Genetic Diversity and Population History of a Critically Endangered Primate, the Northern Muriqui (Brachyteles hypoxanthus)
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{"title"=>"Genetic diversity and population history of a critically endangered primate, the northern muriqui (Brachyteles hypoxanthus)", "type"=>"journal", "authors"=>[{"first_name"=>"Paulo B.", "last_name"=>"Chaves", "scopus_author_id"=>"15076669100"}, {"first_name"=>"Clara S.", "last_name"=>"Alvarenga", "scopus_author_id"=>"36571331500"}, {"first_name"=>"Carla B.", "last_name"=>"de Possamai", "scopus_author_id"=>"39261348500"}, {"first_name"=>"Luiz G.", "last_name"=>"Dias", "scopus_author_id"=>"7102414973"}, {"first_name"=>"Jean P.", "last_name"=>"Boubli", "scopus_author_id"=>"6506290205"}, {"first_name"=>"Karen B.", "last_name"=>"Strier", "scopus_author_id"=>"7003503557"}, {"first_name"=>"Sérgio L.", "last_name"=>"Mendes", "scopus_author_id"=>"12144332200"}, {"first_name"=>"Valéria", "last_name"=>"Fagundes", "scopus_author_id"=>"6603815782"}], "year"=>2011, "source"=>"PLoS ONE", "identifiers"=>{"scopus"=>"2-s2.0-79958036391", "doi"=>"10.1371/journal.pone.0020722", "sgr"=>"79958036391", "isbn"=>"1932-6203", "pmid"=>"21694757", "issn"=>"19326203", "pui"=>"361895814"}, "id"=>"91f499b3-9685-345e-9f13-4635cbbb8fbc", "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.", "link"=>"http://www.mendeley.com/research/genetic-diversity-population-history-critically-endangered-primate-northern-muriqui-brachyteles-hypo", "reader_count"=>124, "reader_count_by_academic_status"=>{"Unspecified"=>4, "Professor > Associate Professor"=>4, "Researcher"=>22, "Student > Doctoral Student"=>10, "Student > Ph. D. Student"=>29, "Student > Postgraduate"=>4, "Student > Master"=>28, "Other"=>2, "Student > Bachelor"=>16, "Lecturer"=>1, "Lecturer > Senior Lecturer"=>2, "Professor"=>2}, "reader_count_by_user_role"=>{"Unspecified"=>4, "Professor > Associate Professor"=>4, "Researcher"=>22, "Student > Doctoral Student"=>10, "Student > Ph. D. Student"=>29, "Student > Postgraduate"=>4, "Student > Master"=>28, "Other"=>2, "Student > Bachelor"=>16, "Lecturer"=>1, "Lecturer > Senior Lecturer"=>2, "Professor"=>2}, "reader_count_by_subject_area"=>{"Unspecified"=>9, "Environmental Science"=>14, "Biochemistry, Genetics and Molecular Biology"=>2, "Agricultural and Biological Sciences"=>92, "Physics and Astronomy"=>1, "Social Sciences"=>3, "Computer Science"=>1, "Earth and Planetary Sciences"=>1, "Economics, Econometrics and Finance"=>1}, "reader_count_by_subdiscipline"=>{"Social Sciences"=>{"Social Sciences"=>3}, "Physics and Astronomy"=>{"Physics and Astronomy"=>1}, "Earth and Planetary Sciences"=>{"Earth and Planetary Sciences"=>1}, "Economics, Econometrics and Finance"=>{"Economics, Econometrics and Finance"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>92}, "Computer Science"=>{"Computer Science"=>1}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>2}, "Unspecified"=>{"Unspecified"=>9}, "Environmental Science"=>{"Environmental Science"=>14}}, "reader_count_by_country"=>{"Canada"=>1, "Sweden"=>1, "Argentina"=>1, "United States"=>3, "Brazil"=>11, "United Kingdom"=>1, "Malaysia"=>1, "Germany"=>1}, "group_count"=>1}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/768854"], "description"=>"<p>1: ES: Espírito Santo; MG: Minas Gerais; PERD: Parque Estadual do Rio Doce, PNC: Parque Nacional do Caparaó, PESB: Parque Estadual da Serra do Brigadeiro, SMJ: Santa Maria do Jetibá, PEI: Parque Estadual do Ibitipoca, RPPN-FMA: Reserva do Patrimônio Natural Feliciano Miguel Abdala, RPPN-MS: Reserva do Patrimônio Natural Mata do Sossego, FE: Fazenda Esmeralda.</p><p>2: data from October 2005 (27).</p><p>3: one sequence from GenBank, accession no. AF213966 <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0020722#pone.0020722-Collins1\" target=\"_blank\">[36]</a>.</p><p>*Estimated from a total area of 13 partially isolated fragments. 3: Calculated only for populations with more than 10 individuals sampled.</p>", "links"=>[], "tags"=>["sampled", "molecular", "indices", "haplotype", "nucleotide", "polymorphic"], "article_id"=>439213, "categories"=>["Ecology", "Genetics", "Evolutionary Biology"], "users"=>["Paulo B. Chaves", "Clara S. Alvarenga", "Carla de B. Possamai", "Luiz G. Dias", "Jean P. Boubli", "Karen B. Strier", "Sérgio L. Mendes", "Valéria Fagundes"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0020722.t001", "stats"=>{"downloads"=>0, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Sampled_localities_number_of_sampled_individuals_and_molecular_diversity_indices_h_haplotype_diversity_nucleotide_diversity_s_number_of_polymorphic_sites_/439213", "title"=>"Sampled localities, number of sampled individuals, and molecular diversity indices (<i>h</i>, haplotype diversity; π, nucleotide diversity; <i>s</i>, number of polymorphic sites).", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2011-06-03 02:33:33"}
  • {"files"=>["https://ndownloader.figshare.com/files/768463"], "description"=>"<p>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 (<i>t</i> = 12.5, <i>df</i> = 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 (<i>X</i> = 3.5, SD = 0.2) for the groups found in smaller areas (RPPN-FMA/RPPN-MS).</p>", "links"=>[], "tags"=>["changes", "haplotype", "richness", "successive", "increments"], "article_id"=>438822, "categories"=>["Ecology", "Genetics", "Evolutionary Biology"], "users"=>["Paulo B. Chaves", "Clara S. Alvarenga", "Carla de B. Possamai", "Luiz G. Dias", "Jean P. Boubli", "Karen B. Strier", "Sérgio L. Mendes", "Valéria Fagundes"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0020722.g003", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Rarefaction_analysis_showing_the_changes_in_haplotype_richness_relative_to_successive_increments_in_sample_sizes_/438822", "title"=>"Rarefaction analysis showing the changes in haplotype richness relative to successive increments in sample sizes.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-06-03 02:27:02"}
  • {"files"=>["https://ndownloader.figshare.com/files/768336"], "description"=>"<p>Only the four best sampled populations were included (PESB, PERD, RPPN-FMA, and SMJ). The scenarios are organized in three groups of three each. The first group includes scenarios that depicts a rapid or star-like divergence event among the populations (1, 2, and 3). Scenario 1 assumes that one large population split into four populations during the Holocene (t1). Scenarios 2 and 3 push the splitting event further back in time (during the last glacial maximum, t2, and earlier, t3, respectively). The second group includes three scenarios (3, 4, and 5) representing sequential or step-wise divergence among the populations in different times. The third group includes scenarios with sequential divergences and assumes that the population RPPN-FMA (FMA) diverged after an admixture event. Different branch colors represent putative changes in effective population sizes (see <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0020722#pone.0020722.s001\" target=\"_blank\">Figure S1</a> for prior set up). The posterior probability of each scenario is shown on the lower left-hand side of its respective diagram.</p>", "links"=>[], "tags"=>["scenarios", "tested", "approximates", "bayesian", "computation"], "article_id"=>438691, "categories"=>["Ecology", "Genetics", "Evolutionary Biology"], "users"=>["Paulo B. Chaves", "Clara S. Alvarenga", "Carla de B. Possamai", "Luiz G. Dias", "Jean P. Boubli", "Karen B. Strier", "Sérgio L. Mendes", "Valéria Fagundes"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0020722.g002", "stats"=>{"downloads"=>1, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Nine_alternative_scenarios_tested_with_the_Approximates_Bayesian_Computation_approach_/438691", "title"=>"Nine alternative scenarios tested with the Approximates Bayesian Computation approach.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-06-03 02:24:51"}
  • {"files"=>["https://ndownloader.figshare.com/files/768215"], "description"=>"<p>Map highlighting the southeast section of Brazil with sampled populations overlaid on the northern muriqui distribution, which is based on <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0020722#pone.0020722-Collins1\" target=\"_blank\">[36]</a> (left, state acronyms: BA – Bahia, MG – Minas Gerais, ES – Espírito Santo, RJ – Rio de Janeiro). Sampling sites and some of the landscape features at SMJ are shown on the large map (right).</p>", "links"=>[], "tags"=>["sites", "geographic"], "article_id"=>438580, "categories"=>["Ecology", "Genetics", "Evolutionary Biology"], "users"=>["Paulo B. Chaves", "Clara S. Alvarenga", "Carla de B. Possamai", "Luiz G. Dias", "Jean P. Boubli", "Karen B. Strier", "Sérgio L. Mendes", "Valéria Fagundes"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0020722.g001", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Sampling_sites_and_geographic_distribution_of_the_northern_muriqui_/438580", "title"=>"Sampling sites and geographic distribution of the northern muriqui.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-06-03 02:23:00"}
  • {"files"=>["https://ndownloader.figshare.com/files/768611"], "description"=>"<p>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.</p>", "links"=>[], "tags"=>["haplotype", "intrapopulation"], "article_id"=>438978, "categories"=>["Ecology", "Genetics", "Evolutionary Biology"], "users"=>["Paulo B. Chaves", "Clara S. Alvarenga", "Carla de B. Possamai", "Luiz G. Dias", "Jean P. Boubli", "Karen B. Strier", "Sérgio L. Mendes", "Valéria Fagundes"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0020722.g004", "stats"=>{"downloads"=>0, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Haplotype_network_haplotype_distributions_and_intrapopulation_genetic_distances_/438978", "title"=>"Haplotype network, haplotype distributions, and intrapopulation genetic distances.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-06-03 02:29:38"}
  • {"files"=>["https://ndownloader.figshare.com/files/768687"], "description"=>"<p>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 <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0020722#pone-0020722-g002\" target=\"_blank\">Fig. 2</a>). The solid line is the median, and the shaded area around it is the 95% HPD estimate of the historic female effective population size (<i>N<sub>ef</sub></i>) not corrected for generation time (τ). Timing of events was estimated assuming a substitution rate of 3.7×10<sup>−8</sup> s/s/y (2.1×10<sup>−8</sup><<i>μ</i><6.0×10<sup>−8</sup> 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).</p>", "links"=>[], "tags"=>["skyline", "depicting", "muriquis"], "article_id"=>439051, "categories"=>["Ecology", "Genetics", "Evolutionary Biology"], "users"=>["Paulo B. Chaves", "Clara S. Alvarenga", "Carla de B. Possamai", "Luiz G. Dias", "Jean P. Boubli", "Karen B. Strier", "Sérgio L. Mendes", "Valéria Fagundes"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0020722.g005", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Bayesian_skyline_plot_depicting_the_population_size_of_northern_muriquis_over_time_/439051", "title"=>"Bayesian skyline plot depicting the population size of northern muriquis over time.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-06-03 02:30:51"}
  • {"files"=>["https://ndownloader.figshare.com/files/768807"], "description"=>"<p>*P<0.05.</p>", "links"=>[], "tags"=>["muriqui", "groups", "rppn-fma", "santa", "maria"], "article_id"=>439167, "categories"=>["Ecology", "Genetics", "Evolutionary Biology"], "users"=>["Paulo B. Chaves", "Clara S. Alvarenga", "Carla de B. Possamai", "Luiz G. Dias", "Jean P. Boubli", "Karen B. Strier", "Sérgio L. Mendes", "Valéria Fagundes"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0020722.t002", "stats"=>{"downloads"=>1, "page_views"=>10, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Pairwise_ST_between_muriqui_social_groups_for_RPPN_FMA_upper_left_and_Santa_Maria_do_Jetib_225_lower_right_/439167", "title"=>"Pairwise Φ<sub>ST</sub> between muriqui social groups for RPPN-FMA (upper left) and Santa Maria do Jetibá (lower right).", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2011-06-03 02:32:47"}
  • {"files"=>["https://ndownloader.figshare.com/files/386165", "https://ndownloader.figshare.com/files/386214", "https://ndownloader.figshare.com/files/386251", "https://ndownloader.figshare.com/files/386274", "https://ndownloader.figshare.com/files/386297", "https://ndownloader.figshare.com/files/386323"], "description"=>"<div><p>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 (<em>Brachyteles hypoxanthus</em>) 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<sub>ST</sub> = 0.49, Φ<sub>CT</sub> = 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 (<em>θ</em> = 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.</p> </div>", "links"=>[], "tags"=>["critically", "endangered", "muriqui"], "article_id"=>136223, "categories"=>["Ecology", "Genetics", "Evolutionary Biology"], "users"=>["Paulo B. Chaves", "Clara S. Alvarenga", "Carla de B. Possamai", "Luiz G. Dias", "Jean P. Boubli", "Karen B. Strier", "Sérgio L. Mendes", "Valéria Fagundes"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0020722.s001", "https://dx.doi.org/10.1371/journal.pone.0020722.s002", "https://dx.doi.org/10.1371/journal.pone.0020722.s003", "https://dx.doi.org/10.1371/journal.pone.0020722.s004", "https://dx.doi.org/10.1371/journal.pone.0020722.s005", "https://dx.doi.org/10.1371/journal.pone.0020722.s006"], "stats"=>{"downloads"=>25, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Genetic_Diversity_and_Population_History_of_a_Critically_Endangered_Primate_the_Northern_Muriqui_Brachyteles_hypoxanthus_/136223", "title"=>"Genetic Diversity and Population History of a Critically Endangered Primate, the Northern Muriqui (<em>Brachyteles hypoxanthus</em>)", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2011-06-03 01:43:43"}

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