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Rooting phylogenies using gene duplications: an empirical example from the bees (Apoidea).
Mol Phylogenet Evol. 2011 Sep; 60(3):295-304.MP

Abstract

The placement of the root node in a phylogeny is fundamental to characterizing evolutionary relationships. The root node of bee phylogeny remains unclear despite considerable previous attention. In order to test alternative hypotheses for the location of the root node in bees, we used the F1 and F2 paralogs of elongation factor 1-alpha (EF-1α) to compare the tree topologies that result when using outgroup versus paralogous rooting. Fifty-two taxa representing each of the seven bee families were sequenced for both copies of EF-1α. Two datasets were analyzed. In the first (the "concatenated" dataset), the F1 and F2 copies for each species were concatenated and the tree was rooted using appropriate outgroups (sphecid and crabronid wasps). In the second dataset (the "duplicated" dataset), the F1 and F2 copies were aligned to each another and each copy for all taxa were treated as separate terminals. In this dataset, the root was placed between the F1 and F2 copies (e.g., paralog rooting). Bayesian analyses demonstrate that the outgroup rooting approach outperforms paralog rooting, recovering deeper clades and showing stronger support for groups well established by both morphological and other molecular data. Sequence characteristics of the two copies were compared at the amino acid level, but little evidence was found to suggest that one copy is more functionally conserved. Although neither approach yields an unambiguous root to the tree, both approaches strongly indicate that the root of bee phylogeny does not fall near Colletidae, as has been previously proposed. We discuss paralog rooting as a general strategy and why this approach performs relatively poorly with our particular dataset.

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Authors+Show Affiliations

Brady SG
Department of Entomology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560, USA. bradys@si.edu
Litman JR
No affiliation info available
Danforth BN
No affiliation info available

MeSH

AnimalsBayes TheoremBeesEvolution, MolecularGene DuplicationModels, GeneticPeptide Elongation Factor 1PhylogenySequence Analysis, DNA

Pub Type(s)

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

Language

eng

PubMed ID

21600997

Citation

Brady, Seán G., et al. "Rooting Phylogenies Using Gene Duplications: an Empirical Example From the Bees (Apoidea)." Molecular Phylogenetics and Evolution, vol. 60, no. 3, 2011, pp. 295-304.
Brady SG, Litman JR, Danforth BN. Rooting phylogenies using gene duplications: an empirical example from the bees (Apoidea). Mol Phylogenet Evol. 2011;60(3):295-304.
Brady, S. G., Litman, J. R., & Danforth, B. N. (2011). Rooting phylogenies using gene duplications: an empirical example from the bees (Apoidea). Molecular Phylogenetics and Evolution, 60(3), 295-304. https://doi.org/10.1016/j.ympev.2011.05.002
Brady SG, Litman JR, Danforth BN. Rooting Phylogenies Using Gene Duplications: an Empirical Example From the Bees (Apoidea). Mol Phylogenet Evol. 2011;60(3):295-304. PubMed PMID: 21600997.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Rooting phylogenies using gene duplications: an empirical example from the bees (Apoidea). AU - Brady,Seán G, AU - Litman,Jessica R, AU - Danforth,Bryan N, Y1 - 2011/05/12/ PY - 2010/07/12/received PY - 2011/04/26/revised PY - 2011/05/03/accepted PY - 2011/5/24/entrez PY - 2011/5/24/pubmed PY - 2011/12/20/medline SP - 295 EP - 304 JF - Molecular phylogenetics and evolution JO - Mol Phylogenet Evol VL - 60 IS - 3 N2 - The placement of the root node in a phylogeny is fundamental to characterizing evolutionary relationships. The root node of bee phylogeny remains unclear despite considerable previous attention. In order to test alternative hypotheses for the location of the root node in bees, we used the F1 and F2 paralogs of elongation factor 1-alpha (EF-1α) to compare the tree topologies that result when using outgroup versus paralogous rooting. Fifty-two taxa representing each of the seven bee families were sequenced for both copies of EF-1α. Two datasets were analyzed. In the first (the "concatenated" dataset), the F1 and F2 copies for each species were concatenated and the tree was rooted using appropriate outgroups (sphecid and crabronid wasps). In the second dataset (the "duplicated" dataset), the F1 and F2 copies were aligned to each another and each copy for all taxa were treated as separate terminals. In this dataset, the root was placed between the F1 and F2 copies (e.g., paralog rooting). Bayesian analyses demonstrate that the outgroup rooting approach outperforms paralog rooting, recovering deeper clades and showing stronger support for groups well established by both morphological and other molecular data. Sequence characteristics of the two copies were compared at the amino acid level, but little evidence was found to suggest that one copy is more functionally conserved. Although neither approach yields an unambiguous root to the tree, both approaches strongly indicate that the root of bee phylogeny does not fall near Colletidae, as has been previously proposed. We discuss paralog rooting as a general strategy and why this approach performs relatively poorly with our particular dataset. SN - 1095-9513 UR - https://www.unboundmedicine.com/medline/citation/21600997/Rooting_phylogenies_using_gene_duplications:_an_empirical_example_from_the_bees__Apoidea__ L2 - https://linkinghub.elsevier.com/retrieve/pii/S1055-7903(11)00222-3 DB - PRIME DP - Unbound Medicine ER -