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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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Haplotype network, haplotype distributions, and intrapopulation genetic distances.Median-joining network depicting haplotype relationships is shown on the left side. The areas of the circles are proportional to the relative abundance of each haplotype (the smallest circle represents 1 sample, the largest circle represents 33 samples). Each node between two haplotypes or median vectors (small open circles) accounts for one mutational step (transition or transversion), unless indicated by two vertical dashes, which account for two transitions. A star shows the single transversion detected in the respective node (h21–h22). The map on the right side shows the haplotype frequencies (pie charts) within each population. Each color represents one of the 23 haplotypes. The chart area is scaled to the sample size. The bar graph (inset) in the center of the figure displays the lower and upper bound genetic distances calculated between pairs of haplotypes within each proposed management unit (MU) population. While the lower bound distances were the same in all groups (0.3%, gray section of each bar), intrapopulation divergences (black sections of each bar) did not deviate substantially from the overall (TOTAL) level.
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pone-0020722-g004: Haplotype network, haplotype distributions, and intrapopulation genetic distances.Median-joining network depicting haplotype relationships is shown on the left side. The areas of the circles are proportional to the relative abundance of each haplotype (the smallest circle represents 1 sample, the largest circle represents 33 samples). Each node between two haplotypes or median vectors (small open circles) accounts for one mutational step (transition or transversion), unless indicated by two vertical dashes, which account for two transitions. A star shows the single transversion detected in the respective node (h21–h22). The map on the right side shows the haplotype frequencies (pie charts) within each population. Each color represents one of the 23 haplotypes. The chart area is scaled to the sample size. The bar graph (inset) in the center of the figure displays the lower and upper bound genetic distances calculated between pairs of haplotypes within each proposed management unit (MU) population. While the lower bound distances were the same in all groups (0.3%, gray section of each bar), intrapopulation divergences (black sections of each bar) did not deviate substantially from the overall (TOTAL) level.

Mentions: The overall pattern depicted by the haplotype network is rather complex (Fig. 4), also revealed by shallow phylogenetic trees (data not shown). Most haplotypes differ from their nearest neighbor by one mutation, yielding pairwise distances that range between 0.3 and 3.4%, with an overall average of 1.5% (Table S4). Distant populations shared several nucleotide polymorphisms (Table S1, Table S2), resulting in no correlation between haplotypes and geography. It appears that h3 is the deepest diverged haplotype because it is present in 13 individuals from 3 geographically distant populations (FE, PERD and SMJ) [4], [72].


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)

Haplotype network, haplotype distributions, and intrapopulation genetic distances.Median-joining network depicting haplotype relationships is shown on the left side. The areas of the circles are proportional to the relative abundance of each haplotype (the smallest circle represents 1 sample, the largest circle represents 33 samples). Each node between two haplotypes or median vectors (small open circles) accounts for one mutational step (transition or transversion), unless indicated by two vertical dashes, which account for two transitions. A star shows the single transversion detected in the respective node (h21–h22). The map on the right side shows the haplotype frequencies (pie charts) within each population. Each color represents one of the 23 haplotypes. The chart area is scaled to the sample size. The bar graph (inset) in the center of the figure displays the lower and upper bound genetic distances calculated between pairs of haplotypes within each proposed management unit (MU) population. While the lower bound distances were the same in all groups (0.3%, gray section of each bar), intrapopulation divergences (black sections of each bar) did not deviate substantially from the overall (TOTAL) level.
© Copyright Policy
Related In: Results  -  Collection

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

pone-0020722-g004: Haplotype network, haplotype distributions, and intrapopulation genetic distances.Median-joining network depicting haplotype relationships is shown on the left side. The areas of the circles are proportional to the relative abundance of each haplotype (the smallest circle represents 1 sample, the largest circle represents 33 samples). Each node between two haplotypes or median vectors (small open circles) accounts for one mutational step (transition or transversion), unless indicated by two vertical dashes, which account for two transitions. A star shows the single transversion detected in the respective node (h21–h22). The map on the right side shows the haplotype frequencies (pie charts) within each population. Each color represents one of the 23 haplotypes. The chart area is scaled to the sample size. The bar graph (inset) in the center of the figure displays the lower and upper bound genetic distances calculated between pairs of haplotypes within each proposed management unit (MU) population. While the lower bound distances were the same in all groups (0.3%, gray section of each bar), intrapopulation divergences (black sections of each bar) did not deviate substantially from the overall (TOTAL) level.
Mentions: The overall pattern depicted by the haplotype network is rather complex (Fig. 4), also revealed by shallow phylogenetic trees (data not shown). Most haplotypes differ from their nearest neighbor by one mutation, yielding pairwise distances that range between 0.3 and 3.4%, with an overall average of 1.5% (Table S4). Distant populations shared several nucleotide polymorphisms (Table S1, Table S2), resulting in no correlation between haplotypes and geography. It appears that h3 is the deepest diverged haplotype because it is present in 13 individuals from 3 geographically distant populations (FE, PERD and SMJ) [4], [72].

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