Cryptic diversity and biogeographical patterns within the black salamander (Aneides flavipunctatus) complex

Abstract

Aim Phylogeographical structure in the black salamander (Aneides flavipunctatus) was inferred using two independent genetic datasets. Concordance between the datasets was sought in order to evaluate earlier suggestions of species‐level breaks and evidence of vicariance and long‐term isolation within the complex. We hypothesized that major phylogeographical breaks would either correspond to current tectonic plate boundaries or to historical geological processes. Location North‐western California and southern Oregon (USA). Methods Three mitochondrial DNA (mtDNA) genes were sequenced for 240 black salamanders from 136 localities, and up to 13 nuclear DNA loci were sequenced for 145 black salamanders representing 93 localities. Phylogenetic analysis of our mitochondrial dataset was performed to recover major lineages, while spatial clustering analysis of our nuclear dataset was utilized to identify points of concordance with our mtDNA phylogeny. Levels of gene flow were estimated for all contact zones. Results Our mitochondrial phylogeny recovered four major lineages. Cluster analysis of our nuclear dataset is consistent with a four‐population scheme, with the boundaries matching those of the mtDNA lineages. Gene flow across a contact zone in southern Humboldt between two of the populational units is extremely limited (2Nm < 1). In what is identified as the Central Core population, two distinctive subpopulations were delineated based on nuclear data, but mitochondrial data are discordant. Main conclusions The Aneides flavipunctatus complex comprises at least four species‐level units. Two of the boundaries between these units are associated with current tectonic plate boundaries. The contact zone between our Northwest and Central Core populations lies adjacent to the Mendocino Triple Junction (MTJ), where the Humboldt and North American plates meet, while the area separating the Santa Cruz and Central Core populations corresponds to the boundary between the Pacific and Humboldt tectonic plates. The phylogeographical break within the Central Core population lies in a region in which uplift occurred that is associated with the historical position of the migrating MTJ.

Zoogeography of theSanAndreasFault system:GreatPacificFractureZones correspond with spatially concordant phylogeographic boundaries in westernNorthAmerica

“…In some cases, physical topography and oceanography may directly inhibit dispersal or promote vicariance. This has been demonstrated for sedentary species with narrow physiological limits that may only disperse tens of metres in their lifetimes, such as plethodontid salamanders that show sharp, deep genetic breaks at plate boundaries and appear to simply ride the plates as they migrate over the eons (Wake, ; Reilly & Wake, ). Even the planktonic larvae of many marine species may be physically unable to overcome strong prevailing offshore currents associated with prominent headlands, especially during periods of heavy upwelling (Kelly & Palumbi, ).…”

“…For this reason, this region has been referred to as the 'North Coast Divide' (Reilly, Marks & Jennings, 2012). Perhaps the most clear-cut example of a phylogeographic break associated with the MTJ occurs in the black salamander (Reilly & Wake, 2014). Genetic lineages north and south of the MTJ are strongly differentiated.…”

“…In other cases, the proximate mechanisms promoting divergence are hotly debated, especially for terrestrial taxa spanning the Transverse Ranges (Chatzimanolis & Caterino, 2007) and the mid-peninsular break of Baja California (Leaché, Crews & Hickerson, 2007). However, the phylogeography literature largely has not addressed the relationship between the GPFZs and biogeographic boundaries in North America (but see Cope, 2004;Reilly & Wake, 2014).…”

Cyto‐nuclear discordance suggests complex evolutionary history in the cave‐dwelling salamander, Eurycea lucifuga

“…Published information about the evolutionary history of other salamanders and other cave-dwelling species reveals some general phylogeographic patterns that shape our expectations. Many North American salamander species experienced ancient divergence from sister taxa, on the order of millions of years (Bonett and Chippindale 2004;Kozak et al 2006;Reilly and Wake 2014;Folt et al 2016), but in most species, intraspecific divergences reflect the impacts of climatic fluctuations throughout the Pleistocene (approximately 2.5 Ma-10 Ka; Church et al 2003;Herman and Bouzat 2015;Newman and Austin 2015). The evolutionary history of troglophilic salamanders tends to reflect these same patterns, for example, Hydromantes strinatii, a native to Southern Europe, experienced divergence among major lineages during the Pleistocene (Cimmaruta et al 2015).…”

“…Many North American salamander species experienced ancient divergence from sister taxa, on the order of millions of years (Bonett and Chippindale ; Kozak et al. ; Reilly and Wake ; Folt et al. ), but in most species, intraspecific divergences reflect the impacts of climatic fluctuations throughout the Pleistocene (approximately 2.5 Ma–10 Ka; Church et al.…”