Phylogenomic analyses in Phrymaceae reveal extensive gene tree discordance in relationships among major clades.

Autor: Morales-Briones DF; Department of Plant and Microbial Biology, University of Minnesota-Twin Cities, 1445 Gortner Avenue, St. Paul, Minnesota, 55108-1095, USA.; Systematics, Biodiversity and Evolution of Plants, Department of Biology I, Ludwig-Maximilians-Universität München, Menzinger Strasse 67, 80638, Munich, Germany., Lin N; Department of Plant and Microbial Biology, University of Minnesota-Twin Cities, 1445 Gortner Avenue, St. Paul, Minnesota, 55108-1095, USA.; College of Life Science, Henan Agricultural University, 63 Nongye Road, Zhengzhou, Henan, 450002, China., Huang EY; Department of Plant and Microbial Biology, University of Minnesota-Twin Cities, 1445 Gortner Avenue, St. Paul, Minnesota, 55108-1095, USA., Grossenbacher DL; Biological Sciences Department, California Polytechnic State University, 1 Grand Avenue, San Luis Obispo, California, 93407, USA., Sobel JM; Department of Biological Sciences, Binghamton University (State University of New York), 4400 Vestal Parkway E, Binghamton, New York, 13902, USA., Gilmore CD; Department of Biological Sciences, Binghamton University (State University of New York), 4400 Vestal Parkway E, Binghamton, New York, 13902, USA., Tank DC; Department of Botany & Rocky Mountain Herbarium, University of Wyoming, 1000 E. University Avenue, Laramie, Wyoming, 82071, USA., Yang Y; Department of Plant and Microbial Biology, University of Minnesota-Twin Cities, 1445 Gortner Avenue, St. Paul, Minnesota, 55108-1095, USA.
Jazyk: angličtina
Zdroj: American journal of botany [Am J Bot] 2022 Jun; Vol. 109 (6), pp. 1035-1046. Date of Electronic Publication: 2022 Jun 05.
DOI: 10.1002/ajb2.1860
Abstrakt: Premise: Phylogenomic datasets using genomes and transcriptomes provide rich opportunities beyond resolving bifurcating phylogenetic relationships. Monkeyflower (Phrymaceae) is a model system for evolutionary ecology. However, it lacks a well-supported phylogeny as a basis for a stable taxonomy and for macroevolutionary comparisons.
Methods: We sampled 24 genomes and transcriptomes in Phrymaceae and closely related families, including eight newly sequenced transcriptomes. We reconstructed the phylogeny using IQ-TREE and ASTRAL, evaluated gene tree discordance using PhyParts, Quartet Sampling, and a cloudogram, and carried out reticulation analyses using PhyloNet and HyDe. We searched for whole genome duplication (WGD) events using chromosome numbers, synonymous distances, and gene duplication events as evidence.
Results: Most gene trees support the monophyly of Phrymaceae and each of its tribes. Most gene trees also support tribe Mimuleae being sister to Phrymeae + Diplaceae + Leucocarpeae, with extensive gene tree discordance among the latter three. Despite the discordance, the monophyly of Mimulus s.l. is rejected, and no individual reticulation event among the Phrymaceae tribes is well-supported. Reticulation likely occurred among Erythranthe bicolor and closely related species. No ancient WGD was detected in Phrymaceae. Instead, small-scale duplications are among potential drivers of macroevolutionary diversification of Phrymaceae.
Conclusions: We show that analysis of reticulate evolution is sensitive to taxon sampling and methods used. We also demonstrate that phylogenomic datasets using genomes and transcriptomes present rich opportunities to investigate gene family evolution and genome duplication events involved in lineage diversification and adaptation.
(© 2022 The Authors. American Journal of Botany published by Wiley Periodicals LLC on behalf of Botanical Society of America.)
Databáze: MEDLINE
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