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Genetic diversity and population history of a critically endangered primate, the northern muriqui (Brachyteles hypoxanthus).

Chaves PB, Alvarenga CS, Possamai Cde B, Dias LG, Boubli JP, Strier KB, Mendes SL, Fagundes V - PLoS ONE (2011)

Bottom Line: We analyzed the mitochondrial DNA control region of 152 northern muriquis, or 17.6% of the 864 northern muriquis from 8 of the 12 known extant populations and found no evidence of phylogeographic partitions or past population shrinkage/expansion.In addition, the best scenario supported by an Approximate Bayesian Computation analysis, significant fixation indices (Φ(ST) = 0.49, Φ(CT) = 0.24), and population-specific haplotypes, coupled with the extirpation of intermediate populations, are indicative of a recent geographic structuring of genetic diversity during the Holocene.We suggest that these populations be treated as discrete units for conservation management purposes.

View Article: PubMed Central - PubMed

Affiliation: Departamento de Ciências Biológicas, Universidade Federal do Espírito Santo, Vitória, Espírito Santo, Brazil.

ABSTRACT
Social, ecological, and historical processes affect the genetic structure of primate populations, and therefore have key implications for the conservation of endangered species. The northern muriqui (Brachyteles hypoxanthus) is a critically endangered New World monkey and a flagship species for the conservation of the Atlantic Forest hotspot. Yet, like other neotropical primates, little is known about its population history and the genetic structure of remnant populations. We analyzed the mitochondrial DNA control region of 152 northern muriquis, or 17.6% of the 864 northern muriquis from 8 of the 12 known extant populations and found no evidence of phylogeographic partitions or past population shrinkage/expansion. Bayesian and classic analyses show that this finding may be attributed to the joint contribution of female-biased dispersal, demographic stability, and a relatively large historic population size. Past population stability is consistent with a central Atlantic Forest Pleistocene refuge. In addition, the best scenario supported by an Approximate Bayesian Computation analysis, significant fixation indices (Φ(ST) = 0.49, Φ(CT) = 0.24), and population-specific haplotypes, coupled with the extirpation of intermediate populations, are indicative of a recent geographic structuring of genetic diversity during the Holocene. Genetic diversity is higher in populations living in larger areas (>2,000 hectares), but it is remarkably low in the species overall (θ = 0.018). Three populations occurring in protected reserves and one fragmented population inhabiting private lands harbor 22 out of 23 haplotypes, most of which are population-exclusive, and therefore represent patchy repositories of the species' genetic diversity. We suggest that these populations be treated as discrete units for conservation management purposes.

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Bayesian skyline plot depicting the population size of northern muriquis over time.Bayesian skyline plot showing an overall stable population size in northern muriquis. A modest population decline near the end of the last glacial maximum (roughly 10000 years ago) may have occurred and it is possibly associated with the recent population subdivision shown in the ABC analysis (see Fig. 2). The solid line is the median, and the shaded area around it is the 95% HPD estimate of the historic female effective population size (Nef) not corrected for generation time (τ). Timing of events was estimated assuming a substitution rate of 3.7×10−8 s/s/y (2.1×10−8<μ<6.0×10−8 s/s/y, see text for details). Time is shown from 0 (present) to 120 kya (the lower estimate of the 95% HPD around tMRCA).
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pone-0020722-g005: Bayesian skyline plot depicting the population size of northern muriquis over time.Bayesian skyline plot showing an overall stable population size in northern muriquis. A modest population decline near the end of the last glacial maximum (roughly 10000 years ago) may have occurred and it is possibly associated with the recent population subdivision shown in the ABC analysis (see Fig. 2). The solid line is the median, and the shaded area around it is the 95% HPD estimate of the historic female effective population size (Nef) not corrected for generation time (τ). Timing of events was estimated assuming a substitution rate of 3.7×10−8 s/s/y (2.1×10−8<μ<6.0×10−8 s/s/y, see text for details). Time is shown from 0 (present) to 120 kya (the lower estimate of the 95% HPD around tMRCA).

Mentions: Based on the nonsignificant and near zero results of neutrality tests in the total sample, we could not reject the hypothesis of demographic stability (FS = −4.08, DF = 0.0, F = 0.0, and R2 = 0.09 all P>0.05). Likewise, although the exponential growth rate estimated in LAMARC has a broad confidence interval, the point estimation indicates at most a rather modest growth. We could not reject a nongrowing population scenario with the LAMARC results because the 95% most probable estimate interval includes zero (g = 160, −62<g<591). The demographic scenario recovered in the BSP (Fig. 5) and the one favored by the ABC (Scenario 1, posterior probability 0.67) were in agreement with the previous analyses, and suggest that there is no mtDNA evidence for dramatic population changes in northern muriquis. The ABC analysis also suggests that the current configuration of isolated populations is a more recent and probably occurred in the Holocene (<10,000 years, Scenario 1, Fig. 2), and most likely not before the last glacial maximum about 20,000 years ago (Scenario 2, posterior probability 0.33).


Genetic diversity and population history of a critically endangered primate, the northern muriqui (Brachyteles hypoxanthus).

Chaves PB, Alvarenga CS, Possamai Cde B, Dias LG, Boubli JP, Strier KB, Mendes SL, Fagundes V - PLoS ONE (2011)

Bayesian skyline plot depicting the population size of northern muriquis over time.Bayesian skyline plot showing an overall stable population size in northern muriquis. A modest population decline near the end of the last glacial maximum (roughly 10000 years ago) may have occurred and it is possibly associated with the recent population subdivision shown in the ABC analysis (see Fig. 2). The solid line is the median, and the shaded area around it is the 95% HPD estimate of the historic female effective population size (Nef) not corrected for generation time (τ). Timing of events was estimated assuming a substitution rate of 3.7×10−8 s/s/y (2.1×10−8<μ<6.0×10−8 s/s/y, see text for details). Time is shown from 0 (present) to 120 kya (the lower estimate of the 95% HPD around tMRCA).
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Related In: Results  -  Collection

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getmorefigures.php?uid=PMC3108597&req=5

pone-0020722-g005: Bayesian skyline plot depicting the population size of northern muriquis over time.Bayesian skyline plot showing an overall stable population size in northern muriquis. A modest population decline near the end of the last glacial maximum (roughly 10000 years ago) may have occurred and it is possibly associated with the recent population subdivision shown in the ABC analysis (see Fig. 2). The solid line is the median, and the shaded area around it is the 95% HPD estimate of the historic female effective population size (Nef) not corrected for generation time (τ). Timing of events was estimated assuming a substitution rate of 3.7×10−8 s/s/y (2.1×10−8<μ<6.0×10−8 s/s/y, see text for details). Time is shown from 0 (present) to 120 kya (the lower estimate of the 95% HPD around tMRCA).
Mentions: Based on the nonsignificant and near zero results of neutrality tests in the total sample, we could not reject the hypothesis of demographic stability (FS = −4.08, DF = 0.0, F = 0.0, and R2 = 0.09 all P>0.05). Likewise, although the exponential growth rate estimated in LAMARC has a broad confidence interval, the point estimation indicates at most a rather modest growth. We could not reject a nongrowing population scenario with the LAMARC results because the 95% most probable estimate interval includes zero (g = 160, −62<g<591). The demographic scenario recovered in the BSP (Fig. 5) and the one favored by the ABC (Scenario 1, posterior probability 0.67) were in agreement with the previous analyses, and suggest that there is no mtDNA evidence for dramatic population changes in northern muriquis. The ABC analysis also suggests that the current configuration of isolated populations is a more recent and probably occurred in the Holocene (<10,000 years, Scenario 1, Fig. 2), and most likely not before the last glacial maximum about 20,000 years ago (Scenario 2, posterior probability 0.33).

Bottom Line: We analyzed the mitochondrial DNA control region of 152 northern muriquis, or 17.6% of the 864 northern muriquis from 8 of the 12 known extant populations and found no evidence of phylogeographic partitions or past population shrinkage/expansion.In addition, the best scenario supported by an Approximate Bayesian Computation analysis, significant fixation indices (Φ(ST) = 0.49, Φ(CT) = 0.24), and population-specific haplotypes, coupled with the extirpation of intermediate populations, are indicative of a recent geographic structuring of genetic diversity during the Holocene.We suggest that these populations be treated as discrete units for conservation management purposes.

View Article: PubMed Central - PubMed

Affiliation: Departamento de Ciências Biológicas, Universidade Federal do Espírito Santo, Vitória, Espírito Santo, Brazil.

ABSTRACT
Social, ecological, and historical processes affect the genetic structure of primate populations, and therefore have key implications for the conservation of endangered species. The northern muriqui (Brachyteles hypoxanthus) is a critically endangered New World monkey and a flagship species for the conservation of the Atlantic Forest hotspot. Yet, like other neotropical primates, little is known about its population history and the genetic structure of remnant populations. We analyzed the mitochondrial DNA control region of 152 northern muriquis, or 17.6% of the 864 northern muriquis from 8 of the 12 known extant populations and found no evidence of phylogeographic partitions or past population shrinkage/expansion. Bayesian and classic analyses show that this finding may be attributed to the joint contribution of female-biased dispersal, demographic stability, and a relatively large historic population size. Past population stability is consistent with a central Atlantic Forest Pleistocene refuge. In addition, the best scenario supported by an Approximate Bayesian Computation analysis, significant fixation indices (Φ(ST) = 0.49, Φ(CT) = 0.24), and population-specific haplotypes, coupled with the extirpation of intermediate populations, are indicative of a recent geographic structuring of genetic diversity during the Holocene. Genetic diversity is higher in populations living in larger areas (>2,000 hectares), but it is remarkably low in the species overall (θ = 0.018). Three populations occurring in protected reserves and one fragmented population inhabiting private lands harbor 22 out of 23 haplotypes, most of which are population-exclusive, and therefore represent patchy repositories of the species' genetic diversity. We suggest that these populations be treated as discrete units for conservation management purposes.

Show MeSH
Related in: MedlinePlus