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Conflicting evolutionary patterns due to mitochondrial introgression and multilocus phylogeography of the Patagonian freshwater crab Aegla neuquensis.

Barber BR, Xu J, Pérez-Losada M, Jara CG, Crandall KA - PLoS ONE (2012)

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: Department of Biology, Brigham Young University, Provo, Utah, United States of America. brbarber76@gmail.com

ABSTRACT

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.

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ML trees based on mtDNA haplotypes Aegla neuquensis.Numbers above branches are ML bootstrap supports (pre/) and Bayesian posterior probabilities (post/). Numbers in bold are estimates of the time of most recent common ancestor TMRCA [ka (95% HPD intervals)]. Dashed lines indicate outgroups with branches that were arbitrarily shorted to fit on page. Locality (see Table 1) and number of individuals are shown after that haplotype.
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pone-0037105-g002: ML trees based on mtDNA haplotypes Aegla neuquensis.Numbers above branches are ML bootstrap supports (pre/) and Bayesian posterior probabilities (post/). Numbers in bold are estimates of the time of most recent common ancestor TMRCA [ka (95% HPD intervals)]. Dashed lines indicate outgroups with branches that were arbitrarily shorted to fit on page. Locality (see Table 1) and number of individuals are shown after that haplotype.

Mentions: Mitochondrial and nuclear haplotype diversity was high. We recovered 146 unique haplotypes from 295 individuals in our combined mtDNA data set (Table 1and Fig. 2). Most of the haplotypes (109 of 146, ∼75%) were singletons and only nine occurred in more than one location. The complete mtDNA alignment of fragments of the 16 S, COI, and COII genes is 1699 bp long. The COI (659-bp), COII (568-bp) and 16 S (472-bp) fragments delineated 82, 79 and 39 haplotypes, with 97, 91 and 41 variable sites, respectively, with an average sequence divergence across genes of 2.7% (0–8.5%). In a 1395-bp concatenated alignment of nDNA fragments, 67 haplotypes were identified from 103 crabs (Fig. 3), with an average sequence divergence across loci of 0.6% (0–1.4%). As in the mtDNA, most of the haplotypes (51 of 67, ∼76%) were singletons and only six occur in more than one location. The length of EF1α exon, EF1α intron and ANT intron were 640, 370 and 385 bp respectively defining 13, 21 and 22 haplotypes (phased alleles).


Conflicting evolutionary patterns due to mitochondrial introgression and multilocus phylogeography of the Patagonian freshwater crab Aegla neuquensis.

Barber BR, Xu J, Pérez-Losada M, Jara CG, Crandall KA - PLoS ONE (2012)

ML trees based on mtDNA haplotypes Aegla neuquensis.Numbers above branches are ML bootstrap supports (pre/) and Bayesian posterior probabilities (post/). Numbers in bold are estimates of the time of most recent common ancestor TMRCA [ka (95% HPD intervals)]. Dashed lines indicate outgroups with branches that were arbitrarily shorted to fit on page. Locality (see Table 1) and number of individuals are shown after that haplotype.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3369872&req=5

pone-0037105-g002: ML trees based on mtDNA haplotypes Aegla neuquensis.Numbers above branches are ML bootstrap supports (pre/) and Bayesian posterior probabilities (post/). Numbers in bold are estimates of the time of most recent common ancestor TMRCA [ka (95% HPD intervals)]. Dashed lines indicate outgroups with branches that were arbitrarily shorted to fit on page. Locality (see Table 1) and number of individuals are shown after that haplotype.
Mentions: Mitochondrial and nuclear haplotype diversity was high. We recovered 146 unique haplotypes from 295 individuals in our combined mtDNA data set (Table 1and Fig. 2). Most of the haplotypes (109 of 146, ∼75%) were singletons and only nine occurred in more than one location. The complete mtDNA alignment of fragments of the 16 S, COI, and COII genes is 1699 bp long. The COI (659-bp), COII (568-bp) and 16 S (472-bp) fragments delineated 82, 79 and 39 haplotypes, with 97, 91 and 41 variable sites, respectively, with an average sequence divergence across genes of 2.7% (0–8.5%). In a 1395-bp concatenated alignment of nDNA fragments, 67 haplotypes were identified from 103 crabs (Fig. 3), with an average sequence divergence across loci of 0.6% (0–1.4%). As in the mtDNA, most of the haplotypes (51 of 67, ∼76%) were singletons and only six occur in more than one location. The length of EF1α exon, EF1α intron and ANT intron were 640, 370 and 385 bp respectively defining 13, 21 and 22 haplotypes (phased alleles).

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: Department of Biology, Brigham Young University, Provo, Utah, United States of America. brbarber76@gmail.com

ABSTRACT

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.

Show MeSH
Related in: MedlinePlus