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Song K, Gao B, Halvarsson P, Fang Y, Klaus S, Jiang YX, Swenson JE, Sun YH, Höglund J. Demographic history and divergence of sibling grouse species inferred from whole genome sequencing reveal past effects of climate change. BMC Ecol Evol 2021; 21:194. [PMID: 34689746 PMCID: PMC8543876 DOI: 10.1186/s12862-021-01921-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 10/13/2021] [Indexed: 11/23/2022] Open
Abstract
Background The boreal forest is one of the largest biomes on earth, supporting thousands of species. The global climate fluctuations in the Quaternary, especially the ice ages, had a significant influence on the distribution of boreal forest, as well as the divergence and evolution of species inhabiting this biome. To understand the possible effects of on-going and future climate change it would be useful to reconstruct past population size changes and relate such to climatic events in the past. We sequenced the genomes of 32 individuals from two forest inhabiting bird species, Hazel Grouse (Tetrastes bonasia) and Chinese Grouse (T. sewerzowi) and three representatives of two outgroup species from Europe and China. Results We estimated the divergence time of Chinese Grouse and Hazel Grouse to 1.76 (0.46–3.37) MYA. The demographic history of different populations in these two sibling species was reconstructed, and showed that peaks and bottlenecks of effective population size occurred at different times for the two species. The northern Qilian population of Chinese Grouse became separated from the rest of the species residing in the south approximately 250,000 years ago and have since then showed consistently lower effective population size than the southern population. The Chinese Hazel Grouse population had a higher effective population size at the peak of the Last Glacial Period (approx. 300,000 years ago) than the European population. Both species have decreased recently and now have low effective population sizes. Conclusions Combined with the uplift history and reconstructed climate change during the Quaternary, our results support that cold-adapted grouse species diverged in response to changes in the distribution of palaeo-boreal forest and the formation of the Loess Plateau. The combined effects of climate change and an increased human pressure impose major threats to the survival and conservation of both species. Supplementary Information The online version contains supplementary material available at 10.1186/s12862-021-01921-7.
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Affiliation(s)
- Kai Song
- Animal Ecology, Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, 75236, Uppsala, Sweden. .,Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, 100101, Beijing, People's Republic of China.
| | - Bin Gao
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, 100101, Beijing, People's Republic of China
| | - Peter Halvarsson
- Unit of Parasitology, Department of Biomedicine and Veterinary Public Health, Swedish University of Agricultural Sciences, PO Box 7036, 75007, Uppsala, Sweden
| | - Yun Fang
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, 100101, Beijing, People's Republic of China
| | | | - Ying-Xin Jiang
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, 100101, Beijing, People's Republic of China
| | - Jon E Swenson
- Faculty of Environmental Sciences and Natural Resource Management, Norwegian University of Life Sciences, PO Box 5003, 1432, Ås, Norway
| | - Yue-Hua Sun
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, 100101, Beijing, People's Republic of China.
| | - Jacob Höglund
- Animal Ecology, Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, 75236, Uppsala, Sweden.
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Low neutral and immunogenetic diversity in northern fringe populations of the green toad Bufotes viridis: implications for conservation. CONSERV GENET 2021. [DOI: 10.1007/s10592-021-01407-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
AbstractGenetic variation is often lower at high latitudes, which may compromise the adaptability and hence survival of organisms. Here we show that genetic variability is negatively correlated with northern latitude in European green toads (Bufotes viridis). The result holds true for both putatively neutral microsatellite variation and supposedly adaptive MHC Class IIB variation. In particular, our findings have bearing on the conservation status of this species in Sweden, on the northern limit of its distribution where local populations are small and fragmented. These genetically impoverished populations are closely related to other populations found around the Baltic Sea basin. The low neutral and adaptive variation in these fringe populations compared to population at central ranges confirms a pattern shared across all other amphibians so far studied. In Sweden, the situation of green toads is of concern as the remaining populations may not have the evolutionary potential to cope with present and future environmental challenges.
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Lee-Yaw JA, Zenni RD, Hodgins KA, Larson BMH, Cousens R, Webber BL. Range shifts and local adaptation: integrating data and theory towards a new understanding of species' distributions in the Anthropocene. THE NEW PHYTOLOGIST 2019; 221:644-647. [PMID: 30569613 DOI: 10.1111/nph.15554] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Affiliation(s)
- Julie A Lee-Yaw
- Department of Botany, University of British Columbia, 6270 University Blvd, Vancouver, BC, V6T 1Z4, Canada
| | - Rafael D Zenni
- Department of Biology, Federal University of Lavras, Av. Central, S/N Campus Universitário, Lavras, Minas Gerais, 37200-000, Brazil
| | - Kathryn A Hodgins
- School of Biological Sciences, Monash University, Clayton, Vic, 3800, Australia
| | - Brendon M H Larson
- School of Environment, Resources and Sustainability, University of Waterloo, 200 University Avenue W., Waterloo, ON, N2L 3G1, Canada
| | - Roger Cousens
- School of BioSciences, The University of Melbourne, Melbourne, Vic, 3010, Australia
| | - Bruce L Webber
- CSIRO Land and Water, Centre for Environment and Life Sciences, 147 Underwood Ave, Floreat, WA, 6014, Australia
- School of Biological Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia
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Cortázar-Chinarro M, Lattenkamp EZ, Meyer-Lucht Y, Luquet E, Laurila A, Höglund J. Drift, selection, or migration? Processes affecting genetic differentiation and variation along a latitudinal gradient in an amphibian. BMC Evol Biol 2017; 17:189. [PMID: 28806900 PMCID: PMC5557520 DOI: 10.1186/s12862-017-1022-z] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2017] [Accepted: 07/26/2017] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Past events like fluctuations in population size and post-glacial colonization processes may influence the relative importance of genetic drift, migration and selection when determining the present day patterns of genetic variation. We disentangle how drift, selection and migration shape neutral and adaptive genetic variation in 12 moor frog populations along a 1700 km latitudinal gradient. We studied genetic differentiation and variation at a MHC exon II locus and a set of 18 microsatellites. RESULTS Using outlier analyses, we identified the MHC II exon 2 (corresponding to the β-2 domain) locus and one microsatellite locus (RCO8640) to be subject to diversifying selection, while five microsatellite loci showed signals of stabilizing selection among populations. STRUCTURE and DAPC analyses on the neutral microsatellites assigned populations to a northern and a southern cluster, reflecting two different post-glacial colonization routes found in previous studies. Genetic variation overall was lower in the northern cluster. The signature of selection on MHC exon II was weaker in the northern cluster, possibly as a consequence of smaller and more fragmented populations. CONCLUSION Our results show that historical demographic processes combined with selection and drift have led to a complex pattern of differentiation along the gradient where some loci are more divergent among populations than predicted from drift expectations due to diversifying selection, while other loci are more uniform among populations due to stabilizing selection. Importantly, both overall and MHC genetic variation are lower at northern latitudes. Due to lower evolutionary potential, the low genetic variation in northern populations may increase the risk of extinction when confronted with emerging pathogens and climate change.
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Affiliation(s)
- Maria Cortázar-Chinarro
- Animal Ecology/Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, 75236, Uppsala, Sweden.
| | - Ella Z Lattenkamp
- Animal Ecology/Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, 75236, Uppsala, Sweden
- Present address: Department of Neurogenetics of Vocal Communication, Max Planck Institute of Psycholinguistics, Box 310, 6500, Nijmegen, Netherlands
| | - Yvonne Meyer-Lucht
- Animal Ecology/Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, 75236, Uppsala, Sweden
| | - Emilien Luquet
- Animal Ecology/Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, 75236, Uppsala, Sweden
- Present address: Université Claude Bernard - Lyon I, CNRS, UMR 5023 - LEHNA, 3-6, rue Raphaël Dubois - Bâtiments Darwin C and Forel, 69622 Villeurbanne Cedex 43, Boulevard du 11 novembre, 1918, Lyon, France
| | - Anssi Laurila
- Animal Ecology/Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, 75236, Uppsala, Sweden
| | - Jacob Höglund
- Animal Ecology/Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, 75236, Uppsala, Sweden
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