Inferring Kangaroo Phylogeny from Incongruent Nuclear and Mitochondrial Genes
Publication Date
February 22, 2013
Journal
PLOS ONE
Authors
Matthew J. Phillips, Dalal Haouchar, Renae C. Pratt, Gillian C. Gibb, et al
Volume
8
Issue
2
Pages
e57745
DOI
https://dx.plos.org/10.1371/journal.pone.0057745
Publisher URL
http://journals.plos.org/plosone/article?id=10.1371%2Fjournal.pone.0057745
PubMed
http://www.ncbi.nlm.nih.gov/pubmed/23451266
PubMed Central
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3579791
Europe PMC
http://europepmc.org/abstract/MED/23451266
Web of Science
000316658800117
Scopus
84874292950
Mendeley
http://www.mendeley.com/research/inferring-kangaroo-phylogeny-incongruent-nuclear-mitochondrial-genes
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Mendeley | Further Information

{"title"=>"Inferring Kangaroo Phylogeny from Incongruent Nuclear and Mitochondrial Genes", "type"=>"journal", "authors"=>[{"first_name"=>"Matthew J.", "last_name"=>"Phillips", "scopus_author_id"=>"7402769978"}, {"first_name"=>"Dalal", "last_name"=>"Haouchar", "scopus_author_id"=>"55606083400"}, {"first_name"=>"Renae C.", "last_name"=>"Pratt", "scopus_author_id"=>"23490025300"}, {"first_name"=>"Gillian C.", "last_name"=>"Gibb", "scopus_author_id"=>"7004092131"}, {"first_name"=>"Michael", "last_name"=>"Bunce", "scopus_author_id"=>"55160482300"}], "year"=>2013, "source"=>"PLoS ONE", "identifiers"=>{"scopus"=>"2-s2.0-84874292950", "doi"=>"10.1371/journal.pone.0057745", "sgr"=>"84874292950", "pmid"=>"23451266", "issn"=>"19326203", "pui"=>"368409603"}, "id"=>"464edad9-a5fe-3dec-88df-e86b122fdaea", "abstract"=>"The marsupial genus Macropus includes three subgenera, the familiar large grazing kangaroos and wallaroos of M. (Macropus) and M. (Osphranter), as well as the smaller mixed grazing/browsing wallabies of M. (Notamacropus). A recent study of five concatenated nuclear genes recommended subsuming the predominantly browsing Wallabia bicolor (swamp wallaby) into Macropus. To further examine this proposal we sequenced partial mitochondrial genomes for kangaroos and wallabies. These sequences strongly favour the morphological placement of W. bicolor as sister to Macropus, although place M. irma (black-gloved wallaby) within M. (Osphranter) rather than as expected, with M. (Notamacropus). Species tree estimation from separately analysed mitochondrial and nuclear genes favours retaining Macropus and Wallabia as separate genera. A simulation study finds that incomplete lineage sorting among nuclear genes is a plausible explanation for incongruence with the mitochondrial placement of W. bicolor, while mitochondrial introgression from a wallaroo into M. irma is the deepest such event identified in marsupials. Similar such coalescent simulations for interpreting gene tree conflicts will increase in both relevance and statistical power as species-level phylogenetics enters the genomic age. Ecological considerations in turn, hint at a role for selection in accelerating the fixation of introgressed or incompletely sorted loci. More generally the inclusion of the mitochondrial sequences substantially enhanced phylogenetic resolution. However, we caution that the evolutionary dynamics that enhance mitochondria as speciation indicators in the presence of incomplete lineage sorting may also render them especially susceptible to introgression.", "link"=>"http://www.mendeley.com/research/inferring-kangaroo-phylogeny-incongruent-nuclear-mitochondrial-genes", "reader_count"=>39, "reader_count_by_academic_status"=>{"Unspecified"=>1, "Professor > Associate Professor"=>1, "Researcher"=>5, "Student > Doctoral Student"=>2, "Student > Ph. D. Student"=>14, "Student > Postgraduate"=>2, "Other"=>1, "Student > Master"=>3, "Student > Bachelor"=>8, "Professor"=>2}, "reader_count_by_user_role"=>{"Unspecified"=>1, "Professor > Associate Professor"=>1, "Researcher"=>5, "Student > Doctoral Student"=>2, "Student > Ph. D. Student"=>14, "Student > Postgraduate"=>2, "Other"=>1, "Student > Master"=>3, "Student > Bachelor"=>8, "Professor"=>2}, "reader_count_by_subject_area"=>{"Engineering"=>1, "Unspecified"=>1, "Environmental Science"=>3, "Biochemistry, Genetics and Molecular Biology"=>2, "Agricultural and Biological Sciences"=>28, "Medicine and Dentistry"=>1, "Business, Management and Accounting"=>1, "Computer Science"=>1, "Immunology and Microbiology"=>1}, "reader_count_by_subdiscipline"=>{"Engineering"=>{"Engineering"=>1}, "Medicine and Dentistry"=>{"Medicine and Dentistry"=>1}, "Immunology and Microbiology"=>{"Immunology and Microbiology"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>28}, "Computer Science"=>{"Computer Science"=>1}, "Business, Management and Accounting"=>{"Business, Management and Accounting"=>1}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>2}, "Unspecified"=>{"Unspecified"=>1}, "Environmental Science"=>{"Environmental Science"=>3}}, "reader_count_by_country"=>{"New Zealand"=>1, "United States"=>1, "Brazil"=>1, "Australia"=>1, "France"=>1}, "group_count"=>0}

Scopus | Further Information

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/968454"], "description"=>"<p>(A) concatenated sequences, showing BPP/BP<sub>ML</sub> (<a href=\"mailto:@%E2%80%8A=%E2%80%8A0.89/59\" target=\"_blank\">@ = 0.89/59</a>), (B) *BEAST partitioned between the mtDNA and five nuclear genes, showing BPP values. (C) both MDC and BUCKy, which recovered the same tree from the mt and five nuclear gene trees. (D) Meredith et al. (2008) with BP<sub>ML</sub> values included for comparison. Several supraspecific clades that were identical across all reconstructions were collapsed for visualization convenience. Relationships within each of the collapsed clades were as inferred in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0057745#pone-0057745-g002\" target=\"_blank\">Figure 2</a>. Asterisks indicate full BPP or BP<sub>ML</sub> support.</p>", "links"=>[], "tags"=>["estimates", "mitochondrial", "sequences"], "article_id"=>638014, "categories"=>["Genetics", "Evolutionary Biology"], "users"=>["Matthew J. Phillips", "Dalal Haouchar", "Renae C. Pratt", "Gillian C. Gibb", "Michael Bunce"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0057745.g004", "stats"=>{"downloads"=>1, "page_views"=>10, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Macropodid_species_tree_estimates_from_the_combined_mitochondrial_and_nuclear_sequences_MtNuc_16_/638014", "title"=>"Macropodid species tree estimates from the combined mitochondrial and nuclear sequences (MtNuc<sub>16</sub>).", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-23 10:16:54"}
  • {"files"=>["https://ndownloader.figshare.com/files/968451"], "description"=>"<p>Maximum likelihood phylogenies inferred from the (A) mitochondrial (Mt<sub>16</sub>) and (B) nuclear (Nuc<sub>17</sub>) concatenated datasets, with RAxML bootstrap values (BP<sub>ML</sub>) above branches and MrBayes Bayesian posterior probabilities (BPP) below branches. The mt placement of <i>M. dorsalis</i> is derived from the reduced-length Mt<sub>17</sub> and the mt placements of <i>M. antilopinus</i> and <i>W. bicolor</i> (NSW, New South Wales) are derived from the <i>Cytb</i><sub>18</sub> alignment. Support for grouping <i>M. eugenii</i> and <i>M. agilis</i> increases (BP<sub>ML</sub> = 88; BPP = 0.98) for Mt<sub>16</sub>, which excludes <i>M. dorsalis</i>, but increases sequence length. Asterisks indicate full support. Clades including members of <i>Macropus</i> are shaded.</p>", "links"=>[], "tags"=>["kangaroos"], "article_id"=>638011, "categories"=>["Genetics", "Evolutionary Biology"], "users"=>["Matthew J. Phillips", "Dalal Haouchar", "Renae C. Pratt", "Gillian C. Gibb", "Michael Bunce"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0057745.g002", "stats"=>{"downloads"=>1, "page_views"=>11, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Phylogenetic_analysis_of_kangaroos_and_wallabies_/638011", "title"=>"Phylogenetic analysis of kangaroos and wallabies.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-23 10:15:59"}
  • {"files"=>["https://ndownloader.figshare.com/files/1005235"], "description"=>"<p>Nuclear sequences are partitioned into protein codon positions and mitochondrial sequences are partitioned into protein codon positions and RNA stems and loops.</p><p>Comparisons (A) – (D) employ Mt<sub>16</sub> and Nuc<sub>17</sub>. Comparison (E) employs Mt<sub>17</sub>.</p> ˆ<p>Allowing <i>W. bicolor</i> and <i>M. irma</i> to float unconstrained on the tree</p>#<p>Not including <i>M. irma</i>, which is favoured as sister to <i>M. robustus</i> on the mt data.</p>", "links"=>[], "tags"=>["unbiased"], "article_id"=>665862, "categories"=>["Genetics", "Evolutionary Biology"], "users"=>["Matthew J. Phillips", "Dalal Haouchar", "Renae C. Pratt", "Gillian C. Gibb", "Michael Bunce"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0057745.t001", "stats"=>{"downloads"=>0, "page_views"=>1, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Approximately_unbiased_AU_test_results_/665862", "title"=>"Approximately unbiased (AU) test results.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-02-22 01:37:42"}
  • {"files"=>["https://ndownloader.figshare.com/files/1005202"], "description"=>"<p>ML placements in bold.</p><p>To ensure relevance of the individual gene results to the overall nuclear phylogeny, the relative positions of the outgroups and placements within <i>M. (Macropus)</i>, <i>M. (Osphranter)</i> and core-<i>Notamacropus</i> were fixed (see <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0057745#pone-0057745-g002\" target=\"_blank\">Figure 2</a>).</p>", "links"=>[], "tags"=>["differences", "sh"], "article_id"=>665827, "categories"=>["Genetics", "Evolutionary Biology"], "users"=>["Matthew J. Phillips", "Dalal Haouchar", "Renae C. Pratt", "Gillian C. Gibb", "Michael Bunce"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0057745.t002", "stats"=>{"downloads"=>0, "page_views"=>1, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Individual_nuclear_gene_ln_L_differences_and_SH_test_results_/665827", "title"=>"Individual nuclear gene –ln<i>L</i> differences and SH test results.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-02-22 01:37:07"}
  • {"files"=>["https://ndownloader.figshare.com/files/968453"], "description"=>"<p>(A) Simulation workflow. (B) Mean number of the five nuclear genes supporting each clade in maximum likelihood analyses of 200 simulations of the combined data *BEAST species tree for <i>N</i><sub>e</sub> values of 1,000 (triangle), 10,000 (open circle), 100,000 (square) and 1,000,000 (filled circle). For comparison, the grey bars show the number of genes supporting each clade on the observed data. (C) Percentage of ML analyses supporting each clade among 200 mtDNA simulations on the nuclear-only *BEAST species tree for <i>N</i><sub>e</sub> values set to mitochondrial equivalency for the same populations (one quarter of the corresponding nuclear values). Abbreviations: <i>Lagor</i>.; <i>Lagorchestes</i>, <i>Wall</i>.; <i>Wallabia</i>, <i>M. (Notamac.)</i>; <i>M. (Notamacropus)</i>, <i>M. (Osphran.)</i>; <i>M. (Osphranter)</i>.</p>", "links"=>[], "tags"=>["clade", "datasets", "simulated"], "article_id"=>638013, "categories"=>["Genetics", "Evolutionary Biology"], "users"=>["Matthew J. Phillips", "Dalal Haouchar", "Renae C. Pratt", "Gillian C. Gibb", "Michael Bunce"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0057745.g003", "stats"=>{"downloads"=>1, "page_views"=>9, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Macropodid_clade_support_from_datasets_simulated_under_coalescence_/638013", "title"=>"Macropodid clade support from datasets simulated under coalescence.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-23 10:16:34"}
  • {"files"=>["https://ndownloader.figshare.com/files/968448"], "description"=>"<p>(A) The supertree of Cardillo et al. <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0057745#pone.0057745-Cardillo1\" target=\"_blank\">[6]</a> summarizing previous molecular and morphological phylogenies and (B) Meredith et al.'s <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0057745#pone.0057745-Meredith1\" target=\"_blank\">[7]</a> evolutionary timescale (ave. of four BEAST analyses), showing the 2–2.4 Ma duration divergence cluster. Both trees are modified to include only the taxa sampled in the present study. Dendrolagini was not recovered by Cardillo et al. <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0057745#pone.0057745-Cardillo1\" target=\"_blank\">[6]</a>, however its inclusion in the summary tree is warranted on subsequent strong evidence from morphology <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0057745#pone.0057745-Prideaux1\" target=\"_blank\">[2]</a> and all recent molecular analyses. Photos include (from the top) <i>W. bicolor</i>, <i>M. rufogriseus</i> (left), <i>M. irma</i> (right), <i>M. rufus and M. giganteus</i>. Photo credits – Matt Phillips, except <i>M. irma</i> (Ric Dawson) and <i>M. rufus</i> (Daniel Hoops).</p>", "links"=>[], "tags"=>["relationships"], "article_id"=>638008, "categories"=>["Genetics", "Evolutionary Biology"], "users"=>["Matthew J. Phillips", "Dalal Haouchar", "Renae C. Pratt", "Gillian C. Gibb", "Michael Bunce"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0057745.g001", "stats"=>{"downloads"=>3, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Phylogenetic_relationships_of_Wallabia_and_the_three_Macropus_subgenera_M_Macropus_M_Osphranter_and_M_Notamacropus_/638008", "title"=>"Phylogenetic relationships of <i>Wallabia</i> and the three <i>Macropus</i> subgenera, <i>M. (Macropus)</i>, <i>M. (Osphranter)</i> and <i>M. (Notamacropus)</i>.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-23 10:15:42"}
  • {"files"=>["https://ndownloader.figshare.com/files/1005221"], "description"=>"<p>(A) BEAST analysis of Mt<sub>16</sub>, (B) average of four BEAST analyses on the five nuclear gene concatenate from Meredith et al. <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0057745#pone.0057745-Meredith1\" target=\"_blank\">[7]</a> and (C) *BEAST species tree analysis of MtNuc<sub>16</sub>.</p>", "links"=>[], "tags"=>["divergence", "estimates", "millions", "years"], "article_id"=>665843, "categories"=>["Genetics", "Evolutionary Biology"], "users"=>["Matthew J. Phillips", "Dalal Haouchar", "Renae C. Pratt", "Gillian C. Gibb", "Michael Bunce"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0057745.t003", "stats"=>{"downloads"=>2, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Macropodoid_divergence_time_estimates_in_millions_of_years_before_present_/665843", "title"=>"Macropodoid divergence time estimates in millions of years before present.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-02-22 01:37:23"}
  • {"files"=>["https://ndownloader.figshare.com/files/968457", "https://ndownloader.figshare.com/files/968461", "https://ndownloader.figshare.com/files/968468", "https://ndownloader.figshare.com/files/968470", "https://ndownloader.figshare.com/files/968472"], "description"=>"<div><p>The marsupial genus <i>Macropus</i> includes three subgenera, the familiar large grazing kangaroos and wallaroos of <i>M. (Macropus)</i> and <i>M. (Osphranter)</i>, as well as the smaller mixed grazing/browsing wallabies of <i>M. (Notamacropus)</i>. A recent study of five concatenated nuclear genes recommended subsuming the predominantly browsing <i>Wallabia bicolor</i> (swamp wallaby) into <i>Macropus</i>. To further examine this proposal we sequenced partial mitochondrial genomes for kangaroos and wallabies. These sequences strongly favour the morphological placement of <i>W. bicolor</i> as sister to <i>Macropus</i>, although place <i>M. irma</i> (black-gloved wallaby) within <i>M. (Osphranter)</i> rather than as expected, with <i>M. (Notamacropus)</i>. Species tree estimation from separately analysed mitochondrial and nuclear genes favours retaining <i>Macropus</i> and <i>Wallabia</i> as separate genera. A simulation study finds that incomplete lineage sorting among nuclear genes is a plausible explanation for incongruence with the mitochondrial placement of <i>W. bicolor</i>, while mitochondrial introgression from a wallaroo into <i>M. irma</i> is the deepest such event identified in marsupials. Similar such coalescent simulations for interpreting gene tree conflicts will increase in both relevance and statistical power as species-level phylogenetics enters the genomic age. Ecological considerations in turn, hint at a role for selection in accelerating the fixation of introgressed or incompletely sorted loci. More generally the inclusion of the mitochondrial sequences substantially enhanced phylogenetic resolution. However, we caution that the evolutionary dynamics that enhance mitochondria as speciation indicators in the presence of incomplete lineage sorting may also render them especially susceptible to introgression.</p> </div>", "links"=>[], "tags"=>["inferring", "kangaroo", "phylogeny", "incongruent", "mitochondrial", "genes"], "article_id"=>638017, "categories"=>["Genetics", "Evolutionary Biology"], "users"=>["Matthew J. Phillips", "Dalal Haouchar", "Renae C. Pratt", "Gillian C. Gibb", "Michael Bunce"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0057745.s001", "https://dx.doi.org/10.1371/journal.pone.0057745.s002", "https://dx.doi.org/10.1371/journal.pone.0057745.s003", "https://dx.doi.org/10.1371/journal.pone.0057745.s004", "https://dx.doi.org/10.1371/journal.pone.0057745.s005"], "stats"=>{"downloads"=>36, "page_views"=>38, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Inferring_Kangaroo_Phylogeny_from_Incongruent_Nuclear_and_Mitochondrial_Genes__/638017", "title"=>"Inferring Kangaroo Phylogeny from Incongruent Nuclear and Mitochondrial Genes", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2013-02-23 10:17:17"}

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Relative Metric

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