How to Tackle Phylogenetic Discordance in Recent and Rapidly Radiating Groups? Developing a Workflow Using Loricaria (Asteraceae) as an Example

Result code in IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F67985939%3A_____%2F22%3A00554661" target="_blank" >RIV/67985939:_____/22:00554661 - isvavai.cz</a>

Alternative codes found

RIV/00216208:11310/22:10454019

Result on the web

<a href="https://doi.org/10.3389/fpls.2021.765719" target="_blank" >https://doi.org/10.3389/fpls.2021.765719</a>

DOI - Digital Object Identifier

<a href="http://dx.doi.org/10.3389/fpls.2021.765719" target="_blank" >10.3389/fpls.2021.765719</a>

Result language

angličtina

Original language name

How to Tackle Phylogenetic Discordance in Recent and Rapidly Radiating Groups? Developing a Workflow Using Loricaria (Asteraceae) as an Example

Original language description

A major challenge in phylogenetics andgenomics is to resolve young rapidly radiating groups. The fast succession of species increases the probability of incomplete lineage sorting (ILS), and different topologies of the gene trees are expected, leading to gene tree discordance, i.e., not all gene trees represent the species tree. Phylogenetic discordance is common in phylogenomic datasets, and apart from ILS, additional sources include hybridization, whole-genome duplication, and methodological artifacts. Despite a high degree of gene tree discordance, species trees are often well supported and the sources of discordance are not further addressed in phylogenomic studies, which can eventually lead to incorrect phylogenetic hypotheses, especially in rapidly radiating groups. We chose the high-Andean Asteraceae genus Loricaria to shed light on the potential sources of phylogenetic discordance and generated a phylogenetic hypothesis. By accounting for paralogy during gene tree inference, we generated a species tree based on hundreds of nuclear loci, using Hyb-Seq, and a plastome phylogeny obtained from off-target reads during target enrichment. We observed a high degree of gene tree discordance, which we found implausible at first sight, because the genus did not show evidence of hybridization in previous studies. We used various phylogenomic analyses (trees and networks) as well as the D-statistics to test for ILS and hybridization, which we developed into a workflow on how to tackle phylogenetic discordance in recent radiations. We found strong evidence for ILS and hybridization within the genus Loricaria. Low genetic differentiation was evident between species located in different Andean cordilleras, which could be indicative of substantial introgression between populations, promoted during Pleistocene glaciations, when alpine habitats shifted creating opportunities for secondary contact and hybridization.

Czech name

—

Czech description

—

Type

J_imp - Article in a specialist periodical, which is included in the Web of Science database

CEP classification

—

OECD FORD branch

10611 - Plant sciences, botany

Project

<a href="/en/project/GA20-10878S" target="_blank" >GA20-10878S: Tropical-alpine plant radiations: an intercontinental comparison of timing and the role of allopatry, hybridization and niche differentiation</a><br>

Continuities

I - Institucionalni podpora na dlouhodoby koncepcni rozvoj vyzkumne organizace

Publication year

2022

Confidentiality

S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

Name of the periodical

Frontiers in Plant Science

ISSN

1664-462X

e-ISSN

1664-462X

Volume of the periodical

12

Issue of the periodical within the volume

7 January

Country of publishing house

CH - SWITZERLAND

Number of pages

16

Pages from-to

765719

UT code for WoS article

000758015400001

EID of the result in the Scopus database

2-s2.0-85123208692