Systematic Biology, Vol. 51, pp. 614-625

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Examining Basal Avian Divergences with Mitochondrial Sequences: Model Complexity, Taxon Sampling, and Sequence Length

Edward L. Braun1,* and Rebecca T. Kimball1

Department of Zoology, University of Florida, Gainesville, Florida 32611

Description of Paper, published as a Point of View in Systematic Biology

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

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.

1 E.L.B. and R.T.K. contributed equally to this paper and are listed in alphabetical order.

* Corresponding author

References for the description of this paper on this web site:

  1. Edwards, SV, B Fertil, A Giron & PJ Deschavanne. 2002. A genomic schism in birds revealed by phylogenetic analysis of DNA strings. Systematic Biology 51:599-613.
  2. Garcia-Moreno, J & DP Mindell. 2000. Rooting a phylogeny with homologous genes on opposite sex chromosomes (gametologs): A case study using avian CHD. Molecular Biology and Evolution 17:1826-1832.
  3. Groth, JG & GF Barrowclough. 1999. Basal divegences in birds and the phylogenetic utility of the nuclear RAG-1 gene. Molecular Phylogenetics and Evolution 12:115-123.
  4. Haring, E, L Kruckenhauser, A Gamauf, MJ Riesing & W Pinsker. 2001. The complete sequence of the mitochondrial genome of Buteo buteo (Aves, Accipitridae) indicates and early split in the phylogeny of raptors. Molecular Biology and Evolution 18:1892-1904.
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  8. Slack, KE, A Janke, D Penny & U Arnason. 2003. Two new avian mitochondrial genomes (penguin and goose) and a summary of bird and reptile mitogenomic features. Gene 302:43-52
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