Limits...
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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Haplotype networks with nested clade design for the nuclear EF1α intron and exon.Haplotype circle size is proportional to its frequency. Each haplotypes is numbered. Haplotypes that exceed twenty individuals are labeled with the total number of individuals of that haplotype. Arrow indicates the root haplotype. Black empty circles represent extinct (or unsampled) haplotypes. Color codes indicate the six major rivers.
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pone-0037105-g008: Haplotype networks with nested clade design for the nuclear EF1α intron and exon.Haplotype circle size is proportional to its frequency. Each haplotypes is numbered. Haplotypes that exceed twenty individuals are labeled with the total number of individuals of that haplotype. Arrow indicates the root haplotype. Black empty circles represent extinct (or unsampled) haplotypes. Color codes indicate the six major rivers.

Mentions: Individual haplotype networks from both genomes (Fig. 4, 5, 6, 7, 8, 9) show relationships that are consistent with those recovered in the phylogenetic analyses (Figs. 2, 3); that is, haplotypes from the Neuquen, Negro and Limay rivers are more closely related to one another than to those found in the Chubut-Chico systems. The ANT intron network is an exception because it has one widespread haplotype (#15) that is shared between these two systems and a Limay river haplotype (#20) that is more closely related to Chico-Chubut than it is to the other Negro system haplotypes (Fig. 9). Overall, networks group geographically close haplotypes. Nuclear networks further illustrate the relatively low haplotype diversity observed within the Chico-Chubut river system.


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)

Haplotype networks with nested clade design for the nuclear EF1α intron and exon.Haplotype circle size is proportional to its frequency. Each haplotypes is numbered. Haplotypes that exceed twenty individuals are labeled with the total number of individuals of that haplotype. Arrow indicates the root haplotype. Black empty circles represent extinct (or unsampled) haplotypes. Color codes indicate the six major rivers.
© Copyright Policy
Related In: Results  -  Collection

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

pone-0037105-g008: Haplotype networks with nested clade design for the nuclear EF1α intron and exon.Haplotype circle size is proportional to its frequency. Each haplotypes is numbered. Haplotypes that exceed twenty individuals are labeled with the total number of individuals of that haplotype. Arrow indicates the root haplotype. Black empty circles represent extinct (or unsampled) haplotypes. Color codes indicate the six major rivers.
Mentions: Individual haplotype networks from both genomes (Fig. 4, 5, 6, 7, 8, 9) show relationships that are consistent with those recovered in the phylogenetic analyses (Figs. 2, 3); that is, haplotypes from the Neuquen, Negro and Limay rivers are more closely related to one another than to those found in the Chubut-Chico systems. The ANT intron network is an exception because it has one widespread haplotype (#15) that is shared between these two systems and a Limay river haplotype (#20) that is more closely related to Chico-Chubut than it is to the other Negro system haplotypes (Fig. 9). Overall, networks group geographically close haplotypes. Nuclear networks further illustrate the relatively low haplotype diversity observed within the Chico-Chubut river system.

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