Abstract Detail


Hodel, Richard [1], Zimmer, Elizabeth [2], Wen, Jun [3].

Nuclear phylogenomic analysis resolves the backbone of Prunus and identifies lineages impacted by frequent reticulate evolution.

The genus Prunus (Rosaceae) contains evergreen and deciduous species occurring throughout the temperate regions of the northern hemisphere and in the tropics and subtropics. Phylogenetic studies on Prunus have used several plastid markers, the nuclear ribosomal ITS, and a few nuclear loci and have produced some significant insights, but many questions remain. Phylogenetic relationships within Prunus are not fully resolved, particularly along the backbone of the phylogeny. Cytonuclear discord and multiple copies of low-copy nuclear loci suggest that allopolyploidy and/or ancient hybridization is obscuring phylogenetic relationships. Specifically, chloroplast data show a sister relationship between the diploid solitary and diploid corymbose groups, but nuclear data have not clearly resolved the relationship between the solitary, corymbose, and polyploid racemose groups. There are ample genomic resources for the genus—currently genome assemblies are available for five species—yet there has not been a phylogenomic investigation to resolve relationships within Prunus.           
We used a combination of existing transcriptome assemblies for five species and publicly available RNA-Seq data to generate de novo assembled transcriptomes for 16 species. The 21 species included represent the three major clades in Prunus. We processed the transcriptomes using Markerminer to construct a dataset of 392 putatively single-copy genes with data present for at least 10 species for each gene. We obtained plastome data from NCBI or assembled plastomes using FastPlast for all 21 species. RAxML was used to estimate a phylogeny for each gene tree and for a concatenated supermatrix of all 392 genes, and for the plastome dataset. ASTRAL was used to estimate a coalescent species tree using all 392 gene trees. 
There were several differences between the chloroplast and nuclear phylogenies, although the relationships between all major clades were consistent—the solitary and corymbose groups were sisters.  We investigated conflict in the nuclear trees using phyparts and found several nodes with substantial underlying gene tree conflict, especially along the backbone of the phylogeny. Notably, some nodes had more gene trees in conflict with the species tree than congruent to the species tree.  The node defining the clade of solitary+corymbose had substantial gene tree conflict, with 130 genes with topologies incongruent with the species tree. In summary, the phylogenomic approach resolved the branching order of the backbone of Prunus and identified several key nodes with underlying discord that will be valuable for future investigations of the taxa and/or lineages implicated in ancient polyploidization or hybridization events. 

Related Links:

1 - National Museum of Natural History, Botany, Smithsonian Institution, MRC 166, Washington, DC, 20560-0166, United States
2 - Smithsonian NMNH, Botany MRC 166, P.O. Box 37102, Smithsonian National Museum Of Natural History, Washington, DC, 20013, United States
3 - Botany, MRC-166 National Museum Of Natural History, 10th St. & Constitution Ave., NW, Mrc 166, Washington/DC, 20013, United States

reticulate evolution
gene tree discord

Presentation Type: Oral Paper
Session: PHYL2, Phylogenomics II
Location: Virtual/Virtual
Date: Wednesday, July 29th, 2020
Time: 1:30 PM
Number: PHYL2005
Abstract ID:640
Candidate for Awards:None

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