{"id":262,"date":"2015-05-22T15:34:55","date_gmt":"2015-05-22T19:34:55","guid":{"rendered":"https:\/\/people.clas.ufl.edu\/ebraun\/?page_id=262"},"modified":"2026-03-19T08:29:19","modified_gmt":"2026-03-19T12:29:19","slug":"sb02","status":"publish","type":"page","link":"https:\/\/people.clas.ufl.edu\/ebraun\/publications\/sb02\/","title":{"rendered":"Examining Basal Avian Divergences with Mitochondrial Sequences: Model Complexity, Taxon Sampling, and Sequence Length"},"content":{"rendered":"\r\n
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Examining Basal Avian Divergences with Mitochondrial Sequences: Model Complexity, Taxon Sampling, and Sequence Length<\/h1>\n\n\n\n

Systematic Biology<\/em>, Vol. 51, pp. 614-625<\/p>\n\n\n\n\n\n

Link to\u00a0Systematic Biology<\/a><\/em>\u00a0home page.<\/p>\n\n\n\n\n\n

Full text for this journal is available from the Taylor and Francis\u00a0home page<\/a>.<\/p>\n\n\n\n

Examining Basal Avian Divergences with Mitochondrial Sequences: Model Complexity, Taxon Sampling, and Sequence Length<\/h3>\n\n\n\n

Edward L. Braun1,*<\/sup><\/wbr>\u00a0and<\/wbr>\u00a0Rebecca T. Kimball1<\/sup><\/strong><\/p>\n\n\n\n\n\n

Department of Zoology, University of Florida, Gainesville, Florida 32611<\/p>\n\n\n\n\n\n

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Description of Paper<\/strong>, published as a\u00a0Point of View<\/strong>\u00a0in\u00a0Systematic Biology<\/i><\/p>\n\n\n\n

Traditional avian classificiations\u00a0<\/sup>have generally indicated that\u00a0<\/sup>the paleognathous birds (ratites and\u00a0<\/sup>tinamous) represent the earliest\u00a0<\/sup>divergence within the extant\u00a0<\/sup>birds and the perching birds\u00a0<\/sup>(Passeriformes) represent one of the\u00a0<\/sup>most recently derived\u00a0<\/sup>lineages. However, a\u00a0<\/sup>number of papers using\u00a0<\/sup>complete mitochondrial sequences\u00a0<\/sup>have challenged this\u00a0<\/sup>idea (Mindell et al. 1997, 1999;\u00a0<\/sup>H\u00e4rlid and Arnason 1999;\u00a0<\/sup>Haring et al. 2001;\u00a0<\/sup>Slack et al. 2003).\u00a0<\/sup>These results are\u00a0<\/sup>suprising given the\u00a0support for the\u00a0convential view of\u00a0<\/sup>avian phylogeny from\u00a0<\/sup>analyses of nuclear gene\u00a0<\/sup>sequences (e.g.,\u00a0Groth and Barrowclough 1999;\u00a0<\/sup>Garcia-Moreno and Mindell 2000)\u00a0<\/sup>and other types of\u00a0data (e.g., Edwards et al.\u00a0<\/sup>2002). In this paper,\u00a0<\/sup>we explored the\u00a0<\/sup>sensitivity of estimates\u00a0<\/sup>of avian phylogeny that\u00a0<\/sup>were obtained using complete\u00a0<\/sup>mitochondrial DNA sequences\u00a0<\/sup>to a variety of\u00a0<\/sup>factors that influence\u00a0<\/sup>estimates of phylogeny.\u00a0<\/sup>In this paper we\u00a0<\/sup>show that support for\u00a0<\/sup>traditional relationships inmitochondrial sequence alignments\u00a0<\/sup>is actually surprisingly\u00a0<\/sup>strong.\u00a0<\/sup>There was evidence that\u00a0<\/sup>certain avian taxa were\u00a0<\/sup>especially problematic for\u00a0<\/sup>various methods of\u00a0<\/sup>phylogenetic estimation,\u00a0<\/sup>emphasizing the utility of\u00a0<\/sup>sampling a reasonably large\u00a0<\/sup>set of taxa and evaluating\u00a0<\/sup>the congruence of all\u00a0<\/sup>estimates of phylogeny with\u00a0<\/sup>other estimates of phylogeny\u00a0<\/sup>obtained from anlayses of many\u00a0<\/sup>different types of data.\u00a0<\/sup>In this context, we note\u00a0<\/sup>that Paton et al. (2002)\u00a0<\/sup>also showed that likelihood\u00a0<\/sup>analyses of avian\u00a0<\/sup>mitochondrial sequence data\u00a0<\/sup>using parameter-rich models\u00a0<\/sup>support a traditional\u00a0<\/sup>placement of the avian root\u00a0<\/sup>and that Slack et al. (2003)\u00a0<\/sup>could not exclude the\u00a0<\/sup>traditional placement of\u00a0<\/sup>root. However, this paper\u00a0<\/sup>represents an exploration\u00a0<\/sup>of the impact factors\u00a0<\/sup>such as model complexity, taxon sampling, and amount of data have\u00a0<\/sup>on the estimate of\u00a0<\/sup>phylogeny obtained.<\/p>\n\n\n<\/div>\n\n\n\n

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This work was initiatied while E.L.B. was supported by a fellowship from the U.S. Department of Agriculture (USDA 1999-01582) and R.T.K. was supported by an Ohio State University fellowship.<\/p>\n\n\n\n\n\n

1<\/sup>\u00a0E.L.B. and R.T.K. contributed equally to this paper and are listed in alphabetical order.<\/p>\n\n\n\n\n\n

*<\/sup>\u00a0Corresponding author<\/p>\n\n\n\n

References for the description of this paper on this web site:<\/strong><\/p>\n\n\n\n

  1. Edwards, SV, B Fertil, A Giron & PJ Deschavanne.<\/strong>\u00a02002. A genomic schism in birds revealed by phylogenetic analysis of DNA strings.\u00a0Systematic Biology<\/i>\u00a051:599-613.<\/li>\n
  2. Garcia-Moreno, J & DP Mindell.<\/strong>\u00a02000. Rooting a phylogeny with homologous genes on opposite sex chromosomes (gametologs): A case study using avian CHD.\u00a0Molecular Biology and Evolution<\/i>\u00a017:1826-1832.<\/li>\n
  3. Groth, JG & GF Barrowclough.<\/strong>\u00a01999. Basal divegences in birds and the phylogenetic utility of the nuclear RAG-1 gene.\u00a0Molecular Phylogenetics and Evolution<\/i>\u00a012:115-123.<\/li>\n
  4. Haring, E, L Kruckenhauser, A Gamauf, MJ Riesing & W Pinsker.<\/strong>\u00a02001. The complete sequence of the mitochondrial genome of\u00a0Buteo buteo<\/i>\u00a0(Aves, Accipitridae) indicates and early split in the phylogeny of raptors.\u00a0Molecular Biology and Evolution<\/i>\u00a018:1892-1904.<\/li>\n
  5. H\u00e4rlid, A & U Arnason\u00a0<\/strong>1999. Analyses of mitochondrial DNA nest ratite birds within the Neognathae: Supporting a neotenous origin of ratite morphological characters.\u00a0Proceedings of the Royal Society of London, series B<\/i>\u00a0266:305-309.<\/li>\n
  6. Mindell, DP, MD Sorenson, DE Dimcheff, M Hasegawa, JC Ast & T Yuri.<\/strong>\u00a01999. Interordinal relationships of birds and other reptiles based on whole mitochondrial genomes.\u00a0Systematic Biology<\/i>\u00a048:138-152.<\/li>\n
  7. Mindell, DP, MD Sorenson, CJ Huddleston, HCJ Miranda, A. Knight, SJ Sawchuk & T Yuri.<\/strong>\u00a01997. Phylogenetic relationships among and within select avian orders based on mitochondrial DNA. Pages 214-247\u00a0in<\/i>\u00a0Avian molecular evolution and sytematics (DP Mindell, ed.) Academic Press, San Diego.<\/li>\n
  8. Slack, KE, A Janke, D Penny & U Arnason.<\/strong>\u00a02003. Two new avian mitochondrial genomes (penguin and goose) and a summary of bird and reptile mitogenomic features.\u00a0Gene<\/i>\u00a0302:43-52<\/li>\n
  9. Paton, T, O Haddrath & AJ Baker.<\/strong>\u00a02002. Complete mitochondrial DNA genome sequences show that modern birds are not descended from transitional shorebirds.\u00a0Proceedings of the Royal Society of London, series B<\/i>\u00a0269:839-846.
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