Ancient Rapid Radiation Explains Most Conflicts Among Gene Trees and Well-Supported Phylogenomic Trees of Nostocalean Cyanobacteria
Abstract
Prokaryotic genomes are often considered to be mosaics of genes that do not necessarily share the same evolutionary history due to widespread horizontal gene transfers (HGTs). Consequently, representing evolutionary relationships of prokaryotes as bifurcating trees has long been controversial. However, studies reporting conflicts among gene trees derived from phylogenomic data sets have shown that these conflicts can be the result of artifacts or evolutionary processes other than HGT, such as incomplete lineage sorting, low phylogenetic signal, and systematic errors due to substitution model misspecification. Here, we present the results of an extensive exploration of phylogenetic conflicts in the cyanobacterial order Nostocales, for which previous studies have inferred strongly supported conflicting relationships when using different concatenated phylogenomic data sets. We found that most of these conflicts are concentrated in deep clusters of short internodes of the Nostocales phylogeny, where the great majority of individual genes have low resolving power. We then inferred phylogenetic networks to detect HGT events while also accounting for incomplete lineage sorting. Our results indicate that most conflicts among gene trees are likely due to incomplete lineage sorting linked to an ancient rapid radiation, rather than to HGTs. Moreover, the short internodes of this radiation fit the expectationsmore »
- Authors:
-
- Duke Univ., Durham, NC (United States)
- Univ. of Liege, (Belgium)
- Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
- Univ. of Liege, (Belgium); Sciensano, Brussels (Belgium)
- Botanical Research Institute of Texas, Fort Worth, TX (United States)
- North Carolina State University, Raleigh, NC (United States)
- Publication Date:
- Research Org.:
- Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States)
- Sponsoring Org.:
- USDOE; National Science Foundation (NSF)
- OSTI Identifier:
- 1972571
- Grant/Contract Number:
- AC05-00OR22725; BEE 1929994
- Resource Type:
- Accepted Manuscript
- Journal Name:
- Systematic Biology
- Additional Journal Information:
- Journal Volume: 72; Journal Issue: 3; Journal ID: ISSN 1063-5157
- Publisher:
- Society of Systematic Biologists - Oxford University Press
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; anomaly zone; bacteria; horizontal gene transfer; incomplete lineage sorting; Nostocales; phylogenomic conflict; rapid radiation; Rhizonema
Citation Formats
Pardo-De la Hoz, Carlos J., Magain, Nicolas, Piatkowski, Bryan, Cornet, Luc, Dal Forno, Manuela, Carbone, Ignazio, Miadlikowska, Jolanta, and Lutzoni, François. Ancient Rapid Radiation Explains Most Conflicts Among Gene Trees and Well-Supported Phylogenomic Trees of Nostocalean Cyanobacteria. United States: N. p., 2023.
Web. doi:10.1093/sysbio/syad008.
Pardo-De la Hoz, Carlos J., Magain, Nicolas, Piatkowski, Bryan, Cornet, Luc, Dal Forno, Manuela, Carbone, Ignazio, Miadlikowska, Jolanta, & Lutzoni, François. Ancient Rapid Radiation Explains Most Conflicts Among Gene Trees and Well-Supported Phylogenomic Trees of Nostocalean Cyanobacteria. United States. https://doi.org/10.1093/sysbio/syad008
Pardo-De la Hoz, Carlos J., Magain, Nicolas, Piatkowski, Bryan, Cornet, Luc, Dal Forno, Manuela, Carbone, Ignazio, Miadlikowska, Jolanta, and Lutzoni, François. Fri .
"Ancient Rapid Radiation Explains Most Conflicts Among Gene Trees and Well-Supported Phylogenomic Trees of Nostocalean Cyanobacteria". United States. https://doi.org/10.1093/sysbio/syad008. https://www.osti.gov/servlets/purl/1972571.
@article{osti_1972571,
title = {Ancient Rapid Radiation Explains Most Conflicts Among Gene Trees and Well-Supported Phylogenomic Trees of Nostocalean Cyanobacteria},
author = {Pardo-De la Hoz, Carlos J. and Magain, Nicolas and Piatkowski, Bryan and Cornet, Luc and Dal Forno, Manuela and Carbone, Ignazio and Miadlikowska, Jolanta and Lutzoni, François},
abstractNote = {Prokaryotic genomes are often considered to be mosaics of genes that do not necessarily share the same evolutionary history due to widespread horizontal gene transfers (HGTs). Consequently, representing evolutionary relationships of prokaryotes as bifurcating trees has long been controversial. However, studies reporting conflicts among gene trees derived from phylogenomic data sets have shown that these conflicts can be the result of artifacts or evolutionary processes other than HGT, such as incomplete lineage sorting, low phylogenetic signal, and systematic errors due to substitution model misspecification. Here, we present the results of an extensive exploration of phylogenetic conflicts in the cyanobacterial order Nostocales, for which previous studies have inferred strongly supported conflicting relationships when using different concatenated phylogenomic data sets. We found that most of these conflicts are concentrated in deep clusters of short internodes of the Nostocales phylogeny, where the great majority of individual genes have low resolving power. We then inferred phylogenetic networks to detect HGT events while also accounting for incomplete lineage sorting. Our results indicate that most conflicts among gene trees are likely due to incomplete lineage sorting linked to an ancient rapid radiation, rather than to HGTs. Moreover, the short internodes of this radiation fit the expectations of the anomaly zone, i.e., a region of the tree parameter space where a species tree is discordant with its most likely gene tree. In this work, we demonstrated that concatenation of different sets of loci can recover up to 17 distinct and well-supported relationships within the putative anomaly zone of Nostocales, corresponding to the observed conflicts among well-supported trees based on concatenated data sets from previous studies. Our findings highlight the important role of rapid radiations as a potential cause of strongly conflicting phylogenetic relationships when using phylogenomic data sets of bacteria. We propose that polytomies may be the most appropriate phylogenetic representation of these rapid radiations that are part of anomaly zones, especially when all possible genomic markers have been considered to infer these phylogenies.},
doi = {10.1093/sysbio/syad008},
journal = {Systematic Biology},
number = 3,
volume = 72,
place = {United States},
year = {Fri Feb 24 00:00:00 EST 2023},
month = {Fri Feb 24 00:00:00 EST 2023}
}
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