Abstract
Phylogeographic inference has provided extensive insight into the relative roles of geographical isolation and ecological processes during evolutionary radiations. However, the importance of cross-lineage admixture in facilitating adaptive radiations is increasingly being recognised, and suggested as a main cause of phylogenetic uncertainty. In this study, we used a double digest RADseq protocol to provide a high resolution (~4 Million bp) nuclear phylogeny of the Delphininae. Phylogenetic resolution of this group has been especially intractable, likely because it has experienced a recent species radiation. We carried out cross-lineage reticulation analyses, and tested for several sources of potential bias in determining phylogenies from genome sampling data. We assessed the divergence time and historical demography of T. truncatus and T. aduncus by sequencing the T. aduncus genome and comparing it with the T. truncatus reference genome. Our results suggest monophyly for the genus Tursiops, with the recently proposed T. australis species falling within the T. aduncus lineage. We also show the presence of extensive cross-lineage gene flow between pelagic and European coastal ecotypes of T. truncatus, as well as in the early stages of diversification between spotted (Stenella frontalis; Stenella attenuata), spinner (Stenella longirostris), striped (Stenella coeruleoalba), common (Delphinus delphis), and Fraser’s (Lagenodelphis hosei) dolphins. Our study suggests that cross-lineage gene flow in this group has been more extensive and complex than previously thought. In the context of biogeography and local habitat dependence, these results improve our understanding of the evolutionary processes determining the history of this lineage.
Highlights
The family Delphinidae evolved during the Miocene (~5–20 Ma) through to the Quaternary
Our main objective is to draw inference from the evolutionary history of division and admixture in this lineage, to better understand the relevant eco-evolutionary processes driving their rapid species radiation. To accomplish this we aim to resolve the question of monophyly and lineage structure for the genus Tursiops using high resolution nuclear DNA sequence data, to improve our understanding of these phylogenetic relationships within the broader Delphininae, and to consider evidence for reticulate evolution influencing the pattern of evolutionary radiation for this group in the context of their biogeography and life history
Most missing data occurs on five samples: the two S. bredanensis samples used as an outgroup, one South African T. aduncus, one pelagic T. truncatus and the Pakistani T. aduncus samples
Summary
The family Delphinidae evolved during the Miocene (~5–20 Ma) through to the Quaternary (since ~3 Ma; e.g. Eisenberg, 1983). Beltrán et al, 2002; Joyce et al, 2011; McGowen, 2011; Kozak et al, 2015), especially with respect to the accurate determination of branching order, where different markers typically show inconsistency in the phylogenetic signal (Gatesy et al, 1999; Degnan and Rosenberg, 2009). Due to the large number of sites scattered across the genome, these reconstructions present many challenges regarding the choice of appropriate evolutionary models and partitioning schemes They can produce high resolution phylogenetic trees that avoid the bias of single gene trees typical of mtDNA analyses (Wagner et al, 2012; Malinsky et al, 2015; Moura et al, 2015). They can provide insights into the possibility of reticulate evolution and lead to improved phylogeographic inferences and clarification of evolutionary histories (Eaton and Ree, 2013)
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