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

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 (p ¼ 0.010), a rapid decay of linkage disequilibrium (LD), and a high population recombination rate (r % 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 ST ¼ 0.193), reduced genetic diversity (p ¼ 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.

Z chromosome divergence, polymorphism and relative effective population size in a genus of lekking birds

“…This ratio should theoretically reduce π Z /π A or θ Z /θ A below 0.75 in species with unequal reproductive success between males and females such as sage-grouse. Indeed, diversity ratios well below 0.75 have been reported in many birds with varying degrees of reproductive skew Borge et al, 2005;Balakrishnan and Edwards, 2009;Huynh et al, 2010;Corl and Ellegren, 2012;Hogner et al, 2012).…”

Towards modelling persistence of woodland birds: the role of genetics

“…To test whether genetic drift could explain the morphological divergence observed between Zebra Finch (Taeniopygia guttata) subspecies, Lande's N e * statistic (an estimate of the genetic population size at which drift alone would explain the observed morphological divergence) was assessed alongside estimates of neutral marker and morphological divergence (Balakrishnan and Edwards 2009). Natural selection on traits, not just drift, was inferred to have been important during the ca.…”

“…For example, Balakrishnan and Edwards (2009) reconstructed the history of divergence and demography between subspecies of Zebra Finches. They concluded that both subspecies have experienced population growth during and since divergence, with non-zero but very low gene flow between them, more from the mainland to islands than vice versa.…”

Chromosomal patterns of diversity and differentiation in creepers: a next-gen phylogeographic investigation of Certhia americana

“…More broadly, birds tend to exhibit increased differentiation and reduced genetic diversity on the Z chromosome relative to autosomes (Carling and Brumfield, 2008;Balakrishnan and Edwards, 2009;Ellegren et al, 2012;Rheindt et al, 2013). This may be expected if there are genetic regions under selection on the Z chromosome (for example, to reduce expression of recessive alleles in hemizygous individuals); however, if lineages are diverging largely by genetic drift, the Z chromosome may simply act like a macrochromosome (albeit with a smaller effective population size).…”