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Dufresnes C, Dutoit L, Brelsford A, Goldstein-Witsenburg F, Clément L, López-Baucells A, Palmeirim J, Pavlinić I, Scaravelli D, Ševčík M, Christe P, Goudet J. Inferring genetic structure when there is little: population genetics versus genomics of the threatened bat Miniopterus schreibersii across Europe. Sci Rep 2023; 13:1523. [PMID: 36707640 PMCID: PMC9883447 DOI: 10.1038/s41598-023-27988-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2022] [Accepted: 01/11/2023] [Indexed: 01/28/2023] Open
Abstract
Despite their paramount importance in molecular ecology and conservation, genetic diversity and structure remain challenging to quantify with traditional genotyping methods. Next-generation sequencing holds great promises, but this has not been properly tested in highly mobile species. In this article, we compared microsatellite and RAD-sequencing (RAD-seq) analyses to investigate population structure in the declining bent-winged bat (Miniopterus schreibersii) across Europe. Both markers retrieved general patterns of weak range-wide differentiation, little sex-biased dispersal, and strong isolation by distance that associated with significant genetic structure between the three Mediterranean Peninsulas, which could have acted as glacial refugia. Microsatellites proved uninformative in individual-based analyses, but the resolution offered by genomic SNPs illuminated on regional substructures within several countries, with colonies sharing migrators of distinct ancestry without admixture. This finding is consistent with a marked philopatry and spatial partitioning between mating and rearing grounds in the species, which was suspected from marked-recaptured data. Our study advocates that genomic data are necessary to properly unveil the genetic footprints left by biogeographic processes and social organization in long-distant flyers, which are otherwise rapidly blurred by their high levels of gene flow.
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Affiliation(s)
- Christophe Dufresnes
- Laboratory for Amphibian Systematic and Evolutionary Research, College of Biology and the Environment, Nanjing Forestry University, Nanjing, People's Republic of China.
| | - Ludovic Dutoit
- Department of Ecology and Evolution, University of Lausanne, 1015, Lausanne, Switzerland.,Department of Zoology, University of Otago, Dunedin, New Zealand
| | - Alan Brelsford
- Department of Evolution, Ecology, and Organismal Biology, University of California Riverside, Riverside, CA, USA
| | | | - Laura Clément
- Department of Ecology and Evolution, University of Lausanne, 1015, Lausanne, Switzerland
| | - Adria López-Baucells
- Bat Research Area, Granollers Museum of Natural Sciences, Carrer Palaudaries 102, 08402, Granollers, Spain
| | - Jorge Palmeirim
- Department of Animal Biology, Centre for Ecology, Evolution and Environmental Change - cE3c, University of Lisbon, 1749-016, Lisbon, Portugal
| | - Igor Pavlinić
- Department of Zoology, Croatian Natural History Museum, Demetrova 1, 10000, Zagreb, Croatia
| | - Dino Scaravelli
- Department of Biological, Geological, and Environmental Sciences, University of Bologna, Via Selmi 3, 40126, Bologna, Italy
| | - Martin Ševčík
- Department of Zoology, Faculty of Science, Charles University in Prague, Viničná 7, 128 44, Prague 2, Czech Republic
| | - Philippe Christe
- Department of Ecology and Evolution, University of Lausanne, 1015, Lausanne, Switzerland.
| | - Jérôme Goudet
- Department of Ecology and Evolution, University of Lausanne, 1015, Lausanne, Switzerland.
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Byerly PA, Chesser RT, Fleischer RC, McInerney N, Przelomska NAS, Leberg PL. Museum Genomics Provide Evidence for Persistent Genetic Differentiation in a Threatened Seabird Species in the Western Atlantic. Integr Comp Biol 2022; 62:1838-1848. [PMID: 35781565 DOI: 10.1093/icb/icac107] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 06/18/2022] [Accepted: 06/27/2022] [Indexed: 01/05/2023] Open
Abstract
Connectivity among wildlife populations facilitates exchange of genetic material between groups. Changes to historical connectivity patterns resulting from anthropogenic activities can therefore have negative consequences for genetic diversity, particularly for small or isolated populations. DNA obtained from museum specimens can enable direct comparison of temporal changes in connectivity among populations, which can aid in conservation planning and contribute to the understanding of population declines. However, museum DNA can be degraded and only available in low quantities, rendering it challenging for use in population genomic analyses. Applications of genomic methodologies such as targeted sequencing address this issue by enabling capture of shared variable sites, increasing quantity and quality of recovered genomic information. We used targeted sequencing of ultra-conserved Elements (UCEs) to evaluate potential changes in connectivity and genetic diversity of roseate terns (Sterna dougallii) with a breeding distribution in the northwestern Atlantic and the Caribbean. Both populations experienced range contractions and population declines due to anthropogenic activity in the 20th century, which has the potential to alter historical connectivity regimes. Instead, we found that the two populations were differentiated historically as well as contemporaneously, with little evidence of migration between them for either time period. We also found no evidence for temporal changes in genetic diversity, although these interpretations may have been limited due to sequencing artifacts caused by the degraded nature of the museum samples. Population structuring in migratory seabirds is typically reflective of low rates of divergence and high connectivity among geographically segregated subpopulations. Our contrasting results suggest the potential presence of ecological mechanisms driving population differentiation, and highlight the value of targeted sequencing on DNA derived from museum specimens to uncover long-term patterns of genetic differentiation in wildlife populations.
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Affiliation(s)
- Paige A Byerly
- University of Louisiana at Lafayette, 104 E University Ave, Lafayette, LA 70504, USA.,Smithsonian's National Zoo and Conservation Biology Institute, 3001 Connecticut Avenue, NW, Washington, DC 20008, USA
| | - R Terry Chesser
- Eastern Ecological Science Center, U.S. Geological Survey, 12100 Beech Forest Road, Laurel, MD 20708, USA.,National Museum of Natural History, 10th St. and Constitution Avenue, NW, Washington, DC 20560, USA
| | - Robert C Fleischer
- Smithsonian's National Zoo and Conservation Biology Institute, 3001 Connecticut Avenue, NW, Washington, DC 20008, USA
| | - Nancy McInerney
- Smithsonian's National Zoo and Conservation Biology Institute, 3001 Connecticut Avenue, NW, Washington, DC 20008, USA
| | - Natalia A S Przelomska
- National Museum of Natural History, 10th St. and Constitution Avenue, NW, Washington, DC 20560, USA.,Smithsonian's National Zoo and Conservation Biology Institute, 3001 Connecticut Avenue, NW, Washington, DC 20008, USA.,Royal Botanic Gardens, Kew, Richmond TW9 3AE, UK
| | - Paul L Leberg
- University of Louisiana at Lafayette, 104 E University Ave, Lafayette, LA 70504, USA
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Searching for genetic evidence of demographic decline in an arctic seabird: beware of overlapping generations. Heredity (Edinb) 2022; 128:364-376. [PMID: 35246618 PMCID: PMC9076905 DOI: 10.1038/s41437-022-00515-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 02/12/2022] [Accepted: 02/14/2022] [Indexed: 11/09/2022] Open
Abstract
Genetic data are useful for detecting sudden population declines in species that are difficult to study in the field. Yet this indirect approach has its own drawbacks, including population structure, mutation patterns, and generation overlap. The ivory gull (Pagophila eburnea), a long-lived Arctic seabird, is currently suffering from rapid alteration of its primary habitat (i.e., sea ice), and dramatic climatic events affecting reproduction and recruitment. However, ivory gulls live in remote areas, and it is difficult to assess the population trend of the species across its distribution. Here we present complementary microsatellite- and SNP-based genetic analyses to test a recent bottleneck genetic signal in ivory gulls over a large portion of their distribution. With attention to the potential effects of population structure, mutation patterns, and sample size, we found no significant signatures of population decline worldwide. At a finer scale, we found a significant bottleneck signal at one location in Canada. These results were compared with predictions from simulations showing how generation time and generation overlap can delay and reduce the bottleneck microsatellite heterozygosity excess signal. The consistency of the results obtained with independent methods strongly indicates that the species shows no genetic evidence of an overall decline in population size. However, drawing conclusions related to the species' population trends will require a better understanding of the effect of age structure in long-lived species. In addition, estimates of the effective global population size of ivory gulls were surprisingly low (~1000 ind.), suggesting that the evolutionary potential of the species is not assured.
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Davis SE, Maftei M, Mallory ML. Migratory Connectivity at High Latitudes: Sabine's Gulls (Xema sabini) from a Colony in the Canadian High Arctic Migrate to Different Oceans. PLoS One 2016; 11:e0166043. [PMID: 27973614 PMCID: PMC5156335 DOI: 10.1371/journal.pone.0166043] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Accepted: 10/22/2016] [Indexed: 11/18/2022] Open
Abstract
The world's Arctic latitudes are some of the most recently colonized by birds, and an understanding of the migratory connectivity of circumpolar species offers insights into the mechanisms of range expansion and speciation. Migratory divides exist for many birds, however for many taxa it is unclear where such boundaries lie, and to what extent these affect the connectivity of species breeding across their ranges. Sabine's gulls (Xema sabini) have a patchy, circumpolar breeding distribution and overwinter in two ecologically similar areas in different ocean basins: the Humboldt Current off the coast of Peru in the Pacific, and the Benguela Current off the coasts of South Africa and Namibia in the Atlantic. We used geolocators to track Sabine's gulls breeding at a colony in the Canadian High Arctic to determine their migratory pathways and wintering sites. Our study provides evidence that birds from this breeding site disperse to both the Pacific and Atlantic oceans during the non-breeding season, which suggests that a migratory divide for this species exists in the Nearctic. Remarkably, members of one mated pair wintered in opposite oceans. Our results ultimately suggest that colonization of favorable breeding habitat may be one of the strongest drivers of range expansion in the High Arctic.
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Affiliation(s)
- Shanti E. Davis
- High Arctic Gull Research Group, Victoria, British Columbia, Canada
- Department of Biology, Memorial University of Newfoundland, St. John’s, Newfoundland and Labrador, Canada
- * E-mail:
| | - Mark Maftei
- High Arctic Gull Research Group, Victoria, British Columbia, Canada
| | - Mark L. Mallory
- High Arctic Gull Research Group, Victoria, British Columbia, Canada
- Department of Biology, Acadia University, Wolfville, Nova Scotia, Canada
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