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

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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.

No MeSH data available.


A species tree produced in *BEAST with a strict molecular clock, indicating divergence of the major lineages during the mid‐late Pleistocene. Bars on major splits represent the 95% CI of the age of that node, and posterior probabilities of major lineage divergences are represented on branch labels. Relationships at the tips were not well supported. Taxon labels reflect the number designation given to each population in Figure 1 and Table 1.
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ece32212-fig-0004: A species tree produced in *BEAST with a strict molecular clock, indicating divergence of the major lineages during the mid‐late Pleistocene. Bars on major splits represent the 95% CI of the age of that node, and posterior probabilities of major lineage divergences are represented on branch labels. Relationships at the tips were not well supported. Taxon labels reflect the number designation given to each population in Figure 1 and Table 1.

Mentions: All parameters of the *BEAST analysis, when viewed in Tracer, had ESS values much higher than 200, and the independent runs reached convergence. The species tree produced in *BEAST (Fig. 4) is very similar to those produced using traditional concatenation‐based methods, with the central region forming an outgroup to the eastern and western regions. However, in the species tree, the eastern and western regions are reciprocally monophyletic, whereas the concatenation trees feature the inclusion of the western clade within the eastern populations. Support for all three major clades is high in the species tree; however, support for the internode splitting the eastern and western clades is extremely low (0.43) indicating that there is significant ambiguity in this topology. Examination of the gene trees produced by running each locus individually in MrBayes and RaxML and the gene trees produced in *BEAST shows the majority of the signal in the concatenated and species trees is due to significant clustering from mitochondrial data. As in the concatenated trees, the topology of the species trees is very similar to the cytb and ND2 gene trees, while the POMC gene trees exhibit very little population or regional clustering, indicating that the species tree is largely representative of the mitochondrial history of this species.


Cyto ‐ nuclear discordance suggests complex evolutionary history in the cave ‐ dwelling salamander, E urycea lucifuga
A species tree produced in *BEAST with a strict molecular clock, indicating divergence of the major lineages during the mid‐late Pleistocene. Bars on major splits represent the 95% CI of the age of that node, and posterior probabilities of major lineage divergences are represented on branch labels. Relationships at the tips were not well supported. Taxon labels reflect the number designation given to each population in Figure 1 and Table 1.
© Copyright Policy - creativeCommonsBy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC5016636&req=5

ece32212-fig-0004: A species tree produced in *BEAST with a strict molecular clock, indicating divergence of the major lineages during the mid‐late Pleistocene. Bars on major splits represent the 95% CI of the age of that node, and posterior probabilities of major lineage divergences are represented on branch labels. Relationships at the tips were not well supported. Taxon labels reflect the number designation given to each population in Figure 1 and Table 1.
Mentions: All parameters of the *BEAST analysis, when viewed in Tracer, had ESS values much higher than 200, and the independent runs reached convergence. The species tree produced in *BEAST (Fig. 4) is very similar to those produced using traditional concatenation‐based methods, with the central region forming an outgroup to the eastern and western regions. However, in the species tree, the eastern and western regions are reciprocally monophyletic, whereas the concatenation trees feature the inclusion of the western clade within the eastern populations. Support for all three major clades is high in the species tree; however, support for the internode splitting the eastern and western clades is extremely low (0.43) indicating that there is significant ambiguity in this topology. Examination of the gene trees produced by running each locus individually in MrBayes and RaxML and the gene trees produced in *BEAST shows the majority of the signal in the concatenated and species trees is due to significant clustering from mitochondrial data. As in the concatenated trees, the topology of the species trees is very similar to the cytb and ND2 gene trees, while the POMC gene trees exhibit very little population or regional clustering, indicating that the species tree is largely representative of the mitochondrial history of this species.

View Article: PubMed Central - PubMed

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.

No MeSH data available.