Eco-Geographical Diversification of Bitter Taste Receptor Genes (TAS2Rs) among Subspecies of Chimpanzees (Pan troglodytes)
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{"title"=>"Eco-geographical diversification of bitter taste receptor genes (TAS2Rs) among subspecies of chimpanzees (Pan troglodytes)", "type"=>"journal", "authors"=>[{"first_name"=>"Takashi", "last_name"=>"Hayakawa", "scopus_author_id"=>"55338421600"}, {"first_name"=>"Tohru", "last_name"=>"Sugawara", "scopus_author_id"=>"8407407200"}, {"first_name"=>"Yasuhiro", "last_name"=>"Go", "scopus_author_id"=>"8056604800"}, {"first_name"=>"Toshifumi", "last_name"=>"Udono", "scopus_author_id"=>"57193978506"}, {"first_name"=>"Hirohisa", "last_name"=>"Hirai", "scopus_author_id"=>"7403094599"}, {"first_name"=>"Hiroo", "last_name"=>"Imai", "scopus_author_id"=>"7401873964"}], "year"=>2012, "source"=>"PLoS ONE", "identifiers"=>{"sgr"=>"84865086519", "doi"=>"10.1371/journal.pone.0043277", "pui"=>"365452115", "scopus"=>"2-s2.0-84865086519", "issn"=>"19326203", "pmid"=>"22916235"}, "id"=>"9220120a-64b4-3ae6-a8bb-99168c85b596", "abstract"=>"Chimpanzees (Pan troglodytes) have region-specific difference in dietary repertoires from East to West across tropical Africa. Such differences may result from different genetic backgrounds in addition to cultural variations. We analyzed the sequences of all bitter taste receptor genes (cTAS2Rs) in a total of 59 chimpanzees, including 4 putative subspecies. We identified genetic variations including single-nucleotide variations (SNVs), insertions and deletions (indels), gene-conversion variations, and copy-number variations (CNVs) in cTAS2Rs. Approximately two-thirds of all cTAS2R haplotypes in the amino acid sequence were unique to each subspecies. We analyzed the evolutionary backgrounds of natural selection behind such diversification. Our previous study concluded that diversification of cTAS2Rs in western chimpanzees (P. t. verus) may have resulted from balancing selection. In contrast, the present study found that purifying selection dominates as the evolutionary form of diversification of the so-called human cluster of cTAS2Rs in eastern chimpanzees (P. t. schweinfurthii) and that the other cTAS2Rs were under no obvious selection as a whole. Such marked diversification of cTAS2Rs with different evolutionary backgrounds among subspecies of chimpanzees probably reflects their subspecies-specific dietary repertoires.", "link"=>"http://www.mendeley.com/research/ecogeographical-diversification-bitter-taste-receptor-genes-tas2rs-among-subspecies-chimpanzees-pan", "reader_count"=>31, "reader_count_by_academic_status"=>{"Professor > Associate Professor"=>3, "Researcher"=>10, "Student > Ph. D. Student"=>4, "Student > Postgraduate"=>3, "Student > Master"=>4, "Other"=>2, "Student > Bachelor"=>3, "Lecturer"=>1, "Professor"=>1}, "reader_count_by_user_role"=>{"Professor > Associate Professor"=>3, "Researcher"=>10, "Student > Ph. D. Student"=>4, "Student > Postgraduate"=>3, "Student > Master"=>4, "Other"=>2, "Student > Bachelor"=>3, "Lecturer"=>1, "Professor"=>1}, "reader_count_by_subject_area"=>{"Engineering"=>1, "Biochemistry, Genetics and Molecular Biology"=>5, "Agricultural and Biological Sciences"=>22, "Medicine and Dentistry"=>1, "Psychology"=>1, "Social Sciences"=>1}, "reader_count_by_subdiscipline"=>{"Engineering"=>{"Engineering"=>1}, "Medicine and Dentistry"=>{"Medicine and Dentistry"=>1}, "Social Sciences"=>{"Social Sciences"=>1}, "Psychology"=>{"Psychology"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>22}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>5}}, "reader_count_by_country"=>{"United States"=>1, "Japan"=>1, "Denmark"=>1}, "group_count"=>2}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/591243"], "description"=>"<p>(A) Genomic organization around the large-deletion region based on CGSC 2.1.3/panTro3. An electrophoresis image shows PCR products of each c<i>TAS2R</i> with subject ID numbers at the top. Only subject 156 did not produce amplicons of c<i>TAS2R43</i>, c<i>TAS2R46</i>, and c<i>TAS2R64</i>. In this subject, c<i>TAS2R63P</i>, <i>IntA</i>, and <i>IntB</i> were also not amplified, whereas <i>IntC</i> was amplified (data not shown). (B) Using intC_F and int31-63_R as a PCR primer pair, only subject 153 and 156 produced amplicons of the expected size of 4,760 bp based on CGSC 2.1.3/panTro3. Subjects 153 and 156 were thought to be a heterozygote and a homozygote for the large-deletion variant, respectively. The sequences around the breakpoints of the large-deletion variant had similar arrangements of retrotransposons (<i>AluJr</i>, <i>L1MEg</i>, and <i>L1ME3B</i>), which were annotated with RepeatMasker (<a href=\"http://www.repeatmasker.org\" target=\"_blank\">http://www.repeatmasker.org</a>).</p>", "links"=>[], "tags"=>["large-deletion", "variant", "involving", "whole-gene", "deletions"], "article_id"=>261726, "categories"=>["Physiology", "Biological Sciences", "Neuroscience", "Evolutionary Biology"], "users"=>["Takashi Hayakawa", "Tohru Sugawara", "Yasuhiro Go", "Toshifumi Udono", "Hirohisa Hirai", "Hiroo Imai"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0043277.g001", "stats"=>{"downloads"=>1, "page_views"=>14, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_A_large_deletion_variant_involving_the_whole_gene_deletions_of_c_TAS2R43_c_TAS2R46_c_TAS2R63P_and_c_TAS2R64_/261726", "title"=>"A large-deletion variant involving the whole-gene deletions of c<i>TAS2R43</i>, c<i>TAS2R46</i>, c<i>TAS2R63P</i>, and c<i>TAS2R64</i>.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-08-16 00:28:46"}
  • {"files"=>["https://ndownloader.figshare.com/files/310223", "https://ndownloader.figshare.com/files/310317", "https://ndownloader.figshare.com/files/310497", "https://ndownloader.figshare.com/files/310585", "https://ndownloader.figshare.com/files/310691", "https://ndownloader.figshare.com/files/310747"], "description"=>"<div><p>Chimpanzees (<em>Pan troglodytes</em>) have region-specific difference in dietary repertoires from East to West across tropical Africa. Such differences may result from different genetic backgrounds in addition to cultural variations. We analyzed the sequences of all bitter taste receptor genes (c<em>TAS2R</em>s) in a total of 59 chimpanzees, including 4 putative subspecies. We identified genetic variations including single-nucleotide variations (SNVs), insertions and deletions (indels), gene-conversion variations, and copy-number variations (CNVs) in c<em>TAS2R</em>s. Approximately two-thirds of all c<em>TAS2R</em> haplotypes in the amino acid sequence were unique to each subspecies. We analyzed the evolutionary backgrounds of natural selection behind such diversification. Our previous study concluded that diversification of c<em>TAS2R</em>s in western chimpanzees (<em>P. t. verus</em>) may have resulted from balancing selection. In contrast, the present study found that purifying selection dominates as the evolutionary form of diversification of the so-called human cluster of c<em>TAS2R</em>s in eastern chimpanzees (<em>P. t. schweinfurthii</em>) and that the other c<em>TAS2R</em>s were under no obvious selection as a whole. Such marked diversification of c<em>TAS2R</em>s with different evolutionary backgrounds among subspecies of chimpanzees probably reflects their subspecies-specific dietary repertoires.</p> </div>", "links"=>[], "tags"=>["eco-geographical", "diversification", "receptor", "genes", "subspecies", "chimpanzees"], "article_id"=>121193, "categories"=>["Physiology", "Biological Sciences", "Neuroscience", "Evolutionary Biology"], "users"=>["Takashi Hayakawa", "Tohru Sugawara", "Yasuhiro Go", "Toshifumi Udono", "Hirohisa Hirai", "Hiroo Imai"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0043277.s001", "https://dx.doi.org/10.1371/journal.pone.0043277.s002", "https://dx.doi.org/10.1371/journal.pone.0043277.s003", "https://dx.doi.org/10.1371/journal.pone.0043277.s004", "https://dx.doi.org/10.1371/journal.pone.0043277.s005", "https://dx.doi.org/10.1371/journal.pone.0043277.s006"], "stats"=>{"downloads"=>6, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Eco_Geographical_Diversification_of_Bitter_Taste_Receptor_Genes_TAS2R_s_among_Subspecies_of_Chimpanzees_Pan_troglodytes_/121193", "title"=>"Eco-Geographical Diversification of Bitter Taste Receptor Genes (<em>TAS2R</em>s) among Subspecies of Chimpanzees (<em>Pan troglodytes</em>)", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2012-08-16 00:19:53"}
  • {"files"=>["https://ndownloader.figshare.com/files/591737"], "description"=>"a<p>Abbreviations: del., deletion; ins., insertion; LIC, loss of start (initiation) codon; GTC, gain of stop (termination) codon; WGD, whole-gene deletion; GC, gene conversion. There was no variation of loss of stop codon in c<i>TAS2R</i>s.</p>b<p>The subspecies of the individual was identified only maternally due to the lack of information about the antecedents in captivity.</p>c<p>The alleles have an alternative start codon at nucleotide positions 4 to 6, and thus are expected to be functional.</p>d<p>Gene conversion with c<i>TAS2R31</i> at nucleotide positions 514 to 586, expected to be functional.</p>e<p>Gene conversion with c<i>TAS2R19</i> at nucleotide positions 141 to 273, expected to be functional.</p>", "links"=>[], "tags"=>["whole-gene", "deletion"], "article_id"=>262228, "categories"=>["Physiology", "Biological Sciences", "Neuroscience", "Evolutionary Biology"], "users"=>["Takashi Hayakawa", "Tohru Sugawara", "Yasuhiro Go", "Toshifumi Udono", "Hirohisa Hirai", "Hiroo Imai"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0043277.t001", "stats"=>{"downloads"=>1, "page_views"=>14, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Variations_of_loss_of_start_codon_gain_of_stop_codon_indel_gene_conversion_and_whole_gene_deletion_in_c_TAS2R_s_/262228", "title"=>"Variations of loss of start codon, gain of stop codon, indel, gene conversion, and whole-gene deletion in c<i>TAS2R</i>s.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-08-16 00:37:08"}
  • {"files"=>["https://ndownloader.figshare.com/files/591322"], "description"=>"<p>(A, B) The distribution of all haplotypes in the 4 subspecies. (C, D) The distribution of high-frequency haplotypes in western and eastern chimpanzees. Subspecies of a Nigerian-Cameroonian chimpanzee was identified only maternally due to a lack of information about the antecedents in captivity. The number of non-functional haplotypes (segregating pseudogenes and whole-gene deletions) is indicated in parentheses. High-frequency haplotypes were observed in more than one sampled chromosome.</p>", "links"=>[], "tags"=>["subspecies", "haplotypes", "28"], "article_id"=>261812, "categories"=>["Physiology", "Biological Sciences", "Neuroscience", "Evolutionary Biology"], "users"=>["Takashi Hayakawa", "Tohru Sugawara", "Yasuhiro Go", "Toshifumi Udono", "Hirohisa Hirai", "Hiroo Imai"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0043277.g002", "stats"=>{"downloads"=>0, "page_views"=>1, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_subspecies_distribution_of_the_number_of_haplotypes_in_the_28_c_TAS2R_s_/261812", "title"=>"The subspecies distribution of the number of haplotypes in the 28 c<i>TAS2R</i>s.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-08-16 00:30:12"}
  • {"files"=>["https://ndownloader.figshare.com/files/591696"], "description"=>"a<p>Data from Sugawara et al. <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0043277#pone.0043277-Sugawara1\" target=\"_blank\">[15]</a>.</p>b<p>Nucleotide diversity within the subspecies.</p>c<p>Synonymous diversity within the subspecies.</p>d<p>Non-synonymous diversity within the subspecies.</p>e<p>Tajima’s <i>D</i>. Two-sided Tajima’s <i>D</i> test were conducted using coalescent simulations under 10,000 replicates, assuming no recombination and a Poisson distribution of mutations along the lineages. *<i>P</i><0.05.</p>f<p>Nucleotide divergence beween western and eastern chimpanzees.</p>", "links"=>[], "tags"=>["divergence"], "article_id"=>262192, "categories"=>["Physiology", "Biological Sciences", "Neuroscience", "Evolutionary Biology"], "users"=>["Takashi Hayakawa", "Tohru Sugawara", "Yasuhiro Go", "Toshifumi Udono", "Hirohisa Hirai", "Hiroo Imai"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0043277.t002", "stats"=>{"downloads"=>6, "page_views"=>1, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Nucleotide_diversity_and_divergence_of_c_TAS2R_s_in_western_and_eastern_chimpanzees_/262192", "title"=>"Nucleotide diversity and divergence of c<i>TAS2R</i>s in western and eastern chimpanzees.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-08-16 00:36:32"}
  • {"files"=>["https://ndownloader.figshare.com/files/591602"], "description"=>"<p>This plot was composed from a total of 174 SNVs in western and eastern chimpanzees. Sampled chromosomes carrying whole-gene deletions were omitted from the calculation. Mutation types and amino acid positions of SNVs with higher <i>F</i><sub>ST</sub> are shown. Ancestral and derived amino acids were estimated from the haplotype networks. The protein locations are also shown based on Sugawara et al. <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0043277#pone.0043277-Sugawara1\" target=\"_blank\">[15]</a> (EC, extracellular region; TM, transmembrane region; IC, intracellular region).</p>", "links"=>[], "tags"=>["histogram", "cumulative", "snvs", "28"], "article_id"=>262094, "categories"=>["Physiology", "Biological Sciences", "Neuroscience", "Evolutionary Biology"], "users"=>["Takashi Hayakawa", "Tohru Sugawara", "Yasuhiro Go", "Toshifumi Udono", "Hirohisa Hirai", "Hiroo Imai"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0043277.g004", "stats"=>{"downloads"=>0, "page_views"=>1, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_histogram_and_cumulative_frequency_curve_of_F_ST_in_SNVs_in_the_28_c_TAS2R_s_/262094", "title"=>"The histogram and cumulative frequency curve of <i>F</i><sub>ST</sub> in SNVs in the 28 c<i>TAS2R</i>s.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-08-16 00:34:54"}
  • {"files"=>["https://ndownloader.figshare.com/files/591514"], "description"=>"<p>Circles represent haplotypes. Hap<i>n</i> indicates haplotype <i>n</i> (<a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0043277#pone.0043277.s003\" target=\"_blank\">Table S1</a>). The letter (P) is added to pseudogenes. Color within the circle indicates each subspecies. Areas and numbers within color-coded parts of the circles indicate the numbers of sampled chromosomes. Numbers along branches indicate nucleotide positions of mutation between the haplotypes. Line styles of branches indicate mutation types of nucleotide changes.</p>", "links"=>[], "tags"=>["networks"], "article_id"=>262008, "categories"=>["Physiology", "Biological Sciences", "Neuroscience", "Evolutionary Biology"], "users"=>["Takashi Hayakawa", "Tohru Sugawara", "Yasuhiro Go", "Toshifumi Udono", "Hirohisa Hirai", "Hiroo Imai"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0043277.g003", "stats"=>{"downloads"=>0, "page_views"=>1, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Median_joining_networks_for_c_TAS2R_s_/262008", "title"=>"Median-joining networks for c<i>TAS2R</i>s.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-08-16 00:33:28"}
  • {"files"=>["https://ndownloader.figshare.com/files/591664"], "description"=>"a<p>Two-sided Fisher’s exact test.</p>b<p>Two-sided Wilcoxon rank sum test in comparison with data of non-coding loci from Fischer et al. <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0043277#pone.0043277-Fischer1\" target=\"_blank\">[22]</a>.</p>c<p>Data from Sugawara et al. <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0043277#pone.0043277-Sugawara1\" target=\"_blank\">[15]</a>.</p>", "links"=>[], "tags"=>["physiology", "Computational biology", "neuroscience", "Evolutionary biology"], "article_id"=>262153, "categories"=>["Physiology", "Biological Sciences", "Neuroscience", "Evolutionary Biology"], "users"=>["Takashi Hayakawa", "Tohru Sugawara", "Yasuhiro Go", "Toshifumi Udono", "Hirohisa Hirai", "Hiroo Imai"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0043277.t003", "stats"=>{"downloads"=>2, "page_views"=>1, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Analyses_of_natural_selection_of_c_TAS2R_s_in_western_and_eastern_chimpanzees_/262153", "title"=>"Analyses of natural selection of c<i>TAS2R</i>s in western and eastern chimpanzees.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-08-16 00:35:53"}

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Relative Metric

{"start_date"=>"2012-01-01T00:00:00Z", "end_date"=>"2012-12-31T00:00:00Z", "subject_areas"=>[{"subject_area"=>"/Biology and life sciences/Evolutionary biology", "average_usage"=>[366, 574, 695, 795, 885, 973, 1063, 1148, 1233, 1319, 1389, 1459, 1533, 1611, 1685, 1754, 1820, 1882, 1937, 2001, 2071, 2129, 2219, 2273, 2335]}]}
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