Academic journal article Genetics

Nucleotide Variation, Linkage Disequilibrium and Founder-Facilitated Speciation in Wild Populations of the Zebra Finch (Taeniopygia Guttata)

Academic journal article Genetics

Nucleotide Variation, Linkage Disequilibrium and Founder-Facilitated Speciation in Wild Populations of the Zebra Finch (Taeniopygia Guttata)

Article excerpt

ABSTRACT

The zebra finch has long been an important model system for the study of vocal learning, vocal production, and behavior. With the imminent sequencing of its genome, the zebra finch is now poised to become a model system for population genetics. Using a panel of 30 noncoding loci, we characterized patterns of polymorphism and divergence among wild zebra finch populations. Continental Australian populations displayed little population structure, exceptionally high levels of nucleotide diversity (π = 0.010), a rapid decay of linkage disequilibrium (LD), and a high population recombination rate (ρ [asymptotically =] 0.05), all of which suggest an open and fluid genomic background that could facilitate adaptive variation. By contrast, substantial divergence between the Australian and Lesser Sunda Island populations (K^sub ST^ = 0.193), reduced genetic diversity (π = 0.002), and higher levels of LD in the island population suggest a strong but relatively recent founder event, which may have contributed to speciation between these populations as envisioned under founder-effect speciation models. Consistent with this hypothesis, we find that under a simple quantitative genetic model both drift and selection could have contributed to the observed divergence in six quantitative traits. In both Australian and Lesser Sundas populations, diversity in Z-linked loci was significantly lower than in autosomal loci. Our analysis provides a quantitative framework for studying the role of selection and drift in shaping patterns of molecular evolution in the zebra finch genome.

THE zebra finch Taeniopygia guttata has long been a model system for studies of avian behavior and neurobiology (reviewed in Slater et al. 1988; Zann 1996). As an oscine passerine, or songbird, the zebra finch is part of a diverse clade composed of >4000 species (Raikow 1986; Edwards 1998; Barker et al. 2004) and is a member of the family Estrildidae, which itself includes 140 finch species distributed across Africa and Australasia (Goodwin 1982; Sorenson et al. 2004). The zebra finch has been of particular interest because songbirds, like humans, learn their vocalizations by imprinting on their parents (reviewed in Jarvis 2004). A number of parallels have already been discovered between the genetic underpinnings of vocal learning in humans and songbirds (e.g., Haesler et al. 2004; Teramitsu et al. 2004), and as genomic resources continue to develop, the zebra finch will only increase its importance as a model system for studies of neurobiology. With the production of bacterial artificial chromosome (BAC) libraries, cDNA microarrays (Naurin et al. 2008; Replogle et al. 2008), and the forthcoming complete genome sequence (Clayton et al. 2005), the zebra finch is now also a model system for genomics (Clayton 2004). Indeed, the first large-scale comparisons of orthologous genes in birds have been made possible through analysis of the chicken and zebra finch genomes (Ellegren 2007; Mank et al. 2007; Axelsson et al. 2008). The zebra finch genome will provide valuable insights into whether patterns observed in the chicken can be generalized across all birds or whether there are important differences among avian lineages, such as those that learn songs and those that do not.

Zebra finches are extremely common in the wild, frequenting habitats such as the cattle pastures, small towns, and homesteads of inland Australia. They are thus distributed across all of Australia with the exception of the extreme north and south of the continent (Figure 1). A second zebra finch subspecies, the Timor zebra finch T. guttata guttata (hereafter the "island" population), occurs on the Lesser Sunda Islands of southeast Asia, just north of Australia (Zann 1996). While the subspecies are well characterized behaviorally (Clayton 1990; Clayton et al. 1991), the history of the divergence between them is not well understood. Mayr (1944) analyzed a group of .40 bird species, including zebra finches, with ranges spanning Australia and the Lesser Sunda Islands. …

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