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  • 1.
    Aagaard, Sunniva M. D.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics.
    Greilhuber, Johann
    University of Vienna, Department of Systematic and Evolutionary Botany.
    Zhang, Xian-Chun
    Institute of Botany,Chinese Academy of Sciences .
    Wikström, Niklas
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics.
    Occurrence and evolutionary origins of polyploids in the club moss genus Diphasiastrum (Lycopodiaceae)2009In: Molecular Phylogenetics and Evolution, ISSN 1055-7903, E-ISSN 1095-9513, Vol. 52, no 3, p. 746-754Article in journal (Refereed)
    Abstract [en]

    Two polyploid taxa are commonly recognized in the genus Diphasiastrum, D. wightianum from Asia and D. zanclophyllum from South Africa and Madagascar. Here we present results from Feulgen DNA image densitometry analyses providing the first evidence for the polyploid origin of D. zanclophyllum. Reported for the first time is also data confirming that D. multispicatum and D. veitchii, representing putative parent lineages for D. wightianum, are diploids. Phylogenetic analyses of nuclear regions RPB2, LEAFY and LAMB4 reveal that putative tetraploid accessions are of allopolyploid origin. Diphasiastrum zanclophyllum shows close relationships to the North American taxon D. digitatum on the maternal side, but the paternal relationship is less clear. Two accessions from Asia, both found to be polyploid, have D. veitchii as maternal parent, whereas the paternal paralogs show relationships to D. multispicatum and D. tristachyum, respectively. None of these parental combinations have previously been hypothesized.

  • 2.
    Alström, Per
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology. Swedish Univ Agr Sci, Swedish Species Informat Ctr, Box 7007, SE-75007 Uppsala, Sweden.;Chinese Acad Sci, Inst Zool, Key Lab Zool Systemat & Evolut, Beijing 100101, Peoples R China..
    Cibois, Alice
    Nat Hist Museum Geneva, Dept Mammal & Ornithol, CP 6434, CH-1211 Geneva 6, Switzerland..
    Irestedt, Martin
    Swedish Museum Nat Hist, Dept Bioinformat & Genet, POB 50007, SE-10405 Stockholm, Sweden..
    Zuccon, Dario
    UMS MNHN CNRS 2700 Outils & Methodes Systemat Int, CP 51,57 Rue Cuvier, F-75231 Paris 05, France.;Sorbonne Univ, Museum Natl Hist Nat, UMR7205,EPHE, Inst Systemat,Evolut,Biodiversite,CNRS,MNHN,UPMC, CP 51,57 Rue Cuvier, F-75231 Paris 05, France..
    Gelang, Magnus
    Gothenburg Nat Hist Museum, Box 7283, S-40235 Gothenburg, Sweden..
    Fjeldsa, Jon
    Nat Hist Museum Denmark, Zool Museum, Ctr Macroecol Evolut & Climate, Univ Pk 15, DK-2100 Copenhagen, Denmark..
    Andersen, Michael
    Univ New Mexico, Dept Biol, Albuquerque, NM 87131 USA.;Univ New Mexico, Museum Southwestern Biol, Albuquerque, NM 87131 USA..
    Moyle, Robert
    Univ Kansas, Dept Ecol & Evolutionary Biol, Lawrence, KS 66045 USA.;Univ Kansas, Biodivers Inst, Lawrence, KS 66045 USA..
    Pasquet, Eric
    UMS MNHN CNRS 2700 Outils & Methodes Systemat Int, CP 51,57 Rue Cuvier, F-75231 Paris 05, France.;Sorbonne Univ, Museum Natl Hist Nat, UMR7205,EPHE, Inst Systemat,Evolut,Biodiversite,CNRS,MNHN,UPMC, CP 51,57 Rue Cuvier, F-75231 Paris 05, France..
    Olsson, Urban
    Univ Gothenburg, Dept Biol & Environm Sci Systemat & Biodivers, Box 463, S-40530 Gothenburg, Sweden..
    Comprehensive molecular phylogeny of the grassbirds and allies (Locustellidae) reveals extensive non-monophyly of traditional genera, and a proposal for a new classification2018In: Molecular Phylogenetics and Evolution, ISSN 1055-7903, E-ISSN 1095-9513, Vol. 127, p. 367-375Article in journal (Refereed)
    Abstract [en]

    The widespread Old World avian family Locustellidae ('grassbirds and allies') comprises 62 extant species in 11 genera. In the present study, we used one mitochondrial and, for most species, four nuclear loci to infer the phylogeny of this family. We analysed 59 species, including the five previously unsampled genera plus two genera that had not before been analysed in a densely sampled dataset. This study revealed extensive disagreement with current taxonomy; the genera Bradypterus, Locustella, Megalurus, Megalurulus and Schoenicola were all found to be non-monophyletic. Non-monophyly was particularly pronounced for Megalurus, which was widely scattered across the tree. Three of the five monotypic genera (Amphilais, Buettikoferella and Malia) were nested within other genera; one monotypic genus (Chaetornis) formed a Glade with one of the two species of Schoenicola; whereas the position of the fifth monotypic genus (Elaphrornis) was unresolved. Robsonius was confirmed as sister to the other genera. We propose a phylogenetically informed revision of genus-level taxonomy, including one new generic name. Finally, we highlight several non-monophyletic species complexes and deep intra-species divergences that point to conflict in taxonomy and suggest an underestimation of current species diversity in this group.

  • 3.
    Alström, Per
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Zoology.
    Olsson, Urban
    Lei, Fumin
    Wang, Hai-tao
    Gao, Wei
    Sundberg, Per
    Phylogeny and classification of the Old World Emberizini (Aves, Passeriformes)2008In: Molecular Phylogenetics and Evolution, ISSN 1055-7903, E-ISSN 1095-9513, Vol. 47, no 3, p. 960-973Article in journal (Refereed)
    Abstract [en]

    The phylogeny of the avian genus Emberiza and the monotypic genera Latoucheornis, Melophus and Miliaria (collectively the Old World Emberizini), as well as representatives for the New World Emberizini, the circumpolar genera Calcarius and Plectrophertax and the four other generally recognized tribes in the subfamily Emberizinae was estimated based on the mitochondrial cytochrome b gene and introns 6-7 of the nuclear ornithine decarboxylase (ODC) gene. Our results support monophyly of the Old World Emberizini, but do not corroborate a sister relationship to the New World Emberizini. Calcarius and Plectrophenax form a clade separated from the other Emberizini. This agrees with previous studies, and we recommend the use of the name Calcariini. Latoucheornis, Melophus and Miliaria are nested within Emberiza, and we therefore propose they be synonymized with Emberiza. Emberiza is divided into four main clades, whose relative positions are uncertain, although a sister relation between a clade with six African species and one comprising the rest of the species (30, all Palearctic) is most likely. Most clades agree with traditional, morphology-based, classifications. However, four sister relationships within Emberiza, three of which involve the previously recognized Latoucheornis, Melophus and Miliaria, are unpredicted, and reveal cases of strong morphological divergence. In contrast, the plumage similarity between adult male Emberiza (formerly Latoucheornis) siemsseni and the nominate subspecies of the New World Junco hyemalis is shown to be the result of parallel evolution. A further case of parallel plumage evolution, between African and Eurasian taxa, is pointed out. Two cases of discordance between the mitochondrial and nuclear data with respect to branch lengths and genetic divergences are considered to be the result of introgressive hybridization.

  • 4.
    Alström, Per
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology. Swedish Univ Agr Sci SLU, Swedish Species Informat Ctr, Box 7007, SE-75007 Uppsala, Sweden;Chinese Acad Sci, Inst Zool, Key Lab Zool Systemat & Evolut, Beijing 100101, Peoples R China.
    Rheindt, Frank E.
    Natl Univ Singapore, Dept Biol Sci, 16 Sci Dr 4, Singapore 117558, Singapore.
    Zhang, Ruiying
    Chinese Acad Sci, Inst Zool, Key Lab Zool Systemat & Evolut, Beijing 100101, Peoples R China.
    Zhao, Min
    Chinese Acad Sci, Inst Zool, Key Lab Zool Systemat & Evolut, Beijing 100101, Peoples R China.
    Wang, Jing
    Chinese Acad Sci, Inst Zool, Key Lab Zool Systemat & Evolut, Beijing 100101, Peoples R China.
    Zhu, Xiaojia
    Chinese Acad Sci, Inst Zool, Key Lab Zool Systemat & Evolut, Beijing 100101, Peoples R China.
    Gwee, Chyi Yin
    Natl Univ Singapore, Dept Biol Sci, 16 Sci Dr 4, Singapore 117558, Singapore.
    Hao, Yan
    Chinese Acad Sci, Inst Zool, Key Lab Zool Systemat & Evolut, Beijing 100101, Peoples R China.
    Ohlson, Jan
    Swedish Museum Nat Hist, Dept Bioinformat & Genet, Box 50007, SE-10405 Stockholm, Sweden.
    Jia, Chenxi
    Chinese Acad Sci, Inst Zool, Key Lab Zool Systemat & Evolut, Beijing 100101, Peoples R China.
    Prawiradilaga, Dewi M.
    Indonesian Inst Sci LIPI, Cibinong Sci Ctr, Res Ctr Biol, Jalan Raya Jakarta Bogor KM 46, Bogor 16911, Indonesia.
    Ericson, Per G. P.
    Swedish Museum Nat Hist, Dept Bioinformat & Genet, Box 50007, SE-10405 Stockholm, Sweden.
    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, Box 463, SE-40530 Gothenburg, Sweden.
    Complete species-level phylogeny of the leaf warbler (Aves: Phylloscopidae) radiation2018In: Molecular Phylogenetics and Evolution, ISSN 1055-7903, E-ISSN 1095-9513, Vol. 126, p. 141-152Article in journal (Refereed)
    Abstract [en]

    The leaf warbler radiation (Aves: Phylloscopidae) has undergone a c. 50% increase in the number of recognised species over the last three decades, mainly as a result of analyses of vocalisations and DNA. Using a multilocus dataset for all of the species in this family, and multispecies coalescent-based as well as concatenation methods, we provide the first complete species-level phylogeny for this important group, as well as an estimate of the timing of diversification. The most recent common ancestor for the family was dated at 11.7 million years ago (mya) (95% highest posterior density 9.8-13.7 mya), and divergence times between sister species ranged from 0.5 mya (0.3-0.8 mya) to 6.1 mya (4.8-7.5 mya). Based on our results, we support synonymising Seicercus with Phylloscopus, which results in a monogeneric Phylloscopidae. We discuss the pros and cons of this treatment, and we argue against proliferation of taxonomic names, and conclude that a large monogeneric Phylloscopidae leads to the fewest taxonomic changes compared to traditional classifications. We briefly discuss morphological evolution in the light of the phylogeny. The time calibrated phylogeny is a major improvement compared to previous studies based on a smaller number of species and loci and can provide a basis for future studies of other aspects of phylloscopid evolution.

  • 5.
    Ament-Velásquez, Sandra Lorena
    et al.
    Department of Earth and Environmental Sciences, Paleontology and Geobiology, Ludwig-Maximilians-Universtität München.
    Breedy, Odalisca
    Cortés, Jorge
    Guzman, Hector M.
    Wörheide, Gert
    Vargas, Sergio
    Homoplasious colony morphology and mito-nuclear phylogenetic discordance among Eastern Pacific octocorals2016In: Molecular Phylogenetics and Evolution, ISSN 1055-7903, E-ISSN 1095-9513, Vol. 98, p. 373-381Article in journal (Refereed)
    Abstract [en]

    Octocorals are a diverse and ecologically important group of cnidarians. However, the phylogenetic relationships of many octocoral groups are not well understood and are based mostly on mitochondrial sequence data. In addition, the discovery and description of new gorgonian species displaying unusual or intermediate morphologies and uncertain phylogenetic affinities further complicates the study of octocoral systematics and raises questions about the role played by processes such as plasticity, crypsis, and convergence in the evolution of this group of organisms. Here, we use nuclear (i.e. 28S rDNA) and mitochondrial (mtMutS) markers and a sample of Eastern Pacific gorgonians thought to be remarkable from a morphological point of view to shed light on the morphological diversification among these organisms. Our study reveals the loss of the anastomosed colony morphology in two unrelated lineages of the seafan genusPacifigorgia and offers strong evidence for the independent evolution of a whip-like morphology in two lineages of Eastern Pacific Leptogorgia. Additionally, our data revealed one instance of mito-nuclear discordance in the genera Leptogorgia andEugorgia, which may be the results of incomplete lineage sorting or ancient hybridization–introgression events. Our study stresses the importance of comprehensive taxonomic sampling and the use of independent sources of evidence to address the phylogenetic relationships and clarifying the evolution of octocorals.

  • 6.
    Cai, Tianlong
    et al.
    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;Nat Hist Museum Denmark, Zool Museum, Ctr Macroecol Evolut & Climate, Univ Pk 15, DK-2100 Copenhagen, Denmark.
    Cibois, Alice
    Nat Hist Museum Geneva, CP 6434, CH-1211 Geneva 6, Switzerland.
    Alström, Per
    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, SE-75007 Uppsala, Sweden.
    Moyle, Robert
    Univ Kansas, Dept Ecol & Evolutionary Biol, Lawrence, KS 66045 USA;Univ Kansas, Biodivers Inst, Lawrence, KS 66045 USA.
    Kennedy, Jonathan
    Nat Hist Museum Denmark, Zool Museum, Ctr Macroecol Evolut & Climate, Univ Pk 15, DK-2100 Copenhagen, Denmark.
    Shao, Shimiao
    Southwest Forestry Univ, State Forestry Adm, Key Lab Biodivers Conservat Southwest China, Kunming 650224, Yunnan, Peoples R China.
    Zhang, Ruiying
    Univ Chinese Acad Sci, Coll Life Sci, Beijing 100049, Peoples R China;Chinese Acad Sci, Inst Genet & Dev Biol, Ctr Dev Biol, Beijing, Peoples R China.
    Irestedt, Martin
    Swedish Museum Nat Hist, Dept Bioinformat & Genet, POB 50007, SE-10405 Stockholm, Sweden.
    Ericson, Per
    Swedish Museum Nat Hist, Dept Bioinformat & Genet, POB 50007, SE-10405 Stockholm, Sweden.
    Gelang, Magnus
    Gothenburg Nat Hist Museum, Box 7283, Gothenburg, Sweden.
    Qu, Yanhua
    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.
    Lei, Fumin
    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.
    Fjeldsa, Jon
    Nat Hist Museum Denmark, Zool Museum, Ctr Macroecol Evolut & Climate, Univ Pk 15, DK-2100 Copenhagen, Denmark.
    Near-complete phylogeny and taxonomic revision of the world's babblers (Aves: Passeriformes)2019In: Molecular Phylogenetics and Evolution, ISSN 1055-7903, E-ISSN 1095-9513, Vol. 130, p. 346-356Article in journal (Refereed)
    Abstract [en]

    The babblers are a diverse group of passerine birds comprising 452 species. The group was long regarded as a "scrap basket" in taxonomic classification schemes. Although several studies have assessed the phylogenetic relationships for subsets of babblers during the past two decades, a comprehensive phylogeny of this group has been lacking. In this study, we used five mitochondrial and seven nuclear loci to generate a dated phylogeny for babblers. This phylogeny includes 402 species (ca. 89% of the overall clade) from 75 genera (97%) and all five currently recognized families, providing a robust basis for taxonomic revision. Our phylogeny supports seven major clades and reveals several non-monophyletic genera. Divergence time estimates indicate that the seven major clades diverged around the same time (18-20 million years ago, Ma) in the early Miocene. We use the phylogeny in a consistent way to propose a new taxonomy, with seven families and 64 genera of babblers, and a new linear sequence of names.

  • 7.
    Corcoran, Pádraic
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Dettman, Jeremy
    University of Ottawa.
    Sun, Yu
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Luque, Eva
    Universidad de Sevilla.
    Corrochano, Luis
    Universidad de Sevilla.
    Taylor, John
    University of California Berkeley.
    Lascoux, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Johannesson, Hanna
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    A global multilocus analysis of the model fungus Neurospora reveals a single recent origin of a novel genetic system2014In: Molecular Phylogenetics and Evolution, ISSN 1055-7903, E-ISSN 1095-9513, Vol. 78, p. 136-147Article in journal (Refereed)
    Abstract [en]

    The large diversity of mating systems observed in the fungal kingdom underlines the importance of mating system change in fungal evolution. The selfing species Neurospora tetrasperma has evolved a novel method of achieving self-fertility by a mating system referred to as pseudohomothallism. However, little is known about the origin of N. tetrasperma and its relationship to the self-sterile, heterothallic, Neurospora species. In this study, we used a combination of phylogenetic and population genetic analyses to reconstruct the evolutionary history of N. tetrasperma and its heterothallic relatives. We sequenced 9 unlinked nuclear loci from 106 strains of N. tetrasperma sampled from across the globe, and a sample of 28 heterothallic strains of Neurospora. Our analyses provide strong support for monophyly of N. tetrasperma, but reject the monophyly of N. crassa. We estimate that N. tetrasperma is of a recent origin and that it diverged from the heterothallic species ~1 million years ago. We also extend previous findings on the diversification within the N. tetrasperma clade, with 10 lineages identified. Taken together, these findings indicate that N. tetrasperma is younger than has been previously reported and that a rapid diversification of lineages has occurred within the N. tetrasperma clade.

  • 8.
    Corl, Ammon
    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.
    Sampling strategies for species trees: The effects on phylogenetic inference of the number of genes, number of individuals, and whether loci are mitochondrial, sex-linked, or autosomal2013In: Molecular Phylogenetics and Evolution, ISSN 1055-7903, E-ISSN 1095-9513, Vol. 67, no 2, p. 358-366Article in journal (Refereed)
    Abstract [en]

    Systematists can now use multi-locus data to construct species trees that take into account the stochastic nature of gene tree divergence among populations. There is a need to evaluate the new methods for species tree reconstruction in order to determine what kinds of loci to use and the most effective sampling schemes in terms of numbers of genes and numbers of individuals per species. Here we study sampling strategies with an empirical data set for six shorebird species in which we sequenced I mitochondrial, 12 autosomal, and 12 Z-linked loci for >8 individuals/species. We found that sampling greater numbers of genes resulted in substantial improvements to the resolution of the species tree, but sampling greater numbers of individuals had minor effects. We found that Z-linked loci significantly outperformed autosomal loci at all levels of sampling, which likely resulted from the lower effective population size of the Z-linked loci. Therefore, sex-linked loci are likely to be a powerful tool for multi-locus phylogenetic studies. We found that adding a mitochondria] gene to a set of Z-linked or autosomal loci substantially improved the resolution of the tree. Overall, our results help evaluate how best to maximize phylogenetic resolution while minimizing the costs of sequencing and computation when performing species tree analyses.

  • 9. Crespo, Ana
    et al.
    Lumbsch, H. Thorsten
    Mattsson, Jan-Eric
    Blanco, Oscar
    Divakar, Pradeep K.
    Articus, Kristina
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Botany.
    Wiklund, Elisabeth
    Bawingan, Paulina A.
    Wedin, Mats
    Testing morphology-based hypotheses of phylogenetic relationships in Parmeliaceae (Ascomycota) using three ribosomal markers and the nuclear RPB1 gene2007In: Molecular Phylogenetics and Evolution, ISSN 1055-7903, E-ISSN 1095-9513, Vol. 44, no 2, p. 812-824Article in journal (Refereed)
    Abstract [en]

    Parmeliaceae is the largest family of lichen-forming fungi with more than 2000 species and includes taxa with different growth forms. Morphology was widely employed to distinguish groups within this large, cosmopolitan family. In this study we test these morphology-based groupings using DNA sequence data from three nuclear and one mitochondrial marker from 1.20 taxa that include 59 genera and represent the morphological and chemical diversity in this lineage. Parmeliaceae is strongly supported as monophyletic and six well-supported main clades can be distinguished within the family. The relationships among them remain unresolved. The clades largely agree with the morphology-based groupings and only the placement of four of the genera studied is rejected by molecular data, while four other genera belong to clades previously unrecognised. The classification of these previously misplaced genera, however, has already been questioned by some authors based on morphological evidence. These results support morphological characters as important for the identification of monophyletic clades within Parmeliaceae.

  • 10.
    den Tex, Robert-Jan
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Leonard, Jennifer A.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    A molecular phylogeny of Asian barbets: Speciation and extinction in the tropics2013In: Molecular Phylogenetics and Evolution, ISSN 1055-7903, E-ISSN 1095-9513, Vol. 68, no 1, p. 1-13Article in journal (Refereed)
    Abstract [en]

    We reconstruct the phylogeny of all recognized species of the tropical forest associated Asian barbets based on mitochondrial and nuclear sequence data and test for the monophyly of species and genera. Tropical regions are well known for their extraordinarily high levels of biodiversity, but we still have a poor understanding of how this richness was generated and maintained through evolutionary time. Multiple theoretical frameworks have been developed to explain this diversity, including the Pleistocene pump hypothesis and the museum hypothesis. We use our phylogeny of the Asian barbets to test these hypotheses. Our data do not find an increase in speciation in the Pleistocene as predicted by the Pleistocene pump hypothesis. We do find evidence of extinctions, which apparently contradicts the museum hypothesis. However, the extinctions are only in a part of the phylogeny that is distributed mainly across Sundaland (the Malay peninsula and the islands off southeast Asia). The theory of island biogeography predicts a higher rate of extinction on islands than on mainland areas. The data from the part of the phylogeny primarily distributed on the mainland best fit a pure birth model of speciation, and thus supports the museum hypothesis. 

  • 11.
    den Tex, Robert-Jan
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Thorington, Richard
    Maldonado, Jesus E.
    Leonard, Jennifer A.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Speciation dynamics in the SE Asian tropics: Putting a time perspective on the phylogeny and biogeography of Sundaland tree squirrels, Sundasciurus2010In: Molecular Phylogenetics and Evolution, ISSN 1055-7903, E-ISSN 1095-9513, Vol. 55, no 2, p. 711-720Article in journal (Refereed)
    Abstract [en]

    Tropical rainforests are well known for their extraordinarily high levels of biodiversity. The origin of this species richness is still debated. For instance, the museum hypothesis states that over evolutionary time more and more species will accumulate with relatively few extinctions. In contrast, the Pleistocene diversification model argues that during the last 2 million years, climatic factors (glaciations) caused environmental changes that drove isolation and vicariant speciation events. In this study, we construct a molecular phylogeny of the Sundaland (Malay Peninsula, Sumata, Borneo, Palawan) and Greater Mindanao (Mindanao, Samar, Leyte) tree squirrels (genus Sundasciurus). Our results show that most speciation events in this forest dependent taxon occurred before the Pleistocene and that even the timing of intra-specific splits among populations from different landmasses are relatively old. Additionally, we found unexpectedly high divergence within and between highland populations of S. tenuis on Sumatra and the Malay Peninsula, highlighting the importance of Pliocene events in both speciation and within species divergences in this region. (C) 2010 Elsevier Inc. All rights reserved.

  • 12.
    Dufresnes, Christophe
    et al.
    Univ Lausanne, Lab Conservat Biol, Biophore Bldg, CH-1015 Lausanne, Switzerland; Hintermann & Weber, Ave Alpes 25, CH-1820 Montreux, Switzerland.
    Mazepa, Glib
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology. Univ Lausanne, Dept Ecol & Evolut, Biophore Bldg, CH-1015 Lausanne, Switzerland.
    Jablonski, Daniel
    Comenius Univ, Dept Zool, Ilkovicova 6, Bratislava 84215, Slovakia.
    Oliveira, Ricardo Caliari
    Katholieke Univ Leuven, Zool Inst, Lab Socioecol & Social Evolut, Naamsestr 59, B-3000 Leuven, Belgium.
    Wenseleers, Tom
    Katholieke Univ Leuven, Zool Inst, Lab Socioecol & Social Evolut, Naamsestr 59, B-3000 Leuven, Belgium.
    Shabanov, Dmytro A.
    Kharkov Natl Univ, Dept Zool & Anim Ecol, Svobody Sq 4, UA-61022 Kharkov, Ukraine.
    Auer, Markus
    Senckenberg Nat Hist Collect Dresden, Museum Zool, Konigsbrucker Landstr 159, D-01109 Dresden, Germany.
    Ernst, Raffael
    Senckenberg Nat Hist Collect Dresden, Museum Zool, Konigsbrucker Landstr 159, D-01109 Dresden, Germany.
    Koch, Claudia
    Leibniz Inst Biodiversitat Tiere, Zoolog Forschungsmuseum Alexander Koenig, Bonn, Germany.
    Ramirez-Chaves, Hector E.
    Univ Caldas, Dept Ciencias Biol, Fac Ciencias Exactas & Nat, Calle 65 26-10, Manizales, Caldas, Colombia;Univ Caldas, Museo Hist Nat, Ctr Museos, Calle 65 26-10, Manizales, Caldas, Colombia.
    Mulder, Kevin Patrick
    Univ Porto, Ctr Invest Biodiversidade & Recursos Genet, CIBIO InBIO, Campus Agr Vairao, P-4485661 Vairao, Portugal; Natl Zool Pk, Smithsonian Conservat Biol Inst, Ctr Conservat Genom, 3001 Connecticut Ave NW, Washington, DC 20008 USA; Natl Museum Nat Hist, Smithsonian Inst, Dept Vertebrate Zool, 10th St & Constitution Ave NW, Washington, DC 20560 USA.
    Simonov, Evgeniy
    Russian Acad Sci, Res Grp Physiol & Genet Hydrobionts, Siberian Branch, Inst Systemat & Ecol Anim, Novosibirsk 630091, Russia; Russian Acad Sci, Siberian Branch, Krasnoyarsk Sci Ctr, Fed Res Ctr,Lab Genom Res & Biotechnol, Krasnoyarsk 660036, Russia.
    Tiutenko, Arthur
    Univ Erlangen Nurnberg, Schlosspl 6, D-91054 Erlangen, Germany.
    Kryvokhyzha, Dmytro
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Wennekes, Paul L.
    Univ Reading, Sch Biol Sci, Plant Syst & Evolut, Philip Lyle Bldg 208, Reading RG6 6LA, Berks, England.
    Zinenko, Oleksandr I.
    Kharkov Natl Univ, Dept Zool & Anim Ecol, Svobody Sq 4, UA-61022 Kharkov, Ukraine; Kharkov Natl Univ, Museum Nat, Trinkler St 8, UA-61058 Kharkov, Ukraine.
    Korshunov, Oleksiy V.
    Kharkov Natl Univ, Dept Zool & Anim Ecol, Svobody Sq 4, UA-61022 Kharkov, Ukraine.
    Al-Johany, Awadh M.
    King Saud Univ, Dept Zool, Riyadh 11451, Saudi Arabia.
    Peregontsev, Evgeniy A.
    Zoocomplex MChJ, Gagarin Vil 14, Tashkent 100149, Uzbekistan.
    Masroor, Rafaqat
    Pakistan Museum Nat Hist, Garden Ave, Islamabad 44000, Pakistan.
    Betto-Colliard, Caroline
    Univ Lausanne, Dept Ecol & Evolut, Biophore Bldg, CH-1015 Lausanne, Switzerland.
    Denoel, Mathieu
    Univ Liege, Freshwater & OCean Sci Unit Res FOCUS, Behav Biol Grp, Lab Fish & Amphibian Ethol, Liege, Belgium.
    Borkin, Leo J.
    Russian Acad Sci, Zool Inst, Dept Herpetol, St Petersburg 199034, Russia.
    Skorinov, Dmitriy V.
    Russian Acad Sci, Inst Cytol, St Petersburg, Russia.
    Pasynkova, Roza A.
    Russian Acad Sci, Inst Cytol, St Petersburg, Russia.
    Mazanaeva, Lyudmila F.
    Dagestan State Univ, Makhachkala, Russia.
    Rosanov, Juriy M.
    Russian Acad Sci, Inst Cytol, St Petersburg, Russia.
    Dubey, Sylvain
    Hintermann & Weber, Ave Alpes 25, CH-1820 Montreux, Switzerland; Univ Lausanne, Dept Ecol & Evolut, Biophore Bldg, CH-1015 Lausanne, Switzerland; Agrosustain SA, Route Duillier 50, CH-1260 Nyon, Switzerland.
    Litvinchuk, Spartak
    Russian Acad Sci, Inst Cytol, St Petersburg, Russia; Dagestan State Univ, Makhachkala, Russia.
    Fifteen shades of green: The evolution of Bufotes toads revisited2019In: Molecular Phylogenetics and Evolution, ISSN 1055-7903, E-ISSN 1095-9513, Vol. 141, article id 106615Article in journal (Refereed)
    Abstract [en]

    The radiation of Palearctic green toads (Bufotes) holds great potential to evaluate the role of hybridization in phylogeography at multiple stages along the speciation continuum. With fifteen species representing three ploidy levels, this model system is particularly attractive to examine the causes and consequences of allopoly-ploidization, a prevalent yet enigmatic pathway towards hybrid speciation. Despite substantial efforts, the evolutionary history of this species complex remains largely blurred by the lack of consistency among the corresponding literature. To get a fresh, comprehensive view on Bufotes phylogeography, here we combined genome-wide multilocus analyses (RAD-seq) with an extensive compilation of mitochondrial, genome size, niche modelling, distribution and phenotypic (bioacoustics, morphometrics, toxin composition) datasets, representing hundreds of populations throughout Eurasia. We provide a fully resolved nuclear phylogeny for Bufotes and highlight exceptional cyto-nuclear discordances characteristic of complete mtDNA replacement (in 20% of species), mitochondrial surfing during post-glacial expansions, and the formation of homoploid hybrid populations. Moreover, we traced the origin of several allopolyploids down to species level, showing that all were exclusively fathered by the West Himalayan B. latastii but mothered by several diploid forms inhabiting Central Asian lowlands, an asymmetry consistent with hypotheses on mate choice and Dobzhansky-Muller incompatibilities. Their intermediate call phenotypes potentially allowed for rapid reproductive isolation, while toxin compositions converged towards the ecologically-closest parent. Across the radiation, we pinpoint a stepwise progression of reproductive isolation through time, with a threshold below which hybridizability is irrespective of divergence (< 6My), above which species barely admix and eventually evolve different mating calls (6-10My), or can successfully cross-breed through allopolyploidization (> 15My). Finally, we clarified the taxonomy of Bufotes (including genetic analyses of type series) and formally described two new species, B. cypriensis sp. nov. (endemic to Cyprus) and B. perrini sp. nov. (endemic to Central Asia). Embracing the genomic age, our framework marks the advent of a new exciting era for evolutionary research in these iconic amphibians.

  • 13.
    Ekenäs, Catarina
    et al.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Medicinal Chemistry, Division of Pharmacognosy. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Heidari, Nahid
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Andreasen, Katarina
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Arnica (Asteraceae) phylogeny revisited using RPB2: Complex patterns and multiple d-paralogues2012In: Molecular Phylogenetics and Evolution, ISSN 1055-7903, E-ISSN 1095-9513, Vol. 64, no 2, p. 261-270Article in journal (Refereed)
    Abstract [en]

    The region coding for the second largest subunit of RNA polymerase II (RPB2) was explored for resolving interspecific relationships in Arnica and lower level taxa in general. The region between exons 17 and 23 was cloned and sequenced for 33 accessions of Arnica and four outgroup taxa. Three paralogues of the RPB2-d copy (RPB2-dA, B and C) were detected in Arnica and outgroup taxa, indicating that the duplications must have occurred before the divergence of Arnica. Parsimony and Bayesian analyses of separate alignments of the three copies reveal complex patterns in Arnica, likely reflecting a history of lineage sorting in combination with apomixis, polyploidization, and possibly hybridization. Cloned sequences of some taxa do not form monophyletic clades within paralogues, but form multiple strongly supported clades with sequences of other taxa. Some well supported groups are present in more than one paralogue and many groups are in line with earlier hypotheses regarding interspecific relationships within the genus. Low levels of homoplasy in combination with relatively high sequence variation indicates that the introns of the RPB2 region could be suitable for phylogenetic studies in low level taxonomy.

  • 14.
    Erixon, Per
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Botany.
    Oxelman, Bengt
    Reticulate or treelike chloroplast DNA evolution in Sileneae (Caryophyllaceae)?2008In: Molecular Phylogenetics and Evolution, ISSN 1055-7903, E-ISSN 1095-9513, Vol. 48, no 1, p. 313-325Article in journal (Refereed)
    Abstract [en]

    Despite sampling of up to 25 kb of chloroplast DNA sequence from 24 species in Sileneae a number of nodes in the phylogeny remain poorly supported and it is not expected that additional sequence sampling will converge to a reliable phylogenetic hypothesis in these parts of the tree. The main reason for this is probably a combination of rapid radiation and substitution rate heterogeneity. Poor resolution among closely related species are often explained by low levels of variation in chloroplast data, but the problem with our data appear to be high levels of homoplasy. Tree-like cpDNA evolution cannot be rejected, but apparent incongruent patterns between different regions are evaluated with the possibility of ancient interspecific chloroplast recombination as explanatory model. However, several major phylogenetic relationships, previously not recognized, are confidently resolved, e.g. the grouping of the two SW Anatolian taxa S. cryptoneura and S. sordida strongly disagrees with previous studies on nuclear DNA sequence data, and indicate a possible case of homoploid hybrid origin. The closely related S. atocioides and S. aegyptiaca form a sister group to Lychnis and the rest of Silene, thus suggesting that Silene may be paraphyletic, despite recent revisions based on molecular data.

  • 15. Foerschler, Marc I.
    et al.
    Carlos Senar, Juan
    Perret, Philippe
    Björklund, Mats
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Evolution, Animal Ecology.
    The species status of the Corsican finch Carduelis corsicana assessed by three genetic markers with different rates of evolution2009In: Molecular Phylogenetics and Evolution, ISSN 1055-7903, E-ISSN 1095-9513, Vol. 52, no 1, p. 234-240Article in journal (Refereed)
    Abstract [en]

    Citril finches Carduelis c. citrinella and Corsican finches Carduelis c. corsicana represent two closely related forms, endemic to European mountains and some Mediterranean Islands. Their taxonomic status has recently been disputed based on the results from mitochondrial genes. We show that the use of different genetic markers may lead to different results in these two putative species. Using the mitochondrial ATP8 + 6 we found a clear difference between C. c. citrinella and C. c. corsicana (3.2%) suggesting a divergence time of 1.2 MYR. In contrast, no clear difference was found using two nuclear genes. The mismatch between the different markers suggests that the separation of C. c. citrinella and C. c. corsicana is likely to be a rather recent event, involving bottlenecks, which have enhanced the divergence in the mtDNA. Our results call for caution when using mtDNA alone for assessing times of divergence and rates of evolution. We did not find any support for the view that C. c. corsicana is more related to Carduelis carduelis than C. c. citrinella as proposed by previous studies. (C) 2009 Elsevier Inc. All rights reserved.

  • 16.
    Frajman, Božo
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Botany.
    Oxelman, Bengt
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Botany.
    Reticulate phylogenetics and phytogeographical structure of Heliosperma (Sileneae, Caryophyllaceae) inferred from chloroplast and nuclear DNA sequences2007In: Molecular Phylogenetics and Evolution, ISSN 1055-7903, E-ISSN 1095-9513, Vol. 43, no 1, p. 140-155Article in journal (Refereed)
    Abstract [en]

    The Balkan Peninsula is known to be one of the most diverse and species-rich parts of Europe, but its biota has gained much less attention in phylogenetic and evolutionary studies compared to other southern European mountain systems. We used nuclear ribosomal internal transcribed spacer (ITS) sequences and intron sequences of the chloroplast gene rps16 to examine phylogenetic and biogeographical patterns within the genus Heliosperma (Sileneae, Caryophyllaceae). The ITS and rps16 intron sequences both support monophyly of Heliosperma, but the data are not conclusive with regard to its exact origin. Three strongly supported clades are found in both data sets, corresponding to Heliosperma alpestre, Heliosperma macranthum and the Heliosperma pusillum clade, including all other taxa. The interrelationships among these three differ between the nuclear and the plastid data sets. Hierarchical relationships within the H. pusillum clade are poorly resolved by the ITS data, but the rps16 intron sequences form two well-supported clades which are geographically, rather than taxonomically, correlated. A similar geographical structure is found in the ITS data, when analyzed with the NeighbourNet method. The apparent rate of change within Heliosperma is slightly higher for rps16 as compared to ITS. In contrast, in the Sileneae outgroup, ITS substitution rates are more than twice as high as those for rps16, a situation more in agreement with what has been found in other rate comparisons of noncoding cpDNA and ITS. Unlike most other Sileneae ITS sequences, the H. pusillum group sequences display extensive polymorphism. A possible explanation to these patterns is extensive hybridization and gene flow within Heliosperma, which together with concerted evolution may have eradicated the ancient divergence suggested by the rps16 data. The morphological differentiation into high elevation, mainly widely distributed taxa, and low elevation narrow endemics is not correlated with the molecular data, and is possibly a result of ecological differentiation.

  • 17.
    Fridmanis, Davids
    et al.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Neuroscience.
    Fredriksson, Robert
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Neuroscience.
    Kapa, Ivo
    Schiöth, Helgi B.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Neuroscience.
    Klovins, Janis
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Neuroscience.
    Formation of new genes explains lower intron density in mammalian Rhodopsin G protein-coupled receptors2007In: Molecular Phylogenetics and Evolution, ISSN 1055-7903, E-ISSN 1095-9513, Vol. 43, no 3, p. 864-880Article in journal (Refereed)
    Abstract [en]

    Mammalian G protein-coupled receptor (GPCR) genes are characterised by a large proportion of intronless genes or a lower density of introns when compared with GPCRs of invertebrates. It is unclear which mechanisms have influenced intron density in this protein family, which is one of the largest in the mammalian genomes. We used a combination of Hidden Markov Models (HMM) and BLAST searches to establish the comprehensive repertoire of Rhodopsin GPCRs from seven species and performed overall alignments and phylogenetic analysis using the maximum parsimony method for over 1400 receptors in 12 subgroups. We identified 14 different Ancestral Receptor Groups (ARGs) that have members in both vertebrate and invertebrate species. We found that there exists a remarkable difference in the intron density among ancestral and new Rhodopsin GPCRs. The intron density among ARGs members was more than 3.5-fold higher than that within non-ARG members and more than 2-fold higher when considering only the 7TM region. This suggests that the new GPCR genes have been predominantly formed intronless while the ancestral receptors likely accumulated introns during their evolution. Many of the intron positions found in mammalian ARG receptor sequences were found to be present in orthologue invertebrate receptors suggesting that these intron positions are ancient. This analysis also revealed that one intron position is much more frequent than any other position and it is common for a number of phylogenetically different Rhodopsin GPCR groups. This intron position lies within a functionally important, conserved, DRY motif which may form a proto-splice site that could contribute to positional intron insertion. Moreover, we have found that other receptor motifs, similar to DRY, also contain introns between the second and third nucleotide of the arginine codon which also forms a proto-splice site. Our analysis presents compelling evidence that there was not a major loss of introns in mammalian GPCRs and formation of new GPCRs among mammals explains why these have fewer introns compared to invertebrate GPCRs. We also discuss and speculate about the possible role of different RNA- and DNA-based mechanisms of intron insertion and loss.

  • 18. Funk, Stephan M.
    et al.
    Verma, Sunil Kumar
    Larson, Greger
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
    Prasad, Kasturi
    Singh, Laiji
    Narayan, Goutarn
    Fa, John E.
    The pygmy hog is a unique genus: 19th century taxonomists got it right first time round2007In: Molecular Phylogenetics and Evolution, ISSN 1055-7903, E-ISSN 1095-9513, Vol. 45, no 2, p. 427-436Article in journal (Refereed)
    Abstract [en]

    The pygmy hog, Sus salvanius, the smallest and rarest extant suid was first described as the only member of the genus Porcula. It is currently regarded as member of the genus Sus and a sister taxon of the domestic pig/Eurasian wild boar (Sus scrofa). Phylogenctic analyses of 2316 bp from three mtDNA loci (control-region, cytochrome b, 16S) by Bayesian inference and statistical testing of alternative phylogenetic hypotheses all support the original classification of the pygmy hog as a unique genus. Thus, we propose that the species name Porcula salvania should be resurrected. The reclassification will heighten awareness of the need for the future protection and survival of this unique species.

  • 19.
    Goropashnaya, Anna V
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Evolution, Conservation Biology and Genetics.
    Fedorov, Vadim B
    Pamilo, Pekka
    Recent speciation in the Formica rufa group ants (Hymenoptera, Formicidae): inference from mitochondrial DNA phylogeny2004In: Molecular Phylogenetics and Evolution, ISSN 1055-7903, E-ISSN 1095-9513, Vol. 32, no 1, p. 198-206Article in journal (Refereed)
    Abstract [en]

    This study examines phylogenetic relationships among six species of the Formica rufa group ants (F. polyctena, F. rufa, F. lugubris, F. paralugubris, F. aquilonia, and F. pratensis). The phylogeny based on a 2051bp fragment of mtDNA including cyt b, tRNASer, and ND1 genes supports the division of the group into three major clusters: one with the species F. polyctena and F. rufa, one with F. aquilonia, F. lugubris, and F. paralugubris, and the third one with F. pratensis. The interspecific divergence estimates (mean 0.98 +/- 0.15% for the main phylogenetic groups) imply that radiation took place during the Pleistocene. Comparison of the divergence estimates among the F. rufa group species with divergence estimates among other closely related species of insects suggests that speciation in the group was relatively fast, and the mitochondrial lineages of F. polyctena and F. rufa have not fully separated. The haplotype tree shows also signs of transfer of mtDNA between species through hybridisation. The distribution of polygyny (multiple queens per nest) along the branches of the tree indicates that the social type characterised by highly polygynous societies and large colonial networks, has originated at least three times. The species F. aquilonia and F. paralugubris that build such large supercolonies, cluster tightly together with very little nucleotide variation, suggesting that this type of social organisation could be a factor promoting speciation in the ants.

  • 20. Guayasamin, Juan M.
    et al.
    Castroviejo-Fisher, Santiago
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Ayarzagüena, José
    Trueb, Linda
    Vilà, Carles
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Phylogenetic relationships of glassfrogs (Centrolenidae) based on mitochondrial and nuclear genes2008In: Molecular Phylogenetics and Evolution, ISSN 1055-7903, E-ISSN 1095-9513, Vol. 48, no 2, p. 574-595Article, review/survey (Refereed)
    Abstract [en]

    Glassfrogs (family Centrolenidae) represent an exceptionally diverse group among Neotropical anurans, but their evolutionary relationships never have been assessed from a molecular perspective. Mitochondrial and nuclear markers were used to develop a novel hypothesis of centrolenid phylogeny. Ingroup sampling included 100 terminals, with 78 (53%) of the named species in the family, representing most of the phenotypic diversity described for the group. Thirty-five species representing taxa traditionally associated with glassfrogs were used as outgroups. Gene sampling consisted of complete or partial sequences of three mitochondrial (12S, 16S, ND1) and three nuclear markers (c-myc exon 2, RAG1, POMC) for a total of ∼4362 bp. Phylogenies were estimated using maximum parsimony, maximum likelihood, and Bayesian analyses for individual genes and combined datasets. The separate analysis of mitochondrial and nuclear datasets allowed us to clarify the relationships within glassfrogs; also, we corroborate the sister-group relationship between Allophryne ruthveni and glassfrogs. The new phylogeny differs significantly from all previous morphology-based hypotheses of relationships, and shows that hypotheses based on few traits are likely to misrepresent evolutionary history. Traits previously hypothesized as unambiguous synapomorphies are shown to be homoplastic, and all genera in the current taxonomy (Centrolene, Cochranella, Hyalinobatrachium, Nymphargus) are found to be poly- or paraphyletic. The new topology implies a South American origin of glassfrogs and reveals allopatric speciation as the most important speciation mechanism. The phylogeny profoundly affects the traditional interpretations of glassfrog taxonomy, character evolution, and biogeography-topics that now require more extensive evaluation in future studies.

  • 21.
    Harris, Rebecca B.
    et al.
    Univ Washington, Dept Biol, Seattle, WA 98195 USA.;Burke Museum Nat Hist & Culture, Seattle, WA 98195 USA..
    Alström, Per
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology. Swedish Univ Agr Sci, Swedish Species Informat Ctr, Uppsala, Sweden.;Chinese Acad Sci, Inst Zool, Key Lab Zool Systemat & Evolut, Beijing, Peoples R China.
    Ödeen, Anders
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Leache, Adam D.
    Univ Washington, Dept Biol, Seattle, USA.;Burke Museum Nat Hist & Culture, Seattle, WA 98195 USA..
    Discordance between genomic divergence and phenotypic variation in a rapidly evolving avian genus (Motacilla)2018In: Molecular Phylogenetics and Evolution, ISSN 1055-7903, E-ISSN 1095-9513, Vol. 120, p. 183-195Article in journal (Refereed)
    Abstract [en]

    Generally, genotypes and phenotypes are expected to be spatially congruent; however, in widespread species complexes with few barriers to dispersal, multiple contact zones, and limited reproductive isolation, discordance between phenotypes and phylogeographic groups is more probable. Wagtails (Motacilla) are a genus of birds with striking plumage pattern variation across the Old World. Up to 13 subspecies are recognized within a single species, yet previous studies using mitochondrial DNA have supported polyphyletic phylogeographic groups that are inconsistent with subspecies plumage characteristics. In this study, we investigate the link between phenotypes and genotype by taking a phylogenetic approach. We use genome-wide SNPs, nuclear introns, and mitochondrial DNA to estimate population structure, isolation by distance, and species relationships. Together, our genetic sampling includes complete species-level sampling and comprehensive coverage of the three most phenotypically diverse Palearctic species. Our study provides strong evidence for species-level patterns of differentiation, however population-level differentiation is less pronounced. SNPs provide a robust estimate of species-level relationships, which are mostly corroborated by a combined analysis of mtDNA and nuclear introns (the first time-calibrated species tree for the genus). However, the mtDNA tree is strongly incongruent and is considered to misrepresent the species phylogeny. The extant wagtail lineages originated during the Pliocene and the Eurasian lineage underwent rapid diversification during the Pleistocene. Three of four widespread Eurasian species exhibit an east-west divide that contradicts both subspecies taxonomy and phenotypic variation. Indeed, SNPs fail to distinguish between phenotypically distinct subspecies within the M. alba and M. flava complexes, and instead support geographical regions, each of which is home to two or more different looking subspecies. This is a major step towards our understanding of wagtail phylogeny compared to previous analyses of fewer species and considerably less sequence data.

  • 22.
    He, Ding
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Sierra, Roberto
    Pawlowski, Jan
    Baldauf, Sandra
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Reducing long-branch effects in multi-protein data uncovers a close relationship between Alveolata and Rhizaria2016In: Molecular Phylogenetics and Evolution, ISSN 1055-7903, E-ISSN 1095-9513, Vol. 101, p. 1-7Article in journal (Refereed)
    Abstract [en]

    Rhizaria is a major eukaryotic group of tremendous diversity, including amoebae with spectacular skele- tons or tests (Radiolaria and Foraminifera), plasmodial parasites (Plasmodiophorida) and secondary endosymbionts (Chlorarachniophyta). Current phylogeny places Rhizaria in an unresolved trichotomy with Stramenopila and Alveolata (supergroup ‘‘SAR”). We assembled a 147-protein data set with exten- sive rhizarian coverage (M147), including the first transcriptomic data for a euglyphid amoeba. Phylogenetic pre-screening of individual proteins indicated potential problems with radically misplaced sequences due either to contamination of rhizarian sequences amplified from wild collected material and/or extremely long branches (xLBs). Therefore, two data subsets were extracted containing either all proteins consistently recovering rhizarian monophyly (M34) or excluding all proteins with P3 xLBs (defined as P2? the average terminal branch length for the tree). Phylogenetic analyses of M147 give conflicting results depending on the outgroup and method of analysis but strongly support an exclusive Rhizaria + Alveolata (R + A) clade with both data subsets (M34 and M37) regardless of phylogenetic method used. Support for an R + A clade is most consistent when a close outgroup is used and decreases with more distant outgroups, suggesting that support for alternative SAR topologies may reflect a long-branch attraction artifact. A survey of xLB distribution among taxa and protein functional category indicates that small ‘‘informational” proteins in particular have highly variable evolutionary rates with no consistent pattern among taxa.

  • 23.
    Hooper, Daniel M.
    et al.
    Univ Chicago, Comm Evolutionary Biol, Chicago, IL 60637 USA..
    Olsson, Urban
    Gothenburg Univ, Dept Zool, Systemat & Biodivers, Box 463, SE-40530 Gothenburg, Sweden..
    Alström, Per
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology. Swedish Univ Agr Sci, Swedish Species Informat Ctr, POB 7007, SE-75007 Uppsala, Sweden.;Chinese Acad Sci, Inst Zool, Key Lab Zool Systemat & Evolut, Beijing 100101, Peoples R China..
    The Rusty-tailed Flycatcher (Muscicapa ruficauda; Ayes: Muscicapidae) is a member of the genus Ficedula2016In: Molecular Phylogenetics and Evolution, ISSN 1055-7903, E-ISSN 1095-9513, Vol. 102, p. 56-61Article in journal (Refereed)
    Abstract [en]

    The phylogenetic relationships of the avian family Muscicapidae (Old World chats and flycatchers) have historically been enigmatic and remain an active area of study. Widespread instances of non-monophyly resulting from misleading morphological and behavioral similarities have merited numerous taxonomic revisions to the group. Here we report one such instance with regard to the Rusty-tailed Flycatcher Muscicapa ruficauda, which has recently been placed in the newly proposed monotypic genus Ripleyia, due to inferred sister relationship to the genus Muscicapa and related genera (Voelker et al., 2016a). This name was later replaced by Ripleyornis, as it was realized that Ripleyia is a junior homonym of a genus of Mollusca (Voelker et al., 2016b). Using a Bayesian phylogenetic assessment of the Muscicapidae with near-complete taxon sampling of the genus Ficedula for five loci, along with an acoustic comparison of M. ruficauda to a subset of other flycatcher species, we show that this species should be reassigned to the genus Ficedula and accordingly that the names Ripleyia and Ripleyornis are both junior synonyms of Ficedula.

  • 24.
    Irwin, Nicholas
    et al.
    Univ British Columbia, Dept Bot, Vancouver, BC V6T 1Z4, Canada.
    Tikhonenkov, Denis
    Univ British Columbia, Dept Bot, Vancouver, BC V6T 1Z4, Canada;Russian Acad Sci, Inst Biol Inland Waters, Borok 152742, Russia.
    Hehenberger, Elisabeth
    Univ British Columbia, Dept Bot, Vancouver, BC V6T 1Z4, Canada;Monterey Bay Aquarium Res Inst, Moss Landing, CA USA.
    Mylnikov, Alexander
    Russian Acad Sci, Inst Biol Inland Waters, Borok 152742, Russia.
    Burki, Fabien
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology. Uppsala University, Science for Life Laboratory, SciLifeLab. Univ British Columbia, Dept Bot, Vancouver, BC V6T 1Z4, Canada.
    Keeling, Patrick
    Univ British Columbia, Dept Bot, Vancouver, BC V6T 1Z4, Canada.
    Phylogenomics supports the monophyly of the Cercozoa2019In: Molecular Phylogenetics and Evolution, ISSN 1055-7903, E-ISSN 1095-9513, Vol. 130, p. 416-423Article in journal (Refereed)
    Abstract [en]

    The phylum Cercozoa consists of a diverse assemblage of amoeboid and flagellated protists that forms a major component of the supergroup, Rhizaria. However, despite its size and ubiquity, the phylogeny of the Cercozoa remains unclear as morphological variability between cercozoan species and ambiguity in molecular analyses, including phylogenomic approaches, have produced ambiguous results and raised doubts about the monophyly of the group. Here we sought to resolve these ambiguities using a 161-gene phylogenetic dataset with data from newly available genomes and deeply sequenced transcriptomes, including three new transcriptomes from Aurigamonas soils, Abollifer prolabens, and a novel species, Lapot gusevi n. gen. n. sp. Our phylogenomic analysis strongly supported a monophyletic Cercozoa, and approximately-unbiased tests rejected the paraphyletic topologies observed in previous studies. The transcriptome of L. gusevi represents the first transcriptomic data from the large and recently characterized Aquavolonidae-Treumulida-'Novel Clade 12' group, and phylogenomics supported its position as sister to the cercozoan subphylum, Endomyxa. These results provide insights into the phylogeny of the Cercozoa and the Rhizaria as a whole.

  • 25. Jesus Garcia-Pereira, Maria
    et al.
    Carvajal-Rodriguez, Antonio
    Whelan, Simon
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Caballero, Armando
    Quesada, Humberto
    Impact of deep coalescence and recombination on the estimation of phylogenetic relationships among species using AFLP markers2014In: Molecular Phylogenetics and Evolution, ISSN 1055-7903, E-ISSN 1095-9513, Vol. 76, p. 102-109Article in journal (Refereed)
    Abstract [en]

    Deep coalescence and the nongenealogical pattern of descent caused by recombination have emerged as a common problem for phylogenetic inference at the species level. Here we use computer simulations to assess whether AFLP-based phylogenies are robust to the uncertainties introduced by these factors. Our results indicate that phylogenetic signal can prevail even in the face of extensive deep coalescence allowing recovering the correct species tree topology. The impact of recombination on tree accuracy was related to total tree depth and species effective population size. The correct tree topology could be recovered upon many simulation settings due to a trade-off between the conflicting signals resulting from intra-locus recombination and the benefits of the joint consideration of unlinked loci that better matched overall the true species tree. Errors in tree topology were not only determined by deep coalescence, but also by the timing of divergence and the tree-building errors arising from an insufficient number of characters. DNA sequences generally outperformed AFLPs upon any simulated scenario, but this difference in performance was nearly negligible when a sufficient number of AFLP characters were sampled. Our simulations suggest that the impact of deep coalescence and intra-locus recombination on the reliability of AFLP trees could be minimal for effective population sizes equal to or lower than 10,000 (typical of many vertebrates and tree plants) given tree depths above 0.02 substitutions per site.

  • 26. Johansson, Ulf S.
    et al.
    Ekman, Jan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Bowie, Rauri C. K.
    Halvarsson, Peter
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Ohlson, Jan I.
    Price, Trevor D.
    Ericson, Per G. P.
    A complete multilocus species phylogeny of the tits and chickadees (Aves:Paridae)2013In: Molecular Phylogenetics and Evolution, ISSN 1055-7903, E-ISSN 1095-9513, Vol. 69, no 3, p. 852-860Article in journal (Refereed)
    Abstract [en]

    The avian family Paridae (tits and chickadees) contains c. 55 species distributed in the Palearctic, Nearctic, Afrotropics and Indomalaya. The group includes some of the most well-known and extensively studied avian species, and the evolutionary history, in particular the post-glacial colonization of the northern latitudes, has been comparably well-studied for several species. Yet a comprehensive phylogeny of the whole clade is lacking. Here, we present the first complete species phylogeny for the group based on sequence data front two nuclear introns and one mitochondrial gene for 67 taxa of parids. Our results strongly support the inclusion of the Fire-capped Tit (Cephalopyrus flammiceps), currently placed in the Remizidae, as the most basal member of the Paridae. The Yellow-browed Tit (Sylviparus modestus) and the Sultan Tit (Melanochlora sultanea) constitute the next two sequential branches whereas the remaining tits fall into two large clades, one of which contains the seed hoarding and nest excavating species. The indicated clades within these two groups are largely congruent with recent classifications, but with several unforeseen relationships, such as non-monophyly of the Sombre Tit (Poecile lugubris) and the Marsh Tit (Poecile palustris), as well as non-monophyly of both the African gray and the African black tits. Further, our results support a close relationship between the White-fronted Tit (Parus semilarvatus) and the varied Tit (Poecile varius) as well as a close relationship between the White-naped Tit (Parus nuchalis) and the Yellow-cheeked and Black-bred tits (Parus spilonotus and P. xanthogenys). Finally, Hume's Ground-tit (Pseudopodoces humilis) is found to be closely related to the Green-backed Tit (Parus monticolus) and the Great Tit (Parus major). We propose a new classification that is in accordance with this phylogeny. 

  • 27.
    Koblmueller, Stephan
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolutionary Biology.
    Schliewen, Ulrich K.
    Duftner, Nina
    Sefc, Kristina M.
    Katongo, Cyprian
    Sturmbauer, Christian
    Age and spread of the haplochromine cichlid fishes in Africa2008In: Molecular Phylogenetics and Evolution, ISSN 1055-7903, E-ISSN 1095-9513, Vol. 49, no 1, p. 153-169Article in journal (Refereed)
    Abstract [en]

    The Haplochromini are by far the most species-rich cichlid fish tribe that originated along with the so-called primary radiation of the Lake Tanganyika cichlid species flock, i.e. at the same time during which the majority of the endemic Lake Tanganyika cichlid tribes emerged. Unlike the other tribes, the haplochromines are not restricted to Lake Tanganyika but distributed throughout Africa, except for the northwestern part of the continent. Haplochromine cichlids seeded the adaptive radiation of cichlid fishes in Lakes Malawi, Kivu, Victoria, Turkana, as well as in the now extinct paleo-Lake Makgadikgadi. Here we present a comprehensive phylogenetic and phylogeographic analysis of haplochromine cichlids that is based upon DNA sequences of two mitochondrial gene segments of riverine taxa covering all major African biogeographic regions where haplochromines are found. Our analysis revealed that six lineages of haplochromines originated within a short period of time, about 5.3-4.4 MYA. These haplochromine lineages show a highly complex phylogeographic pattern, probably severely influenced by climate- and/or geology-induced changes of the environment, with river capture events most likely playing an important role for species dispersal. (C) 2008 Elsevier Inc. All rights reserved.

  • 28.
    Korall, Petra
    et al.
    Department of Botany, Stockholm University, SE-106 91 Stockholm, Sweden, and Molecular Systematics Laboratory, Swedish Museum of Natural History, Box 50007, SE-104 05 Stockholm, Sweden.
    Kenrick, P
    The phylogenetic history of Selaginellaceae based on DNA sequences from the plastid and nucleus: extreme substitution rates and rate heterogeneity2004In: Molecular Phylogenetics and Evolution, ISSN 1055-7903, E-ISSN 1095-9513, Vol. 31, p. 852-864Article in journal (Refereed)
  • 29.
    Korall, Petra
    et al.
    Department of Biology, Duke University, Durham, NC 27708, USA, Department of Phanerogamic Botany, Swedish Museum of Natural History, Stockholm, Sweden.
    Pryer, K A
    Metzgar, J S
    Schneider, H
    Conant, D S
    Tree ferns: Monophyletic groups and their relationships as revealed by four protein-coding plastid loci2006In: Molecular Phylogenetics and Evolution, ISSN 1055-7903, E-ISSN 1095-9513, Vol. 39, no 3, p. 830-845Article in journal (Refereed)
    Abstract [en]

    Tree ferns are a well-established clade within leptosporangiate ferns. Most of the 600 species (in seven families and 13 genera) are arborescent, but considerable morphological variability exists, spanning the giant scaly tree ferns (Cyatheaceae), the low, erect plants (Plagiogyriaceae), and the diminutive endemics of the Guayana Highlands (Hymenophyllopsidaceae). In this study, we investigate phylogenetic relationships within tree ferns based on analyses of four protein-coding, plastid loci (atpA, atpB, rbeL, and rps4). Our results reveal four well-supported clades, with genera of Dicksoniaceae (sensu Kubitzki, 1990) interspersed among them: (A) (Loxomataceae, (Culcita, Plagiogyriaceae)), (B) (Calochlaena, (Dicksonia, Lophosoriaceae)), (C) Cibotium, and (D) Cyatheaceae, with Hymenophyllopsidaceae nested within. How these four groups are related to one other, to Thyrsopteris, or to Metaxyaceae is weakly supported. Our results show that Dicksoniaceae and Cyatheaceae, as currently recognised, are not monophyletic and new circumscriptions for these families are needed. (c) 2006 Elsevier Inc. All rights reserved.

  • 30.
    Krishnan, Arunkumar
    et al.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Neuroscience, Functional Pharmacology.
    Mustafa, Arshi
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Neuroscience, Functional Pharmacology.
    Almén, Markus Sällman
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Neuroscience, Functional Pharmacology.
    Fredriksson, Robert
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Neuroscience, Functional Pharmacology.
    Williams, Michael J
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Neuroscience, Functional Pharmacology.
    Schiöth, Helgi B.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Neuroscience, Functional Pharmacology.
    Evolutionary hierarchy of vertebrate-like heterotrimeric G protein families2015In: Molecular Phylogenetics and Evolution, ISSN 1055-7903, E-ISSN 1095-9513, Vol. 91, p. 27-40Article in journal (Refereed)
    Abstract [en]

    Heterotrimeric G proteins perform a crucial role as molecular switches controlling various cellular responses mediated by G protein-coupled receptor (GPCR) signaling pathway. Recent data have shown that the vertebrate-like G protein families are found across metazoans and their closest unicellular relatives. However, an overall evolutionary hierarchy of vertebrate-like G proteins, including gene family annotations and in particular mapping individual gene gain/loss events across diverse holozoan lineages is still incomplete. Here, with more expanded invertebrate taxon sampling, we have reconstructed phylogenetic trees for each of the G protein classes/families and provide a robust classification and hierarchy of vertebrate-like heterotrimeric G proteins. Our results further extend the evidence that the common ancestor (CA) of holozoans had at least five ancestral Gα genes corresponding to all major vertebrate Gα classes and contain a total of eight genes including two Gβ and one Gγ. Our results also indicate that the GNAI/O-like gene likely duplicated in the last CA of metazoans to give rise to GNAI- and GNAO-like genes, which are conserved across invertebrates. Moreover, homologs of GNB1-4 paralogon- and GNB5 family-like genes are found in most metazoans and that the unicellular holozoans encode two ancestral Gβ genes. Similarly, most bilaterian invertebrates encode two Gγ genes which include a representative of the GNG gene cluster and a putative homolog of GNG13. Interestingly, our results also revealed key evolutionary events such as the Drosophila melanogaster eye specific Gβ subunit that is found conserved in most arthropods and several previously unidentified species specific expansions within Gαi/o, Gαs, Gαq, Gα12/13 classes and the GNB1-4 paralogon. Also, we provide an overall proposed evolutionary scenario on the expansions of all G protein families in vertebrate tetraploidizations. Our robust classification/hierarchy is essential to further understand the differential roles of GPCR/G protein mediated intracellular signaling system across various metazoan lineages.

  • 31. Kårehed, Jesper
    et al.
    Groeninckx, I
    Dessein, S
    Motley, T. J.
    Bremer, B
    The phylogenetic utility of chloroplast and nuclear DNA markers and the phylogeny of the Rubiaceae tribe Spermacoceae2008In: Molecular Phylogenetics and Evolution, ISSN 1055-7903, E-ISSN 1095-9513, Vol. 49, p. 843-866Article in journal (Refereed)
  • 32. Lopez-Vaamonde, Carlos
    et al.
    Wikström, Niklas
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Biology.
    Kjer, M
    Weiblen, D
    Rasplus, Yves
    Machado, A
    Cook, James M.
    Molecular dating and biogeography of fig-pollinating wasps2009In: Molecular Phylogenetics and Evolution, ISSN 1055-7903, E-ISSN 1095-9513, Vol. 52, no 3, p. 715-726Article in journal (Refereed)
    Abstract [en]

    Figs and fig-pollinating wasps are obligate mutualists that have coevolved for over 60 million years. But when and where did pollinating fig wasps (Agaonidae) originate? Some studies suggest that agaonids arose in the Late Cretaceous and the current distribution of fig-wasp faunas can be explained by the break-up of the Gondwanan landmass. However, recent molecular-dating studies suggest divergence time estimates that are inconsistent with the Gondwanan vicariance hypothesis and imply that long distance oceanic dispersal could have been an important process for explaining the current distribution of both figs and fig wasps. Here, we use a combination of phylogenetic and biogeographical data to infer the age, the major period of diversification, and the geographic origin of pollinating fig wasps. Age estimates ranged widely depending on the molecular-dating method used and even when using the same method but with slightly different constraints, making it difficult to assess with certainty a Gondwanan origin of agaonids. The reconstruction of ancestral areas suggests that the most recent common ancestor of all extant fig-pollinating wasps was most likely Asian, although a southern Gondwana origin cannot be rejected. Our analysis also suggests that dispersal has played a more important role in the development of the fig-wasp biota than previously assumed. (C) 2009 Elsevier Inc. All rights reserved.

  • 33. Lucchini, V
    et al.
    Hoglund, J
    Klaus, S
    Swenson, J
    Randi, E
    Historical biogeography and a mitochondrial DNA phylogeny of grouse and ptarmigan2001In: Molecular Phylogenetics and Evolution, ISSN 1055-7903, E-ISSN 1095-9513, Vol. 20, no 1, p. 149-162Article in journal (Refereed)
  • 34. Millanes, Ana M.
    et al.
    Diederich, Paul
    Ekman, Stefan
    Uppsala University, Music and Museums, Museum of Evolution.
    Wedin, Mats
    Phylogeny and character evolution in the jelly fungi (Tremellomycetes, Basidiomycota, Fungi)2011In: Molecular Phylogenetics and Evolution, ISSN 1055-7903, E-ISSN 1095-9513, Vol. 61, no 1, p. 12-28Article in journal (Refereed)
    Abstract [en]

    The Tremellomycetes (Agaricomycotina, Basidiomycota, Fungi) are a nutritionally heterogeneous group comprising saprotrophs, animal parasites, and fungicolous species (fungal-inhabiting, including lichen-inhabiting). The relationships of many species, particularly those with a lichenicolous habit, have never been investigated by molecular methods. We present a phylogeny of the Tremellomycetes based on three nuclear DNA ribosomal markers (nSSU, 5.8S and nLSU), representing all main taxonomic groups and life forms, including lichenicolous taxa. The Cystofilobasidiales, Filobasidiales, Holtermanniales, and Tremellales (including the Trichosporonales) are recovered as monophyletic, but this is not the case for the Tremellomycetes. We suggest, however, that the Cystofilobasidiales tentatively continue to be included in the Tremellomycetes. As currently circumscribed, the Filobasidiaceae, Sirobasidiaceae, Syzygosporaceae and Tremellaceae are non-monophyletic. Cuniculitremaceae, Sirobasidiaceae and Tetragoniomycetaceae are nested within Tremellaceae. The lichenicolous species currently included within the Tremellomycetes belong in this group, distributed across the Filobasidiales and Tremellales. Lichen-inhabiting taxa do not form a monophyletic group; they are distributed in several clades and sometimes intermixed with taxa of other nutritional habits. Character state reconstruction indicates that two morphological traits claimed to characterize groups in the Tremellomycetes (the basidium habit and basidium septation) are highly homoplastic. Comparative phylogenetic methods suggest that the transitions between single and catenulate basidia in the Tremellales are consistent with a punctuational model of evolution whereas basidium septation is likely to have evolved under a graduational model in the clade comprising the Holtermanniales, Filobasidiales, and Tremellales.

  • 35.
    Nabholz, Benoit
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Jarvis, Erich D.
    Ellegren, Hans
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Obtaining mtDNA genomes from next-generation transcriptome sequencing: A case study on the basal Passerida (Aves: Passeriformes) phylogeny2010In: Molecular Phylogenetics and Evolution, ISSN 1055-7903, E-ISSN 1095-9513, Vol. 57, no 1, p. 466-470Article in journal (Refereed)
    Abstract [en]

    Classically, the mitochondrial genome is sequenced by a series of amplicons using conserved PCR primers. Here we show how shot-gun transcriptome sequencing can be used to obtain the complete set of protein-coding genes from the mtDNA of four passerine bird species. With these sequences, we address the still unresolved basal Passerida relationships (Ayes: Passeriformes). Our analysis suggests a new hypothesis for the basal relationships of Passerida, namely a clade grouping Sylvioidea and Passeroidea, with Paridae and Muscicapidae as successive sister groups to this clade. This study demonstrates the usefulness of next-generation sequencing transcriptome sequencing for obtaining new mtDNA genomes.

  • 36.
    Nygren, Kristiina
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Strandberg, Rebecka
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Wallberg, Andreas
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Nabholz, Benoit
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Gustafsson, Tim
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    García, Dania
    Unitat de Microbiologia, Facultat de Medicina i Ciències de la Salut, ISPV, Universitat Rovira i Virgili, 43201 Reus, Tarragona, Spain.
    Cano, José
    Unitat de Microbiologia, Facultat de Medicina i Ciències de la Salut, ISPV, Universitat Rovira i Virgili, 43201 Reus, Tarragona, Spain.
    Guarro, Josep
    Unitat de Microbiologia, Facultat de Medicina i Ciències de la Salut, ISPV, Universitat Rovira i Virgili, 43201 Reus, Tarragona, Spain.
    Johannesson, Hanna
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    A comprehensive phylogeny of Neurospora reveals a link between reproductive mode and molecular evolution in fungi2011In: Molecular Phylogenetics and Evolution, ISSN 1055-7903, E-ISSN 1095-9513, Vol. 59, no 3, p. 649-663Article in journal (Refereed)
    Abstract [en]

    The filamentous ascomycete genus Neurospora encompasses taxa with a wide range of reproductive modes. Sexual reproduction in this genus can be divided into three major modes; heterothallism (self-incompatibility), homothallism (self-compatibility) and pseudohomothallism (partial self-compatibility). In addition to the sexual pathway, most of the heterothallic taxa propagate with morphologically distinct, vegetative dissemination propagules (macroconidia), while this feature is undetected in the majority of the homothallic taxa. In this study, we used sequence information of seven nuclear gene loci from 43 taxa (295 of the possible 301 locus-by-taxon combinations) to create a phylogeny of Neurospora. The results suggest that transitions in reproductive mode have occurred at multiple times within this group of fungi. Although a homothallic ancestor would imply fewer switches in reproductive mode, we argue that the ancestor of Neurospora was likely heterothallic and that homothallism has evolved independently at least six times in the evolutionary history of the genus. Furthermore, the two pseudohomothallic taxa of Neurospora (N. tetrasperma and N. tetraspora) represent two independent origins of pseudohomothallism. Likelihood ratio tests of substitution rates among branches in the phylogeny indicate that reproductive mode is an important factor driving genome evolution in Neurospora. First, an increased level of non-synonymous/synonymous substitutions in branches delineating homothallic taxa was found, suggesting a reduced efficiency of purifying selection in these taxa. Furthermore, elevated nucleotide substitution rates were found in heterothallic, conidia-producing, lineages as compared to the homothallic non-conidiating lineages. The latter finding is likely due to the presence of conidia, i.e., a higher rate of mitotic divisions inducing mutations, and/or that the homothallic taxa have evolved a lower mutation rate to avoid genomic degeneration.

  • 37.
    Nygren, Kristiina
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Strandberg, Rebecka
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Wallberg, Andreas
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Nabholz, Benoit
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Gustafsson, Tim
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    García, Dania
    Cano, José
    Guarro, Josep
    Johannesson, Hanna
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    A comprehensive phylogeny of Neurospora reveals a link between reproductive mode and molecular evolution in fungi2011In: Molecular Phylogenetics and Evolution, ISSN 1055-7903, E-ISSN 1095-9513, Vol. 59, no 3, p. 649-663Article in journal (Refereed)
    Abstract [en]

    The filamentous ascomycete genus Neurospora encompasses taxa with a wide range of reproductive modes. Sexual reproduction in this genus can be divided into three major modes; heterothallism (self-incompatibility), homothallism (self-compatibility) and pseudohomothallism (partial self-compatibility). In addition to the sexual pathway, most of the heterothallic taxa propagate with morphologically distinct, vegetative dissemination propagules (macroconidia), while this feature is undetected in the majority of the homothallic taxa. In this study, we used sequence information of seven nuclear gene loci from 43 taxa (295 of the possible 301 locus-by-taxon combinations) to create a phylogeny of Neurospora. The results suggest that transitions in reproductive mode have occurred at multiple times within this group of fungi. Although a homothallic ancestor would imply fewer switches in reproductive mode, we argue that the ancestor of Neurospora was likely heterothallic and that homothallism has evolved independently at least six times in the evolutionary history of the genus. Furthermore, the two pseudohomothallic taxa of Neurospora (N. tetrasperma and N. tetraspora) represent two independent origins of pseudohomothallism. Likelihood ratio tests of substitution rates among branches in the phylogeny indicate that reproductive mode is an important factor driving genome evolution in Neurospora. First, an increased level of non-synonymous/synonymous substitutions in branches delineating homothallic taxa was found, suggesting a reduced efficiency of purifying selection in these taxa. Furthermore, elevated nucleotide substitution rates were found in heterothallic, conidia-producing, lineages as compared to the homothallic non-conidiating lineages. The latter finding is likely due to the presence of conidia, i.e., a higher rate of mitotic divisions inducing mutations, and/or that the homothallic taxa have evolved a lower mutation rate to avoid genomic degeneration.

  • 38. Olivieri, Gillian
    et al.
    Zimmermann, Elke
    Randrianambinina, Blanchard
    Rasoloharijaona, Solofonirina
    Rakotondravony, Daniel
    Guschanski, Katerina
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Radespiel, Ute
    The ever-increasing diversity in mouse lemurs: Three new species in north and northwestern Madagascar2007In: Molecular Phylogenetics and Evolution, ISSN 1055-7903, E-ISSN 1095-9513, Vol. 43, no 1, p. 309-327Article in journal (Refereed)
  • 39. Olsson, Urban
    et al.
    Alström, Per
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Zoology.
    Gelang, Magnus
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Zoology.
    Ericson, Per G. P.
    Sundberg, Per
    Phylogeography of Indonesian and Sino-Himalayan region bush warblers (Cettia, Aves)2006In: Molecular Phylogenetics and Evolution, ISSN 1055-7903, E-ISSN 1095-9513, Vol. 41, no 3, p. 556-565Article in journal (Refereed)
    Abstract [en]

    We present a hypothesis for the phylogeny and phylogeography of a group of bush warblers in the genus Cettia, based on parts of the mitochondrial Cytochrome b gene and the nuclear myoglobin intron II (in all similar to 1.7 kb). Ancestral areas were reconstructed by dispersal-vicariance analysis and constrained Bayesian inference. The results suggest that the insular taxa in the Cettia vulcania group are most closely related to Cettia flavolivacea, and originated from a dispersal by an ancestral population in the Himalayas towards the south, to the Sunda region. From this population, a second dispersal along a different route colonized China and northern Vietnam. Hence, the Chinese taxon intricata and Vietnamese oblita, currently allocated to C. flavoliuacea, are more closely related to the vulcania group than to the other taxa in the flavolivacea group, and we propose that they be treated as conspecific with C vulcania, restricting C. flavolivacea to Myanmar and the Himalayas.

  • 40.
    Olsson, Urban
    et al.
    Univ Gothenburg, Dept Biol & Environm Sci Systemat & Biodivers, Box 463, SE-40530 Gothenburg, Sweden..
    Rguibi-Idrissi, Hamid
    Univ Chouaib Doukkali, Fac Sci, Equipe Rech Valorisat Ressources Nat & Biodiversi, El Jadida, Morocco..
    Luis Copete, Jose
    Martinez de la Rosa 27 Pral 3a, Barcelona 08012, Spain..
    Arroyo Matos, Jose Luis
    CSIC, Donana Biol Stn, Nat Proc Monitoring Team, C Amer Vespucio S-N, E-41092 Seville, Spain..
    Provost, Pascal
    2 Route Radome, F-22560 Pleumeur Bodou, France..
    Amezian, Mohamed
    Abdelmalek Essaadi Univ, Fac Sci, Dept Biol, MHannech 2, Tetouan 93030, Morocco..
    Alström, Per
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology. Swedish Univ Agr Sci, Swedish Species Informat Ctr, Box 7007, SE-75007 Uppsala, Sweden..
    Jiguet, Frederic
    Ctr Rech Biol Populat Oiseaux, UMR7204 Sorbonne Univ MNHN CNRS UPMC, CESCO, CP 135,43 Rue Buffon, F-75005 Paris, France..
    Mitochondrial phylogeny of the Eurasian/African reed warbler complex (Acrocephalus, Aves). Disagreement between morphological and molecular evidence and cryptic divergence: A case for resurrecting Calamoherpe ambigua Brehm 18572016In: Molecular Phylogenetics and Evolution, ISSN 1055-7903, E-ISSN 1095-9513, Vol. 102, p. 30-44Article in journal (Refereed)
    Abstract [en]

    A tree based on the mitochondrial cyt b gene for 278 samples from throughout the range of the Eurasian Reed Warbler Acrocephalus scirpaceus - African Reed Warbler A. baeticatus complex shows well supported geographically structured divergence for eight distinct lineages. The phylogenetic structuring together with the clarification of priority, provided by sequence data from seven type specimens, suggests that both taxonomy and distribution boundaries are in need of revision. The Iberian and Moroccan populations form a well-supported Glade, and we propose that these are treated as taxonomically distinct, under the name ambiguus (Brehm, 1857). We propose that the names scirpaceus, fuscus, avicenniae, ambiguus, minor, cinnamomeus, hallae and baeticatus are used for the well supported clades in the complex, which we recommend to treat as one polytypic species, A. scirpaceus, pending studies of gene flow and assortative mating in the contact zones.

  • 41.
    Padial, Jose Manuel
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Castroviejo-Fisher, Santiago
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    De la Riva, Ignacio
    The phylogenetic relationships of Yunganastes revisited (Anura: Terrarana)2009In: Molecular Phylogenetics and Evolution, ISSN 1055-7903, E-ISSN 1095-9513, Vol. 52, no 3, p. 911-915Article in journal (Refereed)
  • 42.
    Palanisamy, Navaneethan
    et al.
    Heidelberg Univ, BioQuant, Mol & Cellular Engn Grp, Heidelberg, Germany.;Heidelberg Univ, Hartmut Hoffmann Berling Int Grad Sch Mol & Cellu, Heidelberg, Germany..
    Akaberi, Dario
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Clinical Microbiology.
    Lennerstrand, Johan
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Clinical Microbiology.
    Protein backbone flexibility pattern is evolutionarily conserved in the Flaviviridae family: A case of NS3 protease in Flavivirus and Hepacivirus2018In: Molecular Phylogenetics and Evolution, ISSN 1055-7903, E-ISSN 1095-9513, Vol. 118, p. 58-63Article in journal (Refereed)
    Abstract [en]

    Viruses belonging to the Flaviviridae family have been an important health concern for humans, animals and birds alike. No specific treatment is available yet for many of the viral infections caused by the members of this family. Lack of specific drugs against these viruses is mainly due to lack of protein structure information. It has been known that protein backbone fluctuation pattern is highly conserved in protein pairs with similar folds, in spite of the lack of sequence similarity. We hypothesized that this concept should also hold true for proteins (especially enzymes) of viruses included in different genera of the Flaviviridae family, as we know that the sequence similarity between them is low. Using available NS3 protease crystal structures of the Flaviviridae family, our preliminary results have shown that the C alpha (i.e. backbone) fluctuation patterns are highly similar between Flaviviruses and a Hepacivirus (i.e. hepatitis C virus, HCV). This has to be validated further experimentally.

  • 43. Pleijel, F.
    et al.
    Jondelius, U.
    Norlinder, E.
    Nygren, A.
    Oxelman, B.
    Schander, C.
    Sundberg, P.
    Thollesson, M.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics.
    Phylogenies without roots? A plea for the use of vouchers in molecular phylogenetic studies2008In: Molecular Phylogenetics and Evolution, ISSN 1055-7903, E-ISSN 1095-9513, Vol. 48, no 1, p. 369-371Article in journal (Refereed)
  • 44.
    Rautenberg, Anja
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organism Biology, Systematic Biology.
    Hathaway, Louise
    Oxelman, Bengt
    Prentice, Honor C.
    Geographic and phylogenetic patterns in Silene section Melandrium (Caryophyllaceae) as inferred from chloroplast and nuclear DNA sequences2010In: Molecular Phylogenetics and Evolution, ISSN 1055-7903, E-ISSN 1095-9513, Vol. 57, no 3, p. 978-991Article in journal (Refereed)
    Abstract [en]

    The phylogenetic relationships between the five dioecious species in Silene section Melandrium (Caryophyllaceae) and their putative hermaphrodite relatives are investigated based on an extensive geographic and taxonomic sample, using DNA sequence data from the chloroplast genome and the nuclear ribosomal ITS region. The hermaphrodite S. noctiflora (the type species of section Elisanthe) is distantly related to the dioecious species. With the exception of chloroplast sequences in one S. latifolia population from Turkey, the dioecious taxa form a strongly supported monophyletic group (Silene section Melandrium). The phylogenetic structure within section Melandrium differs between chloroplast and nuclear sequences. While there is extensive sharing of chloroplast haplotypes among all the dioecious species (the observed patterns reflect geographic structure), the nuclear ITS phylogeny shows a higher degree of taxonomic structure. Chloroplast-sharing by the section Melandrium species is most plausibly explained by a history of hybridization and extensive backcrossing.

  • 45.
    Rest, Joshua S
    et al.
    University of Michigan, Museum of Zoology and Department of Ecology and Evolutionary Biology.
    Ast, Jennifer C
    University of Michigan, Museum of Zoology and Department of Ecology and Evolutionary Biology.
    Austin, Christopher C
    Waddell, Peter J
    Tibbetts, Elizabeth A
    University of Michigan, Museum of Zoology and Department of Ecology and Evolutionary Biology.
    Hay, Jennifer M
    Mindell, David P
    University of Michigan, Museum of Zoology and Department of Ecology and Evolutionary Biology.
    Molecular systematics of primary reptilian lineages and the tuatara mitochondrial genome.2003In: Molecular Phylogenetics and Evolution, ISSN 1055-7903, E-ISSN 1095-9513, Vol. 29, no 2, p. 289-97Article in journal (Refereed)
    Abstract [en]

    We provide phylogenetic analyses for primary Reptilia lineages including, for the first time, Sphenodon punctatus (tuatara) using data from whole mitochondrial genomes. Our analyses firmly support a sister relationship between Sphenodon and Squamata, which includes lizards and snakes. Using Sphenodon as an outgroup for select squamates, we found evidence indicating a sister relationship, among our study taxa, between Serpentes (represented by Dinodon) and Varanidae. Our analyses support monophyly of Archosauria, and a sister relationship between turtles and archosaurs. This latter relationship is congruent with a growing set of morphological and molecular analyses placing turtles within crown Diapsida and recognizing them as secondarily anapsid (lacking a skull fenestration). Inclusion of Sphenodon, as the only surviving member of Sphenodontia (with fossils from the mid-Triassic), helps to fill a sampling gap within previous analyses of reptilian phylogeny. We also report a unique configuration for the mitochondrial genome of Sphenodon, including two tRNA(Lys) copies and an absence of ND5, tRNA(His), and tRNA(Thr) genes.

  • 46. Roquet, Cristina
    et al.
    Sanmartin, Isabel
    Garcia-Jacas, Nuria
    Saez, Llorenc
    Susanna, Alfonso
    Wikström, Niklas
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics.
    Jose Aldasoro, Juan
    Reconstructing the history of Campanulaceae with a Bayesian approach to molecular dating and dispersal-vicariance analyses2009In: Molecular Phylogenetics and Evolution, ISSN 1055-7903, E-ISSN 1095-9513, Vol. 52, no 3, p. 575-587Article, review/survey (Refereed)
    Abstract [en]

    We reconstruct here the spatial and temporal evolution of the Campanula alliance in order to better understand its evolutionary history. To increase phylogenetic resolution among major groups (Wahlenbergieae-Campanuleae), new sequences from the rbcL region were added to the trnL-F dataset obtained in a previous Study. These phylogenies were used to infer ancestral areas and divergence times in Campanula and related genera using a Bayesian approach to molecular dating and dispersal-vicariance analyses that takes into account phylogenetic uncertainty. The new phylogenetic analysis confirms Platycodoneae as the sister group of Wahlenbergieae-Campanuleae, the two last ones inter-graded into a well-supported clade. Biogeographic and dating analyses suggest that Western Asia and the Eastern Mediterranean have played a major role as centers of migration and diversification within the Campanula alliance, probably in relation to the intense orogenic activity that took place in this region during the Late Neogene, and that could have promoted isolation and allopatric speciation within lineages. Diversification rates within several Campanula lineages would have increased at the end of the Miocene, coinciding with the Messinian Stage. Strong selective pressures from climate changes and the expansion of mountainous regions during this period are suggested to explain the adaptation to drought, cold or disturbed environments observed in many Campanula species. Several independent long-distance dispersal events to North America are inferred within the Ropunculus clade, which seem to be related to high ploidy levels.

  • 47. Sauquet, Herve
    et al.
    Weston, H
    Barker, P
    Anderson, Cajsa Lisa
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Biology.
    Cantrill, J
    Savolainen, Vincent
    Using fossils and molecular data to reveal the origins of the Cape proteas (subfamily Proteoideae)2009In: Molecular Phylogenetics and Evolution, ISSN 1055-7903, E-ISSN 1095-9513, Vol. 51, no 1, p. 31-43Article in journal (Refereed)
    Abstract [en]

    The angiosperm family Proteaceae is a distinct component of the Cape Floristic Region biodiversity hot-spot with 330 endemic species. Phylogenetic analyses of subfamily Proteoideae using sequence data from one nuclear and six plastid loci show that most of this diversity is contained in two distinct Cape floral clades. Molecular dating analyses, using Bayesian and penalized likelihood methods and four phylogenetically supported fossil age constraints. reveal contrasting histories for these two clades. The genus Protea belongs to a lineage that may have been in Africa since the Late Cretaceous but began to diversify in the Cape only 5-18 Myr ago. In contrast, the Leucadendrinae clade presumably arrived in the region no earlier than 46 Myr ago by long-distance dispersal from an Australian ancestor and the extant members of this clade began to diversify in the Cape 22-39 Myr ago. These results join a growing number of case studies that challenge the commonly accepted view that most of the Cape flora radiated synchronously in the Late Miocene and Early Pliocene when a Mediterranean climate settled in the region. (C) 2008 Elsevier Inc. All rights reserved.

  • 48.
    Schweizer, Manuel
    et al.
    Nat Hist Museum Burgergemeinde Bern, Bernastr 15, CH-3005 Bern, Switzerland.
    Warmuth, Vera M.
    Ludwig Maximilians Univ Munchen, Dept Biol 2, Evolutionary Biol, Biozentrum Martinsried, D-82152 Martinsried, Germany.
    Kakhki, Niloofar Alaei
    Ferdowsi Univ Mashhad, Fac Sci, Dept Biol, Mashhad, Razavi Khorasan, Iran;Ferdowsi Univ Mashhad, RDZI, Inst Appl Zool, Mashhad, Razavi Khorasan, Iran.
    Aliabadian, Mansour
    Ferdowsi Univ Mashhad, Fac Sci, Dept Biol, Mashhad, Razavi Khorasan, Iran;Ferdowsi Univ Mashhad, RDZI, Inst Appl Zool, Mashhad, Razavi Khorasan, Iran.
    Foerschler, Marc
    Dept Ecosyst Monitoring Res & Conservat, Black Forest Natl Pk, D-72250 Freudenstadt, Germany.
    Shirihai, Hadoram
    Ausserdorfstr 6, CH-8052 Zurich, Switzerland.
    Ewels, Phil
    Stockholm Univ, Dept Biochem & Biophys, Sci Life Lab, SE-10691 Stockholm, Sweden.
    Gruselius, Joel
    Karolinska Inst, Dept Biosci & Nutr, Sci Life Lab, Stockholm, Sweden.
    Olsen, Remi-Andre
    Stockholm Univ, Dept Biochem & Biophys, Sci Life Lab, SE-10691 Stockholm, Sweden.
    Schielzeth, Holger
    Friedrich Schiller Univ Jena, Inst Ecol & Evolut, Dept Populat Ecol, D Dornburger Str 159, D-07743 Jena, Germany.
    Suh, Alexander
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Burri, Reto
    Friedrich Schiller Univ Jena, Inst Ecol & Evolut, Dept Populat Ecol, D Dornburger Str 159, D-07743 Jena, Germany.
    Genome-wide evidence supports mitochondrial relationships and pervasive parallel phenotypic evolution in open-habitat chats2019In: Molecular Phylogenetics and Evolution, ISSN 1055-7903, E-ISSN 1095-9513, Vol. 139, article id 106568Article in journal (Refereed)
    Abstract [en]

    In wheatears and related species ('open-habitat chats'), molecular phylogenetics has led to a comprehensively revised understanding of species relationships and species diversity. Phylogenetic analyses have suggested that, in many cases, phenotypic similarities do not reflect species' relationships, revealing traditionally defined genera as non-monophyletic. This led to the suggestion of pervasive parallel evolution of open-habitat chats' plumage coloration and ecological phenotypes. However, to date, the molecular evidence for the phylogenetic relationships among open-habitat chats is mainly limited to mitochondrial DNA. Here, we assessed whether the mitochondrial relationships are supported by genome-wide data. To this end, we reconstructed the species tree among 14 open-habitat chat taxa using multi-species coalescent analyses based on similar to 1'300 SNPs. Our results confirm previous ones based chiefly on mitochondrial DNA; notably the paraphyly of the Oenanthe lugens complex and the clustering of individual species formerly placed in the genera Cercomela and Myrmecocichla within Oenanthe. Since several variable morphological and ecological characteristics occur in multiple places across the open-habitat chat phylogeny, our study consolidates the evidence for pervasive parallel evolution in the plumage coloration and ecology of open-habitat chats.

  • 49.
    Semerikova, Svetlana A.
    et al.
    Russian Acad Sci, Ural Branch, Inst Plant & Anim Ecol, 8 Marta Str,202, Ekaterinburg 620144, Russia.
    Khrunyk, Yuliya Y.
    Russian Acad Sci, Ural Branch, Inst Plant & Anim Ecol, 8 Marta Str,202, Ekaterinburg 620144, Russia;Ural Fed Univ, Mira St 19, Ekaterinburg 620002, Russia.
    Lascoux, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Semerikov, Vladimir L.
    Russian Acad Sci, Ural Branch, Inst Plant & Anim Ecol, 8 Marta Str,202, Ekaterinburg 620144, Russia.
    From America to Eurasia: a multigenomes history of the genus Abies2018In: Molecular Phylogenetics and Evolution, ISSN 1055-7903, E-ISSN 1095-9513, Vol. 125, p. 14-28Article in journal (Refereed)
    Abstract [en]

    The origin of conifer genera, the main components of mountain temperate and boreal forests, was deemed to arise in the Mesozoic, although paleontological records and molecular data point to a recent diversification, presumably related to Neogene cooling. The geographical area(s) where the modern lines of conifers emerged remains uncertain, as is the sequence of events leading to their present distribution. To gain further insights into the biogeography of firs (Abies), we conducted phylogenetic analyses of chloroplast, mitochondrial and nuclear markers. The species tree, generated from ten single-copy nuclear genes, yielded probably the best phylogenetic hypothesis available for Abies. The tree obtained from five regions of chloroplast DNA largely corresponded to the nuclear species tree. Ancestral area reconstructions based on fossil calibrated chloroplast DNA and nuclear DNA trees pointed to repeated intercontinental migrations. The mitochondrial DNA haplotype tree, however, disagreed with nuclear and chloroplast DNA trees. It consisted of two clusters: one included mainly American haplotypes, while the other was composed of only Eurasian haplotypes. Presumably, this conflict is due to intercontinental migrations and introgressive hybridization, accompanied by the capture of the mitotypes from aboriginal species by the invading firs. Given that several species inhabiting Northeastern Asia carry American mitotypes and mutations typical for the American cluster, whereas no Asian mitotypes were detected within the American species, we hypothesize that Abies migrated from America to Eurasia, but not in the opposite direction. The direction and age of intercontinental migrations in firs are congruent with other conifers, such as spruces and pines of subsection Strobus, suggesting that these events had the same cause.

  • 50.
    Sheikh, Sanea
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Glöeckner, Gernot
    Kuwayama, Hidekazu
    Schaap, Pauline
    Urushihara, Hideko
    Baldauf, Sandra L.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Root of Dictyostelia based on 213 universal proteins2015In: Molecular Phylogenetics and Evolution, ISSN 1055-7903, E-ISSN 1095-9513, Vol. 92, p. 53-62Article in journal (Refereed)
    Abstract [en]

    Dictyostelia are common soil microbes that can aggregate when starved to form multicellular fruiting bodies, a characteristic that has also led to their long history of study and widespread use as model systems. Ribosomal RNA phylogeny of Dictyostelia identified four major divisions (Groups 1–4), none of which correspond to traditional genera. Group 1 was also tentatively identified as sister lineage to the other three Groups, although not consistently or with strong support. We tested the dictyostelid root using universal protein-coding genes identified by exhaustive comparison of six completely sequenced dictyostelid genomes, which include representatives of all four major molecular Groups. A set of 213 genes are low-copy number in all genomes, present in at least one amoebozoan outgroup taxon (Acanthamoeba castellanii or Physarum polycephalum), and phylogenetically congruent. Phylogenetic analysis of a concatenation of the deduced protein sequences produces a single topology dividing Dictyostelia into two major divisions: Groups 1 + 2 and Groups 3 + 4. All clades in the tree are fully supported by maximum likelihood and Bayesian inference, and all alternative roots are unambiguously rejected by the approximately unbiased (AU) test. The 1 + 2, 3 + 4 root is also fully supported even after deleting clusters with strong individual support for this root, or concatenating all clusters with low support for alternative roots. The 213 putatively ancestral amoebozoan proteins encode a wide variety of functions including 21 KOG categories out of a total of 25. These comprehensive analyses and consistent results indicate that it is time for full taxonomic revision of Dictyostelia, which will also enable more effective exploitation.

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