NUCLEAR LOCI AND COALESCENT METHODS SUPPORT ANCIENT HYBRIDIZATION AS CAUSE OF MITOCHONDRIAL PARAPHYLY BETWEEN GADWALL AND FALCATED DUCK (ANASSPP.)

Abstract

Many species have mitochondrial DNA lineages that are phylogenetically intermixed with other species, but studies have rarely tested the cause of such paraphyly. In this study, we tested two hypotheses that could explain mitochondrial paraphyly of Holarctic gadwalls (Anas strepera) with respect to Asian falcated ducks (A. falcata). First, hybridization could have resulted in falcated duck mitochondrial DNA (mtDNA) introgressing into the gadwall gene pool. Second, gadwalls and falcated ducks could have diverged so recently that mtDNA lineages have not sorted to reciprocal monophyly. We used coalescent analyses of three independent loci to distinguish between these two hypotheses. Two lines of evidence support introgression. First, analyses of the three loci combined show that some introgression is necessary to explain current genetic diversity in gadwalls. Second, we generated alternative predictions regarding time since divergence estimated from mtDNA: falcated ducks and gadwalls would have diverged between 65,000 and 700,000 years before present (ybp) under the introgression hypothesis and between 11,000 and 76,000 ybp under the incomplete lineage sorting hypothesis. The two independent nuclear introns indicated that these species diverged between 210,000 and 5,200,000 ybp, which did not overlap the predicted time for incomplete lineage sorting. These analyses also suggested that ancient introgression (∼14,000 ybp) has resulted in the widespread distribution and high frequency of falcated-like mtDNA (5.5% of haplotypes) in North America. This is the first study to use a rigorous quantitative framework to reject incomplete lineage sorting as the cause of mitochondrial paraphyly.

Phylogeography: its development and impact in Australo-Papuan ornithology with special reference to paraphyly in Australian birds

“…Thus, the key output of IM, in Bayesian parlance, is credibility intervals for each parameter -the 90% highest posterior densities (HPDs). Joseph et al (in press) apply this to paraphyly among Grey and Chestnut Teal and conclude that ILS is the more likely explanation of the data (see non-Australian example in Peters et al 2007). More generally, multiple loci and rigorous coalescent methods can help understand paraphyly and a wide range of other topics in phylogeography and recent speciation.…”

“…This work is underway using an expanded sample of luteus that has since been collected (n = 6 in earlier studies), more dense geographical sampling (especially near the western contact zone between the species), multiple loci, and currently available analytical methods especially coalescent approaches. Rigorous statistical analyses are needed to reject the possibility of ILS (Peters et al 2007;see below). We now review how ILS occurs and provide likely Australian examples.…”

Introgression as a likely cause of mtDNA paraphyly in two allopatric skippers (Lepidoptera: Hesperiidae)

“…Although a rigorous statistical framework is generally required to distinguish ILS from introgression (Peters et al, 2007), three main approaches have been commonly used to delineate the competing hypotheses when the requirements for a statistical test cannot be met (for example, due to limited sample size). First, examination of mtDNA tree topology serves as a heuristic method to reveal the cause of paraphyly (Baker et al, 2003).…”

“…Owing to the lack of recombination (but see Slate and Phua, 2003;Rokas et al, 2003), mtDNA genes are inherited as a single linkage group, but the mitochondrial genome does not necessarily reflect the entirety of a species' evolution or population history (Ballard and Whitlock, 2004). Examples for such exceptions include paralog gene evolution due to the appearance of nuclear pseudogenes with mitochondrial origin (Bensasson et al, 2001;Thalmann et al, 2004); the finding that mtDNA may not evolve in a pattern consistent with a strictly neutral equilibrium model because mtDNA variation influences organismal fitness (Ballard and Rand, 2005); and many species have mtDNA lineages that are phylogenetically intermixed with other species (Wahlberg et al, 2003;Peters et al, 2007).…”

East–west genetic differentiation in Musk Ducks (Biziura lobata) of Australia suggests late Pleistocene divergence at the Nullarbor Plain

“…We sequenced both 205 strands of the mtDNA, but nuclear introns were only sequenced in one direction 206 unless the individual was found to be heterozygous for an insertion/deletion (indel), in 207 which case both strands were sequenced to resolve the indel (e.g. Peters et al 2007). 208 209 We sequenced 652bp from the 5' end of the mtDNA control region of birds collected 210 for this study and 373bp from most recent samples obtained from museum study 211 skins.…”