Y Fuse? Sex Chromosome Fusions in Fishes and Reptiles
Publication Date
May 20, 2015
Journal
PLOS Genetics
Authors
Matthew W. Pennell, Mark Kirkpatrick, Sarah P. Otto, Jana C. Vamosi, et al
Volume
11
Issue
5
Pages
e1005237
DOI
https://dx.plos.org/10.1371/journal.pgen.1005237
Publisher URL
http://journals.plos.org/plosgenetics/article?id=10.1371%2Fjournal.pgen.1005237
PubMed
http://www.ncbi.nlm.nih.gov/pubmed/25993542
PubMed Central
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4439076
Europe PMC
http://europepmc.org/abstract/MED/25993542
Web of Science
000355305200047
Scopus
84930798450
Mendeley
http://www.mendeley.com/research/y-fuse-sex-chromosome-fusions-fishes-reptiles
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Mendeley | Further Information

{"title"=>"Y Fuse? Sex Chromosome Fusions in Fishes and Reptiles", "type"=>"journal", "authors"=>[{"first_name"=>"Matthew W.", "last_name"=>"Pennell", "scopus_author_id"=>"55261367000"}, {"first_name"=>"Mark", "last_name"=>"Kirkpatrick", "scopus_author_id"=>"7103091513"}, {"first_name"=>"Sarah P.", "last_name"=>"Otto", "scopus_author_id"=>"7101616327"}, {"first_name"=>"Jana C.", "last_name"=>"Vamosi", "scopus_author_id"=>"6602117604"}, {"first_name"=>"Catherine L.", "last_name"=>"Peichel", "scopus_author_id"=>"6602163057"}, {"first_name"=>"Nicole", "last_name"=>"Valenzuela", "scopus_author_id"=>"6701409094"}, {"first_name"=>"Jun", "last_name"=>"Kitano", "scopus_author_id"=>"6603793505"}], "year"=>2015, "source"=>"PLoS Genetics", "identifiers"=>{"scopus"=>"2-s2.0-84930798450", "doi"=>"10.1371/journal.pgen.1005237", "sgr"=>"84930798450", "isbn"=>"1553-7404", "pmid"=>"25993542", "issn"=>"15537404", "pui"=>"604817995"}, "id"=>"de6675a5-f8a0-37fc-bfa1-0d4d2152e80c", "abstract"=>"Chromosomal fusion plays a recurring role in the evolution of adaptations and reproductive isolation among species, yet little is known of the evolutionary drivers of chromosomal fusions. Because sex chromosomes (X and Y in male heterogametic systems, Z and W in female heterogametic systems) differ in their selective, mutational, and demographic environments, those differences provide a unique opportunity to dissect the evolutionary forces that drive chromosomal fusions. We estimate the rate at which fusions between sex chromosomes and autosomes become established across the phylogenies of both fishes and squamate reptiles. Both the incidence among extant species and the establishment rate of Y-autosome fusions is much higher than for X-autosome, Z-autosome, or W-autosome fusions. Using population genetic models, we show that this pattern cannot be reconciled with many standard explanations for the spread of fusions. In particular, direct selection acting on fusions or sexually antagonistic selection cannot, on their own, account for the predominance of Y-autosome fusions. The most plausible explanation for the observed data seems to be (a) that fusions are slightly deleterious, and (b) that the mutation rate is male-biased or the reproductive sex ratio is female-biased. We identify other combinations of evolutionary forces that might in principle account for the data although they appear less likely. Our results shed light on the processes that drive structural changes throughout the genome.", "link"=>"http://www.mendeley.com/research/y-fuse-sex-chromosome-fusions-fishes-reptiles", "reader_count"=>70, "reader_count_by_academic_status"=>{"Unspecified"=>1, "Professor > Associate Professor"=>1, "Student > Doctoral Student"=>5, "Researcher"=>12, "Student > Ph. D. Student"=>24, "Student > Postgraduate"=>5, "Student > Master"=>9, "Other"=>1, "Student > Bachelor"=>10, "Professor"=>2}, "reader_count_by_user_role"=>{"Unspecified"=>1, "Professor > Associate Professor"=>1, "Student > Doctoral Student"=>5, "Researcher"=>12, "Student > Ph. D. Student"=>24, "Student > Postgraduate"=>5, "Student > Master"=>9, "Other"=>1, "Student > Bachelor"=>10, "Professor"=>2}, "reader_count_by_subject_area"=>{"Unspecified"=>2, "Environmental Science"=>2, "Biochemistry, Genetics and Molecular Biology"=>14, "Agricultural and Biological Sciences"=>49, "Medicine and Dentistry"=>1, "Neuroscience"=>1, "Social Sciences"=>1}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>1}, "Neuroscience"=>{"Neuroscience"=>1}, "Social Sciences"=>{"Social Sciences"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>49}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>14}, "Unspecified"=>{"Unspecified"=>2}, "Environmental Science"=>{"Environmental Science"=>2}}, "reader_count_by_country"=>{"Netherlands"=>1, "Sweden"=>1, "Czech Republic"=>1, "United States"=>3, "Australia"=>1, "Germany"=>1}, "group_count"=>0}

CrossRef

Scopus | Further Information

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/2076382"], "description"=>"<p>The plot illustrates the difference in fusion rates over the last 40,000 steps of an MCMC chain, with the 95% credibility intervals shown by the horizontal bars below the figure.</p>", "links"=>[], "tags"=>["Sex chromosomes", "Reptiles Chromosomal fusion", "heterogametic systems", "drive chromosomal fusions", "Sex Chromosome Fusions"], "article_id"=>1421197, "categories"=>["Biological Sciences"], "users"=>["Matthew W. Pennell", "Mark Kirkpatrick", "Sarah P. Otto", "Jana C. Vamosi", "Catherine L. Peichel", "Nicole Valenzuela", "Jun Kitano"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1005237.g004", "stats"=>{"downloads"=>0, "page_views"=>11, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Posterior_probability_density_of_the_difference_in_fixation_rates_of_fusions_between_autosomes_and_sex_chromosomes_rates_in_XY_species_minus_in_ZW_species_/1421197", "title"=>"Posterior probability density of the difference in fixation rates of fusions between autosomes and sex chromosomes (rates in XY species minus in ZW species).", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-05-20 03:37:54"}
  • {"files"=>["https://ndownloader.figshare.com/files/2076376"], "description"=>"<p>(A) In XY systems, X-autosome (X-A) and Y-autosome fusions (Y-A) make XY<sub>1</sub>Y<sub>2</sub> and X<sub>1</sub>X<sub>2</sub>Y systems, respectively. (B) In ZW systems, Z-autosome (Z-A) and W-autosome fusions (W-A) make ZW<sub>1</sub>W<sub>2</sub> and Z<sub>1</sub>Z<sub>2</sub>W systems, respectively.</p>", "links"=>[], "tags"=>["Sex chromosomes", "Reptiles Chromosomal fusion", "heterogametic systems", "drive chromosomal fusions", "Sex Chromosome Fusions"], "article_id"=>1421191, "categories"=>["Biological Sciences"], "users"=>["Matthew W. Pennell", "Mark Kirkpatrick", "Sarah P. Otto", "Jana C. Vamosi", "Catherine L. Peichel", "Nicole Valenzuela", "Jun Kitano"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1005237.g001", "stats"=>{"downloads"=>1, "page_views"=>11, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Sex_chromosome_autosome_fusions_create_multiple_sex_chromosome_systems_/1421191", "title"=>"Sex chromosome-autosome fusions create multiple sex chromosome systems.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-05-20 03:37:54"}
  • {"files"=>["https://ndownloader.figshare.com/files/2076377"], "description"=>"<p>The vast majority of fusions occur in XY systems (aqua) and involve Y-A fusions (brown).</p>", "links"=>[], "tags"=>["Sex chromosomes", "Reptiles Chromosomal fusion", "heterogametic systems", "drive chromosomal fusions", "Sex Chromosome Fusions"], "article_id"=>1421192, "categories"=>["Biological Sciences"], "users"=>["Matthew W. Pennell", "Mark Kirkpatrick", "Sarah P. Otto", "Jana C. Vamosi", "Catherine L. Peichel", "Nicole Valenzuela", "Jun Kitano"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1005237.g002", "stats"=>{"downloads"=>2, "page_views"=>20, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Sex_chromosome_fusions_outer_circle_and_sex_determination_system_inner_circle_mapped_onto_the_phylogenetic_tree_of_fishes_/1421192", "title"=>"Sex chromosome fusions (outer circle) and sex determination system (inner circle) mapped onto the phylogenetic tree of fishes.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-05-20 03:37:54"}
  • {"files"=>["https://ndownloader.figshare.com/files/2076395"], "description"=>"<p>Only X<sub>1</sub>X<sub>2</sub>Y, XY<sub>1</sub>Y<sub>2</sub>, Z<sub>1</sub>Z<sub>2</sub>W, and ZW<sub>1</sub>W<sub>2</sub> systems are counted here.</p><p>*<i>Erythrinus erythrinus</i> was counted as a Y-A fusion (B-D sub-populations), although unfused chromosomes also exist in this species [<a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1005237#pgen.1005237.ref050\" target=\"_blank\">50</a>].</p><p><sup>★</sup>In addition, <i>Ancistrus</i> sp.2 exhibits both W-A and Z-A fusions (Z<sub>1</sub>Z<sub>2</sub>W<sub>1</sub>W<sub>2</sub>)</p><p><sup>#</sup> In addition, <i>Ornithorhynchus anatinus</i> (X<sub>1</sub>X<sub>2</sub>X<sub>3</sub>X<sub>4</sub>X<sub>5</sub>Y<sub>1</sub>Y<sub>2</sub>Y<sub>3</sub>Y<sub>4</sub>Y<sub>5</sub>) and <i>Tachyglossus aculeatus</i> (X<sub>1</sub>X<sub>2</sub>X<sub>3</sub>X<sub>4</sub>X<sub>5</sub>Y<sub>1</sub>Y<sub>2</sub>Y<sub>3</sub>Y<sub>4</sub>) exhibit both Y-A and X-A fusions.</p><p><sup>§</sup>XO systems (<i>n</i> = 12 in fishes, <i>n</i> = 3 in mammals), ZO systems (<i>n</i> = 3 in fishes), and WO systems (<i>n</i> = 1 in amphibians) are not included, nor are cases with multiple segregating sex determining mechanisms (<i>n</i> = 8 in mammals).</p><p>Observed number of species with multiple sex chromosome systems in vertebrates.</p>", "links"=>[], "tags"=>["Sex chromosomes", "Reptiles Chromosomal fusion", "heterogametic systems", "drive chromosomal fusions", "Sex Chromosome Fusions"], "article_id"=>1421201, "categories"=>["Biological Sciences"], "users"=>["Matthew W. Pennell", "Mark Kirkpatrick", "Sarah P. Otto", "Jana C. Vamosi", "Catherine L. Peichel", "Nicole Valenzuela", "Jun Kitano"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1005237.t001", "stats"=>{"downloads"=>1, "page_views"=>19, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Observed_number_of_species_with_multiple_sex_chromosome_systems_in_vertebrates_/1421201", "title"=>"Observed number of species with multiple sex chromosome systems in vertebrates.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2015-05-20 03:37:54"}
  • {"files"=>["https://ndownloader.figshare.com/files/2076394"], "description"=>"<p>The fusion is assumed to be neutral except for the effects of the sexually antagonistic allele that it captures. The fittest allele in each sex has a 10% advantage when homozygous and a 9% advantage when heterozygous (results are robust to these exact numbers). (<i>A</i>) Effect of sex ratio bias among reproductive adults, <i>N</i><sup><i>m</i></sup> / (<i>N</i><sup><i>f</i></sup> + <i>N</i><sup><i>m</i></sup>), assuming <i>μ</i><sup><i>m</i></sup> = <i>μ</i><sup><i>f</i></sup>. (<i>B</i>) Effect of the relative mutation rate for fusions in males versus females, <i>μ</i><sup><i>m</i></sup> / <i>μ</i><sup><i>f</i></sup>, assuming <i>N</i><sup><i>f</i></sup> = <i>N</i><sup><i>m</i></sup>. Parameters: <i>N</i><sup><i>f</i></sup> + <i>N</i><sup><i>m</i></sup> = 10000.</p>", "links"=>[], "tags"=>["Sex chromosomes", "Reptiles Chromosomal fusion", "heterogametic systems", "drive chromosomal fusions", "Sex Chromosome Fusions"], "article_id"=>1421200, "categories"=>["Biological Sciences"], "users"=>["Matthew W. Pennell", "Mark Kirkpatrick", "Sarah P. Otto", "Jana C. Vamosi", "Catherine L. Peichel", "Nicole Valenzuela", "Jun Kitano"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1005237.g006", "stats"=>{"downloads"=>1, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Establishment_rates_of_sex_chromosome_autosome_fusions_as_a_result_of_sexually_antagonistic_selection_relative_to_the_rate_for_X_A_fusions_/1421200", "title"=>"Establishment rates of sex chromosome-autosome fusions as a result of sexually antagonistic selection, relative to the rate for X-A fusions.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-05-20 03:37:54"}
  • {"files"=>["https://ndownloader.figshare.com/files/2076383"], "description"=>"<p>(<i>A</i>), (<i>B</i>) Effect of sex ratio bias among reproductive adults, <i>N</i><sup><i>m</i></sup>/(<i>N</i><sup><i>f</i></sup> + <i>N</i><sup><i>m</i></sup>), assuming <i>μ</i><sup><i>m</i></sup> = <i>μ</i><sup><i>f</i></sup>. (<i>C</i>), (<i>D</i>) Effect of the relative mutation rate for fusions in males versus females, <i>μ</i><sup><i>m</i></sup>/<i>μ</i><sup><i>f</i></sup>, assuming <i>N</i><sup><i>f</i></sup> = <i>N</i><sup><i>m</i></sup>. Mutations are deleterious (<i>s</i> = -0.0003) in panels (<i>A</i>), (<i>C</i>) and beneficial (s = 0.0003) in panels (<i>B</i>), (<i>D</i>). Parameters: <i>N</i><sup><i>f</i></sup> + <i>N</i><sup><i>m</i></sup> = 10000.</p>", "links"=>[], "tags"=>["Sex chromosomes", "Reptiles Chromosomal fusion", "heterogametic systems", "drive chromosomal fusions", "Sex Chromosome Fusions"], "article_id"=>1421198, "categories"=>["Biological Sciences"], "users"=>["Matthew W. Pennell", "Mark Kirkpatrick", "Sarah P. Otto", "Jana C. Vamosi", "Catherine L. Peichel", "Nicole Valenzuela", "Jun Kitano"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1005237.g005", "stats"=>{"downloads"=>0, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Establishment_rates_of_sex_chromosome_autosome_fusions_under_direct_selection_relative_to_the_rate_for_X_A_fusions_/1421198", "title"=>"Establishment rates of sex chromosome-autosome fusions under direct selection, relative to the rate for X-A fusions.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-05-20 03:37:54"}
  • {"files"=>["https://ndownloader.figshare.com/files/2076379"], "description"=>"<p>The vast majority of fusions occur in XY systems (aqua) and involve Y-A fusions (brown).</p>", "links"=>[], "tags"=>["Sex chromosomes", "Reptiles Chromosomal fusion", "heterogametic systems", "drive chromosomal fusions", "Sex Chromosome Fusions"], "article_id"=>1421194, "categories"=>["Biological Sciences"], "users"=>["Matthew W. Pennell", "Mark Kirkpatrick", "Sarah P. Otto", "Jana C. Vamosi", "Catherine L. Peichel", "Nicole Valenzuela", "Jun Kitano"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1005237.g003", "stats"=>{"downloads"=>1, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Sex_chromosome_fusions_outer_circle_and_sex_determination_system_inner_circle_mapped_onto_the_phylogenetic_tree_of_squamate_reptiles_/1421194", "title"=>"Sex chromosome fusions (outer circle) and sex determination system (inner circle) mapped onto the phylogenetic tree of squamate reptiles.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-05-20 03:37:54"}
  • {"files"=>["https://ndownloader.figshare.com/files/2076401", "https://ndownloader.figshare.com/files/2076402", "https://ndownloader.figshare.com/files/2076403", "https://ndownloader.figshare.com/files/2076404", "https://ndownloader.figshare.com/files/2076405", "https://ndownloader.figshare.com/files/2076406", "https://ndownloader.figshare.com/files/2076407"], "description"=>"<div><p>Chromosomal fusion plays a recurring role in the evolution of adaptations and reproductive isolation among species, yet little is known of the evolutionary drivers of chromosomal fusions. Because sex chromosomes (X and Y in male heterogametic systems, Z and W in female heterogametic systems) differ in their selective, mutational, and demographic environments, those differences provide a unique opportunity to dissect the evolutionary forces that drive chromosomal fusions. We estimate the rate at which fusions between sex chromosomes and autosomes become established across the phylogenies of both fishes and squamate reptiles. Both the incidence among extant species and the establishment rate of Y-autosome fusions is much higher than for X-autosome, Z-autosome, or W-autosome fusions. Using population genetic models, we show that this pattern cannot be reconciled with many standard explanations for the spread of fusions. In particular, direct selection acting on fusions or sexually antagonistic selection cannot, on their own, account for the predominance of Y-autosome fusions. The most plausible explanation for the observed data seems to be (a) that fusions are slightly deleterious, and (b) that the mutation rate is male-biased or the reproductive sex ratio is female-biased. We identify other combinations of evolutionary forces that might in principle account for the data although they appear less likely. Our results shed light on the processes that drive structural changes throughout the genome.</p></div>", "links"=>[], "tags"=>["Sex chromosomes", "Reptiles Chromosomal fusion", "heterogametic systems", "drive chromosomal fusions", "Sex Chromosome Fusions"], "article_id"=>1421207, "categories"=>["Biological Sciences"], "users"=>["Matthew W. Pennell", "Mark Kirkpatrick", "Sarah P. Otto", "Jana C. Vamosi", "Catherine L. Peichel", "Nicole Valenzuela", "Jun Kitano"], "doi"=>["https://dx.doi.org/10.1371/journal.pgen.1005237.s001", "https://dx.doi.org/10.1371/journal.pgen.1005237.s002", "https://dx.doi.org/10.1371/journal.pgen.1005237.s003", "https://dx.doi.org/10.1371/journal.pgen.1005237.s004", "https://dx.doi.org/10.1371/journal.pgen.1005237.s005", "https://dx.doi.org/10.1371/journal.pgen.1005237.s006", "https://dx.doi.org/10.1371/journal.pgen.1005237.s007"], "stats"=>{"downloads"=>8, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Y_Fuse_Sex_Chromosome_Fusions_in_Fishes_and_Reptiles_/1421207", "title"=>"Y Fuse? Sex Chromosome Fusions in Fishes and Reptiles", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2015-05-20 03:37:54"}

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  • {"unique-ip"=>"24", "full-text"=>"27", "pdf"=>"2", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"7", "cited-by"=>"0", "year"=>"2019", "month"=>"9"}
  • {"unique-ip"=>"131", "full-text"=>"142", "pdf"=>"3", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"1", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"10"}
  • {"unique-ip"=>"23", "full-text"=>"22", "pdf"=>"4", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"1", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"12"}
  • {"unique-ip"=>"39", "full-text"=>"40", "pdf"=>"4", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"2", "cited-by"=>"0", "year"=>"2020", "month"=>"2"}
  • {"unique-ip"=>"27", "full-text"=>"28", "pdf"=>"4", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2020", "month"=>"3"}
  • {"unique-ip"=>"23", "full-text"=>"25", "pdf"=>"1", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2020", "month"=>"4"}
  • {"unique-ip"=>"15", "full-text"=>"15", "pdf"=>"3", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2020", "month"=>"5"}
  • {"unique-ip"=>"18", "full-text"=>"15", "pdf"=>"4", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"1", "cited-by"=>"0", "year"=>"2020", "month"=>"6"}
  • {"unique-ip"=>"13", "full-text"=>"21", "pdf"=>"1", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2020", "month"=>"7"}
  • {"unique-ip"=>"10", "full-text"=>"11", "pdf"=>"1", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2020", "month"=>"8"}
  • {"unique-ip"=>"18", "full-text"=>"16", "pdf"=>"3", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2020", "month"=>"9"}

Relative Metric

{"start_date"=>"2015-01-01T00:00:00Z", "end_date"=>"2015-12-31T00:00:00Z", "subject_areas"=>[]}
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