Robbery in progress: Historical museum collections bring to light a mitochondrial capture within a bird species widespread across southern Australia, the Copperback Quail‐thrush Cinclosoma clarum

Abstract

We surveyed mitochondrial, autosomal, and Z chromosome diversity within and between the Copperback Quail‐thrush Cinclosoma clarum and Chestnut Quail‐thrush C. castanotum, which together span the arid and semi‐arid zones of southern Australia, and primarily from specimens held in museum collections. We affirm the recent taxonomic separation of the two species and then focus on diversity within the more widespread of the two species, C. clarum. To guide further study of the system and what it offers to understanding the genomics of the differentiation and speciation processes, we develop and present a hypothesis to explain mitonuclear discordance that emerged in ourdata. Following a period of historical allopatry, secondary contact has resulted in an eastern mitochondrial genome replacing the western mitochondrial genome in western populations. This is predicted under a population‐level invasion in the opposite direction, that of the western population invading the range of the eastern one. Mitochondrial captures can be driven by neutral, demographic processes, or adaptive mechanisms, and we favor the hypothesized capture being driven by neutral means. We cannot fully reject the adaptive process but suggest how these alternatives may be further tested. We acknowledge an alternative hypothesis, which finds some support in phenotypic data published elsewhere, namely that outcomes of secondary contact have been more complex than our current genomic data suggest. Discriminating and reconciling these two alternative hypotheses, which may not be mutually exclusive, could be tested with closer sampling at levels of population, individual, and nucleotide than has so far been possible. This would be further aided by knowledge of the genetic basis to phenotypic variation described elsewhere.

Sustained plumage divergence despite weak genomic differentiation and broad sympatry in sister species of Australian woodswallows (Artamus spp.)

“…This is likely why we failed to detect population structure. The higher migration rate from white-browed into masked woodswallow is consistent with a scenario where the range of the masked woodswallow invaded the white-browed’s range thereby retaining more of the native species’ alleles in the invading species’ genome (Joseph et al, 2006; McElroy et al, 2020; Rheindt & Edwards, 2011). This contrasts with the scenario where alleles of the population with the lower effective population size (i.e., white-browed woodswallow) are purged due to high deleterious load (Moran et al, 2021).…”

Sustained plumage divergence despite weak genomic differentiation and broad sympatry in sister species of Australian woodswallows (Artamus spp.)

“…This scenario is not unlike another Australian arid‐adapted species, the butcherbirds Cracticus spp, which experienced range expansion and secondary contact during the LGM (Kearns et al, 2014). The higher migration rate from white‐browed into masked woodswallow is consistent with a scenario where the masked woodswallow invaded the white‐browed's range thereby retaining more of the native species' alleles in the invading species' genome (Joseph et al, 2006; McElroy et al, 2020; Rheindt & Edwards, 2011). This contrasts with the scenario where alleles of the population with the lower effective population size are purged due to high deleterious load (Moran et al, 2021) as both species have similarly large population sizes.…”

Power of Bayesian and Heuristic Tests to Detect Cross-Species Introgression with Reference to Gene Flow in the Tamias quadrivittatus Group of North American Chipmunks

“…Given the extensive mitochondrial introgression in the Tamias group (Sullivan et al, 2014;Sarver et al, 2017Sarver et al, , 2021, introgression affecting the nuclear genome was expected, and the failure to detect any significant evidence for it in the HyDe analysis was surprising (Sarver et al, 2021). Sarver et al (2021) discussed the evidence for cytonuclear discordance in the pattern of introgression (Bonnet et al, 2017;McElroy et al, 2020;Sarver et al, 2021), as well as possible roles of purifying selection affecting the coding genes or exons that make up the nuclear dataset being analyzed. Our results suggest a simpler explanation, that gene flow in the Tamias group is of a wrong type or in the wrong direction, undetectable by HyDe.…”