PT  - JOURNAL ARTICLE
AU  - Michael S. Barker
AU  - Zheng Li
AU  - Thomas I. Kidder
AU  - Chris R. Reardon
AU  - Zhao Lai
AU  - Luiz O. Oliveira
AU  - Moira Scascitelli
AU  - Loren H. Rieseberg
TI  - Most Compositae are descendants of a paleohexaploid and all share a paleotetraploid ancestor with the Calyceraceae
AID  - 10.1101/043455
DP  - 2016 Jan 01
TA  - bioRxiv
PG  - 043455
4099  - http://biorxiv.org/content/early/2016/03/12/043455.short
4100  - http://biorxiv.org/content/early/2016/03/12/043455.full
AB  - Premise of the study Like many other flowering plants, members of the Compositae (Asteraceae) have a polyploid ancestry. Previous analyses have found evidence for an ancient duplication or possibly triplication in the early evolutionary history of the family. We sought to better place this paleopolyploidy in the phylogeny and assess its nature.Methods We sequenced new transcriptomes for Barnadesia, the lineage sister to all other Compositae, and four representatives of closely related families. Using a recently developed algorithm, MAPS, we analyzed nuclear gene family phylogenies for evidence of paleopolyploidy.Key results We found that the previously recognized Compositae paleopolyploidy is also in the ancestry of the Calyceraceae. Our phylogenomic analyses uncovered evidence for a successive second round of genome duplication among all sampled Compositae except Barnadesia.Conclusions Our analyses of new samples with new tools provide a revised view of paleopolyploidy in the Compositae. Together with results from recent linkage maps, our results suggest that the Compositae and Calyceraceae have a common paleotetraploid ancestor and most Compositae are descendants of a paleohexaploid. Although paleohexaploids have been previously identified, this is the first example where the paleotetraploid and paleohexaploid lineages have survived over tens of millions of years. The complex polyploidy in the ancestry of the Compositae and Calyceraceae represents a unique opportunity to study the long-term evolutionary fates and consequences of different ploidal levels.