Trait Variation in Yeast Is Defined by Population History
Publication Date
June 16, 2011
Journal
PLOS Genetics
Authors
Jonas Warringer, Enikö Zörgö, Francisco A. Cubillos, Amin Zia, et al
Volume
7
Issue
6
Pages
e1002111
DOI
https://dx.plos.org/10.1371/journal.pgen.1002111
Publisher URL
http://journals.plos.org/plosgenetics/article?id=10.1371%2Fjournal.pgen.1002111
PubMed
http://www.ncbi.nlm.nih.gov/pubmed/21698134
PubMed Central
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3116910
Europe PMC
http://europepmc.org/abstract/MED/21698134
Web of Science
000292386300069
Scopus
79959847334
Mendeley
http://www.mendeley.com/research/trait-variation-yeast-defined-population-history-8
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CiteULike | Further Information

Mendeley | Further Information

{"title"=>"Trait variation in yeast is defined by population history", "type"=>"journal", "authors"=>[{"first_name"=>"Jonas", "last_name"=>"Warringer", "scopus_author_id"=>"6507234725"}, {"first_name"=>"Enikö", "last_name"=>"Zörgö", "scopus_author_id"=>"37087952600"}, {"first_name"=>"Francisco A.", "last_name"=>"Cubillos", "scopus_author_id"=>"55498073900"}, {"first_name"=>"Amin", "last_name"=>"Zia", "scopus_author_id"=>"6602868410"}, {"first_name"=>"Arne", "last_name"=>"Gjuvsland", "scopus_author_id"=>"15834440000"}, {"first_name"=>"Jared T.", "last_name"=>"Simpson", "scopus_author_id"=>"26641454000"}, {"first_name"=>"Annabelle", "last_name"=>"Forsmark", "scopus_author_id"=>"11839833300"}, {"first_name"=>"Richard", "last_name"=>"Durbin", "scopus_author_id"=>"7102868950"}, {"first_name"=>"Stig W.", "last_name"=>"Omholt", "scopus_author_id"=>"6603707763"}, {"first_name"=>"Edward J.", "last_name"=>"Louis", "scopus_author_id"=>"7202755363"}, {"first_name"=>"Gianni", "last_name"=>"Liti", "scopus_author_id"=>"6508269095"}, {"first_name"=>"Alan", "last_name"=>"Moses", "scopus_author_id"=>"56839913500"}, {"first_name"=>"Anders", "last_name"=>"Blomberg", "scopus_author_id"=>"56348611800"}], "year"=>2011, "source"=>"PLoS Genetics", "identifiers"=>{"issn"=>"15537390", "scopus"=>"2-s2.0-79959847334", "sgr"=>"79959847334", "pui"=>"362058254", "isbn"=>"1553-7404 (Electronic)\\n1553-7390 (Linking)", "pmid"=>"21698134", "doi"=>"10.1371/journal.pgen.1002111"}, "id"=>"69b5aceb-9007-3299-89c5-20d1c381c31c", "abstract"=>"A fundamental goal in biology is to achieve a mechanistic understanding of how and to what extent ecological variation imposes selection for distinct traits and favors the fixation of specific genetic variants. Key to such an understanding is the detailed mapping of the natural genomic and phenomic space and a bridging of the gap that separates these worlds. Here we chart a high-resolution map of natural trait variation in one of the most important genetic model organisms, the budding yeast Saccharomyces cerevisiae, and its closest wild relatives and trace the genetic basis and timing of major phenotype changing events in its recent history. We show that natural trait variation in S. cerevisiae exceeds that of its relatives, despite limited genetic variation, and follows the population history rather than the source environment. In particular, the West African population is phenotypically unique, with an extreme abundance of low-performance alleles, notably a premature translational termination signal in GAL3 that cause inability to utilize galactose. Our observations suggest that many S. cerevisiae traits may be the consequence of genetic drift rather than selection, in line with the assumption that natural yeast lineages are remnants of recent population bottlenecks. Disconcertingly, the universal type strain S288C was found to be highly atypical, highlighting the danger of extrapolating gene-trait connections obtained in mosaic, lab-domesticated lineages to the species as a whole. Overall, this study represents a step towards an in-depth understanding of the causal relationship between co-variation in ecology, selection pressure, natural traits, molecular mechanism, and alleles in a key model organism.", "link"=>"http://www.mendeley.com/research/trait-variation-yeast-defined-population-history-8", "reader_count"=>274, "reader_count_by_academic_status"=>{"Unspecified"=>3, "Professor > Associate Professor"=>18, "Researcher"=>62, "Student > Doctoral Student"=>11, "Student > Ph. D. Student"=>84, "Student > Postgraduate"=>12, "Student > Master"=>36, "Other"=>6, "Student > Bachelor"=>21, "Lecturer"=>1, "Professor"=>20}, "reader_count_by_user_role"=>{"Unspecified"=>3, "Professor > Associate Professor"=>18, "Researcher"=>62, "Student > Doctoral Student"=>11, "Student > Ph. D. Student"=>84, "Student > Postgraduate"=>12, "Student > Master"=>36, "Other"=>6, "Student > Bachelor"=>21, "Lecturer"=>1, "Professor"=>20}, "reader_count_by_subject_area"=>{"Unspecified"=>6, "Agricultural and Biological Sciences"=>200, "Arts and Humanities"=>1, "Chemical Engineering"=>2, "Chemistry"=>2, "Computer Science"=>2, "Engineering"=>2, "Environmental Science"=>1, "Biochemistry, Genetics and Molecular Biology"=>47, "Nursing and Health Professions"=>1, "Medicine and Dentistry"=>6, "Physics and Astronomy"=>3, "Immunology and Microbiology"=>1}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>6}, "Physics and Astronomy"=>{"Physics and Astronomy"=>3}, "Unspecified"=>{"Unspecified"=>6}, "Environmental Science"=>{"Environmental Science"=>1}, "Chemical Engineering"=>{"Chemical Engineering"=>2}, "Arts and Humanities"=>{"Arts and Humanities"=>1}, "Engineering"=>{"Engineering"=>2}, "Chemistry"=>{"Chemistry"=>2}, "Immunology and Microbiology"=>{"Immunology and Microbiology"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>200}, "Computer Science"=>{"Computer Science"=>2}, "Nursing and Health Professions"=>{"Nursing and Health Professions"=>1}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>47}}, "reader_count_by_country"=>{"Colombia"=>2, "United States"=>13, "United Kingdom"=>4, "Thailand"=>1, "Portugal"=>1, "Spain"=>2, "Canada"=>3, "Austria"=>1, "Belgium"=>1, "Norway"=>1, "Denmark"=>1, "Brazil"=>1, "Chile"=>3, "France"=>1}, "group_count"=>14}

CrossRef

Scopus | Further Information

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/764201"], "description"=>"<p>Hierarchical clustering of <i>Saccharomyces sensu stricto</i> isolates based on trait profiles over 600 traits (all proliferation variables) performed using a centered Pearson correlation metric and average linkage mapping. Species are indicated by line color. For <i>S. cerevisiae</i> isolates, source habitats (shape) and populations (color) are indicated with symbols. Heat map depicts the relative proliferation rate (Log<sub>2</sub> [BY4741/strain]); relative proliferation lag and efficiency are given in <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1002111#pgen.1002111.s008\" target=\"_blank\">Figure S7</a>. Green = inferior proliferation, red = superior proliferation, black = BY4741 proliferation, grey = missing data.</p>", "links"=>[], "tags"=>["variations", "sensu"], "article_id"=>434562, "categories"=>["Genetics", "Microbiology"], "users"=>["Jonas Warringer", "Enikö Zörgö", "Francisco A. Cubillos", "Amin Zia", "Arne Gjuvsland", "Jared T. Simpson", "Annabelle Forsmark", "Richard Durbin", "Stig W. Omholt", "Edward J. Louis", "Gianni Liti", "Alan Moses", "Anders Blomberg"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1002111.g002", "stats"=>{"downloads"=>2, "page_views"=>9, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Trait_variations_within_Saccharomyces_sensu_stricto_species_/434562", "title"=>"Trait variations within <i>Saccharomyces sensu stricto</i> species.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-06-16 01:16:02"}
  • {"files"=>["https://ndownloader.figshare.com/files/764396"], "description"=>"<p>A <i>S. cerevisiae</i> mean trait profile was calculated and the similarity (Pearson correlation) between the trait profile of each individual <i>S. cerevisiae</i> isolate and the <i>S. cerevisiae</i> mean trait profile was obtained. Strains were ranked according to degree of similarity. The universal reference strain S288C (arrow) was found to be a phenotypic extreme. * = Isolates with auxotrophic markers; these were excluded from calculations of the mean trait profile.</p>", "links"=>[], "tags"=>["s288c", "phenotypic"], "article_id"=>434756, "categories"=>["Genetics", "Microbiology"], "users"=>["Jonas Warringer", "Enikö Zörgö", "Francisco A. Cubillos", "Amin Zia", "Arne Gjuvsland", "Jared T. Simpson", "Annabelle Forsmark", "Richard Durbin", "Stig W. Omholt", "Edward J. Louis", "Gianni Liti", "Alan Moses", "Anders Blomberg"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1002111.g003", "stats"=>{"downloads"=>1, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_S_cerevisiae_type_strain_S288C_is_a_phenotypic_extreme_/434756", "title"=>"The <i>S. cerevisiae</i> type strain S288C is a phenotypic extreme.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-06-16 01:19:16"}
  • {"files"=>["https://ndownloader.figshare.com/files/764492"], "description"=>"<p>The frequency of population specific traits for each <i>S. cerevisiae</i> population mapped onto a recently established population genomics tree based on low coverage genome sequence data <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1002111#pgen.1002111-Liti2\" target=\"_blank\">[16]</a>. Population specific traits were defined as traits for which the performance of one population deviated significantly from the performance of isolates in all other populations (FDR = 2%), Percentages indicate frequency of population specific traits. Total number of population specific traits: West African = 190, European = 30, North American = 13, Malaysian = 13 and Sake = 3.</p>", "links"=>[], "tags"=>["phenotypic"], "article_id"=>434858, "categories"=>["Genetics", "Microbiology"], "users"=>["Jonas Warringer", "Enikö Zörgö", "Francisco A. Cubillos", "Amin Zia", "Arne Gjuvsland", "Jared T. Simpson", "Annabelle Forsmark", "Richard Durbin", "Stig W. Omholt", "Edward J. Louis", "Gianni Liti", "Alan Moses", "Anders Blomberg"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1002111.g004", "stats"=>{"downloads"=>1, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Reconstructing_the_phenotypic_history_of_S_cerevisiae_/434858", "title"=>"Reconstructing the phenotypic history of <i>S. cerevisiae</i>.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-06-16 01:20:58"}
  • {"files"=>["https://ndownloader.figshare.com/files/764922"], "description"=>"<p>A) A copy number variation in <i>ENA</i> gene locus associates to Na<sup>+</sup> and Li<sup>+</sup> tolerance in natural <i>S. cerevisiae</i> isolates. Strains were divided into equally sized bins on the basis of an estimate of <i>ENA</i> copy numbers, log[(1+observed reads)/(1+expected reads)], and the average proliferative efficiency in presence of Na<sup>+</sup> and Li<sup>+</sup> was determined in each bin. Error bars = standard errors. B) Linkage analysis of crosses between representatives of natural yeast populations supports co-segregation of the marker closest to the <i>ENA</i> locus and proliferation during Li<sup>+</sup> (left panel) and Na<sup>+</sup> (right panel) exposure. Left panel: a cross between the West African DBVPG6044 and the European DBVPG6765, right panel: a cross between the Sake Y12 and the European DBVPG6765. For each cross, 96 haploid F1 offspring were obtained, genotyped for parental genotype at 130 chromosomal markers loci and the proliferative ability in presence of 1 M NaCl and 0.225 mM LiCl was determined. Chromosome numbers indicate centromere position and tick marks indicate marker position. C) Unrooted N-J tree based on a multiple alignment of <i>ENA1, 2</i> and <i>5</i> from the <i>S. cerevisiae</i> reference genome, <i>ENA6</i> obtained from the mosaic CEN.PK2 strain <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1002111#pgen.1002111-DaranLapujade1\" target=\"_blank\">[37]</a>, and all <i>ENA</i> genes detected in <i>S. paradoxus</i>, <i>S. bayanus</i> and <i>S. mikatae</i>. D) <i>ENA6</i> from the West African derived SK1 was transferred to an <i>ENA</i> triple deletion (<i>ena1</i>Δ<i>2</i>Δ<i>5</i>Δ) in the mostly European BY4741. The proliferative rate (doubling time, h) and efficiency (density change, OD units) of the WT (<i>ENA1,2,5</i>), <i>ena1</i>Δ<i>2</i>Δ<i>5</i>Δ, and <i>ena1</i>Δ<i>2</i>Δ<i>5</i>Δ+<i>ENA6</i> strains (n = 4–8, error bars = standard errors) in 0.5 M NaCl, 1.4 M NaCl and 0.3 M LiCl were measured. E) The proliferative rate (doubling time, h) and lag (adaptation time, h) of the WT (<i>ENA1,2,5</i>), <i>ena1</i>Δ<i>2</i>Δ<i>5</i>Δ, and <i>ena1</i>Δ<i>2</i>Δ<i>5</i>Δ+<i>ENA6</i> strains (n = 4–8, error bars = standard errors) in pH 7, 1 mM CuCl<sub>2</sub>, 2 M KCl, 10 mM methylglyoxal and 80 mM dihydoxyacetone (DHA).</p>", "links"=>[], "tags"=>["introgressed", "serially", "amplified", "paradoxus", "causes", "pleiotropy"], "article_id"=>435275, "categories"=>["Genetics", "Microbiology"], "users"=>["Jonas Warringer", "Enikö Zörgö", "Francisco A. Cubillos", "Amin Zia", "Arne Gjuvsland", "Jared T. Simpson", "Annabelle Forsmark", "Richard Durbin", "Stig W. Omholt", "Edward J. Louis", "Gianni Liti", "Alan Moses", "Anders Blomberg"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1002111.g007", "stats"=>{"downloads"=>1, "page_views"=>13, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_An_introgressed_and_serially_amplified_S_paradoxus_ENA_gene_causes_pleiotropy_in_S_cerevisiae_/435275", "title"=>"An introgressed and serially amplified <i>S. paradoxus ENA</i> gene causes pleiotropy in <i>S. cerevisiae</i>.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-06-16 01:27:55"}
  • {"files"=>["https://ndownloader.figshare.com/files/384460", "https://ndownloader.figshare.com/files/384481", "https://ndownloader.figshare.com/files/384524", "https://ndownloader.figshare.com/files/384576", "https://ndownloader.figshare.com/files/384619", "https://ndownloader.figshare.com/files/384660", "https://ndownloader.figshare.com/files/384705", "https://ndownloader.figshare.com/files/384746", "https://ndownloader.figshare.com/files/384852", "https://ndownloader.figshare.com/files/384900", "https://ndownloader.figshare.com/files/384937", "https://ndownloader.figshare.com/files/384975", "https://ndownloader.figshare.com/files/385003", "https://ndownloader.figshare.com/files/385035", "https://ndownloader.figshare.com/files/385073", "https://ndownloader.figshare.com/files/385094", "https://ndownloader.figshare.com/files/385127", "https://ndownloader.figshare.com/files/385265", "https://ndownloader.figshare.com/files/385302", "https://ndownloader.figshare.com/files/385347", "https://ndownloader.figshare.com/files/385418", "https://ndownloader.figshare.com/files/385497", "https://ndownloader.figshare.com/files/385557", "https://ndownloader.figshare.com/files/385604", "https://ndownloader.figshare.com/files/385687", "https://ndownloader.figshare.com/files/385721"], "description"=>"<div><p>A fundamental goal in biology is to achieve a mechanistic understanding of how and to what extent ecological variation imposes selection for distinct traits and favors the fixation of specific genetic variants. Key to such an understanding is the detailed mapping of the natural genomic and phenomic space and a bridging of the gap that separates these worlds. Here we chart a high-resolution map of natural trait variation in one of the most important genetic model organisms, the budding yeast <em>Saccharomyces cerevisiae</em>, and its closest wild relatives and trace the genetic basis and timing of major phenotype changing events in its recent history. We show that natural trait variation in <em>S. cerevisiae</em> exceeds that of its relatives, despite limited genetic variation, and follows the population history rather than the source environment. In particular, the West African population is phenotypically unique, with an extreme abundance of low-performance alleles, notably a premature translational termination signal in <em>GAL3</em> that cause inability to utilize galactose. Our observations suggest that many <em>S. cerevisiae</em> traits may be the consequence of genetic drift rather than selection, in line with the assumption that natural yeast lineages are remnants of recent population bottlenecks. Disconcertingly, the universal type strain S288C was found to be highly atypical, highlighting the danger of extrapolating gene-trait connections obtained in mosaic, lab-domesticated lineages to the species as a whole. Overall, this study represents a step towards an in-depth understanding of the causal relationship between co-variation in ecology, selection pressure, natural traits, molecular mechanism, and alleles in a key model organism.</p> </div>", "links"=>[], "tags"=>["yeast", "defined"], "article_id"=>135916, "categories"=>["Genetics", "Microbiology"], "users"=>["Jonas Warringer", "Enikö Zörgö", "Francisco A. Cubillos", "Amin Zia", "Arne Gjuvsland", "Jared T. Simpson", "Annabelle Forsmark", "Richard Durbin", "Stig W. Omholt", "Edward J. Louis", "Gianni Liti", "Alan Moses", "Anders Blomberg"], "doi"=>["https://dx.doi.org/10.1371/journal.pgen.1002111.s001", "https://dx.doi.org/10.1371/journal.pgen.1002111.s002", "https://dx.doi.org/10.1371/journal.pgen.1002111.s003", "https://dx.doi.org/10.1371/journal.pgen.1002111.s004", "https://dx.doi.org/10.1371/journal.pgen.1002111.s005", "https://dx.doi.org/10.1371/journal.pgen.1002111.s006", "https://dx.doi.org/10.1371/journal.pgen.1002111.s007", "https://dx.doi.org/10.1371/journal.pgen.1002111.s008", "https://dx.doi.org/10.1371/journal.pgen.1002111.s009", "https://dx.doi.org/10.1371/journal.pgen.1002111.s010", "https://dx.doi.org/10.1371/journal.pgen.1002111.s011", "https://dx.doi.org/10.1371/journal.pgen.1002111.s012", "https://dx.doi.org/10.1371/journal.pgen.1002111.s013", "https://dx.doi.org/10.1371/journal.pgen.1002111.s014", "https://dx.doi.org/10.1371/journal.pgen.1002111.s015", "https://dx.doi.org/10.1371/journal.pgen.1002111.s016", "https://dx.doi.org/10.1371/journal.pgen.1002111.s017", "https://dx.doi.org/10.1371/journal.pgen.1002111.s018", "https://dx.doi.org/10.1371/journal.pgen.1002111.s019", "https://dx.doi.org/10.1371/journal.pgen.1002111.s020", "https://dx.doi.org/10.1371/journal.pgen.1002111.s021", "https://dx.doi.org/10.1371/journal.pgen.1002111.s022", "https://dx.doi.org/10.1371/journal.pgen.1002111.s023", "https://dx.doi.org/10.1371/journal.pgen.1002111.s024", "https://dx.doi.org/10.1371/journal.pgen.1002111.s025", "https://dx.doi.org/10.1371/journal.pgen.1002111.s026"], "stats"=>{"downloads"=>34, "page_views"=>18, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Trait_Variation_in_Yeast_Is_Defined_by_Population_History/135916", "title"=>"Trait Variation in Yeast Is Defined by Population History", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2011-06-16 01:38:36"}
  • {"files"=>["https://ndownloader.figshare.com/files/764812"], "description"=>"<p>A) A gene amplification of <i>CUP1</i> associates strongly to copper tolerance in <i>S. cerevisiae</i>. The proliferative efficiency of each <i>S. cerevisiae</i> isolate in presence of 0.75 mM CuCl<sub>2</sub> versus the <i>CUP1</i> gene number estimate for each strain is displayed. The gene number estimate was defined as log[(1+observed reads)/(1+expected reads)]. Linear correlation is displayed. B) To verify a causative link between the <i>CUP1</i> CNV and copper tolerance, the European DBVPG6765 was crossed to the North American YPS128, 96 haploid offspring were obtained after meiotic recombination and co-inheritance of the proliferation performance during 0.75 mM CuCl2 exposure and 130 chromosomal markers was investigated using linkage analysis <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1002111#pgen.1002111-Cubillos1\" target=\"_blank\">[26]</a>. Chromosome numbers indicate centromere position on each chromosome and tick marks marker position. C) The <i>CUP1</i> region in the West African DBVPG6044, the Sake Y12 and the European derived mosaic W303, was determined by high coverage (25–31×) sequencing. The gene arrangement in DBVPG6044 agreed with the <i>S. paradoxus</i> reference assembly and no amplifications were detected. For Y12 and W303, amplified segments, but not gene arrangements, could be unambiguously determined. Two independent segment amplifications were detected in Y12, encompassing only <i>CUP1</i> and <i>CUP1</i> plus 1624 bp of the neighboring <i>RSC30</i> respectively. One amplified segment, encompassing <i>CUP1</i> plus 1069 bp of <i>RSC30</i>, was detected in W303. Breakpoints were completely strain specific: no Y12 reads matched the W303 breakpoint and no W303 reads matched the Y12 breakpoints. The W303 amplification matched the known amplification in the S288C reference genome.</p>", "links"=>[], "tags"=>["amplifications", "populations", "convergent", "copper"], "article_id"=>435170, "categories"=>["Genetics", "Microbiology"], "users"=>["Jonas Warringer", "Enikö Zörgö", "Francisco A. Cubillos", "Amin Zia", "Arne Gjuvsland", "Jared T. Simpson", "Annabelle Forsmark", "Richard Durbin", "Stig W. Omholt", "Edward J. Louis", "Gianni Liti", "Alan Moses", "Anders Blomberg"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1002111.g006", "stats"=>{"downloads"=>2, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Parallel_amplifications_of_CUP1_in_S_cerevisiae_populations_reflect_convergent_evolution_for_copper_tolerance_/435170", "title"=>"Parallel amplifications of <i>CUP1</i> in <i>S. cerevisiae</i> populations reflect convergent evolution for copper tolerance.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-06-16 01:26:10"}
  • {"files"=>["https://ndownloader.figshare.com/files/764670"], "description"=>"<p>A) Potential loss-of-function polymorphisms in the galactose utilization pathway in the West African population; a premature stop codon in <i>GAL3</i> and out of frame deletions in <i>GAL2</i> and <i>GAL4</i>. B) A TGC→TGA (C→Stop) mutation in <i>GAL3</i> associates (Bonferroni corrected Student's t-test p<0.015 and Kolmygorov-Smirnov p<0.15) to the proliferative lag during initiation of galactose proliferation in natural <i>S. cerevisiae</i> strains. Three West African derived genomes contain the variant mutation, 18 other strains contain the reference sequence. C) Linkage analysis of a cross between the West African DBVPG6044 and the North American YPS128 supports a link between <i>GAL3</i> and poor galactose utilization. 96 haploid F1 offspring were genotyped at 130 chromosomal markers and the degree of galactose growth was determined. Chromosome numbers indicate centromere position and tick marks indicate marker position. D) Proliferation of hemizygote BY4741 (<i>gal3</i>Δ)×DBVPG6044 (n = 3), and the parentals DBVPG6044 (n = 2) and BY4741 (n = 2) using galactose as carbon source. E) Population doubling time (rate) and total change in population density (efficiency) of the hemizygote BY4741 (<i>galx</i>Δ)×273614N as compared to the parentals BY4741 and 273614 (n = 3) using galactose as carbon source. Error bars = standard errors. F) Average proliferative rates of strains in the Malaysian population (including the partially Malaysian UWOPS87-2421), the West African population (including the partially West African Y55) and all other <i>S. cerevisiae</i> strains, using melibiose as carbon source. Error bars = standard errors. G) Rooted N-J tree based on a multiple alignment of <i>MEL1</i> from the <i>S. cerevisiae</i> Malaysian (UWOPS05_217_3) and West African (Y55) populations, a <i>S. paradoxus</i> Hawaiian isolate (UWOPS91-917.1), the <i>S. cerevisiae MEL1</i> sequence stored in SGD, and previously reported <i>MEL1</i> sequences from <i>S. mikatae</i> (S.m), <i>S. bayanus</i> (S.b) and <i>S. paradoxus</i> (S.p) <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1002111#pgen.1002111-Naumova1\" target=\"_blank\">[53]</a>.</p>", "links"=>[], "tags"=>["parallel", "inactivation", "galactose", "utilization"], "article_id"=>435031, "categories"=>["Genetics", "Microbiology"], "users"=>["Jonas Warringer", "Enikö Zörgö", "Francisco A. Cubillos", "Amin Zia", "Arne Gjuvsland", "Jared T. Simpson", "Annabelle Forsmark", "Richard Durbin", "Stig W. Omholt", "Edward J. Louis", "Gianni Liti", "Alan Moses", "Anders Blomberg"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1002111.g005", "stats"=>{"downloads"=>2, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Recent_parallel_inactivation_of_galactose_utilization_in_multiple_S_cerevisiae_lineages_/435031", "title"=>"Recent, parallel inactivation of galactose utilization in multiple <i>S. cerevisiae</i> lineages.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-06-16 01:23:51"}
  • {"files"=>["https://ndownloader.figshare.com/files/764075"], "description"=>"<p>A) The proliferative lag (time to initiate proliferation), proliferative rate (population doubling time) and proliferative efficiency (change in population density) were extracted from high density growth curves (n = 2) of 86 <i>Saccharomyces sensu stricto</i> isolates over ∼200 environments. B) The fitness components proliferative lag, rate and efficiency were compared over all isolates and environments. Black line depicts linear correlation between the proliferative rate and efficiency (Pearson, r = 0.77). C) Hierarchical clustering of species trait averages. D) Comparing trait averages of the <i>S. bayanus</i>/<i>S. kudriavzevii</i>/<i>S. arboricolus</i> clade versus the <i>S. cerevisiae</i>/<i>S. paradoxus</i>/<i>S. mikatae</i> clade over all traits. Line indicates 1∶1 correlation. E) Frequency of significant (Student's t-test, Bonferroni correction, p<0.1) trait differences between the <i>S. bayanus</i>/<i>S. kudriavzevii</i>/<i>S. arboricolus</i> clade and the <i>S. cerevisiae</i>/<i>S. paradoxus</i>/<i>S. mikatae</i> clade, considering each class of environmental variation individually. F) Frequency of significant (Student's t-test, Bonferroni correction, p<0.1) trait differences for each species in comparison to <i>S. cerevisiae</i>.</p>", "links"=>[], "tags"=>["sensu"], "article_id"=>434428, "categories"=>["Genetics", "Microbiology"], "users"=>["Jonas Warringer", "Enikö Zörgö", "Francisco A. Cubillos", "Amin Zia", "Arne Gjuvsland", "Jared T. Simpson", "Annabelle Forsmark", "Richard Durbin", "Stig W. Omholt", "Edward J. Louis", "Gianni Liti", "Alan Moses", "Anders Blomberg"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1002111.g001", "stats"=>{"downloads"=>1, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Trait_variation_between_Saccharomyces_sensu_stricto_species_/434428", "title"=>"Trait variation between <i>Saccharomyces sensu stricto</i> species.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-06-16 01:13:48"}

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  • {"unique-ip"=>"27", "full-text"=>"27", "pdf"=>"6", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"12", "cited-by"=>"0", "year"=>"2019", "month"=>"5"}
  • {"unique-ip"=>"18", "full-text"=>"14", "pdf"=>"1", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"4", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"8"}
  • {"unique-ip"=>"13", "full-text"=>"13", "pdf"=>"4", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"1", "cited-by"=>"0", "year"=>"2019", "month"=>"9"}

Relative Metric

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