Evolutionary factors affecting the cross‐species utility of newly developed microsatellite markers in seabirds |
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Authors: | Yoshan Moodley Juan F Masello Theresa L Cole Luciano Calderon Gopi K Munimanda Marco R Thali Rachael Alderman Richard J Cuthbert Manuel Marin Melanie Massaro Joan Navarro Richard A Phillips Peter G Ryan Cristián G Suazo Yves Cherel Henri Weimerskirch Petra Quillfeldt |
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Institution: | 1. Department of Zoology, University of Venda, Private Bag X5050, South Africa;2. Department of Integrative Biology and Evolution, Konrad Lorenz Institute for Ethology, University of Veterinary Medicine Vienna, Vienna, Austria;3. Justus Liebig University Giessen, Department of Animal Ecology & Systematics, Giessen, Germany;4. Trace and Environmental DNA Laboratory, Department of Environment and Agriculture, Curtin University, Perth, WA, Australia;5. Ecogenics GmbH, Zurich‐Schlieren, Switzerland;6. Department of Primary Industries, Parks, Water and Environment, Hobart, Tas., Australia;7. Royal Society for the Protection of Birds (RSPB), The Lodge, Sandy, Bedfordshire, UK;8. Section of Ornithology, Natural History Museum of Los Angeles County, Los Angeles, CA, USA;9. Feather Link Inc., Cincinnati, OH, USA;10. School of Environmental Sciences, Charles Sturt University, Albury, NSW, Australia;11. Department of Conservation Biology, Estación Biológica de Do?ana (EBD‐CSIC), Seville, Spain;12. British Antarctic Survey, Natural Environment Research Council, Cambridge, UK;13. Percy FitzPatrick Institute, DST/NRF Centre of Excellence, University of Cape Town, Rondebosch, South Africa;14. Centre d'Etudes Biologiques de Chizé, UMR 7372 CNRS‐Université de La Rochelle, Villiers‐en‐Bois, France |
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Abstract: | Microsatellite loci are ideal for testing hypotheses relating to genetic segregation at fine spatio‐temporal scales. They are also conserved among closely related species, making them potentially useful for clarifying interspecific relationships between recently diverged taxa. However, mutations at primer binding sites may lead to increased nonamplification, or disruptions that may result in decreased polymorphism in nontarget species. Furthermore, high mutation rates and constraints on allele size may also with evolutionary time, promote an increase in convergently evolved allele size classes, biasing measures of interspecific genetic differentiation. Here, we used next‐generation sequencing to develop microsatellite markers from a shotgun genome sequence of the sub‐Antarctic seabird, the thin‐billed prion (Pachyptila belcheri), that we tested for cross‐species amplification in other Pachyptila and related sub‐Antarctic species. We found that heterozygosity decreased and the proportion of nonamplifying loci increased with phylogenetic distance from the target species. Surprisingly, we found that species trees estimated from interspecific FST provided better approximations of mtDNA relationships among the studied species than those estimated using DC, even though FST was more affected by null alleles. We observed a significantly nonlinear second order polynomial relationship between microsatellite and mtDNA distances. We propose that the loss of linearity with increasing mtDNA distance stems from an increasing proportion of homoplastic allele size classes that are identical in state, but not identical by descent. Therefore, despite high cross‐species amplification success and high polymorphism among the closely related Pachyptila species, we caution against the use of microsatellites in phylogenetic inference among distantly related taxa. |
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Keywords: | cross‐species transferability genetic diversity microsatellite null alleles Pachyptila Procellariiformes |
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