Resolving higher-level phylogenetic networks with repeated hybridization in a complex of polytypic salamanders (Plethodontidae: Desmognathus)


Repeated hybridization between newly forming lineages is a common feature of ecological speciation and ecomorphological diversification. However, computational constraints currently limit our ability to reconstruct network radiations from gene-tree data. Available methods are limited to level-1 networks wherein reticulations do not share edges, and higher-level networks may be non-identifiable in many cases. We present a heuristic method for recovering information from higher-level networks across a range of potentially identifiable empirical scenarios, supported by a theorem and success in simulated data. When extrinsic data are available indicating recent or ancestral hybridization events, the method we propose can yield successful estimates of non-level-1 networks, or at least a reduced possible set thereof. We apply this technique to the Pisgah clade of Desmognathus salamanders, which contains four to seven species exhibiting two discrete phenotypes, aquatic "Shovel-nosed" and semi-aquatic "Black-bellied" forms. Phylogenomic data strongly support a single backbone topology with up to five distinct, overlapping hybrid edges. These reticulations suggest an unusual mechanism of ecomorphological hybrid speciation, wherein a binary threshold trait causes hybrid lineages to shift between two microhabitat niches, promoting ecological divergence between syntopic hybrids and parentals. This contrasts with other well-known systems in which hybrids exhibit intermediate, novel, or transgressive phenotypes. Adjacent populations of both phenotypes exhibit admixture and backcrossing, and at least two Black-bellied lineages have been produced via reticulations between Shovel-nosed parentals, suggesting complex transmission dynamics across multiple hybridization events. The genetic basis of these phenotypes is unclear and further data are needed to clarify the nature of selection and speciation in the group.

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