Molecular systematics of Batrachoseps (Caudata, Plethodontidae) in southern California and Baja California: Mitochondrial-nuclear DNA discordance and the evolutionary history of B. major

Abstract

Inferences about species boundaries and evolutionary history are often complicated by discordance between datasets. In recent times, considerable effort has been devoted to understanding the causes of discordance between the patterns of genetic variation and structure shown by different unlinked molecular markers. The genus Batrachoseps (Caudata, Plethodontidae), the most diverse group of salamanders in western North America, is characterized by limited morphological variation and discordance between molecular datasets, making it a challenging group for taxonomists but also a good model to test newly developed analytical methods to sort out possible sources of discordance. In this study, we present a comprehensive assessment of the evolutionary history of B. major, one of the most widespread species in the genus, based on extensive sampling and phylogenetic and coalescent analyses of data from mitochondrial and nuclear markers. We found non-monophyly of mtDNA in B. major, with two lineages (northern and southern) that are more closely related to other species in the genus than to each other, but this division was not apparent in nuclear DNA. Despite non-monophyly in gene trees, species tree analyses recovered a sister group relationship between the two lineages of B. major, and coalescent simulations suggested that there is no need to invoke gene flow to account for the discordance across gene trees. The possibility that these two lineages represent sister, cryptic taxa, is discussed in the context of Bayesian methods of species/lineage delineation. Contrary to prior expectations, B. major has experienced extensive diversification on the Baja California Peninsula, where four endemic lineages have persisted for at least 4 million years.

Hydrologic and geologic history of the Ozark Plateau drive phylogenomic patterns in a cave‐obligate salamander

“…Furthermore, genetic distances among clades (10.6% mtDNA, 1.1% nucDNA) are greater than other salamanders recognized as distinct species (e.g. Baird et al., ; Martínez‐Solano et al., ; Parra‐Olea, García‐París & Wake, ). Caution is needed when delimiting species based on the multispecies coalescent (Sukumaran & Knowles, ), however, support for strong levels of genetic isolation, mito‐nuclear concordance and deeper divergences than other plethodontids recognized as distinct species.…”

Range‐wide phylogeography of the four‐toed salamander: out of Appalachia and into the glacial aftermath

“…A cautionary statement regarding the limitations of using phylogenies based solely on mitochondrial DNA may be warranted, as Edwards & Bensch () and Towes & Brelsford () emphasized that phylogenetic discordance between mitochondrial and nuclear markers may be an important phenomenon. For example, mito‐nuclear discordance has been reported in other Plethodontid salamanders of the genus Batrachoseps (Martínez‐Solano et al ., ). Discordance in this and other taxa may arise as a result of incomplete lineage sorting in nuclear DNA, or due to demographic asymmetries such as sex‐biased dispersal and hybridization, in addition to secondary contact events (Towes & Brelsford, ).…”

New species in the Sitalcina sura species group (Opiliones, Laniatores, Phalangodidae), with evidence for a biogeographic link between California desert canyons and Arizona sky islands

“…Despite this fact, we have found relatively few animal taxa that show biogeographic patterns similar to those observed in Sitalcina . Salamanders in the Batrachoseps pacificus group have a distribution much like the coastal clade (from Monterey south to northern Baja, almost all populations restricted to Pacific plate, Jockusch et al 2014), and the group includes isolated southern California desert populations, but these populations have apparent western ancestry (Martínez-Solano et al 2012,). Aptostichus trapdoor spiders include many California coastal, California desert canyon, and Arizona sky island species (Bond 2012), but phylogenetic details remain uncertain.…”