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Extensive gene tree discordance and hemiplasy shaped the genomes of North American columnar cacti.

Authors :
Copetti D
Búrquez A
Bustamante E
Charboneau JLM
Childs KL
Eguiarte LE
Lee S
Liu TL
McMahon MM
Whiteman NK
Wing RA
Wojciechowski MF
Sanderson MJ
Source :
Proceedings of the National Academy of Sciences of the United States of America [Proc Natl Acad Sci U S A] 2017 Nov 07; Vol. 114 (45), pp. 12003-12008. Date of Electronic Publication: 2017 Oct 23.
Publication Year :
2017

Abstract

Few clades of plants have proven as difficult to classify as cacti. One explanation may be an unusually high level of convergent and parallel evolution (homoplasy). To evaluate support for this phylogenetic hypothesis at the molecular level, we sequenced the genomes of four cacti in the especially problematic tribe Pachycereeae, which contains most of the large columnar cacti of Mexico and adjacent areas, including the iconic saguaro cactus ( Carnegiea gigantea ) of the Sonoran Desert. We assembled a high-coverage draft genome for saguaro and lower coverage genomes for three other genera of tribe Pachycereeae ( Pachycereus , Lophocereus , and Stenocereus ) and a more distant outgroup cactus, Pereskia We used these to construct 4,436 orthologous gene alignments. Species tree inference consistently returned the same phylogeny, but gene tree discordance was high: 37% of gene trees having at least 90% bootstrap support conflicted with the species tree. Evidently, discordance is a product of long generation times and moderately large effective population sizes, leading to extensive incomplete lineage sorting (ILS). In the best supported gene trees, 58% of apparent homoplasy at amino sites in the species tree is due to gene tree-species tree discordance rather than parallel substitutions in the gene trees themselves, a phenomenon termed "hemiplasy." The high rate of genomic hemiplasy may contribute to apparent parallelisms in phenotypic traits, which could confound understanding of species relationships and character evolution in cacti.<br />Competing Interests: The authors declare no conflict of interest.<br /> (Published under the PNAS license.)

Details

Language :
English
ISSN :
1091-6490
Volume :
114
Issue :
45
Database :
MEDLINE
Journal :
Proceedings of the National Academy of Sciences of the United States of America
Publication Type :
Academic Journal
Accession number :
29078296
Full Text :
https://doi.org/10.1073/pnas.1706367114