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Pârâu LG, Wink M. Common patterns in the molecular phylogeography of western palearctic birds: a comprehensive review. JOURNAL OF ORNITHOLOGY 2021; 162:937-959. [PMID: 34007780 PMCID: PMC8118378 DOI: 10.1007/s10336-021-01893-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/03/2020] [Revised: 04/26/2021] [Accepted: 05/02/2021] [Indexed: 06/12/2023]
Abstract
UNLABELLED A plethora of studies have offered crucial insights in the phylogeographic status of Western Palearctic bird species. However, an overview integrating all this information and analyzing the combined results is still missing. In this study, we compiled all published peer-reviewed and grey literature available on the phylogeography of Western Palearctic bird species. Our literature review indicates a total number of 198 studies, with the overwhelming majority published as journal articles (n = 186). In total, these literature items offer information on 145 bird species. 85 of these species are characterized by low genetic differentiation, 46 species indicate genetic variation but no geographic structuring i.e. panmixia, while 14 species show geographically distinct lineages and haplotypes. Majority of bird species inhabiting the Western Palearctic display genetic admixture. The glaciation cycles in the past few million years were pivotal factors in shaping this situation: during warm periods many species expanded their distribution range to the north over wide areas of Eurasia; whereas, during ice ages most areas were no longer suitable and species retreated to refugia, where lineages mixed. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s10336-021-01893-x.
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Affiliation(s)
- Liviu G. Pârâu
- Institute of Pharmacy and Molecular Biotechnology, Department Biology, Heidelberg University, Im Neuenheimer Feld 364, 4 OG, Heidelberg, Germany
- Present Address: SARS-CoV-2 Data Evaluation Office, Eurofins Genomics Europe Applied Genomics GmbH, Anzinger Straße 7a, 85560 Ebersberg, Germany
| | - Michael Wink
- Institute of Pharmacy and Molecular Biotechnology, Department Biology, Heidelberg University, Im Neuenheimer Feld 364, 4 OG, Heidelberg, Germany
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Asgharzadeh A, Kaboli M, Rajabi-Maham H, Naderi M. Phylogeny and genetic structure of the Yellow ground squirrel, Spermophilus fulvus (Lichtenstein, 1823), in Iran. Mamm Biol 2019. [DOI: 10.1016/j.mambio.2019.09.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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3
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Chen YC, Nazarizadeh M, Lei FM, Yang XJ, Yao CT, Dong F, Dong L, Zou FS, Drovetski SV, Liu Y, Huang CC, Hung CM. The niches of nuthatches affect their lineage evolution differently across latitude. Mol Ecol 2018; 28:803-817. [PMID: 30565765 DOI: 10.1111/mec.14980] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Revised: 12/07/2018] [Accepted: 12/10/2018] [Indexed: 11/28/2022]
Abstract
Ecological niche evolution can promote or hinder the differentiation of taxa and determine their distribution. Niche-mediated evolution may differ among climatic regimes, and thus, species that occur across a wide latitudinal range offer a chance to test these heterogeneous evolutionary processes. In this study, we examine (a) how many lineages have evolved across the continent-wide range of the Eurasian nuthatch (Sitta europaea), (b) whether the lineages' niches are significantly divergent or conserved and (c) how their niche evolution explains their geographic distribution. Phylogenetic reconstruction and ecological niche models (ENMs) showed that the Eurasian nuthatch contained six parapatric lineages that diverged within 2 Myr and did not share identical climatic niches. However, the niche discrepancy between these distinct lineages was relatively conserved compared with the environmental differences between their ranges and thus was unlikely to drive lineage divergence. The ENMs of southern lineages tended to cross-predict with their neighbouring lineages whereas those of northern lineages generally matched with their abutting ranges. The coalescence-based analyses revealed more stable populations for the southern lineages than the northern ones during the last glaciation cycle. In contrast to the overlapping ENMs, the smaller parapatric distribution suggests that the southern lineages might have experienced competitive exclusion to prevent them from becoming sympatric. On the other hand, the northern lineages have expanded their ranges and their current abutting distribution might have resulted from lineages adapting to different climatic conditions in allopatry. This study suggests that niche evolution may affect lineage distribution in different ways across latitude.
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Affiliation(s)
- Yu-Chi Chen
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | | | - Fu-Min Lei
- Chinese Academy of Sciences, Institute of Zoology, Beijing, China
| | - Xiao-Jun Yang
- Kunming Institute Zoology, Chinese Academy of Sciences, Kunming, China
| | - Cheng-Te Yao
- Division of Zoology, Endemic Species Research Institute, Nantou, Taiwan
| | - Feng Dong
- Kunming Institute Zoology, Chinese Academy of Sciences, Kunming, China
| | - Lu Dong
- Department of Life Science, Beijing Normal University, Beijing, China
| | - Fa-Sheng Zou
- South China Institute of Endangered Animals, Guangzhou, China
| | - Sergei V Drovetski
- Laboratories of Analytical Biology, National Museum of Natural History, Smithsonian Institution, Washington, District of Columbia
| | - Yang Liu
- State Key Laboratory of Biocontrol, Department of Ecology and School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | | | - Chih-Ming Hung
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
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4
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Kamp L, Pasinelli G, Milanesi P, Drovetski SV, Kosiński Z, Kossenko S, Robles H, Schweizer M. Significant Asia‐Europe divergence in the middle spotted woodpecker (Aves, Picidae). ZOOL SCR 2018. [DOI: 10.1111/zsc.12320] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Laura Kamp
- Naturhistorisches Museum der Burgergemeinde Bern Bern Switzerland
- Institute of Ecology and Evolution Universität Bern Bern Switzerland
- Swiss Ornithological Station Sempach Switzerland
| | | | | | - Sergei V. Drovetski
- Laboratories of Analytical Biology, National Museum of Natural History Smithsonian Institution Washington DC
| | - Ziemowit Kosiński
- Department of Avian Biology and Ecology, Institute of Environmental Biology, Faculty of Biology Adam Mickiewicz University Poznań Poland
| | - Serguei Kossenko
- State Nature Biosphere Reserve "Bryansky Les," Nerussa Station Bryansk Region Russia
| | - Hugo Robles
- Evolutionary Ecology Group (EVECO) University of Antwerp Wilrijk Belgium
| | - Manuel Schweizer
- Naturhistorisches Museum der Burgergemeinde Bern Bern Switzerland
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Drovetski SV, Fadeev IV, Raković M, Lopes RJ, Boano G, Pavia M, Koblik EA, Lohman YV, Red'kin YA, Aghayan SA, Reis S, Drovetskaya SS, Voelker G. A test of the European Pleistocene refugial paradigm, using a Western Palaearctic endemic bird species. Proc Biol Sci 2018; 285:rspb.2018.1606. [PMID: 30355709 DOI: 10.1098/rspb.2018.1606] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Accepted: 10/01/2018] [Indexed: 11/12/2022] Open
Abstract
Hewitt's paradigm for effects of Pleistocene glaciations on European populations assumes their isolation in peninsular refugia during glacial maxima, followed by re-colonization of broader Europe during interstadials. This paradigm is well supported by studies of poorly dispersing taxa, but highly dispersive birds have not been included. To test this paradigm, we use the dunnock (Prunella modularis), a Western Palaearctic endemic whose range includes all major European refugia. MtDNA gene tree, multilocus species tree and species delimitation analyses indicate the presence of three distinct lineages: one in the Iberian refugium, one in the Caucasus refugium, and one comprising the Italian and Balkan refugia and broader Europe. Our gene flow analysis suggests isolation of both the Iberian and Caucasus lineages but extensive exchange between Italy, the Balkans and broader Europe. Demographic stability could not be rejected for any refugial population, except the very recent expansion in the Caucasus. By contrast, northern European populations may have experienced two expansion periods. Iberia and Caucasus had much smaller historical populations than other populations. Although our results support the paradigm, in general, they also suggest that in highly dispersive taxa, isolation of neighbouring refugia was incomplete, resulting in large super-refugial populations.
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Affiliation(s)
- Sergei V Drovetski
- Laboratories of Analytical Biology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20004, USA
| | - Igor V Fadeev
- Department of Collections, State Darwin Museum, Vavilova St. 57, 117292 Moscow, Russia
| | - Marko Raković
- Natural History Museum Belgrade, Njegoševa 51, 11000 Belgrade, Serbia
| | - Ricardo J Lopes
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos da Universidade do Porto, InBIO Laboratório Associado, Universidade do Porto, Campus Agrário de Vairão, 4485-661 Vairão, Portugal
| | - Giovanni Boano
- Natural History Museum of Carmagnola, San Francesco di Sales 188, 10022 Carmagnola, Italy
| | - Marco Pavia
- Department of Earth Sciences, University of Turin, Valperga Caluso 35, 10125 Turin, Italy
| | - Evgeniy A Koblik
- Department of Ornithology, Zoological Museum of Moscow State University, Bol'shaya Nikitskaya Street 6, 103009 Moscow, Russia
| | | | - Yaroslav A Red'kin
- Department of Ornithology, Zoological Museum of Moscow State University, Bol'shaya Nikitskaya Street 6, 103009 Moscow, Russia
| | - Sargis A Aghayan
- Laboratory of Zoology, Research Institute of Biology, Yerevan State University, Alex Manoogian 1, Yerevan, Armenia
| | - Sandra Reis
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos da Universidade do Porto, InBIO Laboratório Associado, Universidade do Porto, Campus Agrário de Vairão, 4485-661 Vairão, Portugal
| | | | - Gary Voelker
- Department of Wildlife and Fisheries Sciences, Texas A&M University, College Station, 77843 TX, USA
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Alireza M, Morteza N, Reza RH, Mohammad K. Population Genetic Structure of Transcaucasian Mole Vole (Ellobius lutescens) Along Zagros Mountains, Iran. CONTEMP PROBL ECOL+ 2018. [DOI: 10.1134/s1995425518020075] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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7
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Drovetski SV, Reeves AB, Red'kin YA, Fadeev IV, Koblik EA, Sotnikov VN, Voelker G. Multi-locus reassessment of a striking discord between mtDNA gene trees and taxonomy across two congeneric species complexes. Mol Phylogenet Evol 2017; 120:43-52. [PMID: 29224786 DOI: 10.1016/j.ympev.2017.11.023] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Revised: 11/30/2017] [Accepted: 11/30/2017] [Indexed: 11/19/2022]
Abstract
Resolving relationships among members of the yellow and citrine wagtail species complexes is among the greatest challenges in avian systematics due to arguably the most dramatic disagreements between traditional taxonomy and mtDNA phylogeny. Each species complex is divided into three geographically cohesive mtDNA clades. Each clade from one species complex has a sister from the other complex. Furthermore, one cross-complex pair is more distantly related to the remaining two pairs than are several other wagtail species. To test mtDNA gene tree topology, we sequenced the mtDNA ND2 gene and 11 nuclear introns for seven wagtail species. Our mtDNA gene tree reconstruction supported the results of previous studies, thereby confirming the disagreement between mtDNA phylogeny and taxonomy. However, our multi-locus species tree which used mtDNA clades as "taxa" was consistent with traditional taxonomy regardless of whether mtDNA was included in the analysis or not. Our multi-locus data suggest that despite the presence of strongly supported, geographically structured mtDNA variation, the mtDNA gene tree misrepresents the evolutionary history of the yellow and citrine wagtail complexes. This mito-nuclear discord results from mtDNA representing the biogeographic, but not evolutionary history of these recently radiated Palearctic wagtails.
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Affiliation(s)
- Sergei V Drovetski
- Division of Birds, National Museum of Natural History, Smithsonian Institution, 1000 Constitution Ave NW, Washington, DC 20004, USA.
| | - Andrew B Reeves
- Department of Biological Sciences, University of Alaska Anchorage, 3211 Providence Dr, Anchorage, AK 99508, USA.
| | - Yaroslav A Red'kin
- Department of Ornithology, Zoological Museum of Moscow State University, 6 Bol'shaya Nikitskaya St, Moscow 103009, Russia.
| | - Igor V Fadeev
- Department of Collections, State Darwin Museum, 57/1 Vavilova St, Moscow 117292, Russia.
| | - Evgeniy A Koblik
- Department of Ornithology, Zoological Museum of Moscow State University, 6 Bol'shaya Nikitskaya St, Moscow 103009, Russia.
| | | | - Gary Voelker
- Department of Wildlife and Fisheries Sciences, Texas A&M University, 454 Throckmorton St, College Station, TX 77843, USA.
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8
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Hung C, Drovetski SV, Zink RM. The roles of ecology, behaviour and effective population size in the evolution of a community. Mol Ecol 2017; 26:3775-3784. [DOI: 10.1111/mec.14152] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Revised: 04/14/2017] [Accepted: 04/17/2017] [Indexed: 01/06/2023]
Affiliation(s)
- Chih‐Ming Hung
- Biodiversity Research Center Academia Sinica Taipei Taiwan
| | - Sergei V. Drovetski
- Division of Birds National Museum of Natural History Smithsonian Institution Washington DC USA
| | - Robert M. Zink
- School of Natural Resources Nebraska State Museum, and School of Biological Sciences University of Nebraska Lincoln NE USA
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Hung CM, Drovetski SV, Zink RM. Matching loci surveyed to questions asked in phylogeography. Proc Biol Sci 2016; 283:20152340. [PMID: 26962145 DOI: 10.1098/rspb.2015.2340] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Although mitochondrial DNA (mtDNA) has long been used for assessing genetic variation within and between populations, its workhorse role in phylogeography has been criticized owing to its single-locus nature. The only choice for testing mtDNA results is to survey nuclear loci, which brings into contrast the difference in locus effective size and coalescence times. Thus, it remains unclear how erroneous mtDNA-based estimates of species history might be, especially for evolutionary events in the recent past. To test the robustness of mtDNA and nuclear sequences in phylogeography, we provide one of the largest paired comparisons of summary statistics and demographic parameters estimated from mitochondrial, five Z-linked and 10 autosomal genes of 30 avian species co-distributed in the Caucasus and Europe. The results suggest that mtDNA is robust in estimating inter-population divergence but not in intra-population diversity, which is sensitive to population size change. Here, we provide empirical evidence showing that mtDNA was more likely to detect population divergence than any other single locus owing to its smaller Ne and thus faster coalescent time. Therefore, at least in birds, numerous studies that have based their inferences of phylogeographic patterns solely on mtDNA should not be readily dismissed.
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Affiliation(s)
- Chih-Ming Hung
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Sergei V Drovetski
- Division of Birds, National Museum of Natural History, Smithsonian Institution, Washington, DC 20004, USA
| | - Robert M Zink
- Bell Museum and Department of Ecology, Evolution and Behavior, University of Minnesota, St Paul, MN, USA
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10
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Nazarizadeh M, Kaboli M, Rezaie HR, Harisini JI, Pasquet E. Phylogenetic relationships of Eurasian Nuthatches (Sitta europaea Linnaeus, 1758) from the Alborz and Zagros Mountains, Iran. ZOOLOGY IN THE MIDDLE EAST 2016. [DOI: 10.1080/09397140.2016.1226547] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- Masoud Nazarizadeh
- Department of Environmental Sciences, Faculty of Natural Resources, University of Tehran, Karaj, Iran
| | - Mohammad Kaboli
- Department of Environmental Sciences, Faculty of Natural Resources, University of Tehran, Karaj, Iran
| | - Hamid Reza Rezaie
- Department of Environmental Sciences, Gorgan University of Agricultural Sciences and Natural Resources, Gorgan, Iran
| | - Jalil Imani Harisini
- Department of Environmental Sciences, Gorgan University of Agricultural Sciences and Natural Resources, Gorgan, Iran
| | - Eric Pasquet
- Muséum National d’Histoire Naturelle, Paris, France
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11
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Ottenburghs J, Megens HJ, Kraus RH, Madsen O, van Hooft P, van Wieren SE, Crooijmans RP, Ydenberg RC, Groenen MA, Prins HH. A tree of geese: A phylogenomic perspective on the evolutionary history of True Geese. Mol Phylogenet Evol 2016; 101:303-313. [DOI: 10.1016/j.ympev.2016.05.021] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2015] [Revised: 04/27/2016] [Accepted: 05/20/2016] [Indexed: 11/26/2022]
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12
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Mechanisms of global diversification in the marine species Madeiran Storm-petrel Oceanodroma castro and Monteiro’s Storm-petrel O. monteiroi: Insights from a multi-locus approach. Mol Phylogenet Evol 2016; 98:314-23. [DOI: 10.1016/j.ympev.2016.02.014] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2015] [Revised: 02/07/2016] [Accepted: 02/18/2016] [Indexed: 01/19/2023]
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13
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Hope AG, Malaney JL, Bell KC, Salazar-Miralles F, Chavez AS, Barber BR, Cook JA. Revision of widespread red squirrels (genus: Tamiasciurus) highlights the complexity of speciation within North American forests. Mol Phylogenet Evol 2016; 100:170-182. [PMID: 27083861 DOI: 10.1016/j.ympev.2016.04.014] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2015] [Revised: 04/07/2016] [Accepted: 04/11/2016] [Indexed: 11/27/2022]
Abstract
Integration of molecular methods, ecological modeling, and statistical hypothesis testing are increasing our understanding of differentiation within species and phylogenetic relationships among species by revealing environmental connections to evolutionary processes. Within mammals, novel diversity is being discovered and characterized as more complete geographic sampling is coupled with newer multi-disciplinary approaches. North American red squirrels exemplify a forest obligate genus whose species are monitored as indicators of forest ecosystem condition, yet phylogenetic relationships reflecting evolutionary history within this genus remain tentative. Through testing of competing systematic and niche-based divergence hypotheses, we recognize three species, Tamiasciurus douglasii, T. hudsonicus, and T. fremonti. Our data provide evidence of regional differences in evolutionary dynamics and continental gradients of complexity that are important both for future management and for investigating multiple pathways that can lead to the formation of new species.
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Affiliation(s)
- Andrew G Hope
- Division of Biology, Kansas State University, Manhattan, KS 66506, USA.
| | - Jason L Malaney
- Department of Biology, Austin Peay State University, Clarksville, TN 37044, USA.
| | - Kayce C Bell
- Department of Biology and Museum of Southwestern Biology, University of New Mexico, Albuquerque, NM 87131, USA.
| | - Fernando Salazar-Miralles
- Department of Biology and Museum of Southwestern Biology, University of New Mexico, Albuquerque, NM 87131, USA.
| | - Andreas S Chavez
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California-Berkeley, Berkeley, CA 94720, USA.
| | - Brian R Barber
- Biodiversity Institute, University of Wyoming, Laramie, WY 82071, USA.
| | - Joseph A Cook
- Department of Biology and Museum of Southwestern Biology, University of New Mexico, Albuquerque, NM 87131, USA.
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14
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Williford D, Deyoung RW, Honeycutt RL, Brennan LA, Hernández F. Phylogeography of the bobwhite (Colinus) quails. WILDLIFE MONOGRAPHS 2015. [DOI: 10.1002/wmon.1017] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Damon Williford
- Caesar Kleberg Wildlife Research Institute; Texas A&M University-Kingsville; 700 University Boulevard MSC 218; Kingsville TX 78363 USA
| | - Randy W. Deyoung
- Caesar Kleberg Wildlife Research Institute; Texas A&M University-Kingsville; 700 University Boulevard MSC 218; Kingsville TX 78363 USA
| | - Rodney L. Honeycutt
- Natural Science Division; Pepperdine University, 24255 Pacific Coast Highway; Malibu CA 90263 USA
| | - Leonard A. Brennan
- Caesar Kleberg Wildlife Research Institute; Texas A&M University-Kingsville; 700 University Boulevard MSC 218; Kingsville TX 78363 USA
| | - Fidel Hernández
- Caesar Kleberg Wildlife Research Institute; Texas A&M University-Kingsville; 700 University Boulevard MSC 218; Kingsville TX 78363 USA
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15
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Silva MC, Matias R, Wanless RM, Ryan PG, Stephenson BM, Bolton M, Ferrand N, Coelho MM. Understanding the mechanisms of antitropical divergence in the seabird White-faced Storm-petrel (Procellariiformes: Pelagodroma marina) using a multilocus approach. Mol Ecol 2015; 24:3122-37. [PMID: 25903359 DOI: 10.1111/mec.13212] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2013] [Revised: 04/16/2015] [Accepted: 04/21/2015] [Indexed: 11/27/2022]
Abstract
Analytical methods that apply coalescent theory to multilocus data have improved inferences of demographic parameters that are critical to understanding population divergence and speciation. In particular, at the early stages of speciation, it is important to implement models that accommodate conflicting gene trees, and benefit from the presence of shared polymorphisms. Here, we employ eleven nuclear loci and the mitochondrial control region to investigate the phylogeography and historical demography of the pelagic seabird White-faced Storm-petrel (Pelagodroma marina) by sampling subspecies across its antitropical distribution. Groups are all highly differentiated: global mitochondrial ΦST = 0.89 (P < 0.01) and global nuclear ΦST varies between 0.22 and 0.83 (all P < 0.01). The complete lineage sorting of the mitochondrial locus between hemispheres is corroborated by approximately half of the nuclear genealogies, suggesting a long-term antitropical divergence in isolation. Coalescent-based estimates of demographic parameters suggest that hemispheric divergence of P. marina occurred approximately 840 000 ya (95% HPD 582 000-1 170 000), in the absence of gene flow, and divergence within the Southern Hemisphere occurred 190 000 ya (95% HPD 96 000-600 000), both probably associated with the profound palaeo-oceanographic changes of the Pleistocene. A fledgling sampled in St Helena (tropical South Atlantic) suggests recent colonization from the Northern Hemisphere. Despite the great potential for long-distance dispersal, P. marina antitropical groups have been evolving as independent, allopatric lineages, and divergence is probably maintained by philopatry coupled with asynchronous reproductive phenology and local adaptation.
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Affiliation(s)
- Mónica C Silva
- Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, 1749-016, Lisboa, Portugal
| | - Rafael Matias
- Centre for Ecology and Conservation, School of Biosciences, University of Exeter, Penryn, TR10 9EZ, UK.,Marine and Environmental Sciences Centre, ISPA-Instituto Universitário, 1149-041, Lisboa, Portugal
| | - Ross M Wanless
- Percy FitzPatrick Institute of African Ornithology, DST-NRF Centre of Excellence, University of Cape Town, Rondebosch, 7701, South Africa.,Seabird Conservation Program, BirdLife South Africa, PO Box 7119, Roggebaai, 8012, South Africa
| | - Peter G Ryan
- Percy FitzPatrick Institute of African Ornithology, DST-NRF Centre of Excellence, University of Cape Town, Rondebosch, 7701, South Africa
| | - Brent M Stephenson
- Eco-Vista: Photography & Research Ltd, PO Box 157, Bay View, Napier, 4149, New Zealand
| | - Mark Bolton
- RSPB Centre for Conservation Science, Royal Society for the Protection of Birds, The Lodge, Sandy, Beds, SG19 2DL, UK
| | - Nuno Ferrand
- CIBIO, Universidade do Porto, Campus Agrário Vairão, 4485-661, Vairão, Portugal
| | - M Manuela Coelho
- Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, 1749-016, Lisboa, Portugal
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16
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Pons JM, Thibault JC, Fournier J, Olioso G, Rakovic M, Tellini Florenzano G, Fuchs J. Genetic variation among Corsican and continental populations of the Eurasian treecreeper (Aves:Certhia familiaris) reveals the existence of a palaeoendemic mitochondrial lineage. Biol J Linn Soc Lond 2015. [DOI: 10.1111/bij.12485] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Jean-Marc Pons
- Institut de Systématique, Evolution, Biodiversité, UMR 7205 CNRS MNHN UPMC EPHE; Département Systématique et Evolution; Muséum national d'Histoire naturelle; Case Postale 51 55 rue Buffon F-75005 Paris France
- UMS MNHN/CNRS 2700 Outils et Méthodes de la Systématique Intégrative (OMSI); Muséum National d'Histoire Naturelle; 57 rue Cuvier F-75231 Paris Cedex 05 France
| | - Jean-Claude Thibault
- Institut de Systématique, Evolution, Biodiversité, UMR 7205 CNRS MNHN UPMC EPHE; Département Systématique et Evolution; Muséum national d'Histoire naturelle; Case Postale 51 55 rue Buffon F-75005 Paris France
| | - Jérôme Fournier
- Centre de Recherche sur la Biologie des Populations d'Oiseaux; Département Ecologie et Gestion de la Biodiversité; Muséum National d'Histoire Naturelle; Case Postale 51 55 rue Buffon F-75005 Paris France
| | | | - Marko Rakovic
- Natural History Museum of Belgrade; Njegoseva 51 Serbia
| | | | - Jérôme Fuchs
- Institut de Systématique, Evolution, Biodiversité, UMR 7205 CNRS MNHN UPMC EPHE; Département Systématique et Evolution; Muséum national d'Histoire naturelle; Case Postale 51 55 rue Buffon F-75005 Paris France
- UMS MNHN/CNRS 2700 Outils et Méthodes de la Systématique Intégrative (OMSI); Muséum National d'Histoire Naturelle; 57 rue Cuvier F-75231 Paris Cedex 05 France
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17
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Voelker G, Semenov G, Fadeev IV, Blick A, Drovetski SV. The biogeographic history ofPhoenicurusredstarts reveals an allopatric mode of speciation and an out-of-Himalayas colonization pattern. SYST BIODIVERS 2015. [DOI: 10.1080/14772000.2014.992380] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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Hung CM, Hung HY, Yeh CF, Fu YQ, Chen D, Lei F, Yao CT, Yao CJ, Yang XJ, Lai YT, Li SH. Species delimitation in the Chinese bamboo partridgeBambusicola thoracica(Phasianidae; Aves). ZOOL SCR 2014. [DOI: 10.1111/zsc.12071] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Chih-Ming Hung
- Department of Life Science; National Taiwan Normal University; Taipei 11677 Taiwan
| | - Hsin-Yi Hung
- Department of Life Science; National Taiwan Normal University; Taipei 11677 Taiwan
| | - Chia-Fen Yeh
- Department of Life Science; National Taiwan Normal University; Taipei 11677 Taiwan
| | - Yi-Qiang Fu
- College of Life Science; Leshan Normal University; Leshan 614000 China
| | - De Chen
- Department of Life Science; College of Life Sciences; Beijing Normal University; Beijing 100875 China
| | - Fumin Lei
- Key Laboratory of Zoological Systematics and Evolution; Institute of Zoology; Chinese Academy of Sciences; Beijing 100101 China
| | - Cheng-Te Yao
- Division of Zoology; Endemic Species Research Institute; Chi-chi Nantou 55244 Taiwan
| | - Chiou-Ju Yao
- Department of Biology; National Museum of Natural Science; Taichung 40453 Taiwan
| | - Xiao-Jun Yang
- Kunming Institute Zoology; Chinese Academy of Sciences; Kunming Yunnan China
| | - Yu-Ting Lai
- Department of Life Science; National Taiwan Normal University; Taipei 11677 Taiwan
| | - Shou-Hsien Li
- Department of Life Science; National Taiwan Normal University; Taipei 11677 Taiwan
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Distinguishing the effects of selection from demographic history in the genetic variation of two sister passerines based on mitochondrial-nuclear comparison. Heredity (Edinb) 2014; 113:42-51. [PMID: 24619180 DOI: 10.1038/hdy.2014.9] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2013] [Revised: 12/01/2013] [Accepted: 01/09/2014] [Indexed: 11/08/2022] Open
Abstract
Determining the mechanisms responsible for the distribution of genetic diversity in natural populations has occupied a central role in molecular evolution. Our study was motivated by the unprecedented observation that a widespread Eurasian flycatcher, Ficedula albicilla, exhibited no variation at the mitochondrial DNA (mtDNA) ND2 gene in 75 individuals sampled over a 5000-km distance. In contrast, its sister species, F. parva, had low but considerably higher levels of mtDNA variation. We assessed whether natural selection or demographic factors could explain the absence of mtDNA variation in F. albicilla. Eighteen nuclear genes were sequenced to estimate the two species' phylogeographic histories, and for comparison to the mtDNA data. Multilocus coalescence analyses suggested that F. albicilla experienced a population expansion perhaps following a population bottleneck. Simulations based on this demographic history, however, did not replicate the extremely low level of mtDNA variation. Historical range changes based on ecological niche models also failed to explain the observed mtDNA patterns. Neutrality tests (DHEW and ML-HKA) suggested a non-neutral pattern in the mtDNA of F. albicilla. We found a transmembrane-skewed distribution of nonsynonymous substitutions between the two species, three of which caused functional change; the results implied that positive selection could have targeted mtDNA. Several lines of evidence support selection rather than demographic history as the main force influencing the patterns of mtDNA variation. Despite the influence of natural selection, many of the phylogeographic inferences derived from mtDNA were robust, including species limits and a high level of gene flow among populations within species.
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Limited phylogeographic signal in sex-linked and autosomal loci despite geographically, ecologically, and phenotypically concordant structure of mtDNA variation in the Holarctic avian genus Eremophila. PLoS One 2014; 9:e87570. [PMID: 24498139 PMCID: PMC3907499 DOI: 10.1371/journal.pone.0087570] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2013] [Accepted: 12/23/2013] [Indexed: 11/22/2022] Open
Abstract
Phylogeographic studies of Holarctic birds are challenging because they involve vast geographic scale, complex glacial history, extensive phenotypic variation, and heterogeneous taxonomic treatment across countries, all of which require large sample sizes. Knowledge about the quality of phylogeographic information provided by different loci is crucial for study design. We use sequences of one mtDNA gene, one sex-linked intron, and one autosomal intron to elucidate large scale phylogeographic patterns in the Holarctic lark genus Eremophila. The mtDNA ND2 gene identified six geographically, ecologically, and phenotypically concordant clades in the Palearctic that diverged in the Early - Middle Pleistocene and suggested paraphyly of the horned lark (E. alpestris) with respect to the Temminck's lark (E. bilopha). In the Nearctic, ND2 identified five subclades which diverged in the Late Pleistocene. They overlapped geographically and were not concordant phenotypically or ecologically. Nuclear alleles provided little information on geographic structuring of genetic variation in horned larks beyond supporting the monophyly of Eremophila and paraphyly of the horned lark. Multilocus species trees based on two nuclear or all three loci provided poor support for haplogroups identified by mtDNA. The node ages calculated using mtDNA were consistent with the available paleontological data, whereas individual nuclear loci and multilocus species trees appeared to underestimate node ages. We argue that mtDNA is capable of discovering independent evolutionary units within avian taxa and can provide a reasonable phylogeographic hypothesis when geographic scale, geologic history, and phenotypic variation in the study system are too complex for proposing reasonable a priori hypotheses required for multilocus methods. Finally, we suggest splitting the currently recognized horned lark into five Palearctic and one Nearctic species.
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Sağlam İK, Küçükyıldırım S, Çağlar SS. Diversification of montane species via elevation shifts: the case of the Kaçkar cricket Phonochorion
(Orthoptera). J ZOOL SYST EVOL RES 2013. [DOI: 10.1111/jzs.12051] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- İsmail K. Sağlam
- Department of Biology; Faculty of Science; Hacettepe University; Beytepe, Ankara Turkey
| | - Sibel Küçükyıldırım
- Department of Biology; Faculty of Science; Hacettepe University; Beytepe, Ankara Turkey
| | - Selim S. Çağlar
- Department of Biology; Faculty of Science; Hacettepe University; Beytepe, Ankara Turkey
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Pérez T, Essler S, Palacios B, Albornoz J, Domínguez A. Evolution of the melanocortin-1 receptor gene (MC1R) in chamois (Rupicapra spp.). Mol Phylogenet Evol 2013; 67:621-5. [PMID: 23499612 DOI: 10.1016/j.ympev.2013.02.027] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2012] [Revised: 02/27/2013] [Accepted: 02/28/2013] [Indexed: 10/27/2022]
Abstract
The taxonomy of chamois and the effects of historical and evolutionary events on its diversification are still under discussion given that different morphological and genetic features presented partially discordant views. One of the morphological features that differentiate the two currently considered species, Rupicapra pyrenaica (southern chamois) and R. rupicapra (northern chamois) is coat color pattern. The melanocortin-1 receptor gene (MC1R) is related with differences in coloration in different mammals and was analyzed here in a sample of 25 chamois covering the 10 subspecies recognized, three in R. pyrenaica, (parva, pyrenaica and ornata) and seven in R. rupicapra (cartusiana, rupicapra, tatrica, carpatica, balcanica, asiatica and caucasica). Comparison with other caprinae showed that the MC1R gene has evolved under strong purifying selection. Three well differentiated haplotypes were identified: one shared by the seven subspecies of R. rupicapra, other common to the two Iberian chamois, both of the species R. pyrenaica, and a third haplotype, basal in the phylogenetic tree, unique to the subspecies from the Apennines, R. pyrenaica ornata. This pattern of variation, with three conspicuous clades, concurs with previous findings on microsatellites and mtDNA and argues in favor of the old classifications that distinguished the species R. ornata.
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Affiliation(s)
- Trinidad Pérez
- Universidad de Oviedo, Biología Funcional, Genética, Julián Clavería 6, 33071 Oviedo, Spain
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A multimarker phylogeography of crested newts (Triturus cristatus superspecies) reveals cryptic species. Mol Phylogenet Evol 2013; 67:167-75. [PMID: 23353071 DOI: 10.1016/j.ympev.2013.01.009] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2012] [Revised: 01/09/2013] [Accepted: 01/10/2013] [Indexed: 11/21/2022]
Abstract
The crested newt Triturus cristatus superspecies is composed of five recognized species. One of these, T. karelinii sensu lato, comprises three geographically structured mitochondrial DNA lineages: 'eastern', 'central' and 'western T. karelinii'. Genetic divergence among these lineages is comparable to that of recognized crested newt species, but morphologically they are indistinguishable. Here, we conduct a multimarker phylogeographical survey to explore the evolutionary independence of these mitochondrial DNA lineages and we include representatives of the other species to guide our interpretation of the results. All markers show distinct patterns when analyzed singly (as a phylogeny or haplotype network) and none of them sort haplotypes fully in line with species or mitochondrial DNA lineage. A multilocus approach (BAPS and *BEAST) on the other hand shows that not only the recognized species, but also the three mitochondrial DNA lineages represent discrete nuclear DNA gene pools. A mismatch is found in the northwest of Asiatic Turkey, where several populations identified as 'central T. karelinii' based on nuclear DNA possesses 'western T. karelinii' mitochondrial DNA. We invoke asymmetric mitochondrial DNA introgression to explain this pattern and support this with a historical biogeographical scenario. The three spatial groups in T. karelinii sensu lato should be regarded as distinct species.
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Hung CM, Drovetski SV, Zink RM. Recent allopatric divergence and niche evolution in a widespread Palearctic bird, the common rosefinch (Carpodacus erythrinus). Mol Phylogenet Evol 2012; 66:103-11. [PMID: 23022139 DOI: 10.1016/j.ympev.2012.09.012] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2011] [Revised: 09/08/2012] [Accepted: 09/14/2012] [Indexed: 10/27/2022]
Abstract
A previously published phylogeographic analysis of mtDNA sequences from the widespread Palearctic common rosefinch (Carpodacus erythrinus) suggested the existence of three recently diverged groups, corresponding to the Caucasus, central-western Eurasia, and northeastern Eurasia. We re-evaluated the mtDNA data using coalescence methods and added sequence data from a sex-linked gene. The mtDNA gene tree and SAMOVA supported the distinctiveness of the Caucasian group but not the other two groups. However, UPGMA clustering of mtDNA Φ(ST)-values among populations recovered the three groups. The sex-linked gene tree recovered no phylogeographic signal, which was attributed to recent divergence and insufficient time for sorting of alleles. Overall, coalescence methods indicated a lack of gene flow among the three groups, and population expansion in the central-western and northeastern Eurasia groups. These three groups corresponded to named subspecies, further supporting their validity. A species distribution model revealed potential refugia at the Last Glacial Maximum. These three groups, which we hypothesized are in the early stages of speciation, provided an opportunity for testing tenets of ecological speciation. We showed that the early stages of speciation were not accompanied by ecological niche divergence, consistent with other avian studies.
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Affiliation(s)
- Chih-Ming Hung
- Bell Museum, University of Minnesota, St Paul, MN 55108, USA.
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