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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, 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.

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  • 4.
    Alavioon, Ghazal
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Garcia, Andrea Cabrera
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    LeChatelier, Magali
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    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 Res Pk, Norwich, 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 Res Pk, Norwich, Norfolk, England.
    Selection for longer lived sperm within ejaculate reduces reproductive ageing in offspring2019In: Evolution Letters, E-ISSN 2056-3744, Vol. 3, no 2, p. 198-206Article in journal (Refereed)
    Abstract [en]

    Males produce numerous sperm in a single ejaculate that greatly outnumber their potential egg targets. Recent studies found that phenotypic and genotypic variation among sperm in a single ejaculate of a male affects the fitness and performance of the resulting offspring. Specifically, within-ejaculate sperm selection for sperm longevity increased the performance of the resulting offspring in several key life-history traits in early life. Because increased early-life reproductive performance often correlates with rapid ageing, it is possible that within-ejaculate sperm selection increases early-life fitness at the cost of accelerated senescence. Alternatively, within-ejaculate sperm selection could improve offspring quality throughout the life cycle, including reduced age-specific deterioration. We tested the two alternative hypotheses in an experimental setup using zebrafish Danio rerio. We found that within-ejaculate sperm selection for sperm longevity reduced age-specific deterioration of fecundity and offspring survival but had no effect on fertilization success in males. Remarkably, we found an opposing effect of within-ejaculate sperm selection on female fecundity, where selection for sperm longevity resulted in increased early-life performance followed by a slow decline, while females sired by unselected sperm started low but increased their fecundity with age. Intriguingly, within-ejaculate sperm selection also reduced the age-specific decline in fertilization success in females, suggesting that selection for sperm longevity improves at least some aspects of female reproductive ageing. These results demonstrate that within-ejaculate variation in sperm phenotype contributes to individual variation in animal life histories in the two sexes and may have important implications for assisted fertilization programs in livestock and humans.

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  • 5.
    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.

  • 6.
    Aleix-Mata, Gael
    et al.
    Jaen Univ, Dept Expt Biol, E-23071 Jaen, Spain.;Jaen Univ, Dept Anim & Plant Biol & Ecol, E-23071 Jaen, Spain..
    Exposito, Miriam
    Jaen Univ, Dept Expt Biol, E-23071 Jaen, Spain..
    Ruiz-Ruano, Francisco J.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology. Granada Univ, Fac Sci, Dept Genet, E-18071 Granada, Spain..
    Maria Lopez-Beceiro, Ana
    Univ Santiago de Compostela, Dept Anat Anim Prod & Vet Clin Sci, E-27002 Lugo, Spain..
    Fidalgo, Luis E.
    Univ Santiago de Compostela, Dept Anat Anim Prod & Vet Clin Sci, E-27002 Lugo, Spain..
    Martinez-Carrasco, Carlos
    Murcia Univ, Dept Anim Hlth, E-30100 Murcia, Spain..
    Ruiz de Ybanez, Maria Rocio
    Murcia Univ, Dept Anim Hlth, E-30100 Murcia, Spain..
    Boos, Mathieu
    Naturaconst, Res Agcy Appl Ecol, F-67270 Wilshausen, France.;Federat Natl Chasseurs, Pole Sci, 13 Rue Gen Leclerc, F-92136 Issy Les Moulineaux, France..
    Perez, Jesus M.
    Jaen Univ, Dept Anim & Plant Biol & Ecol, E-23071 Jaen, Spain.;Wildlife Ecol & Hlth Grp WE&H, Barcelona, Spain..
    Sanchez, Antonio
    Jaen Univ, Dept Expt Biol, E-23071 Jaen, Spain..
    Development and characterization of 15 novel polymorphic microsatellite loci for two important bot flies (Diptera, Oestridae) by next-generation sequencing2020In: Parasitology Research, ISSN 0932-0113, E-ISSN 1432-1955, Vol. 119, no 9, p. 2829-2835Article in journal (Refereed)
    Abstract [en]

    Cephenemyia stimulatorandOestrus ovisare two important parasitic bot flies (Oestridae) species causing myiasis, with a potential negative impact on the welfare of the host. Using next-generation sequencing approach and bioinformatics tools, a large panel of possible microsatellites loci was obtained in both species. Primer pairs were designed for 15 selected microsatellite loci inC. stimulatorand other 15 loci inO. ovisfor PCR amplification. Loci amplification and analysis were performed in four populations of each species. The results demonstrated that all selected loci were polymorphic, with the number of alleles ranging from 2 to 6 per locus inC. stimulatorand 3 to 13 per locus inO. ovis. This is the first time to describe these microsatellite loci forC. stimulatorandO. ovis. These two sets of microsatellite markers could be further used for biogeographic and population genetics studies.

  • 7.
    Alfjorden, Anders
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology. Department of Animal Health and Antimicrobial Strategies, National Veterinary Institute (SVA), Uppsala, Sweden.
    Onut-Brännström, Ioana
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology. Natural History Museum, University of Oslo, Oslo, Norway.
    Wengström, Niklas
    Kristmundsson, Arni
    Jamy, Mahwash
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Persson, B. David
    Burki, Fabien
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Identification of a new gregarine parasite associated with mass mortality events of freshwater pearl mussels (Margaritifera margaritifera) in Sweden2024In: Journal of Eukaryotic Microbiology, ISSN 1066-5234, E-ISSN 1550-7408, Vol. 71, no 3, article id e13021Article in journal (Refereed)
    Abstract [en]

    Freshwater bivalves play key ecological roles in lakes and rivers, largely contributing to healthy ecosystems. The freshwater pearl mussel, Margaritifera margaritifera, is found in Europe and on the East coast of North America. Once common in oxygenated streams, M. margaritifera is rapidly declining and consequently assessed as a threatened species worldwide. Deterioration of water quality has been considered the main factor for the mass mortality events affecting this species. Yet, the role of parasitic infections has not been investigated. Here, we report the discovery of three novel protist lineages found in Swedish populations of M. margaritifera belonging to one of the terrestrial groups of gregarines (Eugregarinorida, Apicomplexa). These lineages are closely related–but clearly separated–from the tadpole parasite Nematopsis temporariae. In one lineage, which is specifically associated with mortality events of M. margaritifera, we found cysts containing single vermiform zoites in the gills and other organs of diseased individuals using microscopy and in situ hybridization. This represents the first report of a parasitic infection in M. margaritifera that may be linked to the decline of this mussel species. We propose a tentative life cycle with the distribution of different developmental stages and potential exit from the host into the environment.

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  • 8.
    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.

  • 9.
    Ali, Raja Hashim
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology. Ghulam Ishaq Khan Inst Engn Sci & Technol, Fac Comp Sci & Engn, Topi, Pakistan.
    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.
    Identifying Clusters of High Confidence Homologies in Multiple Sequence Alignments2019In: Molecular biology and evolution, ISSN 0737-4038, E-ISSN 1537-1719, Vol. 36, no 10, p. 2340-2351Article in journal (Refereed)
    Abstract [en]

    Multiple sequence alignment (MSA) is ubiquitous in evolution and bioinformatics. MSAs are usually taken to be a known and fixed quantity on which to perform downstream analysis despite extensive evidence that MSA accuracy and uncertainty affect results. These errors are known to cause a wide range of problems for downstream evolutionary inference, ranging from false inference of positive selection to long branch attraction artifacts. The most popular approach to dealing with this problem is to remove (filter) specific columns in the MSA that are thought to be prone to error. Although popular, this approach has had mixed success and several studies have even suggested that filtering might be detrimental to phylogenetic studies. We present a graph-based clustering method to address MSA uncertainty and error in the software Divvier (available at https://github.com/simonwhelan/Divvier), which uses a probabilistic model to identify clusters of characters that have strong statistical evidence of shared homology. These clusters can then be used to either filter characters from the MSA (partial filtering) or represent each of the clusters in a new column (divvying). We validate Divvier through its performance on real and simulated benchmarks, finding Divvier substantially outperforms existing filtering software by retaining more true pairwise homologies calls and removing more false positive pairwise homologies. We also find that Divvier, in contrast to other filtering tools, can alleviate long branch attraction artifacts induced by MSA and reduces the variation in tree estimates caused by MSA uncertainty.

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  • 10. 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, 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.

  • 11.
    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, 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.

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  • 12.
    Amaya-Marquez, Marisol
    et al.
    Univ Nacl Colombia, Inst Ciencias Nat, Bogota 111321, Colombia.
    Tusso Gomez, Sergio
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology. Uppsala University, Science for Life Laboratory, SciLifeLab. Ludwig Maximilians Univ Munchen, Div Evolutionary Biol, Fac Biol, 82152 Grosshaderner Str, Planegg Martinsried, Germany.
    Hernandez, Juan
    Univ Nacl Colombia, Inst Ciencias Nat, Bogota 111321, Colombia.
    Dario Jimenez, Juan
    Univ Nacl Colombia, Inst Ciencias Nat, Bogota 111321, Colombia.
    Wells, Harrington
    Tulsa Univ, Dept Biol, Tulsa, OK 74104 USA.
    Abramson, Charles, I
    Oklahoma State Univ, Dept Psychol, Stillwater, OK 74078 USA.
    Olfactory Learning in the Stingless Bee Melipona eburnea Friese (Apidae: Meliponini)2019In: Insects, E-ISSN 2075-4450, Vol. 10, no 11, article id 412Article in journal (Refereed)
    Abstract [en]

    Olfactory learning and floral scents are co-adaptive traits in the plant-pollinator relationship. However, how scent relates to cognition and learning in the diverse group of Neotropical stingless bees is largely unknown. Here we evaluated the ability of Melipona eburnea to be conditioned to scent using the proboscis extension reflex (PER) protocol. Stingless bees did not show PER while harnessed but were able to be PER conditioned to scent when free-to-move in a mini-cage (fmPER). We evaluated the effect of: 1) unconditioned stimulus (US) reward, and 2) previous scent-reward associations on olfactory learning performance. When using unscented-US, PER-responses were low on day 1, but using scented-US reward the olfactory PER-response increased on day 1. On day 2 PER performance greatly increased in bees that previously had experienced the same odor and reward combination, while bees that experienced a different odor on day 2 showed poor olfactory learning. Bees showed higher olfactory PER conditioning to guava than to mango odor. The effect of the unconditioned stimulus reward was not a significant factor in the model on day 2. This indicates that olfactory learning performance can increase via either taste receptors or accumulated experience with the same odor. Our results have application in agriculture and pollination ecology.

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  • 13. Ament-Velásquez, Sandra Lorena
    et al.
    Vogan, Aaron A.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Wallerman, Ola
    Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology. Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology, Medicinsk genetik och genomik.
    Hartmann, Fanny
    Gautier, Valérie
    Silar, Philippe
    Giraud, Tatiana
    Johannesson, Hanna
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    The evolution of the allorecognition gene repertoire in the Podospora anserina species complexManuscript (preprint) (Other academic)
    Abstract [en]

    Across the Tree of Life, self/non-self recognition is typically achieved through highly polymorphic loci under balancing selection. In fungi, vegetative conspecific recognition, or allorecognition, is defined by the compatibility interactions between loci known as het genes. In this study we explore the evolution of the het genes in the model fungus Podospora anserina and its closest relatives (the Podospora anserina species complex). First, we used chromosome-level genome assemblies to resolve their phylogenetic relationships. We found that the species in the complex are well defined but diversified recently and rapidly, leading to high degrees of conflict at deep branches of the phylogeny. Unlike typical orthologous genes from the complex, some allorecognition genes (het-z and het-s) show trans-species polymorphism, a hallmark of long-term balancing selection. By contrast, the het genes belonging to the HNWD family exhibit a high turn-over, with losses and duplications happening often. In particular, the species P. pseudocomata has a considerable increase of HNWD genes. Unexpectedly, we show that the HNWD paralogs have clean defined boundaries flanked by a target site duplication (TSD), implicating a DNA transposon-like mechanism in the genesis of new duplicates. Overall, our data highlights the diversity of evolutionary histories behind individual self/non-self recognition genes at short evolutionary timescales.

  • 14.
    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.

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  • 15.
    Anderson, Bruce
    et al.
    Department of Botany & Zoology, Stellenbosch Univ., Cape Town, South Africa..
    Pannell, John
    Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland..
    Billiard, Sylvain
    University Lille, CNRS, UMR 8198 – Evo-Eco-Paleo, 59000 Lille, France..
    Burgarella, Concetta
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    de Boer, Hugo
    Natural History Museum, University of Oslo, 0318 Oslo, Norway..
    Dufay, Mathilde
    CEFE, University Montpellier, CNRS, University Paul Valéry Montpellier 3, Ephe, IRD, Montpellier, France..
    Helmstetter, Andrew J.
    FRB – CESAB, 5 Rue de l’École de Médecine, 34000 Montpellier, France..
    Méndez, Marcos
    Area of Biodiversity and Conservation, Universidad Rey Juan Carlos, Madrid, Spain..
    Otto, Sarah P.
    Department of Zoology, University of British Columbia, Vancouver, BC, Canada.
    Roze, Denis
    IRL 3614, CNRS, Sorbonne Université, Station Biologique de Roscoff, 29688 Roscoff Cedex, France..
    Sauquet, Hervé
    National Herbarium of New South Wales, Royal Botanic Gardens and Domain Trust, Sydney, NSW 2000, Australia.;Evolution and Ecology Research Centre, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW, Australia..
    Schoen, Daniel
    Department of Biology, McGill University, Montreal, QC, Canada..
    Schönenberger, Jürg
    Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, 1030 Vienna, Austria..
    Vallejo‐Marín, Mario
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Zenil-Ferguson, Rosana
    Department of Biology, University of Kentucky, Lexington, KY 40506-0225, USA..
    Käfer, Jos
    Université de Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR 5558, 69622 Villeurbanne, France..
    Glemin, Sylvain
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution. CNRS, Ecosystèmes Biodiversité Evolution (Université de Rennes), 35000 Rennes, France.
    Opposing effects of plant traits on diversification2023In: iScience, E-ISSN 2589-0042, Vol. 26, no 4, article id 106362Article in journal (Refereed)
    Abstract [en]

    Species diversity can vary dramatically across lineages due to differences in speciation and extinction rates. Here, we explore the effects of several plant traits on diversification, finding that most traits have opposing effects on diversification. For example, outcrossing may increase the efficacy of selection and adaptation but also decrease mate availability, two processes with contrasting effects on lineage persistence. Such opposing trait effects can manifest as differences in diversification rates that depend on ecological context, spatiotemporal scale, and associations with other traits. The complexity of pathways linking traits to diversification suggests that the mechanistic underpinnings behind their correlations may be difficult to interpret with any certainty, and context dependence means that the effects of specific traits on diversification are likely to differ across multiple lineages and timescales. This calls for taxonomically and context-controlled approaches to studies that correlate traits and diversification.

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  • 16.
    Anderson, Jennifer L
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Nieuwenhuis, Bart P. S.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology. Division of Evolutionary Biology, Faculty of Biology, Ludwig- Maximilians-Universität München.
    Johannesson, Hanna
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Asexual reproduction and growth rate: independent and plastic lifehistory traits in Neurospora crassa2019In: The ISME Journal, ISSN 1751-7362, E-ISSN 1751-7370, Vol. 13, no 3, p. 780-788Article in journal (Refereed)
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  • 17. 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.

  • 18. 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.

  • 19.
    Armisen, David
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology. Univ Claude Bernard Lyon1, Univ Lyon, CNRS, Inst Genom Fonct Lyon,Unite Mixte Rech 5242,Ecole, F-69007 Lyon, France..
    Viala, Severine
    Univ Claude Bernard Lyon1, Univ Lyon, CNRS, Inst Genom Fonct Lyon,Unite Mixte Rech 5242,Ecole, F-69007 Lyon, France..
    Silva Cordeiro, Isabelle da Rocha
    Fundacao Oswaldo Cruz, Lab Biodiversidade Entomol, Inst Oswaldo Cruz, BR-21040900 Rio De Janeiro, RJ, Brazil..
    Johan Crumiere, Antonin Jean
    Univ Claude Bernard Lyon1, Univ Lyon, CNRS, Inst Genom Fonct Lyon,Unite Mixte Rech 5242,Ecole, F-69007 Lyon, France..
    Hendaoui, Elisa
    Univ Claude Bernard Lyon1, Univ Lyon, CNRS, Inst Genom Fonct Lyon,Unite Mixte Rech 5242,Ecole, F-69007 Lyon, France..
    Le Bouquin, Augustin
    Univ Claude Bernard Lyon1, Univ Lyon, CNRS, Inst Genom Fonct Lyon,Unite Mixte Rech 5242,Ecole, F-69007 Lyon, France.;Univ Toronto, Dept Ecol & Evolutionary Biol, Toronto, ON M5S 3B2, Canada..
    Duchemin, Wandrille
    Univ Basel, Ctr Sci Comp SciCORE, CH-4056 Basel, Switzerland..
    Santos, Emilia
    Univ Claude Bernard Lyon1, Univ Lyon, CNRS, Inst Genom Fonct Lyon,Unite Mixte Rech 5242,Ecole, F-69007 Lyon, France.;Univ Cambridge, Dept Zool, Downing St Cambridge, Cambridge CB2 3EJ, England..
    Toubiana, William
    Univ Claude Bernard Lyon1, Univ Lyon, CNRS, Inst Genom Fonct Lyon,Unite Mixte Rech 5242,Ecole, F-69007 Lyon, France.;Univ Lausanne, Dept Ecol & Evolut, Lausanne, Switzerland..
    Vargas-Lowman, Aidamalia
    Univ Claude Bernard Lyon1, Univ Lyon, CNRS, Inst Genom Fonct Lyon,Unite Mixte Rech 5242,Ecole, F-69007 Lyon, France.;Univ Panama, Estafeta Univ, Dept Genet & Biol Mol, Panama City, Panama..
    Burguez Floriano, Carla Fernanda
    Fundacao Oswaldo Cruz, Lab Biodiversidade Entomol, Inst Oswaldo Cruz, BR-21040900 Rio De Janeiro, RJ, Brazil..
    Polhemus, Dan A.
    Bernice P Bishop Museum, Dept Nat Sci, 1525 Bernice St, Honolulu, HI 96817 USA..
    Wang, Yan-Hui
    Sun Yat Sen Univ, Sch Life Sci, 135 Xingangxi Rd, Guangzhou 510275, Guangdong, Peoples R China..
    Rowe, Locke
    Univ Toronto, Dept Ecol & Evolutionary Biol, Toronto, ON M5S 3B2, Canada..
    Figueiredo Moreira, Felipe Ferraz
    Fundacao Oswaldo Cruz, Lab Biodiversidade Entomol, Inst Oswaldo Cruz, BR-21040900 Rio De Janeiro, RJ, Brazil..
    Khila, Abderrahman
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology. Univ Claude Bernard Lyon1, Univ Lyon, CNRS, Inst Genom Fonct Lyon,Unite Mixte Rech 5242,Ecole, F-69007 Lyon, France..
    Transcriptome-based phylogeny of the semi-aquatic bugs (Hemiptera Heteroptera: Gerromorpha) reveals patterns of lineage expansion in a series of new adaptive zones2022In: Molecular biology and evolution, ISSN 0737-4038, E-ISSN 1537-1719, Vol. 39, no 11, article id msac229Article in journal (Refereed)
    Abstract [en]

    Key innovations enable access to new adaptive zones and are often linked to increased species diversification. As such, innovations have attracted much attention, yet their concrete consequences on the subsequent evolutionary trajectory and diversification of the bearing lineages remain unclear. Water striders and relatives (Hemiptera: Heteroptera: Gerromorpha) represent a monophyletic lineage of insects that transitioned to live on the water-air interface and that diversified to occupy ponds, puddles, streams, mangroves and even oceans. This lineage offers an excellent model to study the patterns and processes underlying species diversification following the conquest of new adaptive zones. However, such studies require a reliable and comprehensive phylogeny of the infraorder. Based on whole transcriptomic datasets of 97 species and fossil records, we reconstructed a new phylogeny of the Gerromorpha that resolved inconsistencies and uncovered strong support for previously unknown relationships between some important taxa. We then used this phylogeny to reconstruct the ancestral state of a set of adaptations associated with water surface invasion (fluid locomotion, dispersal and transition to saline waters) and sexual dimorphism. Our results uncovered important patterns and dynamics of phenotypic evolution, revealing how the initial event of water surface invasion enabled multiple subsequent transitions to new adaptive zones on the water surfaces. This phylogeny and the associated transcriptomic datasets constitute highly valuable resources, making Gerromorpha an attractive model lineage to study phenotypic evolution.

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  • 20.
    Arnqvist, Göran
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Rönn, Johanna
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Watson, Christopher
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Goenaga, Julieta
    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, Evolutionary Biology.
    Concerted evolution of metabolic rate, economics of mating, ecology, and pace of life across seed beetles2022In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 119, no 33, article id e2205564119Article in journal (Refereed)
    Abstract [en]

    Male-female coevolution has taken different paths among closely related species, but our understanding of the factors that govern its direction is limited. While it is clear that ecological factors, life history, and the economics of reproduction are connected, the divergent links are often obscure. We propose that a complete understanding requires the conceptual integration of metabolic phenotypes. Metabolic rate, a nexus of life history evolution, is constrained by ecological factors and may exert important direct and indirect effects on the evolution of sexual dimorphism. We performed standardized experiments in 12 seed beetle species to gain a rich set of sex-specific measures of metabolic phenotypes, life history traits, and the economics of mating and analyzed our multivariate data using phylogenetic comparative methods. Resting metabolic rate (RMR) showed extensive evolution and evolved more rapidly in males than in females. The evolution of RMR was tightly coupled with a suite of life history traits, describing a pace-of-life syndrome (POLS), with indirect effects on the economics of mating. As predicted, high resource competition was associated with a low RMR and a slow POLS. The cost of mating showed sexually antagonistic coevolution, a hallmark of sexual conflict. The sex-specific costs and benefits of mating were predictably related to ecology, primarily through the evolution of male ejaculate size. Overall, our results support the tenet that resource competition affects metabolic processes that, in turn, have predictable effects on both life history evolution and reproduction, such that ecology shows both direct and indirect effects on male-female coevolution.

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  • 21.
    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.

  • 22.
    Arnqvist, Göran
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Westerberg, Ivar
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology. Stockholm Univ, Dept Ecol Environm & Plant Sci, SE-10691 Stockholm, Sweden.
    Galbraith, James
    Univ Adelaide, Sch Biol Sci, Adelaide 5005, Australia.;Univ Exeter, Fac Environm Sci & Econ, Cornwall TR10 9FE, England..
    Sayadi, Ahmed
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Rheumatology.
    Scofield, Douglas G.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Olsen, Remi-André
    Stockholm Univ, Dept Biochem & Biophys, Sci Life Lab, SE-10691 Stockholm, Sweden..
    Immonen, Elina
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Bonath, Franziska
    Stockholm Univ, Wenner Gren Inst, Dept Mol Biosci, Sci Life Lab, SE-10691 Stockholm, Sweden..
    Ewels, Philip
    Seqera Labs, Barcelona 08005, Spain..
    Suh, Alexander
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    A chromosome-level assembly of the seed beetle Callosobruchus maculatus genome with annotation of its repetitive elements2024In: G3: Genes, Genomes, Genetics, E-ISSN 2160-1836, Vol. 14, no 2, article id jkad266Article in journal (Refereed)
    Abstract [en]

    Callosobruchus maculatus is a major agricultural pest of legume crops worldwide and an established model system in ecology and evolution. Yet, current molecular biological resources for this species are limited. Here, we employ Hi-C sequencing to generate a greatly improved genome assembly and we annotate its repetitive elements in a dedicated in-depth effort where we manually curate and classify the most abundant unclassified repeat subfamilies. We present a scaffolded chromosome-level assembly, which is 1.01 Gb in total length with 86% being contained within the 9 autosomes and the X chromosome. Repetitive sequences accounted for 70% of the total assembly. DNA transposons covered 18% of the genome, with the most abundant superfamily being Tc1-Mariner (9.75% of the genome). This new chromosome-level genome assembly of C. maculatus will enable future genetic and evolutionary studies not only of this important species but of beetles more generally.

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  • 23.
    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.

  • 24.
    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, 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.

  • 25.
    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, 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.

  • 26.
    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.

  • 27.
    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.

  • 28.
    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.

  • 29.
    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, 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.

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  • 30.
    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, 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.

  • 31.
    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, 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.

  • 32.
    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.

  • 33. Badou, Sylvestre A.
    et al.
    Furneaux, Brendan R.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    De Kesel, André
    Kalsoom, Faheema
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Houdanon, Roel D.
    Ryberg, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Yorou, Nourou S.
    Paxilloboletus gen. nov., a new lamellate bolete genus from tropical Africa2022In: Mycological progress, ISSN 1617-416X, E-ISSN 1861-8952, Vol. 21, no 1, p. 243-256Article in journal (Refereed)
    Abstract [en]

    This study presents Paxilloboletus gen. nov., a new lamellate bolete genus represented by two tropical African species, Paxilloboletus africanus sp. nov. and Paxilloboletus latisporus sp. nov. Although the new taxa strongly resemble Paxillus (Paxillaceae), they lack clamp connections and form a separate generic clade within the Boletaceae phylogeny. The new species are lookalikes, morphologically only separable by their spore morphology. Descriptions and illustrations of the new genus and new species are given, as well as comments on ecology, distribution, and morphological differences with other gilled Boletaceae.

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  • 34. Bagchi, Basabi
    et al.
    Corbel, Quentin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology. University of Valencia.
    Khan, Imroze
    Payne, Ellen
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Banerji, Devshuvam
    Liljestrand-Rönn, Johanna
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Martinossi-Allibert, Ivain
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Baur, Julian
    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. Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - BMC, Biochemistry.
    Immonen, Elina
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Arnqvist, Göran
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Söderhäll, Irene
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Comparative Physiology.
    Berger, David
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Sexual conflict drives micro- and macroevolution of sexual dimorphism in immunity2021In: BMC Biology, E-ISSN 1741-7007, Vol. 19, no 1, article id 114Article in journal (Refereed)
    Abstract [en]

    BACKGROUND: Sexual dimorphism in immunity is believed to reflect sex differences in reproductive strategies and trade-offs between competing life history demands. Sexual selection can have major effects on mating rates and sex-specific costs of mating and may thereby influence sex differences in immunity as well as associated host-pathogen dynamics. Yet, experimental evidence linking the mating system to evolved sexual dimorphism in immunity are scarce and the direct effects of mating rate on immunity are not well established. Here, we use transcriptomic analyses, experimental evolution and phylogenetic comparative methods to study the association between the mating system and sexual dimorphism in immunity in seed beetles, where mating causes internal injuries in females.

    RESULTS: We demonstrate that female phenoloxidase (PO) activity, involved in wound healing and defence against parasitic infections, is elevated relative to males. This difference is accompanied by concomitant sex differences in the expression of genes in the prophenoloxidase activating cascade. We document substantial phenotypic plasticity in female PO activity in response to mating and show that experimental evolution under enforced monogamy (resulting in low remating rates and reduced sexual conflict relative to natural polygamy) rapidly decreases female (but not male) PO activity. Moreover, monogamous females had evolved increased tolerance to bacterial infection unrelated to mating, implying that female responses to costly mating may trade off with other aspects of immune defence, an hypothesis which broadly accords with the documented sex differences in gene expression. Finally, female (but not male) PO activity shows correlated evolution with the perceived harmfulness of male genitalia across 12 species of seed beetles, suggesting that sexual conflict has a significant influence on sexual dimorphisms in immunity in this group of insects.

    CONCLUSIONS: Our study provides insights into the links between sexual conflict and sexual dimorphism in immunity and suggests that selection pressures moulded by mating interactions can lead to a sex-specific mosaic of immune responses with important implications for host-pathogen dynamics in sexually reproducing organisms.

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  • 35. 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, 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.

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  • 36.
    Baison, John
    et al.
    Swedish Univ Agr Sci, Dept Forest Genet & Plant Physiol, Umea Plant Sci Ctr, Parallellvagen 21, S-90736 Umea, Sweden.
    Vidalis, Amaryllis
    Tech Univ Munich, Sect Populat Epigenet & Epigen, Ctr Life & Food Sci Weihenstephan, Lichtenbergstr 2a, D-85748 Munich, Germany.
    Zhou, Linghua
    Swedish Univ Agr Sci, Dept Forest Genet & Plant Physiol, Umea Plant Sci Ctr, Parallellvagen 21, S-90736 Umea, Sweden.
    Chen, Zhi-Qiang
    Swedish Univ Agr Sci, Dept Forest Genet & Plant Physiol, Umea Plant Sci Ctr, Parallellvagen 21, S-90736 Umea, Sweden.
    Li, Zitong
    Univ Helsinki, Dept Biosci, Ecol Genet Res Unit, POB 65, FI-00014 Helsinki, Finland.
    Sillanpää, Mikko J.
    Univ Oulu, Dept Math Sci, Bioctr Oulu, Pentti Kaiteran Katu 1, Oulu, Finland.
    Bernhardsson, Carolina
    Swedish Univ Agr Sci, Dept Forest Genet & Plant Physiol, Umea Plant Sci Ctr, Parallellvagen 21, S-90736 Umea, Sweden;Umea Univ, Dept Ecol & Environm Sci, Linnaeus Vag 4-6, S-90736 Umea, Sweden.
    Scofield, Douglas
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Forsberg, Nils
    Swedish Univ Agr Sci, Dept Forest Genet & Plant Physiol, Umea Plant Sci Ctr, Parallellvagen 21, S-90736 Umea, Sweden.
    Grahn, Thomas
    RISE Bioecon, Drottning Kristinas Vag 61, SE-11486 Stockholm, Sweden.
    Olsson, Lars
    RISE Bioecon, Drottning Kristinas Vag 61, SE-11486 Stockholm, Sweden.
    Karlsson, Bo
    Skogforsk, Ekebo 2250, SE-26890 Svalov, Sweden.
    Wu, Harry
    Swedish Univ Agr Sci, Dept Forest Genet & Plant Physiol, Umea Plant Sci Ctr, Parallellvagen 21, S-90736 Umea, Sweden.
    Ingvarsson, Pär K:
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology. Umea Univ, Dept Ecol & Environm Sci, Linnaeus Vag 4-6, S-90736 Umea, Sweden.
    Lundqvist, Sven-Olof
    RISE Bioecon, Drottning Kristinas Vag 61, SE-11486 Stockholm, Sweden;IIC, Rosenlundsgatan 48B, SE-11863 Stockholm, Sweden.
    Niittylä, Totte
    Swedish Univ Agr Sci, Dept Forest Genet & Plant Physiol, Umea Plant Sci Ctr, Parallellvagen 21, S-90736 Umea, Sweden.
    Garcia-Gil, M. Rosario
    Swedish Univ Agr Sci, Dept Forest Genet & Plant Physiol, Umea Plant Sci Ctr, Parallellvagen 21, S-90736 Umea, Sweden.
    Genome-wide association study identified novel candidate loci affecting wood formation in Norway spruce2019In: The Plant Journal, ISSN 0960-7412, E-ISSN 1365-313X, Vol. 100, no 1, p. 83-100Article in journal (Refereed)
    Abstract [en]

    Norway spruce is a boreal forest tree species of significant ecological and economic importance. Hence there is a strong imperative to dissect the genetics underlying important wood quality traits in the species. We performed a functional genome-wide association study (GWAS) of 17 wood traits in Norway spruce using 178 101 single nucleotide polymorphisms (SNPs) generated from exome genotyping of 517 mother trees. The wood traits were defined using functional modelling of wood properties across annual growth rings. We applied a Least Absolute Shrinkage and Selection Operator (LASSO-based) association mapping method using a functional multilocus mapping approach that utilizes latent traits, with a stability selection probability method as the hypothesis testing approach to determine a significant quantitative trait locus. The analysis provided 52 significant SNPs from 39 candidate genes, including genes previously implicated in wood formation and tree growth in spruce and other species. Our study represents a multilocus GWAS for complex wood traits in Norway spruce. The results advance our understanding of the genetics influencing wood traits and identifies candidate genes for future functional studies.

  • 37. 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)
  • 38. 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.

  • 39.
    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)
  • 40.
    Bauerfeind, Stephanie S.
    et al.
    Univ Zurich, Dept Evolutionary Biol & Environm Studies, Zurich, Switzerland.
    Schaefer, Martin A.
    Univ Zurich, Dept Evolutionary Biol & Environm Studies, Zurich, Switzerland.
    Berger, David
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology. Univ Zurich, Dept Evolutionary Biol & Environm Studies, Zurich, Switzerland.
    Blanckenhorn, Wolf U.
    Univ Zurich, Dept Evolutionary Biol & Environm Studies, Zurich, Switzerland.
    Fox, Charles W.
    Univ Kentucky, Dept Entomol, S225 Ag Sci Ctr North, Lexington, KY 40546 USA.
    Replicated latitudinal clines in reproductive traits of European and North American yellow dung flies2018In: Oikos, ISSN 0030-1299, E-ISSN 1600-0706, Vol. 127, no 11, p. 1619-1632Article in journal (Refereed)
    Abstract [en]

    Geographic variation in phenotypic traits is commonly correlated with spatial variation in the environment, e.g. seasonality and mean temperature, providing evidence that natural selection generates such patterns. In particular, both body size and egg size of ectothermic animals are commonly larger in northern climates, and temperature induces plastic responses in both traits. Size-independent egg quality can also vary with latitude, though this is rarely investigated. For the widespread yellow dung fly Scathophaga stercoraria (Diptera: Scathophagidae) we investigated whether there are latitudinal clines in reproductive traits (clutch size, egg size and egg composition), whether these clines are due to variation in body and/or egg size, and whether such clines replicate across independent experiments performed on different continents (North America and Europe). Egg size generally increased with latitude (especially in Europe), an effect largely explained by body size of the mother, while clutch size did not; overall reproductive effort thus increased with latitude. Both the absolute and relative (correcting for egg size) amount of egg protein increased with latitude, egg glycogen decreased with latitude, while latitudinal trends for egg lipids and total egg energy content were complex and non-linear. Altitude sometimes showed relationships analogous to those of latitude (egg proteins and glycogen) but occasionally opposite (egg size), possibly because latitude and altitude are negatively related among populations of this cold-adapted species. There was no evidence of a tradeoff between egg size and number across latitudinal populations; if anything, the relationship was positive. All traits, including body and egg size, varied with rearing temperature (12 degrees C, 18 degrees C, 24 degrees C), generally following the temperature-size rule. Clines based on common garden rearing, thus reflecting genetic differentiation, were qualitatively but not always quantitatively consistent between continents, and were similar across rearing temperatures, suggesting they evolved due to natural selection, although the concrete selective mechanisms involved require further study.

  • 41.
    Baur, Julian
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Berger, David
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.