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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
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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Aguilar C, Miller MJ, Loaiza JR, González R, Krahe R, De León LF. Tempo and mode of allopatric divergence in the weakly electric fish Sternopygus dariensis in the Isthmus of Panama. Sci Rep 2019; 9:18828. [PMID: 31827183 PMCID: PMC6906317 DOI: 10.1038/s41598-019-55336-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Accepted: 11/27/2019] [Indexed: 01/12/2023] Open
Abstract
Spatial isolation is one of the main drivers of allopatric speciation, but the extent to which spatially-segregated populations accumulate genetic differences relevant to speciation is not always clear. We used data from ultraconserved elements (UCEs) and whole mitochondrial genomes (i.e., mitogenomes) to explore genetic variation among allopatric populations of the weakly electric fish Sternopygus dariensis across the Isthmus of Panama. We found strong genetic divergence between eastern and western populations of S. dariensis. Over 77% of the UCE loci examined were differentially fixed between populations, and these loci appear to be distributed across the species' genome. Population divergence occurred within the last 1.1 million years, perhaps due to global glaciation oscillations during the Pleistocene. Our results are consistent with a pattern of genetic differentiation under strict geographic isolation, and suggest the presence of incipient allopatric species within S. dariensis. Genetic divergence in S. dariensis likely occurred in situ, long after the closure of the Isthmus of Panama. Our study highlights the contribution of spatial isolation and vicariance to promoting rapid diversification in Neotropical freshwater fishes. The study of spatially-segregated populations within the Isthmus of Panama could reveal how genetic differences accumulate as allopatric speciation proceeds.
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Affiliation(s)
- Celestino Aguilar
- Centro de Biodiversidad y Descubrimiento de Drogas, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT AIP), P. O. Box 0843-01103, Panamá, República de Panamá
- Department of Biotechnology, Acharya Nagarjuna University, Guntur, India
- Smithsonian Tropical Research Institute, Balboa Ancón, P.O. Box 0843-03092, Panamá, República de Panamá
- Department of Biology, University of Massachusetts Boston, Boston, MA, USA
| | - Matthew J Miller
- Centro de Biodiversidad y Descubrimiento de Drogas, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT AIP), P. O. Box 0843-01103, Panamá, República de Panamá
- Sam Noble Oklahoma Museum of Natural History and Department of Biology, University of Oklahoma, Norman, OK, USA
| | - Jose R Loaiza
- Centro de Biodiversidad y Descubrimiento de Drogas, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT AIP), P. O. Box 0843-01103, Panamá, República de Panamá
- Smithsonian Tropical Research Institute, Balboa Ancón, P.O. Box 0843-03092, Panamá, República de Panamá
- Programa Centroamericano de Maestría en Entomología, Universidad de Panamá, Panamá, República de Panamá
| | - Rigoberto González
- Smithsonian Tropical Research Institute, Balboa Ancón, P.O. Box 0843-03092, Panamá, República de Panamá
| | - Rüdiger Krahe
- Institut für Biologie, Humboldt-Universität zu Berlin, Berlin, Germany
- Department of Biology, McGill University, Montreal, QC, Canada
| | - Luis F De León
- Centro de Biodiversidad y Descubrimiento de Drogas, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT AIP), P. O. Box 0843-01103, Panamá, República de Panamá.
- Smithsonian Tropical Research Institute, Balboa Ancón, P.O. Box 0843-03092, Panamá, República de Panamá.
- Department of Biology, University of Massachusetts Boston, Boston, MA, USA.
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Tan HZ, Ng EYX, Tang Q, Allport GA, Jansen JJFJ, Tomkovich PS, Rheindt FE. Population genomics of two congeneric Palaearctic shorebirds reveals differential impacts of Quaternary climate oscillations across habitats types. Sci Rep 2019; 9:18172. [PMID: 31796810 PMCID: PMC6890745 DOI: 10.1038/s41598-019-54715-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Accepted: 11/08/2019] [Indexed: 02/07/2023] Open
Abstract
Intracontinental biotic divisions across the vast Palaearctic region are not well-characterized. Past research has revealed patterns ranging from a lack of population structure to deep divergences along varied lines of separation. Here we compared biogeographic patterns of two Palaearctic shorebirds with different habitat preferences, Whimbrel (Numenius phaeopus) and Eurasian curlew (N. arquata). Using genome-wide markers from populations across the Palaearctic, we applied a multitude of population genomic and phylogenomic approaches to elucidate population structure. Most importantly, we tested for isolation by distance and visualized barriers and corridors to gene flow. We found shallow Palaearctic population structure in subpolar bog and tundra-breeding whimbrels, consistent with other species breeding at a similarly high latitude, indicating connectivity across the tundra belt, both presently and during southward shifts in periods of global cooling. In contrast, the temperate grassland-breeding Eurasian curlew emerged in three distinct clades corresponding to glacial refugia. Barriers to gene flow coincided with areas of topographic relief in the central Palaearctic for whimbrels and further east for Eurasian curlews. Our findings highlight the interplay of historic and ecological factors in influencing present-day population structure of Palaearctic biota.
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Affiliation(s)
- Hui Zhen Tan
- Department of Biological Sciences, National University of Singapore, 16 Science Drive 4, Singapore, 117558, Singapore
| | - Elize Ying Xin Ng
- Department of Biological Sciences, National University of Singapore, 16 Science Drive 4, Singapore, 117558, Singapore
| | - Qian Tang
- Department of Biological Sciences, National University of Singapore, 16 Science Drive 4, Singapore, 117558, Singapore
| | - Gary A Allport
- BirdLife International, The David Attenborough Building, Pembroke Street, Cambridge, CB2 3QZ, UK
| | - Justin J F J Jansen
- Naturalis Biodiversity Center, Leiden, P.O. Box 9517, 2300 RA, Leiden, The Netherlands
| | - Pavel S Tomkovich
- Zoological Museum, Lomonosov Moscow State University, Bolshaya Nikitskaya Str. 2, Moscow, 125009, Russia
| | - Frank E Rheindt
- Department of Biological Sciences, National University of Singapore, 16 Science Drive 4, Singapore, 117558, Singapore.
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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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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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Song G, Zhang R, DuBay SG, Qu Y, Dong L, Wang W, Zhang Y, Lambert DM, Lei F. East Asian allopatry and north Eurasian sympatry in Long-tailed Tit lineages despite similar population dynamics during the late Pleistocene. ZOOL SCR 2015. [DOI: 10.1111/zsc.12148] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Gang Song
- Key Laboratory of Zoological Systematics and Evolution; Institute of Zoology; Chinese Academy of Sciences; Beijing 100101 China
- Environmental Futures Research Institute; Griffith University; Nathan Qld 4111 Australia
| | - Ruiying Zhang
- Key Laboratory of Zoological Systematics and Evolution; Institute of Zoology; Chinese Academy of Sciences; Beijing 100101 China
- Center for Developmental Biology; Institute of Genetics and Developmental Biology; Chinese Academy of Sciences; Beijing 100101 China
| | - Shane G. DuBay
- Committee on Evolutionary Biology; University of Chicago; Chicago IL 60637 USA
- Life Sciences Section; Integrative Research Center; Field Museum of Natural History; Chicago IL 60605 USA
| | - Yanhua Qu
- Key Laboratory of Zoological Systematics and Evolution; Institute of Zoology; Chinese Academy of Sciences; Beijing 100101 China
| | - Lu Dong
- Ministry of Education Key Laboratory for Biodiversity and Ecological Engineering; College of Life Sciences; Beijing Normal University; Beijing 100875 China
| | - Wenjuan Wang
- Center for Watershed Ecology; Institute of Life Science; Nanchang University; Nanchang 330031 China
| | - Yanyun Zhang
- Ministry of Education Key Laboratory for Biodiversity and Ecological Engineering; College of Life Sciences; Beijing Normal University; Beijing 100875 China
| | - David M. Lambert
- Environmental Futures Research Institute; Griffith University; Nathan Qld 4111 Australia
| | - Fumin Lei
- Key Laboratory of Zoological Systematics and Evolution; Institute of Zoology; Chinese Academy of Sciences; Beijing 100101 China
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