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.

Show MeSH

Related in: MedlinePlus

Extended Bayesian skyline plots of historical demographics of the two major river systems [(a) Negro system and (b) Chico-Chubut)] within Aegla neuquensis.The TMRCA is the mean root height. The median estimate (bold line), mean (light line) and 95% HPD limits are dashed. Inset is the number of demographic changes detected for each analysis. Blue bars indicated number of demographic changes that are within the 95% HPD estimates. Red bars are outside the 95% HPD.
© Copyright Policy
Related In: Results  -  Collection


getmorefigures.php?uid=PMC3369872&req=5

pone-0037105-g011: Extended Bayesian skyline plots of historical demographics of the two major river systems [(a) Negro system and (b) Chico-Chubut)] within Aegla neuquensis.The TMRCA is the mean root height. The median estimate (bold line), mean (light line) and 95% HPD limits are dashed. Inset is the number of demographic changes detected for each analysis. Blue bars indicated number of demographic changes that are within the 95% HPD estimates. Red bars are outside the 95% HPD.

Mentions: Contrasting demographic histories between the two major river systems were estimated using EBSP. We cannot reject a constant demographic model for the Negro system (Fig. 11a inset). However, the 95% HPD includes one demographic change. Inspection of the EBSP suggests that this event could have occurred over the last 65 ka (Fig. 6a). In contrast, we can reject a constant demographic model for the Chico-Chubut system because the mode number of changes is one (Fig. 11b inset). The EBSP shows an explosive increase over the last 2–3 thousand years (Fig. 11b). These plots show that the Negro system’s TMRCA is much older than that of the Chico-Chubut, 300 ka and 48 ka, respectively. The effective population size for Chico-Chubut was much lower (near zero) than the Negro’s for most of the history of this population. Each of the three EBSP runs conducted for each system converged on similar estimates for our parameters of interest and these parameters had high (>200) ESS values. See the appendix for the BEAST xml files and plots of TMRCA for each locus.


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)

Extended Bayesian skyline plots of historical demographics of the two major river systems [(a) Negro system and (b) Chico-Chubut)] within Aegla neuquensis.The TMRCA is the mean root height. The median estimate (bold line), mean (light line) and 95% HPD limits are dashed. Inset is the number of demographic changes detected for each analysis. Blue bars indicated number of demographic changes that are within the 95% HPD estimates. Red bars are outside the 95% HPD.
© Copyright Policy
Related In: Results  -  Collection

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

pone-0037105-g011: Extended Bayesian skyline plots of historical demographics of the two major river systems [(a) Negro system and (b) Chico-Chubut)] within Aegla neuquensis.The TMRCA is the mean root height. The median estimate (bold line), mean (light line) and 95% HPD limits are dashed. Inset is the number of demographic changes detected for each analysis. Blue bars indicated number of demographic changes that are within the 95% HPD estimates. Red bars are outside the 95% HPD.
Mentions: Contrasting demographic histories between the two major river systems were estimated using EBSP. We cannot reject a constant demographic model for the Negro system (Fig. 11a inset). However, the 95% HPD includes one demographic change. Inspection of the EBSP suggests that this event could have occurred over the last 65 ka (Fig. 6a). In contrast, we can reject a constant demographic model for the Chico-Chubut system because the mode number of changes is one (Fig. 11b inset). The EBSP shows an explosive increase over the last 2–3 thousand years (Fig. 11b). These plots show that the Negro system’s TMRCA is much older than that of the Chico-Chubut, 300 ka and 48 ka, respectively. The effective population size for Chico-Chubut was much lower (near zero) than the Negro’s for most of the history of this population. Each of the three EBSP runs conducted for each system converged on similar estimates for our parameters of interest and these parameters had high (>200) ESS values. See the appendix for the BEAST xml files and plots of TMRCA for each locus.

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