 14.
    Backström, Niclas
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Adaptive evolution in passerine birds2014In: Encyclopedia of Life Sciences, ISSN 1476-9506, E-ISSN 1476-9506Article in journal (Other academic)
    Abstract [en]

    Adaptive evolution is the process whereby mutations that provide the carrier with a selective advantage increase in frequency in a population via the process of natural selection. Passerines are widespread, common and long-term targets for field study and they demonstrate a copious diversity in physiological and morphological adaptations to varying habitats, for example, beak size and wing shape, and they are, therefore, an important study system to understand adaptive evolution. Recent technological advancements have made it easier to investigate the mechanistic and evolutionary underpinnings of adaptive evolution by allowing genome sequence data to be generated in almost any species of interest. However, it is important to assess the contribution of neutral forces like demographic events and GC-biased gene conversion before concluding that selection has shaped the patterns observed in genomic data. Initial analyses in passerines have identified candidate genes that might be involved in, for example, song learning, beak morphology, disease resistance, high-altitude adaptation and exploratory behavior, but functional verifications are needed to establish a causative relationship between the identified genes and the traits. Key Concepts:Key Concepts: * Passerines are widespread, generally common and easy targets for field study and they demonstrate a copious diversity in physiological and morphological adaptations to varying habitats and they have, therefore, played an important role in previous studies concerning behaviour, ecology and evolution. * A full understanding of passerine adaptations requires an integrative approach aiming at identifying and characterising both proximate (mechanistic) and ultimate (evolutionary) underpinnings to adaptive traits. * The recent advancements in molecular techniques allows for using both comparative genomics, expression profiling, candidate gene approaches and classical association and QTL mapping strategies to identify the genetic basis of adaptive traits in passerines. * Groundwork studies of ecological genetics and genomics using comparative approaches, expression profiling and candidate genes are now accumulating and in a handful of cases we have an idea about the genetic basis of adaptive traits related to, for example, dietary specialisation, learning, exploratory behaviour, immune response and high-altitude adaptations in passerines. * Demographic history and other neutral processes, for example, GC-biased gene conversion (gcBGC), may mimic signals of selection and it is important to verify findings of adaptive evolution using independent methods.

  • 15.
    Backström, Niclas
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Forstmeier, Wolfgang
    Schielzeth, Holger
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Mellenius, Harriet
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Nam, Kiwoong
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Bolund, Elisabeth
    Webster, Matthew T.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Öst, Torbjörn
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences.
    Schneider, Melanie
    Kempenaers, Bart
    Ellegren, Hans
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    The recombination landscape of the zebra finch Taeniopygia guttata genome2010In: Genome Research, ISSN 1088-9051, E-ISSN 1549-5469, Vol. 20, no 4, p. 485-495Article in journal (Refereed)
    Abstract [en]

    Understanding the causes and consequences of variation in the rate of recombination is essential since this parameter is considered to affect levels of genetic variability, the efficacy of selection, and the design of association and linkage mapping studies. However, there is limited knowledge about the factors governing recombination rate variation. We genotyped 1920 single nucleotide polymorphisms in a multigeneration pedigree of more than 1000 zebra finches (Taeniopygia guttata) to develop a genetic linkage map, and then we used these map data together with the recently available draft genome sequence of the zebra finch to estimate recombination rates in 1 Mb intervals across the genome. The average zebra finch recombination rate (1.5 cM/Mb) is higher than in humans, but significantly lower than in chicken. The local rates of recombination in chicken and zebra finch were only weakly correlated, demonstrating evolutionary turnover of the recombination landscape in birds. The distribution of recombination events was heavily biased toward ends of chromosomes, with a stronger telomere effect than so far seen in any organism. In fact, the recombination rate was as low as 0.1 cM/Mb in intervals up to 100 Mb long in the middle of the larger chromosomes. We found a positive correlation between recombination rate and GC content, as well as GC-rich sequence motifs. Levels of linkage disequilibrium (LD) were significantly higher in regions of low recombination, showing that heterogeneity in recombination rates have left a footprint on the genomic landscape of LD in zebra finch populations.

  • 16.
    Backström, Niclas
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Lindell, Johan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Zhang, Yu
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Palkopoulou, Eleftheria
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Qvarnström, Anna
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal Ecology.
    Sætre, Glenn-Peter
    Ellegren, Hans
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    A high-density scan of the Z chromosome in ficedula flycatchers reveals candidate loci for diversifying selection2010In: Evolution, ISSN 0014-3820, E-ISSN 1558-5646, Vol. 64, no 12, p. 3461-3475Article in journal (Refereed)
    Abstract [en]

    Theoretical and empirical data suggest that genes located on sex chromosomes may play an important role both for sexually selected traits and for traits involved in the build-up of hybrid incompatibilities. We investigated patterns of genetic variation in 73 genes located on the Z chromosomes of two species of the flycatcher genus Ficedula, the pied flycatcher and the collared flycatcher. Sequence data were evaluated for signs of selection potentially related to genomic differentiation in these young sister species, which hybridize despite reduced fitness of hybrids. Seven loci were significantly more divergent between the two species than expected under neutrality and they also displayed reduced nucleotide diversity, consistent with having been influenced by directional selection. Two of the detected candidate regions contain genes that are associated with plumage coloration in birds. Plumage characteristics play an important role in species recognition in these flycatchers suggesting that the detected genes may have been involved in the evolution of sexual isolation between the species.

  • 17.
    Backström, Niclas
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Palkopoulou, Eleftheria
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Qvarnström, Anna
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal Ecology.
    Ellegren, Hans
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    No evidence for Z-chromosome rearrangements between the pied flycatcher and the collared flycatcher as judged by gene-based comparative genetic maps2010In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 19, no 16, p. 3394-3405Article in journal (Refereed)
    Abstract [en]

    Revealing the genetic basis of reproductive isolation is fundamental for understanding the speciation process. Chromosome speciation models propose a role for chromosomal rearrangements in promoting the build up of reproductive isolation between diverging populations and empirical data from several animal and plant taxa support these models. The pied flycatcher and the collared flycatcher are two closely related species that probably evolved reproductive isolation during geographical separation in Pleistocene glaciation refugia. Despite the short divergence time and current hybridization, these two species demonstrate a high degree of intrinsic post-zygotic isolation and previous studies have shown that traits involved in mate choice and hybrid viability map to the Z-chromosome. Could rearrangements of the Z-chromosome between the species explain their reproductive isolation? We developed high coverage Z-chromosome linkage maps for both species, using gene-based markers and large-scale SNP genotyping. Best order maps contained 57-62 gene markers with an estimated average density of one every 1-1.5 Mb. We estimated the recombination rates in flycatcher Z-chromosomes to 1.1-1.3 cM/Mb. A comparison of the maps of the two species revealed extensive co-linearity with no strong evidence for chromosomal rearrangements. This study does therefore not provide support the idea that sex chromosome rearrangements have caused the relatively strong post-zygotic reproductive isolation between these two Ficedula species.

  • 18.
    Backström, Niclas
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Saetre, Glenn-Peter
    Ellegren, Hans
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Inferring the demographic history of European Ficedula flycatcher populations2013In: BMC Evolutionary Biology, ISSN 1471-2148, E-ISSN 1471-2148, Vol. 13, p. 2-Article in journal (Refereed)
    Abstract [en]

    Background: Inference of population and species histories and population stratification using genetic data is important for discriminating between different speciation scenarios and for correct interpretation of genome scans for signs of adaptive evolution and trait association. Here we use data from 24 intronic loci re-sequenced in population samples of two closely related species, the pied flycatcher and the collared flycatcher. Results: We applied Isolation-Migration models, assignment analyses and estimated the genetic differentiation and diversity between species and between populations within species. The data indicate a divergence time between the species of <1 million years, significantly shorter than previous estimates using mtDNA, point to a scenario with unidirectional gene-flow from the pied flycatcher into the collared flycatcher and imply that barriers to hybridisation are still permeable in a recently established hybrid zone. Furthermore, we detect significant population stratification, predominantly between the Spanish population and other pied flycatcher populations. Conclusions: Our results provide further evidence for a divergence process where different genomic regions may be at different stages of speciation. We also conclude that forthcoming analyses of genotype-phenotype relations in these ecological model species should be designed to take population stratification into account.

  • 19.
    Backström, Niclas
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Shipilina, Daria
    Bloom, Mozes
    Edwards, Scott
    Cis-regulatory sequence variation and association with Mycoplasma load in natural populations of the house finch (Carpodacus mexicanus)2013In: Ecology and Evolution, ISSN 2045-7758, E-ISSN 2045-7758, Vol. 3, no 3, p. 655-666Article in journal (Refereed)
    Abstract [en]

    Characterization of the genetic basis of fitness traits in natural populations is important for understanding how organisms adapt to the changing environment and to novel events, such as epizootics. However, candidate fitness-influencing loci, such as regulatory regions, are usually unavailable in nonmodel species. Here, we analyze sequence data from targeted resequencing of the cis-regulatory regions of three candidate genes for disease resistance (CD74, HSP90α, and LCP1) in populations of the house finch (Carpodacus mexicanus) historically exposed (Alabama) and naïve (Arizona) to Mycoplasma gallisepticum. Our study, the first to quantify variation in regulatory regions in wild birds, reveals that the upstream regions of CD74 and HSP90α are GC-rich, with the former exhibiting unusually low sequence variation for this species. We identified two SNPs, located in a GC-rich region immediately upstream of an inferred promoter site in the gene HSP90α, that were significantly associated with Mycoplasma pathogen load in the two populations. The SNPs are closely linked and situated in potential regulatory sequences: one in a binding site for the transcription factor nuclear NFYα and the other in a dinucleotide microsatellite ((GC)6). The genotype associated with pathogen load in the putative NFYα binding site was significantly overrepresented in the Alabama birds. However, we did not see strong effects of selection at this SNP, perhaps because selection has acted on standing genetic variation over an extremely short time in a highly recombining region. Our study is a useful starting point to explore functional relationships between sequence polymorphisms, gene expression, and phenotypic traits, such as pathogen resistance that affect fitness in the wild.

  • 20.
    Backström, Niclas
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Väli, Ulo
    Sex- and species-biased gene flow in a spotted eagle hybrid zone.2011In: BMC Evolutionary Biology, ISSN 1471-2148, E-ISSN 1471-2148, Vol. 11Article in journal (Refereed)
    Abstract [en]

    BACKGROUND: Recent theoretical and empirical work points toward a significant role for sex-chromosome linked genes in the evolution of traits that induce reproductive isolation and for traits that evolve under influence of sexual selection. Empirical studies including recently diverged (Pleistocene), short-lived avian species pairs with short generation times have found that introgression occurs on the autosomes but not on the Z-chromosome. Here we study genetic differentiation and gene flow in the long-lived greater spotted eagle (Aquila clanga) and lesser spotted eagle (A. pomarina), two species with comparatively long generation times.

    RESULTS: Our data suggest that there is a directional bias in migration rates between hybridizing spotted eagles in eastern Europe. We find that a model including post divergence gene flow fits our data best for both autosomal and Z-chromosome linked loci but, for the Z-chromosome, the rate is reduced in the direction from A. pomarina to A. clanga.

    CONCLUSIONS: The fact that some introgression still occurs on the Z-chromosome between these species suggests that the differentiation process is in a more premature phase in our study system than in previously studied avian species pairs and that could be explained by a shorter divergence time and/or a longer average generation time in the spotted eagles. The results are in agreement with field observations and provide further insight into the role of sex-linked loci for the build-up of barriers to gene flow among diverging populations and species.

  • 21.
    Backström, Niclas
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Zhang, Qu
    Edwards, Scott V.
    Evidence from a House Finch (Haemorhous mexicanus) Spleen Transcriptome for Adaptive Evolution and Biased Gene Conversion in Passerine Birds2013In: Molecular biology and evolution, ISSN 0737-4038, E-ISSN 1537-1719, Vol. 30, no 5, p. 1046-1050Article in journal (Refereed)
    Abstract [en]

    Identifying genes influenced by natural selection can provide information about lineage-specific adaptations, and transcriptomes generated by next-generation sequencing are a useful resource for identifying such genes. Here, we utilize a spleen transcriptome for the house finch (Haemorhous mexicanus), an emerging model for sexual selection and disease ecology, together with previously sequenced avian genomes (chicken, turkey, and zebra finch), to investigate lineage-specific adaptations within birds. An analysis of 4,398 orthologous genes revealed a significantly higher ratio of nonsynonymous to synonymous substitutions and significantly higher GC content in passerines than in galliforms, an observation deviating from strictly neutral expectations but consistent with an effect of biased gene conversion on the evolutionary rate in passerines. These data also showed that genes exhibiting signs of positive selection and fast evolution in passerines have functional roles related to fat metabolism, neurodevelopment, and ion binding.

  • 22. Bains, Ripudaman K.
    et al.
    Kovacevic, Mirna
    Plaster, Christopher A.
    Tarekegn, Ayele
    Bekele, Endashaw
    Bradman, Neil N.
    Thomas, Mark G.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Molecular diversity and population structure at the Cytochrome P450 3A5 gene in Africa2013In: BMC Genetics, ISSN 1471-2156, E-ISSN 1471-2156, Vol. 14, p. 34-Article in journal (Refereed)
    Abstract [en]

    Background: Cytochrome P450 3A5 (CYP3A5) is an enzyme involved in the metabolism of many therapeutic drugs. CYP3A5 expression levels vary between individuals and populations, and this contributes to adverse clinical outcomes. Variable expression is largely attributed to four alleles, CYP3A5*1 (expresser allele); CYP3A5*3 (rs776746), CYP3A5*6 (rs10264272) and CYP3A5*7 (rs41303343) (low/non-expresser alleles). Little is known about CYP3A5 variability in Africa, a region with considerable genetic diversity. Here we used a multi-disciplinary approach to characterize CYP3A5 variation in geographically and ethnically diverse populations from in and around Africa, and infer the evolutionary processes that have shaped patterns of diversity in this gene. We genotyped 2538 individuals from 36 diverse populations in and around Africa for common low/non-expresser CYP3A5 alleles, and re-sequenced the CYP3A5 gene in five Ethiopian ethnic groups. We estimated the ages of low/non-expresser CYP3A5 alleles using a linked microsatellite and assuming a step-wise mutation model of evolution. Finally, we examined a hypothesis that CYP3A5 is important in salt retention adaptation by performing correlations with ecological data relating to aridity for the present day, 10,000 and 50,000 years ago. Results: We estimate that similar to 43% of individuals within our African dataset express CYP3A5, which is lower than previous independent estimates for the region. We found significant intra-African variability in CYP3A5 expression phenotypes. Within Africa the highest frequencies of high-activity alleles were observed in equatorial and Niger-Congo speaking populations. Ethiopian allele frequencies were intermediate between those of other sub-Saharan African and non-African groups. Re-sequencing of CYP3A5 identified few additional variants likely to affect CYP3A5 expression. We estimate the ages of CYP3A5*3 as similar to 76,400 years and CYP3A5*6 as similar to 218,400 years. Finally we report that global CYP3A5 expression levels correlated significantly with aridity measures for 10,000 [Spearmann's Rho= -0.465, p=0.004] and 50,000 years ago [Spearmann's Rho= -0.379, p=0.02]. Conclusions: Significant intra-African diversity at the CYP3A5 gene is likely to contribute to multiple pharmacogenetic profiles across the continent. Significant correlations between CYP3A5 expression phenotypes and aridity data are consistent with a hypothesis that the enzyme is important in salt-retention adaptation.

  • 23. Balding, David
    et al.
    Weale, Michael
    Richards, Michael
    Thomas, Mark
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Genetic and isotopic analysis and the UK border agency2010In: Significance, Vol. 7, no 2, p. 58-61Article in journal (Refereed)
  • 24. Barnes, Ian
    et al.
    Duda, Anna
    Pybus, Oliver G.
    Thomas, Mark G.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Ancient urbanization predicts genetic resistance to tuberculosis2011In: Evolution, ISSN 0014-3820, E-ISSN 1558-5646, Vol. 65, no 3, p. 842-848Article in journal (Refereed)
    Abstract [en]

    A link between urban living and disease is seen in recent and historical records, but the presence of this association in prehistory has been difficult to assess. If the transition to urban living does result in an increase in disease-based mortality, we might expect to see evidence of increased disease resistance in longer-term urbanized populations, as the result of natural selection. To test this, we determined the frequency of an allele (SLC11A1 1729 + 55del4) associated with natural resistance to intracellular pathogens such as tuberculosis and leprosy. We found a highly significantly correlation with duration of urban settlement-populations with a long history of living in towns are better adapted to resisting these infections. This correlation remains strong when we correct for autocorrelation in allele frequencies due to shared population history. Our results therefore support the interpretation that infectious disease loads became an increasingly important cause of human mortality after the advent of urbanization, highlighting the importance of population density in determining human health and the genetic structure of human populations.

  • 25.
    Barsh, Gregory S.
    et al.
    Stanford University.
    Anderson, Tovi M.
    Stanford University.
    Vonholdt, Bridgett M.
    University of California.
    Candille, Sophie I.
    Stanford University.
    Musiani, Marco
    University of Calgary.
    Stahler, Daniel R.
    University of California.
    Leonard, Jennifer
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Padhukasahasram, Badri
    Cornell University.
    Randi, Ettore
    Instituto Nazionale per la Fauna Selvatica.
    Bustamante, Carlos D.
    Cornell University.
    Ostrander, Elaine A.
    National Human Genome Research Institute, Bethesda.
    Tang, Hua
    Stanford University.
    Wayne, Robert K.
    University of California.
    How the Gray Wolf Got Its Color - Response2009In: Science, ISSN 0036-8075, E-ISSN 1095-9203, Vol. 325, no 5936, p. 34-34Article in journal (Refereed)
  • 26.
    Beekman, Madeleine
    et al.
    Univ Sydney, Sch Life & Environm Sci, Sydney, NSW 2006, Australia..
    Nieuwenhuis, Bart
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Ortiz-Barrientos, Daniel
    Univ Queensland, Sch Biol Sci, St Lucia, Qld, Australia..
    Evans, Jonathan P.
    Univ Western Australia, Sch Anim Biol, Ctr Evolutionary Biol, Nedlands, WA 6009, Australia..
    Sexual selection in hermaphrodites, sperm and broadcast spawners, plants and fungi2016In: Philosophical Transactions of the Royal Society of London. Biological Sciences, ISSN 0962-8436, E-ISSN 1471-2970, Vol. 371, no 1706, article id 20150541Article, review/survey (Refereed)
    Abstract [en]

    Darwin was the first to recognize that sexual selection is a strong evolutionary force. Exaggerated traits allow same-sex individuals to compete over access to mates and provide a mechanism by which mates are selected. It is relatively easy to appreciate how inter-and intrasexual selection work in organisms with the sensory capabilities to perceive physical or behavioural traits that signal mate quality or mate compatibility, and to assess the relative quality of competitors. It is therefore not surprising that most studies of sexual selection have focused on animals with separate sexes and obvious adaptations that function in the context of reproductive competition. Yet, many sexual organisms are both male and female at the same time, often lack sexual dimorphism and never come into direct contact at mating. How does sexual selection act in such species, and what can we learn from them? Here, we address these questions by exploring the potential for sexual selection in simultaneous hermaphrodites, sperm-and broadcast spawners, plants and fungi. Our reviewreveals a range of mechanisms of sexual selection, operating primarily after gametes have been released, which are common in many of these groups and also quite possibly in more familiar (internally fertilizing and sexually dimorphic) organisms. This article is part of the themed issue 'Weird sex: the underappreciated diversity of sexual reproduction'.

  • 27.
    Berger, David
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Walters, R. J.
    Blanckenhorn, W. U.
    Experimental evolution for generalists and specialists reveals multivariate genetic constraints on thermal reaction norms2014In: Journal of Evolutionary Biology, ISSN 1010-061X, E-ISSN 1420-9101, Vol. 27, no 9, p. 1975-1989Article in journal (Refereed)
    Abstract [en]

    Theory predicts the emergence of generalists in variable environments and antagonistic pleiotropy to favour specialists in constant environments, but empirical data seldom support such generalist-specialist trade-offs. We selected for generalists and specialists in the dung fly Sepsis punctum (Diptera: Sepsidae) under conditions that we predicted would reveal antagonistic pleiotropy and multivariate trade-offs underlying thermal reaction norms for juvenile development. We performed replicated laboratory evolution using four treatments: adaptation at a hot (31 degrees C) or a cold (15 degrees C) temperature, or under regimes fluctuating between these temperatures, either within or between generations. After 20 generations, we assessed parental effects and genetic responses of thermal reaction norms for three correlated life-history traits: size at maturity, juvenile growth rate and juvenile survival. We find evidence for antagonistic pleiotropy for performance at hot and cold temperatures, and a temperature-mediated trade-off between juvenile survival and size at maturity, suggesting that trade-offs associated with environmental tolerance can arise via intensified evolutionary compromises between genetically correlated traits. However, despite this antagonistic pleiotropy, we found no support for the evolution of increased thermal tolerance breadth at the expense of reduced maximal performance, suggesting low genetic variance in the generalist-specialist dimension.

  • 28.
    Bischof, Richard
    et al.
    Norwegian Univ Life Sci, Dept Ecol & Nat Resource Management, Hogskoleveien 12, N-1430 As, Norway..
    Gregersen, Espen R.
    Norwegian Univ Life Sci, Dept Ecol & Nat Resource Management, Hogskoleveien 12, N-1430 As, Norway..
    Broseth, Henrik
    Norwegian Inst Nat Res, Tungasletta 2, N-7004 Trondheim, Norway..
    Ellegren, Hans
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Flagstad, Oystein
    Norwegian Inst Nat Res, Tungasletta 2, N-7004 Trondheim, Norway..
    Noninvasive genetic sampling reveals intrasex territoriality in wolverines2016In: Ecology and Evolution, ISSN 2045-7758, E-ISSN 2045-7758, Vol. 6, no 5, p. 1527-1536Article in journal (Refereed)
    Abstract [en]

    Due to its conspicuous manifestations and its capacity to shape the configuration and dynamics of wild populations, territorial behavior has long intrigued ecologists. Territoriality and other animal interactions in situ have traditionally been studied via direct observations and telemetry. Here, we explore whether noninvasive genetic sampling, which is increasingly supplementing traditional field methods in ecological research, can reveal territorial behavior in an elusive carnivore, the wolverine (Gulo gulo). Using the locations of genotyped wolverine scat samples collected annually over a period of 12 years in central Norway, we test three predictions: (1) male home ranges constructed from noninvasive genetic sampling data are larger than those of females, (2) individuals avoid areas used by other conspecifics of the same sex (intrasexual territoriality), and (3) avoidance of same-sex territories diminishes or disappears after the territory owner's death. Each of these predictions is substantiated by our results: sex-specific differences in home range size and intrasexual territoriality in wolverine are patently reflected in the spatial and temporal configuration of noninvasively collected genetic samples. Our study confirms that wildlife monitoring programs can utilize the spatial information in noninvasive genetic sampling data to detect and quantify home ranges and social organization.

  • 29. Blum, Michael G. B.
    et al.
    Jakobsson, Mattias
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Deep Divergences of Human Gene Trees and Models of Human Origins2011In: Molecular biology and evolution, ISSN 0737-4038, E-ISSN 1537-1719, Vol. 28, no 2, p. 889-898Article in journal (Refereed)
    Abstract [en]

    Two competing hypotheses are at the forefront of the debate on modern human origins. In the first scenario, known as the recent Out-of-Africa hypothesis, modern humans arose in Africa about 100,000-200,000 years ago and spread throughout the world by replacing the local archaic human populations. By contrast, the second hypothesis posits substantial gene flow between archaic and emerging modern humans. In the last two decades, the young time estimates-between 100,000 and 200,000 years-of the most recent common ancestors for the mitochondrion and the Y chromosome provided evidence in favor of a recent African origin of modern humans. However, the presence of very old lineages for autosonnal and X-linked genes has often been claimed to be incompatible with a simple, single origin of modern humans. Through the analysis of a public DNA sequence database, we find, similar to previous estimates, that the common ancestors of autosomal and X-linked genes are indeed very old, living, on average, respectively, 1,500,000 and 1,000,000 years ago. However, contrary to previous conclusions, we find that these deep gene genealogies are consistent with the Out-of-Africa scenario provided that the ancestral effective population size was approximately 14,000 individuals. We show that an ancient bottleneck in the Middle Pleistocene, possibly arising from an ancestral structured population, can reconcile the contradictory findings from the mitochondrion on the one hand, with the autosomes and the X chromosome on the other hand.

  • 30.
    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
  • 31.
    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.

  • 32.
    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.

  • 33.
    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.

  • 34. Bollongino, Ruth
    et al.
    Burger, Joachim
    Powell, Adam
    Mashkour, Marjan
    Vigne, Jean-Denis
    Thomas, Mark G.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Modern Taurine Cattle Descended from Small Number of Near-Eastern Founders2012In: Molecular biology and evolution, ISSN 0737-4038, E-ISSN 1537-1719, Vol. 29, no 9, p. 2101-2104Article in journal (Refereed)
    Abstract [en]

    Archaeozoological and genetic data indicate that taurine cattle were first domesticated from local wild ox (aurochs) in the Near East some 10,500 years ago. However, while modern mitochondrial DNA (mtDNA) variation indicates early Holocene founding event(s), a lack of ancient DNA data from the region of origin, variation in mutation rate estimates, and limited application of appropriate inference methodologies have resulted in uncertainty on the number of animals first domesticated. A large number would be expected if cattle domestication was a technologically straightforward and unexacting region-wide phenomenon, while a smaller number would be consistent with a more complex and challenging process. We report mtDNA sequences from 15 Neolithic to Iron Age Iranian domestic cattle and, in conjunction with modern data, use serial coalescent simulation and approximate Bayesian computation to estimate that around 80 female aurochs were initially domesticated. Such a low number is consistent with archaeological data indicating that initial domestication took place in a restricted area and suggests the process was constrained by the difficulty of sustained managing and breeding of the wild progenitors of domestic cattle.

  • 35. Bolund, Elisabeth
    et al.
    Schielzeth, Holger
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Forstmeier, Wolfgang
    Correlates of male fitness in captive zebra finches: a comparison of methods to disentangle genetic and environmental effects2011In: BMC Evolutionary Biology, ISSN 1471-2148, E-ISSN 1471-2148, Vol. 11, p. 327-Article in journal (Refereed)
    Abstract [en]

    Backgound: It is a common observation in evolutionary studies that larger, more ornamented or earlier breeding individuals have higher fitness, but that body size, ornamentation or breeding time does not change despite of sometimes substantial heritability for these traits. A possible explanation for this is that these traits do not causally affect fitness, but rather happen to be indirectly correlated with fitness via unmeasured non-heritable aspects of condition (e. g. undernourished offspring grow small and have low fitness as adults due to poor health). Whether this explanation applies to a specific case can be examined by decomposing the covariance between trait and fitness into its genetic and environmental components using pedigree-based animal models. We here examine different methods of doing this for a captive zebra finch population where male fitness was measured in communal aviaries in relation to three phenotypic traits (tarsus length, beak colour and song rate). Results: Our case study illustrates how methods that regress fitness over breeding values for phenotypic traits yield biased estimates as well as anti-conservative standard errors. Hence, it is necessary to estimate the genetic and environmental covariances between trait and fitness directly from a bivariate model. This method, however, is very demanding in terms of sample sizes. In our study parameter estimates of selection gradients for tarsus were consistent with the hypothesis of environmentally induced bias (beta(A) = 0.035 +/- 0.25 (SE), beta(E) = 0.57 +/- 0.28 (SE)), yet this differences between genetic and environmental selection gradients falls short of statistical significance. Conclusions: To examine the generality of the idea that phenotypic selection gradients for certain traits (like size) are consistently upwardly biased by environmental covariance a meta-analysis across study systems will be needed.

  • 36.
    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.

  • 37. Brace, Selina
    et al.
    Barnes, Ian
    Powell, Adam
    Pearson, Rebecca
    Woolaver, Lance G.
    Thomas, Mark G.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Turvey, Samuel T.
    Population history of the Hispaniolan hutia Plagiodontia aedium (Rodentia Capromyidae): testing the model of ancient differentiation on a geotectonically complex Caribbean island2012In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 21, no 9, p. 2239-2253Article in journal (Refereed)
    Abstract [en]

    Hispaniola is a geotectonically complex island consisting of two palaeo-islands that docked c. 10 Ma, with a further geological boundary subdividing the southern palaeo-island into eastern and western regions. All three regions have been isolated by marine barriers during the late Cenozoic and possess biogeographically distinct terrestrial biotas. However, there is currently little evidence to indicate whether Hispaniolan mammals show distributional patterns reflecting this geotectonic history, as the islands endemic land mammal fauna is now almost entirely extinct. We obtained samples of Hispaniolan hutia (Plagiodontia aedium), one of the two surviving Hispaniolan land mammal species, through fieldwork and historical museum collections from seven localities distributed across all three of the islands biogeographic regions. Phylogenetic analysis using mitochondrial DNA (cytochrome b) reveals a pattern of historical allopatric lineage divergence in this species, with the spatial distribution of three distinct hutia lineages biogeographically consistent with the islands geotectonic history. Coalescent modelling, approximate Bayesian computation and approximate Bayes factor analyses support our phylogenetic inferences, indicating near-complete genetic isolation of these biogeographically separate populations and differing estimates of their effective population sizes. Spatial congruence of hutia lineage divergence is not however matched by temporal congruence with divergences in other Hispaniolan taxa or major events in Hispaniolas geotectonic history; divergence between northern and southern hutia lineages dates to c. 0.6 Ma, significantly later than the unification of the palaeo-islands. The three allopatric Plagiodontia populations should all be treated as distinct management units for conservation, with particular attention required for the northern population (low haplotype diversity) and the south-western population (high haplotype diversity but highly threatened).

  • 38. Brandariz-Fontes, Claudia
    et al.
    Leonard, Jennifer A.
    Luis Vega-Pla, Jose
    Backström, Niclas
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Lindgren, Gabriella
    Lippold, Sebastian
    Rico, Ciro
    Y-Chromosome Analysis in Retuertas Horses2013In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 8, no 5, p. e64985-Article in journal (Refereed)
    Abstract [en]

    Several studies based on a variety of genetic markers have attempted to establish the origins of horse domestication. Thus far a discrepancy between the results of mitochondrial DNA analysis, which show high levels of diversity, and results from the Y-chromosome, with almost no genetic variability, has been identified. Most previous work on the horse Y-chromosome has focused on widespread, popular breeds or local Asian breeds. It is possible that these breeds represent a reduced set of the genetic variation present in the species. Additional genetic variation may be present in local breeds and ancient feral populations, such as the Retuertas horse in Spain. In this study we analyzed the Y-chromosome of the Retuertas horse, a feral horse population on the Iberian Peninsula that is at least several hundred years old, and whose genetic diversity and morphology suggests that it has been reproductively isolated for a long time. Data from the Retuertas horse was compared to another 11 breeds from the region (Portugal, Spain and France) or likely of Iberian origin, and then to data from 15 more breeds from around the globe. We sequenced 31 introns, Zinc finger Y-chromosomal protein (ZFY) and anonymous Y-linked fragments and genotyped 6 microsatellite loci found on the Y-chromosome. We found no sequence variation among all individuals and all breeds studied. However, fifteen differences were discovered between our data set and reference sequences in GenBank. We show that these likely represent errors within the deposited sequences, and suggest that they should not be used as comparative data for future projects.

  • 39.
    Brandström, Mikael
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics. 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 Evolution, Genomics and Systematics. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    The genomic landscape of short insertion and deletion polymorphisms in the chicken (Gallus gallus) genome: A high frequency of deletions in tandem duplicates2007In: Genetics, ISSN 0016-6731, E-ISSN 1943-2631, Vol. 176, no 3, p. 1691-1701Article in journal (Refereed)
    Abstract [en]

    It is increasingly recognized that insertions and deletions(indels) are an important source of genetic as well as phenotypicdivergence and diversity. We analyzed length polymorphisms identifiedthrough partial (0.25x) shotgun sequencing of three breeds ofdomestic chicken made by the International Chicken PolymorphismMap Consortium. A data set of 140,484 short indel polymorphismsin unique DNA was identified after filtering for microsatellitestructures. There was a significant excess of tandem duplicatesat indel sites, with deletions of a duplicate motif outnumberingthe generation of duplicates through insertion. Indel densitywas lower in microchromosomes than in macrochromosomes, in theZ chromosome than in autosomes, and in 100 bp of upstream sequence,5'-UTR, and first introns than in intergenic DNA and in otherintrons. Indel density was highly correlated with single nucleotidepolymorphism (SNP) density. The mean density of indels in pairwisesequence comparisons was 1.9 x 10–4 indel events/bp, 5%the density of SNPs segregating in the chicken genome. The greatmajority of indels involved a limited number of nucleotides(median 1 bp), with A-rich motifs being overrepresented at indelsites. The overrepresentation of deletions at tandem duplicatesindicates that replication slippage in duplicate sequences isa common mechanism behind indel mutation. The correlation betweenindel and SNP density indicates common effects of mutation and/orselection on the occurrence of indels and point mutations.

  • 40. Brandvain, Yaniv
    et al.
    Slotte, Tanja
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Hazzouri, Khaled M.
    Wright, Stephen I.
    Coop, Graham
    Genomic Identification of Founding Haplotypes Reveals the History of the Selfing Species Capsella rubella2013In: PLOS Genetics, ISSN 1553-7390, E-ISSN 1553-7404, Vol. 9, no 9, p. e1003754-Article in journal (Refereed)
    Abstract [en]

    The shift from outcrossing to self-fertilization is among the most common evolutionary transitions in flowering plants. Until recently, however, a genome-wide view of this transition has been obscured by both a dearth of appropriate data and the lack of appropriate population genomic methods to interpret such data. Here, we present a novel population genomic analysis detailing the origin of the selfing species, Capsella rubella, which recently split from its outcrossing sister, Capsella grandiflora. Due to the recency of the split, much of the variation within C. rubella is also found within C. grandiflora. We can therefore identify genomic regions where two C. rubella individuals have inherited the same or different segments of ancestral diversity (i.e. founding haplotypes) present in C. rubella's founder(s). Based on this analysis, we show that C. rubella was founded by multiple individuals drawn from a diverse ancestral population closely related to extant C. grandiflora, that drift and selection have rapidly homogenized most of this ancestral variation since C. rubella's founding, and that little novel variation has accumulated within this time. Despite the extensive loss of ancestral variation, the approximately 25% of the genome for which two C. rubella individuals have inherited different founding haplotypes makes up roughly 90% of the genetic variation between them. To extend these findings, we develop a coalescent model that utilizes the inferred frequency of founding haplotypes and variation within founding haplotypes to estimate that C. rubella was founded by a potentially large number of individuals between 50 and 100 kya, and has subsequently experienced a twenty-fold reduction in its effective population size. As population genomic data from an increasing number of outcrossing/selfing pairs are generated, analyses like the one developed here will facilitate a fine-scaled view of the evolutionary and demographic impact of the transition to self-fertilization.

  • 41.
    Breton, Gwenna
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Schlebusch, Carina M.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology. Uppsala University.
    Lombard, Marlize
    Sjödin, Per
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Soodyall, Himla
    Jakobsson, Mattias
    Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Lactase Persistence Alleles Reveal Partial East African Ancestry of Southern African Khoe Pastoralists2014In: Current Biology, ISSN 0960-9822, E-ISSN 1879-0445, Vol. 24, no 8, p. 852-858Article in journal (Refereed)
    Abstract [en]

    The ability to digest milk into adulthood, lactase persistence (LP), as well as specific genetic variants associated with LP, is heterogeneously distributed in global populations [1-4]. These variants were most likely targets of selection when some populations converted from hunter-gatherer to pastoralist or farming lifestyles [5-7]. Specific LP polymorphisms are associated with particular geographic regions and populations [1-4, 8-10]; however, they have not been extensively studied in southern Africa. We investigate the LP-regulatory region in 267 individuals from 13 southern African populations (including descendants of hunter-gatherers, pastoralists, and agropastoralists), providing the first comprehensive study of the LP-regulatory region in a large group of southern Africans. The "East African" LP single-nucleotide polymorphism (SNP) (14010G>C) was found at high frequency (>20%) in a strict pastoralist Khoe population, the Nama of Namibia, suggesting a connection to East Africa, whereas the "European" LP SNP (13910C>T) was found in populations of mixed ancestry. Using genome-wide data from various African populations, we identify admixture (13%) in the Nama, from an Afro-Asiatic group dating to >1,300 years ago, with the remaining fraction of their genomes being from San hunter-gatherers. We also find evidence of selection around the LCT gene among Khoe-speaking groups, and the substantial frequency of the 14010C variant among the Nama is best explained by adaptation to digesting milk. These genome-local and genome-wide results support a model in which an East African group brought pastoralist practices to southern Africa and admixed with local hunter-gatherers to form the ancestors of Khoe people.

  • 42. Broseth, Henrik
    et al.
    Flagstad, Oystein
    Wärdig, Cecilia
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Johansson, Malin
    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.
    Large-scale noninvasive genetic monitoring of wolverines using scats reveals density dependent adult survival2010In: Biological Conservation, ISSN 0006-3207, E-ISSN 1873-2917, Vol. 143, no 1, p. 113-120Article in journal (Refereed)
    Abstract [en]

    Noninvasive genetic monitoring has the potential to estimate vital rates essential for conservation and management of many species. In a long-term genetic capture-mark-recapture study using scats we evaluated temporal variation in adult survival in a wolverine (Gulo gulo) population in southern Norway. In contrast to most previous studies of large mammals we found evidence for negative density dependence in adult survival in this large carnivore. Both sexes showed the same pattern of density dependence, with higher annual survival rates in adult females than males. In addition, we also found an additive mortality effect of harvesting in the population, resulting in the lowest adult survival rates at a combination of high population density and high harvest rate. The additive effects of density and harvest on adult survival of wolverines have relevance to the conservation and management of solitary carnivores with strong intrasexual territoriality, especially for species where combats among conspecifics can cause serious injury or even mortality.

  • 43. Browning, Sarah L.
    et al.
    Tarekegn, Ayele
    Bekele, Endashaw
    Bradman, Neil
    Thomas, Mark G.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    CYP1A2 is more variable than previously thought: a genomic biography of the gene behind the human drug-metabolizing enzyme2010In: Pharmacogenetics and genomics, ISSN 1744-6872, Vol. 20, no 11, p. 647-664Article in journal (Refereed)
    Abstract [en]

    Background and objectives CYP1A2 metabolizes various drugs, endogenous compounds and procarcinogens. As human genetic diversity has been reported to decrease with distance from Ethiopia, we resequenced CYP1A2 in five Ethiopian ethnic groups representing a rough northeast to southwest transect across Ethiopia to establish: (i) what variation exists in comparison with what is already known globally and (ii) what CYP1A2 pharmacogenetic profiles may be present as several CYP1A2-metabolized drugs are administered to Ethiopians. Results and conclusions We found 49 different variable sites (30 of which are novel), nine nonsynonymous changes (seven of which are novel), one synonymous change and 55 different haplotypes, only three of which are previously reported. When haplotypes were constructed using only nonsynonymous polymorphisms to restrict haplotypes to those most likely to affect enzyme structure/function, 10 haplotypes were identified (seven contain previously unidentified nonsynonymous variants and four are predicted to alter the enzyme structure/function). Most individuals have at least one copy of the ancestral haplotype. Comparing these data with those from publically available databases, Ethiopian groups display twice the variation seen in all other populations combined (gene diversity using nonsynonymous variants): Ethiopia = 0.17 +/- 0.02, other populations = 0.08 +/- 0.03. Across the entire gene, Ethiopia also evidences all common variation found on a global scale. We provide evidence of weak purifying selection acting on CYP1A2 and show that the time to most recent common ancestor, calculated using variation in a nearby microsatellite, places several variants into a period predating the expansion of modern humans out of Africa less than 100 000 years ago. Pharmacogenetics and Genomics 20:647-664 (C) 2010 Wolters Kluwer Health vertical bar Lippincott Williams & Wilkins.

  • 44. Bryan, Heather M
    et al.
    Sim, Kathrin A
    Darimont, Chris T
    Paquet, Paul C
    Wagner, Brent
    Muñoz-Fuentes, Violeta
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Smits, Judit E
    Chilton, Neil B
    Identification of Parelaphostrongylus odocoilei (Nematoda: Protostrongylidae) First-Stage Larvae in the Feces of Gray Wolves (Canis lupus) by Molecular Methods2010In: Journal of Wildlife Diseases, ISSN 0090-3558, E-ISSN 1943-3700, Vol. 46, no 1, p. 297-302Article in journal (Refereed)
    Abstract [en]

    First-stage nematode larvae with a dorsal-spine (E)SI.)),were, detected ill five of, 1,565 fecal samples from gray wolves (Canis lupus) collected ill British Columbia, Canada, between 2005 and 2008. Molecular techniques were used to identify the DSL because it was not possible to determine their species identity using morphologic characters. The DSL were identified as parelaphostrongylus odocoilei based oil the results of single-strand conformation polymorphism (SSCP) analyses and DNA sequencing of the ribosomal DNA First and second internal transcribed spacers. Finding DSL of P. odocoilei in the feces of gray wolves was unexpected because P. odocoilei adults are parasites of cervids and bovids. The most likely explanation for the presence of DSL in wolf feces is that they were ingested along with the viscera of recently consumed prey. This was probably black-tailed deer (Odocoileus hemionus columbianus), which are known in the sampling area to be hosts of P. odocoilei. The present study demonstrates the use of SSCP and DNA sequencing for the identification, to the species level, of,parasitic nematode larvae ill feces.

  • 45.
    Burdon, Rosalie C. F.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Junker, Robert R.
    Scofield, Douglas
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Parachnowitsch, Amy L.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Bacteria colonising Penstemon digitalis show volatile and tissue-specific responses to a natural concentration range of the floral volatile linalool2018In: Chemoecology, ISSN 0937-7409, E-ISSN 1423-0445, Vol. 28, no 1, p. 11-19Article in journal (Refereed)
  • 46.
    Burdon, Rosalie C.F.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Scofield, Douglas G.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Pierce, Ellen
    Worcester Polytechnic Institute, Dept of Biol and Biotech, Worcester, MA, 01609, USA .
    Gegear, Robert J.
    Worcester Polytechnic Institute, Dept of Biol and Biotech, Worcester, MA, 01609, USA .
    Parachnowitsch, Amy L.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Multimodal signal honesty in Penstemon digitalis enhances bumblebee foragingManuscript (preprint) (Other academic)
  • 47.
    Burgevin, Lorraine
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Friberg, Urban
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Maklakov, Alexei A.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Intersexual correlation for same-sex sexual behaviour in an insect2013In: Animal Behaviour, ISSN 0003-3472, E-ISSN 1095-8282, Vol. 85, no 4, p. 759-762Article in journal (Refereed)
    Abstract [en]

    Same-sex sexual behaviour is widespread across taxa and is particularly common in insects, in which up to 50% of copulation attempts by males are directed towards other males in some species. Research effort has focused on male-male same-sex behaviour and the prevailing theory is that benefits of high mating rate combined with poor sex discrimination explain the high incidence of male-male mounting. However, the evolution of female-female mounting is more enigmatic, since females typically do not mount males in order to mate. Using a full-sib design, we found an intersexual correlation for same-sex mounting in the beetle Callosobruchus maculatus. Variation in male-male mounting across families explained over 20% of variation in female-female mounting. Moreover, we found no evidence that same-sex behaviour was related to general activity level in either sex or carried a fitness cost to females. Taken together, our results suggest that female-female mounting is a relatively low-cost behaviour that may be maintained in the population via selection on males.

  • 48.
    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.

  • 49.
    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.

  • 50.
    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.

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