Speciation genomics and a role for the Z chromosome in the early stages of divergence between Mexican ducks and mallards

Abstract

Speciation is a continuous and dynamic process, and studying organisms during the early stages of this process can aid in identifying speciation mechanisms. The mallard (Anas platyrhynchos) and Mexican duck (A. [p.] diazi) are two recently diverged taxa with a history of hybridization and controversial taxonomy. To understand their evolutionary history, we conducted genomic scans to characterize patterns of genetic diversity and divergence across the mitochondrial DNA (mtDNA) control region, 3523 autosomal loci and 172 Z-linked sex chromosome loci. Between the two taxa, Z-linked loci (ΦST = 0.088) were 5.2 times more differentiated than autosomal DNA (ΦST = 0.017) but comparable to mtDNA (ΦST = 0.092). This elevated Z differentiation deviated from neutral expectations inferred from simulated data that incorporated demographic history and differences in effective population sizes between marker types. Furthermore, 3% of Z-linked loci, compared to <0.1% of autosomal loci, were detected as outlier loci under divergent selection with elevated relative (ΦST ) and absolute (dXY ) estimates of divergence. In contrast, the ratio of Z-linked and autosomal differentiation among the seven Mexican duck sampling locations was close to 1:1 (ΦST = 0.018 for both markers). We conclude that between mallards and Mexican ducks, divergence at autosomal markers is largely neutral, whereas greater divergence on the Z chromosome (or some portions thereof) is likely the product of selection that has been important in speciation. Our results contribute to a growing body of literature indicating elevated divergence on the Z chromosome and its likely importance in avian speciation.

Old divergence and restricted gene flow between torrent duck (Merganetta armata) subspecies in the Central and Southern Andes

“…In fact, torrent ducks from Peru had values of mtDNA diversity more similar to those found in other ducks with Ne several orders of magnitude larger Ne (e.g., mallards; Lavretsky et al, 2015). In contrast to mtDNA, diversity estimates from nuclear DNA for the two torrent duck subspecies were lower compared to other waterfowl species (Lavretsky et al, 2015;Lavretsky et al, 2016;Peters et al, 2016;Wilson et al, 2012). In contrast to mtDNA, diversity estimates from nuclear DNA for the two torrent duck subspecies were lower compared to other waterfowl species (Lavretsky et al, 2015;Lavretsky et al, 2016;Peters et al, 2016;Wilson et al, 2012).…”

Migration-Selection Balance Drives Genetic Differentiation in Genes Associated with High-Altitude Function in the Speckled Teal (Anas flavirostris) in the Andes

“…Putative chromosomal locations of each of the autosomal categorized clusters were also identified; although we focus primarily on the Z-chromosome versus autosome comparison due to the tendency for sex chromosomes to house genes related to sexual selection, reproductive isolation, and speciation (Ellegren 2009; Ellegren et al. 2012; Lavretsky et al 2015). …”

“…2011; Martin et al. 2013; Lavretsky et al. 2015), chromosomal inversions, or “supergenes” (Kirkpatrick and Barton 2006; Thompson and Jiggins 2014), and a variety of other genes associated with adaptation to extreme environments (Chapman et al.…”

Crossing species boundaries : the hybrid histories of the true geese

“…Whole genome analyses have recently been used to unravel the phylogenetic relations between the major bird orders (Jarvis et al, 2014, Prum et al, 2015, but our study presents one of the first phylogenomic analyses of a group of closely related bird species (DaCosta andSorenson, 2016, Nater et al, 2015). As both concatenation and consensus methods resulted in the same topology and all nodes on the concatenation tree are supported by high bootstrap values, it is likely that the resulting phylogeny closely approaches the actual species tree for the Anserini.…”

“…A similar hub-species in the Order Anseriformes is the Mallard (Anas platyrhynchos), which has hybridized with at least 39 different species (Figure 9.2). In contrast to the Common Pheasant, several of the hybrid interactions of the Mallard have been studied in greater detail, specifically with closely related species, such as the Black Duck (Anas superciliosa) in Australia and New Zealand (Taysom et al, 2014), the Hawaiian Duck (Anas wylvilliana) on the Hawaiian Islands (Fowler et al, 2009), the American Black Duck (Anas rubripes) and the Mottled Duck (Anas fulvigula) in North America (Mank et al, 2004, Peters et al, 2014a, the Spot-billed Duck (Anas zonorhyncha) in Russia (Kulikova et al, 2004) and the Mexican Duck (Anas diazi) in Mexico (Lavretsky et al, 2015a). Step 2: Quantifying Gene Flow Based on the hybrid network, hypotheses regarding recent and ancient gene flow can be formulated and tested for particular species pairs.…”