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Journal of Heredity Advance Access originally published online on September 4, 2008
Journal of Heredity 2009 100(2):125-136; doi:10.1093/jhered/esn065
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© The American Genetic Association. 2008. All rights reserved. For permissions, please email: journals.permissions@oxfordjournals.org.

Recombination and Nucleotide Diversity in the Sex Chromosomal Pseudoautosomal Region of the Emu, Dromaius novaehollandiae

Daniel E. Janes, Tariq Ezaz, Jennifer A. Marshall Graves, and Scott V. Edwards

Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138 (Janes and Edwards); and Comparative Genomics Group, Research School of Biological Sciences, Australian National University, PO Box 475, Canberra, ACT 2601, Australia (Ezaz and Marshall Graves)

Address correspondence to D. E. Janes at the address above, or e-mail: djanes{at}oeb.harvard.edu.

Pseudoautosomal regions (PARs) shared by avian Z and W sex chromosomes are typically small homologous regions within which recombination still occurs and are hypothesized to share the properties of autosomes. We capitalized on the unusual structure of the sex chromosomes of emus, Dromaius novaehollandiae, which consist almost entirely of PAR shared by both sex chromosomes, to test this hypothesis. We compared recombination, linkage disequilibrium (LD), GC content, and nucleotide diversity between pseudoautosomal and autosomal loci derived from 11 emu bacterial artificial chromosome (BAC) clones that were mapped to chromosomes by fluorescent in situ hybridization. Nucleotide diversity ({pi} = 4Neµ) was not significantly lower in pseudoautosomal loci (14 loci, 1.9 ± 2.4 x 10–3) than autosomal loci (8 loci, 4.2 ± 6.1 x 10–3). By contrast, recombination per site within BAC-end sequences ({rho} = 4Nc) (pseudoautosomal, 3.9 ± 6.9 x 10–2; autosomal, 2.3 ± 3.7 x 10–2) was higher and average LD (D') (pseudoautosomal, 4.2 ± 0.2 x 10–1; autosomal, 4.7 ± 0.5 x 10–1) slightly lower in pseudoautosomal sequences. We also report evidence of deviation from a simple neutral model in the PAR and in autosomal loci, possibly caused by departures from demographic equilibrium, such as population growth. This study provides a snapshot of the population genetics of avian sex chromosomes at an early stage of differentiation.

Key Words: bacterial artificial chromosomes • fluorescent in situ hybridization • nucleotide diversity • pseudoautosomal region • recombination • sex chromosomes

Corresponding Editor: David Burt

Received April 21, 2008
Accepted July 25, 2008


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