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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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Rarefaction analysis showing the changes in haplotype richness relative to successive increments in sample sizes.Rarefaction curves of two groups of populations sampled for at least ten individuals. The test was significant for the differences in haplotype richness between these groups (t = 12.5, df = 19, P<0.0001). The mean number of haplotypes found in 10 samples randomly drawn from the group PERD/PESB/SMJ was 7.0 (SD = 1.3), whereas the mean was roughly half as much (X = 3.5, SD = 0.2) for the groups found in smaller areas (RPPN-FMA/RPPN-MS).
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pone-0020722-g003: Rarefaction analysis showing the changes in haplotype richness relative to successive increments in sample sizes.Rarefaction curves of two groups of populations sampled for at least ten individuals. The test was significant for the differences in haplotype richness between these groups (t = 12.5, df = 19, P<0.0001). The mean number of haplotypes found in 10 samples randomly drawn from the group PERD/PESB/SMJ was 7.0 (SD = 1.3), whereas the mean was roughly half as much (X = 3.5, SD = 0.2) for the groups found in smaller areas (RPPN-FMA/RPPN-MS).

Mentions: The overall haplotype diversity was high (h = 0.905), and the nucleotide diversity was remarkably low (π = 0.0135). Haplotype h16 was found with the highest frequency in the overall sample set (22%) and was twice as frequent as h17, the second most frequent. Both h16 and 17 were exclusive to RPPN-FMA (Table S1). This distribution likely reflects the joint effects of a sampling bias because the RPPN-FMA encompasses 42% of the total sample and the low number of haplotypes in this population. Within each population, the haplotype and nucleotide diversities were relatively low, with RPPN-MS having only one haplotype and thus diversity measures equal to zero (Table 1). From the populations with at least ten individuals sampled, PERD harbors the highest number of haplotypes (8), and RPPN-MS harbors the lowest (1). Almost all haplotypes (19 out of 23) are exclusively found in only one of the eight populations: PERD, PESB, and SMJ (5 haplotypes each), RPPN-FMA (3) and PEI (1). The first four populations together have all haplotypes, except h5. The h3 haplotype, which is found in PERD, SMJ, and FE samples, is identical to the GenBank reference sequence from the FE locality. The rarefaction analysis showed that populations living in larger areas maintain significantly more haplotypes than the ones that are restricted to areas less than 1,000 ha (Fig. 3), whereas the differences among populations from larger areas themselves seem subtle (Table S1).


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)

Rarefaction analysis showing the changes in haplotype richness relative to successive increments in sample sizes.Rarefaction curves of two groups of populations sampled for at least ten individuals. The test was significant for the differences in haplotype richness between these groups (t = 12.5, df = 19, P<0.0001). The mean number of haplotypes found in 10 samples randomly drawn from the group PERD/PESB/SMJ was 7.0 (SD = 1.3), whereas the mean was roughly half as much (X = 3.5, SD = 0.2) for the groups found in smaller areas (RPPN-FMA/RPPN-MS).
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3108597&req=5

pone-0020722-g003: Rarefaction analysis showing the changes in haplotype richness relative to successive increments in sample sizes.Rarefaction curves of two groups of populations sampled for at least ten individuals. The test was significant for the differences in haplotype richness between these groups (t = 12.5, df = 19, P<0.0001). The mean number of haplotypes found in 10 samples randomly drawn from the group PERD/PESB/SMJ was 7.0 (SD = 1.3), whereas the mean was roughly half as much (X = 3.5, SD = 0.2) for the groups found in smaller areas (RPPN-FMA/RPPN-MS).
Mentions: The overall haplotype diversity was high (h = 0.905), and the nucleotide diversity was remarkably low (π = 0.0135). Haplotype h16 was found with the highest frequency in the overall sample set (22%) and was twice as frequent as h17, the second most frequent. Both h16 and 17 were exclusive to RPPN-FMA (Table S1). This distribution likely reflects the joint effects of a sampling bias because the RPPN-FMA encompasses 42% of the total sample and the low number of haplotypes in this population. Within each population, the haplotype and nucleotide diversities were relatively low, with RPPN-MS having only one haplotype and thus diversity measures equal to zero (Table 1). From the populations with at least ten individuals sampled, PERD harbors the highest number of haplotypes (8), and RPPN-MS harbors the lowest (1). Almost all haplotypes (19 out of 23) are exclusively found in only one of the eight populations: PERD, PESB, and SMJ (5 haplotypes each), RPPN-FMA (3) and PEI (1). The first four populations together have all haplotypes, except h5. The h3 haplotype, which is found in PERD, SMJ, and FE samples, is identical to the GenBank reference sequence from the FE locality. The rarefaction analysis showed that populations living in larger areas maintain significantly more haplotypes than the ones that are restricted to areas less than 1,000 ha (Fig. 3), whereas the differences among populations from larger areas themselves seem subtle (Table S1).

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