DOI: 10.5061/dryad.93js1254
title: Data from: Conflicting evolutionary patterns due to mitochondrial introgression and multilocus phylogeography of the Patagonian freshwater crab Aegla neuquensis

description: BACKGROUND: Multiple loci and population genetic methods were employed to
 study the phylogeographic history of the Patagonian freshwater crab Aegla
 neuquensis (Aeglidae: Decopoda). This taxon occurs in two large river
 systems in the Patagonian Steppe, from the foothills of the Andes
 Mountains east to the Atlantic Ocean. METHODOLOGY/PRINCIPAL FINDINGS: A
 nuclear phylogeny and multilocus nested clade phylogeographic analysis
 detected a fragmentation event between the Negro and Chico-Chubut river
 systems. This event occurred approximately 137 thousand years ago. An
 isolation-with-migration analysis and maximum-likelihood estimates of gene
 flow showed asymmetrical exchange of genetic material between these two
 river systems exclusively in their headwaters. We used information theory
 to determine the best-fit demographic history between these two river
 systems under an isolation-with-migration model. The best-fit model
 suggests that the Negro and the ancestral populations have the same
 effective population sizes; whereas the Chico-Chubut population is smaller
 and shows that gene flow from the Chico-Chubut into the Negro is four
 times higher than in the reverse direction. Much of the Chico-Chubut
 system appears to have only been recently colonized while the Negro
 populations appear to have been in place for most of the evolutionary
 history of this taxon. CONCLUSIONS/SIGNIFICANCE: Due to mitochondrial
 introgression, three nuclear loci provided different phylogeographic
 resolution than the three mitochondrial genes for an ancient fragmentation
 event observed in the nuclear phylogeny. However, the mitochondrial locus
 provided greater resolution on more recent evolutionary events. Our study,
 therefore, demonstrates the need to include both nuclear and mitochondrial
 loci for a more complete understanding of evolutionary histories and
 associated phylogeographic events. Our results suggest that gene flow
 between these systems, before and after fragmentation was through periodic
 paleolakes that formed in the headwaters region. Fragmentation between the
 Negro and Chico-Chubut systems was driven by the disappearance of these
 paleolakes during the Patagonian Glaciation.
description: mitochondrial
 16SSequence data from the
 mitochondrial 16S gene obtained from samples of Aegla neuquensis.
 Sequences names are sampleID/population name/major
 river(abbreviation).Aneu16S_295.nexmitochondrial COISequence data from the mitochondrial COI gene obtained from samples of Aegla neuquensis. Sequences names are sampleID/population name/major river(abbreviation).AneuCOI_295.nexmitochondrial COIISequence data from the mitochondrial COII gene obtained from samples of Aegla neuquensis. Sequences names are sampleID/population name/major river(abbreviation).AneuCOII_295.nexANTintronSequence data from the nuclear ANT intron gene obtained from samples of Aegla neuquensis. Sequences names are sampleID/population name/major river(abbreviation).AneuANTintron104.nexEF1intronSequence data from the nuclear EF1 Intron gene obtained from samples of Aegla neuquensis. Sequences names are sampleID/population name/major river(abbreviation).AneuEF1intron101.nexEF1exon122Sequence data from the nuclear EF1 exon gene obtained from samples of Aegla neuquensis. Sequences names are sampleID/population name/major river(abbreviation).AneuEF1exon122.nex