Biogeographic barriers, Pleistocene refugia, and climatic gradients in the southeastern Nearctic drive diversification in cornsnakes (Pantherophis guttatus complex)

Abstract

The southeastern Nearctic is a biodiversity hotspot that is also rich in cryptic species. Numerous hypotheses (e.g., vicariance, local adaptation, and Pleistocene speciation in glacial refugia) have been tested in an attempt to explain diversification and the observed pattern of extant biodiversity. However, previous phylogeographic studies have both supported and refuted these hypotheses. Therefore, while data support one or more of these diversification hypotheses, it is likely that taxa are forming within this region in species‐specific ways. Here, we generate a genomic data set for the cornsnakes (Pantherophis guttatus complex), which are widespread across this region, spanning both biogeographic barriers and climatic gradients. We use phylogeographic model selection combined with hindcast ecological niche models to determine regions of habitat stability through time. This combined approach suggests that numerous drivers of population differentiation explain the current diversity of this group of snakes. The Mississippi River caused initial speciation in this species complex, with more recent divergence events linked to adaptations to ecological heterogeneity and allopatric Pleistocene refugia. Lastly, we discuss the taxonomy of this group and suggest there may be additional cryptic species in need of formal recognition.

Resolving spatial complexities of hybridization in the context of the gray zone of speciation in North American ratsnakes (Pantherophis obsoletuscomplex)

“…These results are consistent with previous mtDNA and morphological conclusions Burbrink et al, 2000). The Mississippi River has served as a strong barrier to gene flow given evidence from historical estimates of increased drainage (Cox et al 2014) and numerous unrelated organisms show genetic disconnection across the river (Robison 1986;Burbrink 2002;Soltis et al 2006;Burbrink et al 2008;Pyron and Burbrink 2009;Brandley et al 2010;Satler and Carstens 2017;Myers et al 2020). Hybridization, while low (1-2 individuals/generation, Fig.3), does occur in a zone (~100km) east of the Mississippi River between the central lineages (P. obsoletus and P. spiloides).…”

“…We used regression-based ANN to determine which variables predict genetic distances and rank those with the highest model importance. To conduct the ANN regressions we used the R package caret (Kuhn 2008) and partitioned the data into the standard 70% training and 30% test sets (Lek et al 1996;Zhang 2010;Burbrink et al 2020). This analysis was run using 1,000 maximum iterations to ensure convergence.…”

“…Lineages within species complexes ranging across heterogeneous landscapes are likely at different stages of the speciation process. These differences may reflect how specific environmental and biogeographic barriers have uniquely altered changes in gene flow and other demographic processes in a particular complex (Myers et al 2020). Even at the same barrier within related groups of organisms, the timing of divergence and degree of gene flow can be species specific and dependent on when they encountered the barrier (Riddle 2016;Myers et al 2019b).…”

“…This complex is a wide-ranging group of four species found throughout the forested regions of the Eastern Nearctic and nearby Chihuahuan Desert that have diverged at three unique biogeographic barriers. The primary divergence in this complex occurred at the Mississippi River, which has consistently been identified as one of the main biogeographic barriers in the ENA (Robison 1986;Burbrink et al 2000;Soltis et al 2006;Brandley et al 2010;Zellmer et al 2012;Myers et al 2020). Further east, the Appalachian Mountains and Apalachicola/Chattahoochee River System (AARS) have noted barrier effects in other organisms and likely contributed to the divergence between P. alleghaniensis and P. spiloides (Walker and Avise 1998;Burbrink et al 2000;Soltis et al 2006).…”

Reticulate Evolutionary History in a Recent Radiation of Montane Grasshoppers Revealed by Genomic Data

“…The Iberian Peninsula and western Maghreb regions present a rich biodiversity and an alike species composition due to their close geographical proximity, similar climatic and ecological conditions, complex topography, and a geological history that has led to multiple episodes of connectivity and isolation for terrestrial biotas distributed in the two continents (Blondel and Aronson 2002; Krijgsman 2002; Meulenkamp and Sissingh 2003). As a result, this region is an important center of diversification for numerous organism groups and considered a hotspot for animal and plant biodiversity (Rodríguez-Sánchez et al 2008; Myers et al 2020). The re-opening of the Strait of Gibraltar at the beginning of the Pliocene led to the loss of the last intercontinental land connection stablished during the desiccation of the Mediterranean Basin in the Messinian Salinity Crisis (Krijgsman 2002; Husemann et al 2014), a phenomenon representing the starting point for the diversification of many lineages whose distributional ranges resulted fragmented under the new geographic setting (e.g., Veith et al 2003; Faille et al 2014).…”