Impact of duplicate gene copies on phylogenetic analysis and divergence time estimates in butterfliesReport as inadecuate




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BMC Evolutionary Biology

, 9:99

First Online: 13 May 2009Received: 10 November 2008Accepted: 13 May 2009

Abstract

BackgroundThe increase in availability of genomic sequences for a wide range of organisms has revealed gene duplication to be a relatively common event. Encounters with duplicate gene copies have consequently become almost inevitable in the context of collecting gene sequences for inferring species trees. Here we examine the effect of incorporating duplicate gene copies evolving at different rates on tree reconstruction and time estimation of recent and deep divergences in butterflies.

ResultsSequences from ultraviolet-sensitive UVRh, blue-sensitive BRh, and long-wavelength sensitive LWRh opsins, EF-1α and COI were obtained from 27 taxa representing the five major butterfly families 5535 bp total. Both BRh and LWRh are present in multiple copies in some butterfly lineages and the different copies evolve at different rates. Regardless of the phylogenetic reconstruction method used, we found that analyses of combined data sets using either slower or faster evolving copies of duplicate genes resulted in a single topology in agreement with our current understanding of butterfly family relationships based on morphology and molecules. Interestingly, individual analyses of BRh and LWRh sequences also recovered these family-level relationships. Two different relaxed clock methods resulted in similar divergence time estimates at the shallower nodes in the tree, regardless of whether faster or slower evolving copies were used, with larger discrepancies observed at deeper nodes in the phylogeny. The time of divergence between the monarch butterfly Danaus plexippus and the queen D. gilippus 15.3–35.6 Mya was found to be much older than the time of divergence between monarch co-mimic Limenitis archippus and red-spotted purple L. arthemis 4.7–13.6 Mya, and overlapping with the time of divergence of the co-mimetic passionflower butterflies Heliconius erato and H. melpomene 13.5–26.1 Mya. Our family-level results are congruent with recent estimates found in the literature and indicate an age of 84–113 million years for the divergence of all butterfly families.

ConclusionThese results are consistent with diversification of the butterfly families following the radiation of angiosperms and suggest that some classes of opsin genes may be usefully employed for both phylogenetic reconstruction and divergence time estimation.

AbbreviationsMamillion years

Myamillion years ago

UVRhultraviolet-sensitive rhodopsin

BRhblue-sensitive rhodopsin

LWRhlong wavelength-sensitive rhodopsin

EF-1αelongation factor 1-alpha

COIcytochrome oxidase I.

Electronic supplementary materialThe online version of this article doi:10.1186-1471-2148-9-99 contains supplementary material, which is available to authorized users.

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Author: Nélida Pohl - Marilou P Sison-Mangus - Emily N Yee - Saif W Liswi - Adriana D Briscoe

Source: https://link.springer.com/article/10.1186/1471-2148-9-99



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