{"id":349,"date":"2015-05-26T10:38:48","date_gmt":"2015-05-26T14:38:48","guid":{"rendered":"https:\/\/people.clas.ufl.edu\/ebraun\/?page_id=349"},"modified":"2026-03-19T08:29:19","modified_gmt":"2026-03-19T12:29:19","slug":"mpe01","status":"publish","type":"page","link":"https:\/\/people.clas.ufl.edu\/ebraun\/publications\/mpe01\/","title":{"rendered":"Evolution of the Mitochondrial DNA Control Region and Cytochrome b Genes and the Inference of Phylogenetic Relationships in the Avian Genus Lophura (Galliformes)"},"content":{"rendered":"\r\n
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Evolution of the Mitochondrial DNA Control Region and Cytochrome b Genes and the Inference of Phylogenetic Relationships in the Avian Genus Lophura (Galliformes)<\/h1>\n\n\n\n

Molecular Phylogenetics and Evolution<\/em>, Vol. 19, pp. 187-201<\/p>\n\n\n\n\n\n

Link to\u00a0Molecular Phylogenetics and Evolution<\/a><\/em>\u00a0home page.<\/p>\n\n\n\n

Evolution of the Mitochondrial DNA Control Region and Cytochrome\u00a0b<\/i>\u00a0Genes and the Inference of Phylogenetic Relationships in the Avian Genus\u00a0Lophura<\/i>\u00a0(Galliformes)<\/h3>\n\n\n\n

Ettore Randi*<\/sup>,<\/wbr>\u00a0Vittorio Lucchini,<\/wbr>\u00a0Alain Hennache,<\/wbr>\u00a0Rebecca T. Kimball,<\/wbr>\u00a0Edward L. Braun,<\/wbr>\u00a0and<\/wbr>\u00a0J. David Ligon\u00a0<\/strong><\/p>\n\n\n\n\n\n

Istituto Nazionale per la Fauna Selvatica, via C\u00e0 Fornacetta 9, 40064, Ozzano dell Emilia, (BO), Italy (V.L., E.R.); Museum National d’Histoire Naturelle, Parc Zoologique de Cl\u00e8res, 76690, Cl\u00e8res, France (A.H.); Department of Biology, University of New Mexico, Albuquerque, NM, 87131, USA (R.T.K., E.L.B., J.D.L); Departments of Evolution, Ecology and Organismal Biology (R.T.K.) and Plant Biology (E.L.B.), Ohio State University, Columbus, OH, 43210, USA;
\nE.L.B.<\/a>\u00a0and\u00a0R.T.K.<\/a>\u00a0are currently in the Department of Zoology at the University of Florida.<\/p>\n\n\n\n\n\n

The entire mitochondrial\u00a0<\/sup>DNA control region (mtDNA\u00a0<\/sup>CR) and cytochrome\u00a0b<\/i>\u00a0<\/sup>(cyt\u00a0b<\/i>) genes were sequenced\u00a0<\/sup>in 10 of the 11 extant\u00a0<\/sup>species of gallopheasants (Lophura<\/i>).\u00a0<\/sup>The cyt\u00a0b<\/i>\u00a0from\u00a0L. diardi<\/i>\u00a0<\/sup>and\u00a0L. ignita<\/i>\u00a0showed unusual\u00a0<\/sup>leucine-coding codons at\u00a0<\/sup>the expected terminal 3′\u00a0<\/sup>end of the gene.\u00a0<\/sup>Presence of conserved functional\u00a0<\/sup>motifs in the\u00a0<\/sup>inferred amino acid sequences,\u00a0<\/sup>conserved secondary structures\u00a0<\/sup>of the flanking tRNAPro<\/sup>\u00a0and tRNAThr<\/sup>, and Southern\u00a0<\/sup>hybridization concordantly suggest\u00a0<\/sup>that these cyt\u00a0b<\/i>\u00a0<\/sup>represent functional mitochondrial\u00a0<\/sup>genes and not nuclear transpositions.\u00a0<\/sup>Functional stop codons can\u00a0<\/sup>be generated by RNA editing\u00a0<\/sup>of the primary transcripts\u00a0<\/sup>rom these sequences. Despite\u00a0<\/sup>strong site and domain substitution\u00a0<\/sup>rate heterogeneity,\u00a0<\/sup>CR and cyt\u00a0b<\/i>\u00a0diverged\u00a0<\/sup>at similar rates,\u00a0<\/sup>on average, and expressed\u00a0<\/sup>congruent phylogenetic signals.Phylogenetic analyses of the\u00a0<\/sup>concatenated sequences split\u00a0<\/sup>Lophura<\/i>\u00a0into five clades\u00a0<\/sup>including (1)\u00a0L. bulweri,<\/i>\u00a0(2)\u00a0<\/sup>L. diardi<\/i>\u2013L. ignita,<\/i>\u00a0<\/sup>(3)\u00a0L. erythrophthalma<\/i>\u2013L. inornata,<\/i>\u00a0<\/sup>(4)\u00a0L. leucomelanos<\/i>\u2013L. nycthemera,<\/i>\u00a0<\/sup>and (5)\u00a0L. swinhoii<\/i>\u2013L. edwardsi<\/i>\u2013L. hatinhensis.<\/i>\u00a0<\/sup>Basal relationships among these\u00a0<\/sup>clades, which include species\u00a0<\/sup>distributed in continental South\u00a0<\/sup>East Asia and the Sundaland archipelago,\u00a0<\/sup>were weakly resolved, suggesting the\u00a0<\/sup>occurrence of rapid\u00a0<\/sup>cladogenic events in the\u00a0<\/sup>early evolutionary history of\u00a0Lophura.<\/i>\u00a0<\/sup>A conventional calibration\u00a0<\/sup>of mtDNA sequence divergence\u00a0<\/sup>indicates a mid to late Pliocene\u00a0<\/sup>evolution of the main clades\u00a0<\/sup>in\u00a0Lophura,<\/i>\u00a0which could\u00a0<\/sup>have diversified in allopatry\u00a0<\/sup>in continental South East Asia.\u00a0<\/sup>Sundaland could have been\u00a0<\/sup>colonized lately and independently\u00a0<\/sup>by the different clades.\u00a0<\/sup>Consequently, cyclic changes in\u00a0<\/sup>late Pleistocene climate and\u00a0<\/sup>landscape might not have\u00a0<\/sup>increased rates of speciation\u00a0<\/sup>in genus\u00a0Lophura<\/i>\u00a0in Sundaland.<\/p>\n\n\n\n

This research was supported by the Museum National d’Histoire Naturelle, Paris, France, by the World Pheasant Association, Lower Basildon, Reading, UK, and by the Istituto Nazionale per la Fauna Selvatica, Bologna, Italy. Some DNA sequencing was performed in the NSF-supported (RIMI Program Grant HRD-9550649) Molecular Biology Facility at the University of New Mexico.<\/p>\n\n\n\n\n\n

*<\/sup>\u00a0Corresponding author<\/p>\n\n\n\r\n\t\t\t<\/div>\r\n\t\t<\/div>\r\n\t<\/div>\r\n<\/section>\r\n","protected":false},"excerpt":{"rendered":"","protected":false},"author":544,"featured_media":0,"parent":19,"menu_order":30,"comment_status":"closed","ping_status":"closed","template":"","meta":{"_acf_changed":false,"featured_post":"","footnotes":"","_links_to":"","_links_to_target":""},"class_list":["post-349","page","type-page","status-publish","hentry"],"acf":[],"_links":{"self":[{"href":"https:\/\/people.clas.ufl.edu\/ebraun\/wp-json\/wp\/v2\/pages\/349","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/people.clas.ufl.edu\/ebraun\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/people.clas.ufl.edu\/ebraun\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/people.clas.ufl.edu\/ebraun\/wp-json\/wp\/v2\/users\/544"}],"replies":[{"embeddable":true,"href":"https:\/\/people.clas.ufl.edu\/ebraun\/wp-json\/wp\/v2\/comments?post=349"}],"version-history":[{"count":5,"href":"https:\/\/people.clas.ufl.edu\/ebraun\/wp-json\/wp\/v2\/pages\/349\/revisions"}],"predecessor-version":[{"id":451,"href":"https:\/\/people.clas.ufl.edu\/ebraun\/wp-json\/wp\/v2\/pages\/349\/revisions\/451"}],"up":[{"embeddable":true,"href":"https:\/\/people.clas.ufl.edu\/ebraun\/wp-json\/wp\/v2\/pages\/19"}],"wp:attachment":[{"href":"https:\/\/people.clas.ufl.edu\/ebraun\/wp-json\/wp\/v2\/media?parent=349"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}