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de Raad J, Päckert M, Irestedt M, Janke A, Kryukov AP, Martens J, Red'kin YA, Sun Y, Töpfer T, Schleuning M, Neuschulz EL, Nilsson MA. Speciation and population divergence in a mutualistic seed dispersing bird. Commun Biol 2022; 5:429. [PMID: 35534538 PMCID: PMC9085801 DOI: 10.1038/s42003-022-03364-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 04/14/2022] [Indexed: 11/29/2022] Open
Abstract
Bird-mediated seed dispersal is crucial for the regeneration and viability of ecosystems, often resulting in complex mutualistic species networks. Yet, how this mutualism drives the evolution of seed dispersing birds is still poorly understood. In the present study we combine whole genome re-sequencing analyses and morphometric data to assess the evolutionary processes that shaped the diversification of the Eurasian nutcracker (Nucifraga), a seed disperser known for its mutualism with pines (Pinus). Our results show that the divergence and phylogeographic patterns of nutcrackers resemble those of other non-mutualistic passerine birds and suggest that their early diversification was shaped by similar biogeographic and climatic processes. The limited variation in foraging traits indicates that local adaptation to pines likely played a minor role. Our study shows that close mutualistic relationships between bird and plant species might not necessarily act as a primary driver of evolution and diversification in resource-specialized birds. Genomic and phylogeographic analyses indicate that resource-specialization did not play a major role in the diversification and speciation of seed dispersing nutcrackers
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Affiliation(s)
- Jordi de Raad
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F, Senckenberganlage 25, 60325, Frankfurt am Main, Germany.,LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Senckenberganlage 25, 60325, Frankfurt, Germany.,Institute for Ecology, Evolution and Diversity, Goethe University, Max-von-Laue-Str. 13, 60438, Frankfurt am Main, Germany
| | - Martin Päckert
- Senckenberg Naturhistorische Sammlungen Dresden, Museum für Tierkunde, Königsbrücker Landstraße 159, 01109, Dresden, Germany
| | - Martin Irestedt
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Frescativägen 40, 114 18, Stockholm, Sweden
| | - Axel Janke
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F, Senckenberganlage 25, 60325, Frankfurt am Main, Germany.,LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Senckenberganlage 25, 60325, Frankfurt, Germany.,Institute for Ecology, Evolution and Diversity, Goethe University, Max-von-Laue-Str. 13, 60438, Frankfurt am Main, Germany
| | - Alexey P Kryukov
- Federal Scientific Center of the East Asia Terrestrial Biodiversity, Russian Academy of Sciences, Stoletiya Avenue 159, 690022, Vladivostok, Russia
| | - Jochen Martens
- Institut für Organismische und Molekulare Evolutionsbiologie (iomE), Johannes Gutenberg-Universität Mainz, 55099, Mainz, Germany
| | - Yaroslav A Red'kin
- Department of Ornithology, Zoological Museum of Moscow State University, Bol'shaya Nikitskaya Street 2, 125009, Moscow, Russia
| | - Yuehua Sun
- Institute of Zoology, Chinese Academy of Sciences, CN-100101, Beijing, PR China
| | - Till Töpfer
- Leibniz Institute for the Analysis of Biodiversity Change, Zoological Research Museum Alexander Koenig, Adenauerallee 127, 53113, Bonn, Germany
| | - Matthias Schleuning
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F, Senckenberganlage 25, 60325, Frankfurt am Main, Germany
| | - Eike Lena Neuschulz
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F, Senckenberganlage 25, 60325, Frankfurt am Main, Germany
| | - Maria A Nilsson
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F, Senckenberganlage 25, 60325, Frankfurt am Main, Germany. .,LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Senckenberganlage 25, 60325, Frankfurt, Germany.
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Artyushin IV, Red'kin YA, Kawai K, Kruskop SV. First Record of the Long-Eared Bat (Plecotus; Chiroptera: Vespertilionidae) on Urup Island Highlights the Obscure Taxonomic Problem. Mammal Study 2020. [DOI: 10.3106/ms2020-0070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Affiliation(s)
- Ilya V. Artyushin
- Department of vertebrate zoology, Moscow State University, Leninskiye Gory, 1(12), 119234 Moscow, Russia
| | - Yaroslav A. Red'kin
- Zoological Museum, Moscow State University, Bolshaya Nikitskaya, 2, 125009 Moscow, Russia
| | - Kuniko Kawai
- School of Biological Sciences, Tokai University, 1-1 1-Chome 5-Jo Minami-sawa, Minami-ku, Sapporo, Hokkaido, Japan
| | - Sergei V. Kruskop
- Zoological Museum, Moscow State University, Bolshaya Nikitskaya, 2, 125009 Moscow, Russia
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Saitoh T, Kawakami K, Red'kin YA, Nishiumi I, Kim CH, Kryukov AP. Cryptic Speciation of the Oriental Greenfinch Chloris sinica on Oceanic Islands. Zoolog Sci 2020; 37:280-294. [PMID: 32549542 DOI: 10.2108/zs190111] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Accepted: 02/21/2020] [Indexed: 11/17/2022]
Abstract
The Oriental greenfinch, Chloris sinica, is a small seed-eating finch that breeds in the eastern Palearctic region, an area that spans from Russia in the east to China, Korea, and Japan in the south and southwest. Several subspecies have been described based on subtle morphological characteristics, although the taxonomy varies among different authors. Although many ecological studies have been performed, there has been no phylogenetic study that encompasses the species' entire geographical range. We used four regions of mitochondrial DNA to analyze the intraspecies genetic phylogeny and diversity of the Oriental greenfinch. In addition, we performed morphometric analyses using museum specimens. Genetic analysis identified two clades that diverged approximately 1.06 million years ago. These were a population from the Ogasawara Islands, Japan (subspecies kittlitzi, Clade B), and the other populations (Clade A, which could not be subdivided according to geographic context). Morphometric analyses showed that the population on the Kuril Islands (subspecies kawarahiba) had the longest mean wing length, whereas C. s. kittlitzi had the shortest wings. Chloris s. kittlitzi also had the longest mean bill length, probably because it has adapted to feeding on the Ogasawara Islands. Based on molecular phylogeny and morphology analyses, we recommend that C. s. kittlitzi should be treated as a completely distinct species, called the Ogasawara greenfinch, Chloris kittlitzi. It is critically endangered and needs to be specially protected.
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Affiliation(s)
- Takema Saitoh
- Yamashina Institute for Ornithology, Division of Natural History, Abiko, Chiba 270-1145, Japan,
| | - Kazuto Kawakami
- Forestry and Forest Products Research Institute, Tsukuba, Ibaraki 305-8687, Japan
| | | | - Isao Nishiumi
- Department of Zoology, National Museum of Nature and Science, Tokyo, Tsukuba, Ibaraki 305-0005, Japan
| | - Chang-Hoe Kim
- Team of National Ecosystem Survey, National Institute of Ecology, Maseo-myeon, Seocheon 33657, Republic of Korea
| | - Alexey P Kryukov
- Federal Scientific Center of the East Asia Terrestrial Biodiversity, Far Eastern Branch of the Russian Academy of Sciences, Pr-t 100-letiya Vladivostoka, Vladivostok 690022, Russia
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Kryukov AP, Spiridonova LN, Mori S, Arkhipov VY, Red'kin YA, Goroshko OA, Lobkov EG, Haring E. Deep Phylogeographic Breaks in Magpie Pica pica Across the Holarctic: Concordance with Bioacoustics and Phenotypes. Zoolog Sci 2019; 34:185-200. [PMID: 28589845 DOI: 10.2108/zs160119] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
We examined sequences of the mitochondrial control region in magpies (Pica pica) from the entire distribution range and found deep genetic splits into four major lineages: (1) group West (Europe-Siberia), (2) group East (southern Far East), (3) P. p. mauritanica (North Africa), and (4) P. p. hudsonia (North America). These lineages show a geographic pattern corresponding to known subspecies or subspecies groups. Genetic variation within the widely-distributed group West is low and neutrality tests supported a recent expansion scenario. The haplotypes from Kamchatka, representing a separated sublineage with clear affinity to the European-Siberian group, are almost identical, implying a recent bottleneck. Group East contained two subclades without clear geographic pattern, presumably due to admixing of populations that had diverged in Pleistocene refuges. The homogeneity of the Kyushu population supports historical reports of introduction of the species from Korea. In contrast, the high variation in the recently established Hokkaido population may reflect an ongoing invasion from several populations of the Far Eastern mainland. Bioacoustic data based on chatter call differentiate groups of subspecies and reflect phylogeographic patterns, i.e., mitochondrial lineages. Furthermore, we report the fast spreading of P. p. jankowskii towards the west along the upper Amur River, and a slower shifting of P. p. leucoptera in the opposite direction thus yielding a new contact zone. Overall, our data support a scenario of divergence in geographic isolation, but the ongoing expansion of distribution ranges may lead to major changes in phylogeographic patterns.
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Affiliation(s)
- Alexey P Kryukov
- 1 Institute of Biology and Soil Science, Russian Academy of Sciences, Vladivostok 690022, Russia
| | - Liudmila N Spiridonova
- 1 Institute of Biology and Soil Science, Russian Academy of Sciences, Vladivostok 690022, Russia
| | - Sayaka Mori
- 2 Rakuno Gakuen University, 582 Midori-machi, Bunkyo-dai, Ebetsu-shi, Hokkaido 069-0836, Japan
| | - Vladimir Yu Arkhipov
- 3 Institute of Theoretical and Experimental Biophysics RAS, Pushchino, Moscow Region 142290, Russia.,4 State Nature Reserve Rdeysky, Kholm, Novgorod 175270, Russia
| | - Yaroslav A Red'kin
- 5 Zoological Museum, Moscow State University, B. Nikitskaya 6, Moscow 125009, Russia
| | - Oleg A Goroshko
- 6 Daursky State Nature Biosphere Reserve, Nizhny Tsasuchey 674480, Russia.,7 Institute of Nature Resources, Ecology and Cryology, Russian Academy of Sciences, Chita 672014, Russia
| | - Evgeny G Lobkov
- 8 Kamchatka State Technical University, Petropavlovsk-Kamchatsky 684010, Russia
| | - Elisabeth Haring
- 9 Museum of Natural History Vienna, Burgring 7, Vienna A-1010, Austria.,10 Department of Integrative Zoology, University of Vienna, Althanstrasse 14, Vienna 1090, Austria
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Semenov GA, Koblik EA, Red'kin YA, Badyaev AV. Extensive phenotypic diversification coexists with little genetic divergence and a lack of population structure in the White Wagtail subspecies complex (Motacilla alba). J Evol Biol 2018; 31:1093-1108. [PMID: 29873425 DOI: 10.1111/jeb.13305] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Revised: 03/27/2018] [Accepted: 05/28/2018] [Indexed: 02/01/2023]
Abstract
Geographically clustered phenotypes often demonstrate consistent patterns in molecular markers, particularly mitochondrial DNA (mtDNA) traditionally used in phylogeographic studies. However, distinct evolutionary trajectories among traits and markers can lead to their discordance. First, geographic structure in phenotypic traits and nuclear molecular markers can be co-aligned but inconsistent with mtDNA (mito-nuclear discordance). Alternatively, phenotypic variation can have little to do with patterns in neither mtDNA nor nuclear markers. Disentangling between these distinct patterns can provide insight into the role of selection, demography and gene flow in population divergence. Here, we examined a previously reported case of strong inconsistency between geographic structure in mtDNA and plumage traits in a widespread polytypic bird species, the White Wagtail (Motacilla alba). We tested whether this pattern is due to mito-nuclear discordance or discrepancy between morphological evolution and both nuclear and mtDNA markers. We analysed population differentiation and structure across six out of nine commonly recognized subspecies using 17 microsatellite loci and a combination of microsatellites and plumage indices in a comprehensively sampled region of a contact between two subspecies. We did not find support for the mito-nuclear discordance hypothesis: nuclear markers indicated a subtle signal of genetic clustering only partially consistent with plumage groups, similar to previous findings that relied on mtDNA. We discuss evolutionary factors that could have shaped the intricate patterns of phenotypic diversification in the White wagtail and the role that repeated selection on plumage 'hotspots' and hybridization may have played.
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Affiliation(s)
- Georgy A Semenov
- Department of Ecology & Evolutionary Biology, University of Colorado, Boulder, CO, USA.,Department of Ecology & Evolutionary Biology, University of Arizona, Tucson, AZ, USA.,Institute of Systematics and Ecology of Animals, Novosibirsk, Russia
| | - Evgeniy A Koblik
- Department of Ornithology, Zoological Museum of Moscow State University, Moscow, Russia
| | - Yaroslav A Red'kin
- Department of Ornithology, Zoological Museum of Moscow State University, Moscow, Russia
| | - Alexander V Badyaev
- Department of Ecology & Evolutionary Biology, University of Arizona, Tucson, AZ, USA
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Drovetski SV, Semenov G, Red'kin YA, Sotnikov VN, Fadeev IV, Koblik EA. Effects of asymmetric nuclear introgression, introgressive mitochondrial sweep, and purifying selection on phylogenetic reconstruction and divergence estimates in the Pacific clade of Locustella warblers. PLoS One 2015; 10:e0122590. [PMID: 25849039 PMCID: PMC4388726 DOI: 10.1371/journal.pone.0122590] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2014] [Accepted: 02/11/2015] [Indexed: 11/18/2022] Open
Abstract
When isolated but reproductively compatible populations expand geographically and meet, simulations predict asymmetric introgression of neutral loci from a local to invading taxon. Genetic introgression may affect phylogenetic reconstruction by obscuring topology and divergence estimates. We combined phylogenetic analysis of sequences from one mtDNA and 12 nuDNA loci with analysis of gene flow among 5 species of Pacific Locustella warblers to test for presence of genetic introgression and its effects on tree topology and divergence estimates. Our data showed that nuDNA introgression was substantial and asymmetrical among all members of superspecies groups whereas mtDNA showed no introgression except a single species pair where the invader's mtDNA was swept by mtDNA of the local species. This introgressive sweep of mtDNA had the opposite direction of the nuDNA introgression and resulted in the paraphyly of the local species' mtDNA haplotypes with respect to those of the invader. Тhe multilocus nuDNA species tree resolved all inter- and intraspecific relationships despite substantial introgression. However, the node ages on the species tree may be underestimated as suggested by the differences in node age estimates based on non-introgressing mtDNA and introgressing nuDNA. In turn, the introgressive sweep and strong purifying selection appear to elongate internal branches in the mtDNA gene tree.
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Affiliation(s)
- Sergei V. Drovetski
- Department of Natural History, Tromsø University Museum, University of Tromsø—The Arctic University of Norway, Tromsø, Norway
- * E-mail:
| | - Georgy Semenov
- Thematic Group on Bird Ecology, Institute of Systematics and Ecology of Animals of Siberian Branch of Russian Academy of Sciences, Novosibirsk, Russia
| | - Yaroslav A. Red'kin
- Department of Ornithology, Zoological Museum of Moscow State University, Moscow, Russia
| | | | - Igor V. Fadeev
- Department of Collections, State Darwin Museum, Moscow, Russia
| | - Evgeniy A. Koblik
- Department of Ornithology, Zoological Museum of Moscow State University, Moscow, Russia
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Drovetski SV, Semenov G, Drovetskaya SS, Fadeev IV, Red'kin YA, Voelker G. Geographic mode of speciation in a mountain specialist Avian family endemic to the Palearctic. Ecol Evol 2013; 3:1518-28. [PMID: 23789064 PMCID: PMC3686188 DOI: 10.1002/ece3.539] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2013] [Revised: 02/27/2013] [Accepted: 03/04/2013] [Indexed: 11/25/2022] Open
Abstract
Mountains host greater avian diversity than lowlands at the same latitude due to their greater diversity of habitats stratified along an elevation gradient. Here we test whether this greater ecological heterogeneity promotes sympatric speciation. We selected accentors (Prunellidae), an avian family associated with mountains of the Palearctic, as a model system. Accentors differ in their habitat/elevation preferences and south-central Siberia and Himalayan regions each host 6 of the 13 species in the family. We used sequences of the mtDNA ND2 gene and the intron 9 of the Z chromosome specific ACO1 gene to reconstruct a complete species-level phylogeny of Prunellidae. The tree based on joint analysis of both loci was used to reconstruct the family's biogeographic history and to date the diversification events. We also analyzed the relationship between the node age and sympatry, to determine the geographic mode of speciation in Prunellidae. Our data suggest a Miocene origin of Prunellidae in the Himalayan region. The major division between alpine species (subgenus Laiscopus) and species associated with shrubs (subgenus Prunella) and initial diversification events within the latter happened within the Himalayan region in the Miocene and Pliocene. Accentors colonized other parts of the Palearctic during the Pliocene-Pleistocene transition. This spread across the Palearctic resulted in rapid diversification of accentors. With only a single exception dating to 0.91 Ma, lineages younger than 1.5 Ma are allopatric. In contrast, sympatry values for older nodes are >0. There was no relationship between node age and range symmetry. Allopatric speciation (not to include peripatric) is the predominant geographic mode of speciation in Prunellidae despite the favorable conditions for ecological diversification in the mountains and range overlaps among species.
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Koblik EA, Red'kin YA, Meer MS, Derelle R, Golenkina SA, Kondrashov FA, Arkhipov VY. Acrocephalus orinus: a case of mistaken identity. PLoS One 2011; 6:e17716. [PMID: 21526114 PMCID: PMC3081296 DOI: 10.1371/journal.pone.0017716] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2010] [Accepted: 02/11/2011] [Indexed: 11/19/2022] Open
Abstract
Recent discovery of the Large-billed Reed Warbler (Acrocephalus orinus) in museums and in the wild significantly expanded our knowledge of its morphological traits and genetic variability, and revealed new data on geographical distribution of the breeding grounds, migration routes and wintering locations of this species. It is now certain that A. orinus is breeding in Central Asia; however, the precise area of distribution remains unclear. The difficulty in the further study of this species lies in the small number of known specimens, with only 13 currently available in museums, and in the relative uncertainty of the breeding area and habitat of this species. Following morphological and genetic analyses from Svensson, et al, we describe 14 new A. orinus specimens from collections of Zoological Museums of the former USSR from the territory of Central Asian states. All of these specimens were erroneously labeled as Blyth's Reed Warbler (A. dumetorum), which is thought to be a breeding species in these areas. The 14 new A. orinus specimens were collected during breeding season while most of the 85 A. dumetorum specimens from the same area were collected during the migration period. Our data indicate that the Central Asian territory previously attributed as breeding grounds of A. dumetorum is likely to constitute the breeding territory of A. orinus. This rare case of a re-description of the breeding territory of a lost species emphasizes the importance of maintenance of museum collections around the world. If the present data on the breeding grounds of A. orinus are confirmed with field observations and collections, the literature on the biology of A. dumetorum from the southern part of its range may have to be reconsidered.
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Affiliation(s)
- Evgeny A. Koblik
- Zoological Museum of the Moscow State University, Moscow, Russia
| | | | - Margarita S. Meer
- Bioinformatics and Genomics Programme, Centre for Genomic Regulation, Barcelona, Spain
| | - Romain Derelle
- Bioinformatics and Genomics Programme, Centre for Genomic Regulation, Barcelona, Spain
| | - Sofia A. Golenkina
- Laboratory of Evolutionary Genomics, Vavilov Institute of General Genetics, Russian Academy of Science, Moscow, Russia
| | - Fyodor A. Kondrashov
- Bioinformatics and Genomics Programme, Centre for Genomic Regulation, Barcelona, Spain
| | - Vladimir Yu. Arkhipov
- Institute of Theoretical & Experimental Biophysics, Russian Academy of Sciences, Pushchino, Moscow Region, Russia
- * E-mail:
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Kerr KC, Birks SM, Kalyakin MV, Red'kin YA, Koblik EA, Hebert PD. Filling the gap - COI barcode resolution in eastern Palearctic birds. Front Zool 2009; 6:29. [PMID: 20003213 PMCID: PMC2796652 DOI: 10.1186/1742-9994-6-29] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2009] [Accepted: 12/09/2009] [Indexed: 11/26/2022] Open
Abstract
Background The Palearctic region supports relatively few avian species, yet recent molecular studies have revealed that cryptic lineages likely still persist unrecognized. A broad survey of cytochrome c oxidase I (COI) sequences, or DNA barcodes, can aid on this front by providing molecular diagnostics for species assignment. Barcodes have already been extensively surveyed in the Nearctic, which provides an interesting comparison to this region; faunal interchange between these regions has been very dynamic. We explored COI sequence divergence within and between species of Palearctic birds, including samples from Russia, Kazakhstan, and Mongolia. As of yet, there is no consensus on the best method to analyze barcode data. We used this opportunity to compare and contrast three different methods routinely employed in barcoding studies: clustering-based, distance-based, and character-based methods. Results We produced COI sequences from 1,674 specimens representing 398 Palearctic species. These were merged with published COI sequences from North American congeners, creating a final dataset of 2,523 sequences for 599 species. Ninety-six percent of the species analyzed could be accurately identified using one or a combination of the methods employed. Most species could be rapidly assigned using the cluster-based or distance-based approach alone. For a few select groups of species, the character-based method offered an additional level of resolution. Of the five groups of indistinguishable species, most were pairs, save for a larger group comprising the herring gull complex. Up to 44 species exhibited deep intraspecific divergences, many of which corresponded to previously described phylogeographic patterns and endemism hotspots. Conclusion COI sequence divergence within eastern Palearctic birds is largely consistent with that observed in birds from other temperate regions. Sequence variation is primarily congruent with taxonomic boundaries; deviations from this trend reveal overlooked biological patterns, and in some cases, overlooked species. More research is needed to further refine the taxonomic status of some Palearctic birds, but large genetic surveys such as this may facilitate this effort. DNA barcodes are a practical means for rapid species assignment, although efficient analytical methods will likely require a two-tiered approach to differentiate closely related pairs of species.
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Affiliation(s)
- Kevin Cr Kerr
- Department of Integrative Biology, Biodiversity Institute of Ontario, University of Guelph, Guelph, Ontario, N1G 2W1, Canada.
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Drovetski SV, Zink RM, Rohwer S, Fadeev IV, Nesterov EV, Karagodin I, Koblik EA, Red'kin YA. Complex biogeographic history of a Holarctic passerine. Proc Biol Sci 2004; 271:545-51. [PMID: 15129966 PMCID: PMC1691619 DOI: 10.1098/rspb.2003.2638] [Citation(s) in RCA: 100] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Our analysis of the ND2 sequences revealed six clades within winter wrens (Troglodytes troglodytes). These clades corresponded to six geographical regions: western Nearctic, eastern Nearctic, eastern Asia, Nepal, Caucasus and Europe, and differed by 3-8.8% of sequence divergence. Differences among regions explained 96% of the sequence variation in winter wren. Differences among individuals within localities explained 3% of the sequence variation, and differences among localities within regions explained 1%. Grouping sequences into subspecies instead of localities did not change these proportions. Proliferation of the six clades coincided with Early and Middle Pleistocene glaciations. The distribution of winter wren clades can be explained by a series of five consecutive vicariant events. Western Nearctic wrens diverged from the Holarctic ancestor 1.6 Myr before the present time (MYBP). Eastern Nearctic and Palaearctic wrens diverged 1 MYBP. Eastern and western Palaearctic birds diverged 0.83 MYBP. Nepalese and east Asian wrens diverged 0.67 MYBP, and Caucasian birds diverged from European wrens 0.54 MYBP. The winter wren has a much greater degree of inter- and intracontinental differentiation than the three other Holarctic birds studied to date--dunlin (Calidris alpina), common raven (Corvus corax) and three-toed woodpecker (Picoides trydactylus)--and represents an example of cryptic speciation that has been overlooked.
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Affiliation(s)
- Sergei V Drovetski
- Department of Ecology, Evolution and Behavior, University of Minnesota, 100 Ecology Building, 1987 Upper Buford Circle, St Paul, MN 55108, USA.
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