Characterizing range-wide divergence in an alpine-endemic bird: a comparison of genetic and genomic approaches

Abstract

The delineation of intraspecific units that are evolutionarily and demographically distinct is an important step in the development of species-specific management plans. Neutral genetic variation has served as the primary data source for delineating “evolutionarily significant units,” but with recent advances in genomic technology, we now have an unprecedented ability to utilize information about neutral and adaptive variation across the entire genome. Here, we use traditional genetic markers (microsatellites) and a newer reduced-representation genomic approach (single nucleotide polymorphisms) to delineate distinct groups of white-tailed ptarmigan (Lagopus leucura), an alpine-obligate species that is distributed in naturally fragmented habitats from Alaska to New Mexico. Five subspecies of white-tailed ptarmigan are currently recognized but their distinctiveness has not been verified with molecular data. Based on analyses of 436 samples at 12 microsatellite loci and 95 samples at 14,866 single nucleotide polymorphism loci, we provide strong support for treating two subspecies as distinct intraspecific units—L. l. altipetens, found in Colorado and neighboring states; and L. l. saxatilis, found on British Columbia’s Vancouver Island—but our findings reveal more moderate patterns of divergence within the remainder of the species’ range. Results based on genetic and genomic datasets generally agreed with one another, indicating that in many cases microsatellite loci may be sufficient for describing major patterns of genetic structure across species’ ranges. This work will inform future conservation and management decisions for the white-tailed ptarmigan, a species that may be vulnerable to future changes in climate.

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Data availability

All datasets are available in the online supplement. In addition, the molecular datasets are archived at https://doi.org/10.5066/F7GM86GZ and the genomic sequencing data are deposited in Genbank (biosample accession numbers: SAMN08132751-SAMN08132845).

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Acknowledgements

We thank Kathryn Bernier, Sharon Birks, John Bulger, Ray Collingwood, Avery Cook, Sarah Hudson, Doug Jury, Lee Kaiser, Richard Merizon, Jason Robinson, Serena Rocksund, William Taylor, and many others for help obtaining ptarmigan samples. We also thank Daniel Taylor for digitizing the morphology data, Kevin Oh for advice on genomic methods, and Christin Pruett and Patricia Stevens for manuscript comments. The University of Washington Burke Museum provided four samples through their tissue collection program. Colorado Parks and Wildlife, the Utah Division of Wildlife Resources, and the Alaska Department of Fish and Game provided samples collected by hunters. Funding was provided by the U.S. Geological Survey, the U.S. National Park Service, the Natural Sciences and Engineering Research Council of Canada, Forest Renewal British Columbia, Environment and Climate Change Canada, Colorado Parks and Wildlife, the Washington Department of Fish and Wildlife, and the Utah Division of Wildlife Resources. Any use of trade, firm, or product names is for descriptive purposes only and does not imply endorsement by the U.S. Government.

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Correspondence to Kathryn M. Langin.

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Langin, K.M., Aldridge, C.L., Fike, J.A. et al. Characterizing range-wide divergence in an alpine-endemic bird: a comparison of genetic and genomic approaches. Conserv Genet 19, 1471–1485 (2018). https://doi.org/10.1007/s10592-018-1115-2

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Keywords

  • Conservation
  • Evolutionarily significant unit
  • Population genetics
  • Population genomics
  • White-tailed ptarmigan