000 02493 am a22002653u 4500
042 _adc
100 1 0 _aChen, Hengchi
_eauthor
_91346
700 1 0 _aFang, Yuhan
_eauthor
_91339
700 1 0 _aZwaenepoel, Arthur
_eauthor
_92384
700 1 0 _aHuang, Sanwen
_eauthor
_91361
700 1 0 _aVan de Peer, Yves
_eauthor
700 1 0 _aLi, Zhen
_eauthor
_91345
245 0 0 _aRevisiting Ancient Polyploidy in Leptosporangiate Ferns
260 _c2022-11-08.
500 _a/pmc/articles/PMC7614084/
500 _a/pubmed/36349406
520 _aFerns, and particularly homosporous ferns, have long been assumed to have experienced recurrent whole-genome duplication (WGD) events because of their substantially large genome sizes, surprisingly high chromosome numbers, and high degrees of polyploidy among many extant members. As the number of sequenced fern genomes is limited, recent studies have employed transcriptome data to find evidence for WGDs in ferns. However, they have reached conflicting results concerning the occurrence of ancient polyploidy, for instance, in the lineage of leptosporangiate ferns. Because identifying WGDs in a phylogenetic context is the foremost step in studying the contribution of ancient polyploidy to evolution, we here revisited earlier identified WGDs in leptosporangiate ferns, mainly the core leptosporangiate ferns, by building K(s)-age distributions and applying substitution rate corrections, and by conducting statistical gene tree - species tree reconciliation analyses. Our integrative analyses confidently identified four ancient WGDs in the sampled core leptosporangiate ferns but also identified false positives and false negatives for WGDs that recent studies have reported earlier. In conclusion, we underscore the significance of substitution rate corrections and uncertainties in gene tree - species tree reconciliations in calling WGD events and advance an exemplar workflow to overcome such often-overlooked issues.
540 _a
540 _ahttps://creativecommons.org/licenses/by/4.0/This work was funded by European Research Council (DOUBLE-TROUBLE 833522). For the purpose of Open Access, the author has applied a CC BY public copyright licence to any Author Accepted Manuscript version arising from this submission. (https://creativecommons.org/licenses/by/4.0/)
546 _aen
690 _aArticle
655 7 _aText
_2local
786 0 _nNew Phytol
856 4 1 _uhttp://dx.doi.org/10.1111/nph.18607
_zConnect to this object online.
999 _c2106
_d2106