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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.


Bayesian phylogeny inferred from the concatenated sequence data of cytb, ND2 and POMC using MrBayes. Pseudotriton ruber was included as an outgroup, but is not shown here for ease of visualization. Posterior support values above 0.5 are shown above, and maximum‐likelihood bootstraps above 50 are shown below branches. Colors correspond to the regions from which samples were collected, as seen in Figure 1.
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ece32212-fig-0003: Bayesian phylogeny inferred from the concatenated sequence data of cytb, ND2 and POMC using MrBayes. Pseudotriton ruber was included as an outgroup, but is not shown here for ease of visualization. Posterior support values above 0.5 are shown above, and maximum‐likelihood bootstraps above 50 are shown below branches. Colors correspond to the regions from which samples were collected, as seen in Figure 1.

Mentions: The ML and Bayesian concatenated trees both recover two well‐supported major clades organized by geographic region; the topologies are very similar with only minor rearrangements within major clades, and therefore, we present here the Bayesian tree with ML bootstrap values shown (Fig. 3). The central clade contains populations in western Tennessee and Indiana, and the eastern/western clade contains the populations within Virginia, West Virginia, eastern Tennessee, Oklahoma, and Missouri. The western populations form a monophyletic clade within the eastern populations. Haplotypes were shared among populations within the major geographic regions; however, support at the tips was very low. Relationships among the clades differ from simple geographic expectations: the western and eastern regions are more closely related to each other than either is to the central clade. Gene trees of individual loci (Figures S1–3, Supporting Information) generally reflect these relationships, although the nuclear locus POMC did not have a large influence on the topology, and as a result, the combined trees generally represent the mitochondrial history of the species.


Cyto ‐ nuclear discordance suggests complex evolutionary history in the cave ‐ dwelling salamander, E urycea lucifuga
Bayesian phylogeny inferred from the concatenated sequence data of cytb, ND2 and POMC using MrBayes. Pseudotriton ruber was included as an outgroup, but is not shown here for ease of visualization. Posterior support values above 0.5 are shown above, and maximum‐likelihood bootstraps above 50 are shown below branches. Colors correspond to the regions from which samples were collected, as seen in Figure 1.
© Copyright Policy - creativeCommonsBy
Related In: Results  -  Collection

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

ece32212-fig-0003: Bayesian phylogeny inferred from the concatenated sequence data of cytb, ND2 and POMC using MrBayes. Pseudotriton ruber was included as an outgroup, but is not shown here for ease of visualization. Posterior support values above 0.5 are shown above, and maximum‐likelihood bootstraps above 50 are shown below branches. Colors correspond to the regions from which samples were collected, as seen in Figure 1.
Mentions: The ML and Bayesian concatenated trees both recover two well‐supported major clades organized by geographic region; the topologies are very similar with only minor rearrangements within major clades, and therefore, we present here the Bayesian tree with ML bootstrap values shown (Fig. 3). The central clade contains populations in western Tennessee and Indiana, and the eastern/western clade contains the populations within Virginia, West Virginia, eastern Tennessee, Oklahoma, and Missouri. The western populations form a monophyletic clade within the eastern populations. Haplotypes were shared among populations within the major geographic regions; however, support at the tips was very low. Relationships among the clades differ from simple geographic expectations: the western and eastern regions are more closely related to each other than either is to the central clade. Gene trees of individual loci (Figures S1–3, Supporting Information) generally reflect these relationships, although the nuclear locus POMC did not have a large influence on the topology, and as a result, the combined trees generally represent the mitochondrial history of the 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.