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

Abstract

Our understanding of the evolutionary history and ecology of cave‐associated species has been driven historically by studies of morphologically adapted cave‐restricted species. Our understanding of the evolutionary history and ecology of nonrestricted cave species, troglophiles, is limited to a few studies, which present differing accounts of troglophiles’ relationship with the cave habitat, and its impact on population dynamics. Here, we used phylogenetics, demographic statistics, and population genetic methods to study lineage divergence, dates of divergence, and population structure in the Cave Salamander, Eurycea lucifuga, across its range. In order to perform these analyses, we sampled 233 individuals from 49 populations, using sequence data from three gene loci as well as genotyping data from 19 newly designed microsatellite markers. We find, as in many other species studied in a phylogeographic context, discordance between patterns inferred from mitochondrial relationships and those inferred by nuclear markers indicating a complicated evolutionary history in this species. Our results suggest Pleistocene‐based divergence among three main lineages within E. lucifuga corresponding to the western, central, and eastern regions of the range, similar to patterns seen in species separated in multiple refugia during climatic shifts. The conflict between mitochondrial and nuclear patterns is consistent with what we would expect from secondary contact between regional populations following expansion from multiple refugia.

Phylogeographic diversification and postglacial range dynamics shed light on the conservation of the kelp Saccharina japonica

“…In contrast, the analyses based on microsatellite data revealed two genetic groups with admixed populations and only 16.5% of the nuclear variance occurred among groups, which is indicative of high levels of mitochondrial genetic structure in the absence of significant nuclear structure in S. japonica . Such “mito‐nuclear” discordance is common in secondary contact zones (Bonnet, Leblois, Rousset, & Crochet, ; Edgington, Ingram, & Taylor, ; Fontenot, Makowsky, & Chippindale, ; Toews & Brelsford, ). We suspect that this phenomenon could be caused by the different introgression degrees observed for the mitochondrial and nuclear markers (e.g., Neiva, Pearson, Valero, & Serrão, ).…”

Genetic Analysis of a Cryptic Contact Zone between Mitochondrial Clades of the Eastern Red-Backed Salamander, Plethodon cinereus

“…Alternatively, the phylogeographic break may reflect ancient allopatry succeeded by secondary contact and lineage merger, in which the microsatellite cline is far wider than our sampling and so not detectable. Some studies have posited that mtDNA can reflect historical processes, such as divergence in multiple refugia or past introgression, whereas nuclear markers more closely track the current demographic dynamics (Jockusch and Wake, 2002;Weisrock et al, 2005;Edgington et al, 2016). Further, by not selecting loci a priori with known clade-specific alleles (e.g., Alexandrino et al, 2005;Kuchta, 2007), we may not have been able to recover a subtle nuclear cline within our transect, although INTROGRESS suggests that none of our 10 loci are consistent with a cline or secondary contact.…”

Where can introduced populations learn their tricks? Searching for the geographical source of a species introduction to the Galápagos archipelago

“…The potential drawbacks of phylogeographic inference from mtDNA alone are well known (Flanders et al 2009), but in combination with nuclear markers, the data can provide valuable understanding of a species' evolutionary trajectory (Lefebvre et al 2016;Mende et al 2016). In particular, it has been suggested that mitochondrial loci might reflect a more ancient evolutionary history (Edgington et al 2016).…”