Multilocus phylogeographic assessment of the California Mountain Kingsnake (Lampropeltis zonata) suggests alternative patterns of diversification for the California Floristic Province

Abstract

Phylogeographic inference can determine the timing of population divergence, historical demographic processes, patterns of migration, and when extended to multiple species, the history of communities. Single-locus analyses can mislead interpretations of the evolutionary history of taxa and comparative analyses. It is therefore important to revisit previous single-locus phylogeographic studies, particularly those that have been used to propose general patterns for regional biotas and the processes responsible for generating inferred patterns. Here, we employ a multilocus statistical approach to re-examine the phylogeography of Lampropeltis zonata. Using nonparametic and Bayesian species delimitation, we determined that there are two well-supported species within L. zonata. Ecological niche modelling supports the delimitation of these taxa, suggesting that the two species inhabit distinct climatic environments. Gene flow between the two taxa is low and appears to occur unidirectionally. Further, our data suggest that gene flow was mediated by females, a rare pattern in snakes. In contrast to previous analyses, we determined that the divergence between the two lineages occurred in the late Pliocene (c. 2.07 Ma). Spatially and temporally, the divergence of these lineages is associated with the inundation of central California by the Monterey Bay. The effective population sizes of the two species appear to have been unaffected by Pleistocene glaciation. Our increased sampling of loci for L. zonata, combined with previously published multilocus analyses of other sympatric species, suggests that previous conclusions reached by comparative phylogeographic studies conducted within the California Floristic Province should be reassessed.

Both traits and phylogenetic history influence community structure in snakes over steep environmental gradients

“…As noted by Mayfield and Levine (2010), it is possible that competition will not produce an even or diverged distribution of traits in communities, but rather yield single directional trends (clumped) as species compete for similar recourses. Third, the continued delimitation of species in this region , Myers et al 2013, Ruane et al 2014) and the use of species trees may have important effects on downstream phylogenetic community analyses as has been shown in comparative phylogenetic studies (Burbrink and Pyron 2011). Causes for latitudinal gradients have been discussed in detail elsewhere (Rohde and Heap 1998, Willig et al 2003, Kozak and Wiens 2007, Pyron and Burbrink 2009b but generally fall into categories of ecological (dispersal and survival is limited at northern latitudes), evolutionary (speciation is higher at lower latitudes or extinction is greater at higher latitudes), or biogeographic (southern regions were occupied earlier or more often; Willig et al 2003, Mittelbach et al 2007.…”

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

“…4a) and climatic conditions connecting the two regions may have been more suitable at that time. The pattern of a trans-valley leak from the Coast Ranges to the central Sierra Nevada across the Central Valley has been observed in many other species including Batrachoseps attenuatus [7], Ensatina eschscholtzii xanthoptica [6], Contia tenuis [10], Lampropeltis zonata [47], and California Turret Spiders [66].…”

Gene Flow Results in High Genetic Similarity between Sibiraea (Rosaceae) Species in the Qinghai-Tibetan Plateau

“…Genetic differentiation between distinct lineages can be quickly and easily determined by DNA fragment sequences (e.g., DNA barcodes) for multiple individuals (Mallet, 1995). Although, DNA fragment sequences revealed numerous cryptic species lacking morphological differentiation in both animals and plants (Myers et al, 2013; Su et al, 2015), they sometimes fail when groups are closely related species, let alone evolutionary complex. At present, simple sequence repeats (SSR) are widely used to characterize divergence among closely related species (e.g., Surget-Groba and Kay, 2013; Yan et al, 2015; Duncan et al, 2016).…”