Abstract Detail



Phylogenomics

Song, Michael [1], Rothfels, Carl [2], Igic, Boris [3].

Difficulties in the Inference of Ancient Whole-Genome Duplications.

Polyploids—those individuals that have experienced whole genome duplications (WGDs)—were classically regarded as evolutionary dead ends. In a remarkable shift of scientific opinion, the seemingly opposing view—that ancient WGDs are commonplace in the ancestry of many extant lineages—has recently come to predominate, such that most evolutionary biologists accept that many genomes (including those of nearly all plants) have been shaped by of multiple rounds of WGD. This rapid shift in viewpoint was brought about the increased availability of genome-scale data and by a novel set of inference methods, which have changed the way we think about plant genome evolution and its relationship to patterns of angiosperm diversification. Here, we caution that our overconfidence in the widely employed inference methods. One inference method forms a disproportionate basis of evidence supporting WGDs and their ages. It relies on distributions of nucleotide distances of synonymous mutations (Ks) among paralogous genes. The models that shape our expectations of Ks distributions, and the associated statistical tests, may not have the advertised ability to reliably discern ancient polyploidization events from a number of confounding processes. As a consequence, it is possible that we have vastly overestimated the prevalence of ancient WGDs.


1 - University of California, Berkeley, UC Berkeley, Berkeley, CA, 94720, United States
2 - University Of California Berkeley, University Herbarium And Departmenty Of Integrative Biology, 1001 Valley Life Science Building, Berkeley, CA, 94720, United States
3 - University of Illinois Chicago, Chicago, IL

Keywords:
Polyploidy
whole genome duplication
ks plot.

Presentation Type: Poster
Number: PPH001
Abstract ID:135
Candidate for Awards:None


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