title: Exonic versus intronic SNPs: contrasting roles in revealing the population genetic differentiation of a widespread bird species.
abstract: Recent years have seen considerable progress in applying single nucleotide polymorphisms (SNPs) to population genetics studies. However, relatively few have attempted to use them to study the genetic differentiation of wild bird populations and none have examined possible differences of exonic and intronic SNPs in these studies. Here, using 144 SNPs, we examined population genetic differentiation in the saker falcon (Falco cherrug) across Eurasia. The position of each SNP was verified using the recently sequenced saker genome with 108 SNPs positioned within the introns of 10 fragments and 36 SNPs in the exons of six genes, comprising MHC, MC1R and four others. In contrast to intronic SNPs, both Bayesian clustering and principal component analyses using exonic SNPs consistently revealed two genetic clusters, within which the least admixed individuals were found in Europe/central Asia and Qinghai (China), respectively. Pairwise D analysis for exonic SNPs showed that the two populations were significantly differentiated and between the two clusters the frequencies of five SNP markers were inferred to be influenced by selection. Central Eurasian populations clustered in as intermediate between the two main groups, consistent with their geographic position. But the westernmost populations of central Europe showed evidence of demographic isolation. Our work highlights the importance of functional exonic SNPs for studying population genetic pattern in a widespread avian species.
authors: 1] Organisms and Environment Division, Cardiff School of Biosciences, Cardiff University, Cardiff, UK [2] Key Lab of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.
authors: X
authors: X
authors: Zhan
authors: International Wildlife Consultants Ltd., Carmarthen, UK.
authors: A
authors: A
authors: Dixon
authors: Wildlife Science and Conservation Centre, Ulaanbaatar, Mongolia.
authors: N
authors: N
authors: Batbayar
authors: Naurzum National Nature Reserve, Kostanay State Pedagogical Institute, Kostanay, Kazakhstan.
authors: E
authors: E
authors: Bragin
authors: Department of Biology, Hacettepe University, Ankara, Turkey.
authors: Z
authors: Z
authors: Ayas
authors: Raptor Protection of Slovakia, Bratislava, Slovakia.
authors: L
authors: L
authors: Deutschova
authors: Raptor Protection of Slovakia, Bratislava, Slovakia.
authors: J
authors: J
authors: Chavko
authors: Ukrainian Birds of Prey Research Centre, c/o Kryvyi Rih State Pedagogical University, Kryvyi Rih, Ukraine.
authors: S
authors: S
authors: Domashevsky
authors: Danube Delta National Institute for Research and Development, Tulcea, Romania.
authors: A
authors: A
authors: Dorosencu
authors: MME/BirdLife Hungary, Budapest, Hungary.
authors: J
authors: J
authors: Bagyura
authors: Zoology Department, National University of Mongolia, Ulaanbaatar, Mongolia.
authors: S
authors: S
authors: Gombobaatar
authors: Nature Society 'Drava', Virovitica, Croatia.
authors: I D
authors: ID
authors: Grlica
authors: Institute of Zoology, National Academy of Sciences, Almaty, Kazakhstan.
authors: A
authors: A
authors: Levin
authors: Ukrainian Birds of Prey Research Centre, c/o Kryvyi Rih State Pedagogical University, Kryvyi Rih, Ukraine.
authors: Y
authors: Y
authors: Milobog
authors: Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China.
authors: M
authors: M
authors: Ming
authors: MME/BirdLife Hungary, Budapest, Hungary.
authors: M
authors: M
authors: Prommer
authors: Wildlife Science and Conservation Centre, Ulaanbaatar, Mongolia.
authors: G
authors: G
authors: Purev-Ochir
authors: Institute of Biodiversity and Ecosystem Research, Bulgarian Academy of Sciences, Sofia, Bulgaria.
authors: D
authors: D
authors: Ragyov
authors: Institute of Zoology, Moldovan Academy of Science, Chişinău, Republic of Moldova.
authors: V
authors: V
authors: Tsurkanu
authors: Ukrainian Birds of Prey Research Centre, c/o Kryvyi Rih State Pedagogical University, Kryvyi Rih, Ukraine.
authors: V
authors: V
authors: Vetrov
authors: Institute of Zoology, Moldovan Academy of Science, Chişinău, Republic of Moldova.
authors: N
authors: N
authors: Zubkov
authors: Organisms and Environment Division, Cardiff School of Biosciences, Cardiff University, Cardiff, UK.
authors: M W
authors: MW
authors: Bruford
mesh_terms: D000818:Animals; D001208:Asia; D001499:Bayes Theorem; D005060:Europe; D005091:Exons; D046093:Falconiformes / Q000235:genetics*; D005241:Feathers; D005787:Gene Frequency; D005819:Genetic Markers; D005828:Genetics, Population; D005843:Geography; D007438:Introns; D008969:Molecular Sequence Data; D020641:Polymorphism, Single Nucleotide; D025341:Principal Component Analysis; D012641:Selection, Genetic; D017422:Sequence Analysis, DNA
chemical_list: D005819:Genetic Markers