title: Genome-wide linkage disequilibrium in nine-spined stickleback populations.
abstract: Variation in the extent and magnitude of genome-wide linkage disequilibrium (LD) among populations residing in different habitats has seldom been studied in wild vertebrates. We used a total of 109 microsatellite markers to quantify the level and patterns of genome-wide LD in 13 Fennoscandian nine-spined stickleback (Pungitius pungitius) populations from four (viz. marine, lake, pond, and river) different habitat types. In general, high magnitude (D' > 0.5) of LD was found both in freshwater and marine populations, and the magnitude of LD was significantly greater in inland freshwater than in marine populations. Interestingly, three coastal freshwater populations located in close geographic proximity to the marine populations exhibited similar LD patterns and genetic diversity as their marine neighbors. The greater levels of LD in inland freshwater compared with marine and costal freshwater populations can be explained in terms of their contrasting demographic histories: founder events, long-term isolation, small effective sizes, and population bottlenecks are factors likely to have contributed to the high levels of LD in the inland freshwater populations. In general, these findings shed new light on the patterns and extent of variation in genome-wide LD, as well as the ecological and evolutionary factors driving them.
authors.affiliation: CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing 100101, China.
authors.forename: Ji
authors.initials: J
authors.lastname: Yang
authors.affiliation: Ecological Genetics Research Unit, Department of Biosciences, FIN-00014 University of Helsinki, Finland.
authors.forename: Takahito
authors.initials: T
authors.lastname: Shikano
authors.affiliation: CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing 100101, China menghua.li@ioz.ac.cn.
authors.forename: Meng-Hua
authors.initials: MH
authors.lastname: Li
authors.affiliation: Ecological Genetics Research Unit, Department of Biosciences, FIN-00014 University of Helsinki, Finland.
authors.forename: Juha
authors.initials: J
authors.lastname: Merilä
mesh_terms: D000818:Animals; D002874:Chromosome Mapping; D014644:Genetic Variation; D005828:Genetics, Population; D016678:Genome; D006239:Haplotypes; D015810:Linkage Disequilibrium; D018895:Microsatellite Repeats; D040641:Quantitative Trait Loci; D023701:Smegmamorpha / Q000235:genetics*
keywords: Pungitius pungitius; genetic variation; linkage disequilibrium; microsatellite