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A partitioned likelihood analysis of swallowtail butterfly phylogeny (Lepidoptera:Papilionidae).
Syst Biol. 2001 Feb; 50(1):106-27.SB

Abstract

Although it is widely agreed that data from multiple sources are necessary to confidently resolve phylogenetic relationships, procedures for accommodating and incorporating heterogeneity in such data remain underdeveloped. We explored the use of partitioned, model-based analyses of heterogeneous molecular data in the context of a phylogenetic study of swallowtail butterflies (Lepidoptera: Papilionidae). Despite substantial basic and applied study, phylogenetic relationships among the major lineages of this prominent group remain contentious. We sequenced 3.3 kb of mitochondrial and nuclear DNA (2.3 kb of cytochrome oxidase I and II and 1.0 kb of elongation factor-1 alpha, respectively) from 22 swallowtails, including representatives of Baroniinae, Parnassiinae, and Papilioninae, and from several moth and butterfly outgroups. Using parsimony, we encountered considerable difficulty in resolving the deepest splits among these taxa. We therefore chose two outgroups with undisputed relationships to each other and to Papilionidae and undertook detailed likelihood analyses of alternative topologies. Following from previous studies that have demonstrated substantial heterogeneity in the evolutionary dynamics among process partitions of these genes, we estimated evolutionary parameters separately for gene-based and codon-based partitions. These values were then used as the basis for examining the likelihoods of possible resolutions and rootings under several partitioned and unpartitioned likelihood models. Partitioned models gave markedly better fits to the data than did unpartitioned models and supported different topologies. However, the most likely topology varied from model to model. The most likely ingroup topology under the best-fitting, six-partition GTR + gamma model favors a paraphyletic Parnassiinae. However, when examining the likelihoods of alternative rootings of this tree relative to rootings of the classical hypothesis, two rootings of the latter emerge as most likely. Of these two, the most likely rooting is within the Papilioninae, although a rooting between Baronia and the remaining Papilionidae is only nonsignificantly less likely.

Authors+Show Affiliations

Division of Insect Biology, 201 Wellman Hall, University of California, Berkeley, CA 94720-3112, USA. histerid@nhm.ac.ukNo affiliation info availableNo affiliation info availableNo affiliation info available

Pub Type(s)

Journal Article
Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.

Language

eng

PubMed ID

12116588

Citation

Caterino, M S., et al. "A Partitioned Likelihood Analysis of Swallowtail Butterfly Phylogeny (Lepidoptera:Papilionidae)." Systematic Biology, vol. 50, no. 1, 2001, pp. 106-27.
Caterino MS, Reed RD, Kuo MM, et al. A partitioned likelihood analysis of swallowtail butterfly phylogeny (Lepidoptera:Papilionidae). Syst Biol. 2001;50(1):106-27.
Caterino, M. S., Reed, R. D., Kuo, M. M., & Sperling, F. A. (2001). A partitioned likelihood analysis of swallowtail butterfly phylogeny (Lepidoptera:Papilionidae). Systematic Biology, 50(1), 106-27.
Caterino MS, et al. A Partitioned Likelihood Analysis of Swallowtail Butterfly Phylogeny (Lepidoptera:Papilionidae). Syst Biol. 2001;50(1):106-27. PubMed PMID: 12116588.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - A partitioned likelihood analysis of swallowtail butterfly phylogeny (Lepidoptera:Papilionidae). AU - Caterino,M S, AU - Reed,R D, AU - Kuo,M M, AU - Sperling,F A, PY - 2002/7/16/pubmed PY - 2002/8/13/medline PY - 2002/7/16/entrez SP - 106 EP - 27 JF - Systematic biology JO - Syst Biol VL - 50 IS - 1 N2 - Although it is widely agreed that data from multiple sources are necessary to confidently resolve phylogenetic relationships, procedures for accommodating and incorporating heterogeneity in such data remain underdeveloped. We explored the use of partitioned, model-based analyses of heterogeneous molecular data in the context of a phylogenetic study of swallowtail butterflies (Lepidoptera: Papilionidae). Despite substantial basic and applied study, phylogenetic relationships among the major lineages of this prominent group remain contentious. We sequenced 3.3 kb of mitochondrial and nuclear DNA (2.3 kb of cytochrome oxidase I and II and 1.0 kb of elongation factor-1 alpha, respectively) from 22 swallowtails, including representatives of Baroniinae, Parnassiinae, and Papilioninae, and from several moth and butterfly outgroups. Using parsimony, we encountered considerable difficulty in resolving the deepest splits among these taxa. We therefore chose two outgroups with undisputed relationships to each other and to Papilionidae and undertook detailed likelihood analyses of alternative topologies. Following from previous studies that have demonstrated substantial heterogeneity in the evolutionary dynamics among process partitions of these genes, we estimated evolutionary parameters separately for gene-based and codon-based partitions. These values were then used as the basis for examining the likelihoods of possible resolutions and rootings under several partitioned and unpartitioned likelihood models. Partitioned models gave markedly better fits to the data than did unpartitioned models and supported different topologies. However, the most likely topology varied from model to model. The most likely ingroup topology under the best-fitting, six-partition GTR + gamma model favors a paraphyletic Parnassiinae. However, when examining the likelihoods of alternative rootings of this tree relative to rootings of the classical hypothesis, two rootings of the latter emerge as most likely. Of these two, the most likely rooting is within the Papilioninae, although a rooting between Baronia and the remaining Papilionidae is only nonsignificantly less likely. SN - 1063-5157 UR - https://www.unboundmedicine.com/medline/citation/12116588/A_partitioned_likelihood_analysis_of_swallowtail_butterfly_phylogeny__Lepidoptera:Papilionidae__ DB - PRIME DP - Unbound Medicine ER -