scholarly journals Using Genomic Location and Coalescent Simulation to Investigate Gene Tree Discordance in Medicago L.

2017 ◽  
Vol 66 (6) ◽  
pp. 934-949 ◽  
Author(s):  
F. Sousa ◽  
Y. J. K. Bertrand ◽  
J. J. Doyle ◽  
B. Oxelman ◽  
B. E. Pfeil
Keyword(s):  
Gene Tree ◽  
Coalescent Simulation ◽  
Genomic Location ◽  
Gene Tree Discordance

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

2022 ◽  
Vol 12 ◽  
Author(s):  
Martha Kandziora ◽  
Petr Sklenář ◽  
Filip Kolář ◽  
Roswitha Schmickl
Keyword(s):  
Incomplete Lineage Sorting ◽  
Gene Tree ◽  
Species Tree ◽  
Secondary Contact ◽  
Gene Trees ◽  
Species Trees ◽  
Lineage Sorting ◽  
Phylogenetic Discordance ◽  
Gene Tree Discordance ◽  
High Degree

A major challenge in phylogenetics and -genomics 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.

scholarly journals Deep-Time Demographic Inference Suggests Ecological Release as Driver of Neoavian Adaptive Radiation

Diversity ◽  
2020 ◽  
Vol 12 (4) ◽  
pp. 164 ◽  
Author(s):  
Peter Houde ◽  
Edward L. Braun ◽  
Lawrence Zhou
Keyword(s):  
Evolutionary Biology ◽  
Gene Tree ◽  
Difficult Problem ◽  
Gene Trees ◽  
Effective Population ◽  
Deep Time ◽  
Ecological Release ◽  
Population Sizes ◽  
Demographic Inference ◽  
Gene Tree Discordance

Assessing the applicability of theory to major adaptive radiations in deep time represents an extremely difficult problem in evolutionary biology. Neoaves, which includes 95% of living birds, is believed to have undergone a period of rapid diversification roughly coincident with the Cretaceous–Paleogene (K-Pg) boundary. We investigate whether basal neoavian lineages experienced an ecological release in response to ecological opportunity, as evidenced by density compensation. We estimated effective population sizes (Ne) of basal neoavian lineages by combining coalescent branch lengths (CBLs) and the numbers of generations between successive divergences. We used a modified version of Accurate Species TRee Algorithm (ASTRAL) to estimate CBLs directly from insertion–deletion (indel) data, as well as from gene trees using DNA sequence and/or indel data. We found that some divergences near the K-Pg boundary involved unexpectedly high gene tree discordance relative to the estimated number of generations between speciation events. The simplest explanation for this result is an increase in Ne, despite the caveats discussed herein. It appears that at least some early neoavian lineages, similar to the ancestor of the clade comprising doves, mesites, and sandgrouse, experienced ecological release near the time of the K-Pg mass extinction.

scholarly journals Disentangling Sources of Gene Tree Discordance in Phylogenomic Data Sets: Testing Ancient Hybridizations in Amaranthaceae s.l

2020 ◽  
Author(s):  
Diego F Morales-Briones ◽  
Gudrun Kadereit ◽  
Delphine T Tefarikis ◽  
Michael J Moore ◽  
Stephen A Smith ◽  
...  
Keyword(s):  
Network Inference ◽  
Incomplete Lineage Sorting ◽  
Gene Tree ◽  
Phylogenetic Network ◽  
Species Tree ◽  
Data Sets ◽  
Species Trees ◽  
Lineage Sorting ◽  
Data Set ◽  
Gene Tree Discordance

Abstract Gene tree discordance in large genomic data sets can be caused by evolutionary processes such as incomplete lineage sorting and hybridization, as well as model violation, and errors in data processing, orthology inference, and gene tree estimation. Species tree methods that identify and accommodate all sources of conflict are not available, but a combination of multiple approaches can help tease apart alternative sources of conflict. Here, using a phylotranscriptomic analysis in combination with reference genomes, we test a hypothesis of ancient hybridization events within the plant family Amaranthaceae s.l. that was previously supported by morphological, ecological, and Sanger-based molecular data. The data set included seven genomes and 88 transcriptomes, 17 generated for this study. We examined gene-tree discordance using coalescent-based species trees and network inference, gene tree discordance analyses, site pattern tests of introgression, topology tests, synteny analyses, and simulations. We found that a combination of processes might have generated the high levels of gene tree discordance in the backbone of Amaranthaceae s.l. Furthermore, we found evidence that three consecutive short internal branches produce anomalous trees contributing to the discordance. Overall, our results suggest that Amaranthaceae s.l. might be a product of an ancient and rapid lineage diversification, and remains, and probably will remain, unresolved. This work highlights the potential problems of identifiability associated with the sources of gene tree discordance including, in particular, phylogenetic network methods. Our results also demonstrate the importance of thoroughly testing for multiple sources of conflict in phylogenomic analyses, especially in the context of ancient, rapid radiations. We provide several recommendations for exploring conflicting signals in such situations. [Amaranthaceae; gene tree discordance; hybridization; incomplete lineage sorting; phylogenomics; species network; species tree; transcriptomics.]

scholarly journals DiscoVista: Interpretable visualizations of gene tree discordance

2018 ◽  
Vol 122 ◽  
pp. 110-115 ◽  
Author(s):  
Erfan Sayyari ◽  
James B. Whitfield ◽  
Siavash Mirarab
Keyword(s):  
Gene Tree ◽  
Gene Tree Discordance

scholarly journals Symbiosis genes show a unique pattern of introgression and selection within a Rhizobium leguminosarum species complex

2020 ◽  
Vol 6 (4) ◽  
Author(s):  
Maria Izabel A. Cavassim ◽  
Sara Moeskjær ◽  
Camous Moslemi ◽  
Bryden Fields ◽  
Asger Bachmann ◽  
...  
Keyword(s):  
Species Complex ◽  
Rhizobium Leguminosarum ◽  
De Novo ◽  
Gene Tree ◽  
Species Boundaries ◽  
Content Type ◽  
Genomic Location ◽  
Tree Traversal ◽  
Four Blocks ◽  
Core Genes

Rhizobia supply legumes with fixed nitrogen using a set of symbiosis genes. These can cross rhizobium species boundaries, but it is unclear how many other genes show similar mobility. Here, we investigate inter-species introgression using de novo assembly of 196 Rhizobium leguminosarum sv. trifolii genomes. The 196 strains constituted a five-species complex, and we calculated introgression scores based on gene-tree traversal to identify 171 genes that frequently cross species boundaries. Rather than relying on the gene order of a single reference strain, we clustered the introgressing genes into four blocks based on population structure-corrected linkage disequilibrium patterns. The two largest blocks comprised 125 genes and included the symbiosis genes, a smaller block contained 43 mainly chromosomal genes, and the last block consisted of three genes with variable genomic location. All introgression events were likely mediated by conjugation, but only the genes in the symbiosis linkage blocks displayed overrepresentation of distinct, high-frequency haplotypes. The three genes in the last block were core genes essential for symbiosis that had, in some cases, been mobilized on symbiosis plasmids. Inter-species introgression is thus not limited to symbiosis genes and plasmids, but other cases are infrequent and show distinct selection signatures.

scholarly journals Sage Insights Into the Phylogeny of Salvia: Dealing With Sources of Discordance Within and Across Genomes

2021 ◽  
Vol 12 ◽  
Author(s):  
Jeffrey P. Rose ◽  
Ricardo Kriebel ◽  
Larissa Kahan ◽  
Alexa DiNicola ◽  
Jesús G. González-Gallegos ◽  
...  
Keyword(s):  
Incomplete Lineage Sorting ◽  
Gene Tree ◽  
Divergence Time ◽  
Time Estimation ◽  
Single Copy ◽  
Lineage Sorting ◽  
Divergence Time Estimation ◽  
Sequencing Technologies ◽  
Plastid Genomes ◽  
Gene Tree Discordance

Next-generation sequencing technologies have facilitated new phylogenomic approaches to help clarify previously intractable relationships while simultaneously highlighting the pervasive nature of incongruence within and among genomes that can complicate definitive taxonomic conclusions. Salvia L., with ∼1,000 species, makes up nearly 15% of the species diversity in the mint family and has attracted great interest from biologists across subdisciplines. Despite the great progress that has been achieved in discerning the placement of Salvia within Lamiaceae and in clarifying its infrageneric relationships through plastid, nuclear ribosomal, and nuclear single-copy genes, the incomplete resolution has left open major questions regarding the phylogenetic relationships among and within the subgenera, as well as to what extent the infrageneric relationships differ across genomes. We expanded a previously published anchored hybrid enrichment dataset of 35 exemplars of Salvia to 179 terminals. We also reconstructed nearly complete plastomes for these samples from off-target reads. We used these data to examine the concordance and discordance among the nuclear loci and between the nuclear and plastid genomes in detail, elucidating both broad-scale and species-level relationships within Salvia. We found that despite the widespread gene tree discordance, nuclear phylogenies reconstructed using concatenated, coalescent, and network-based approaches recover a common backbone topology. Moreover, all subgenera, except for Audibertia, are strongly supported as monophyletic in all analyses. The plastome genealogy is largely resolved and is congruent with the nuclear backbone. However, multiple analyses suggest that incomplete lineage sorting does not fully explain the gene tree discordance. Instead, horizontal gene flow has been important in both the deep and more recent history of Salvia. Our results provide a robust species tree of Salvia across phylogenetic scales and genomes. Future comparative analyses in the genus will need to account for the impacts of hybridization/introgression and incomplete lineage sorting in topology and divergence time estimation.

scholarly journals Phylogenomic analyses using genomes and transcriptomes do not resolve relationships among major clades in Phrymaceae

2021 ◽  
Author(s):  
Diego F. Morales-Briones ◽  
Nan Lin ◽  
Eileen Y. Huang ◽  
Dena L. Grossenbacher ◽  
James M. Sobel ◽  
...  
Keyword(s):  
Phylogenetic Relationships ◽  
Evolutionary Ecology ◽  
Gene Tree ◽  
Phylogenetic Network ◽  
Reticulate Evolution ◽  
Small Scale ◽  
Gene Trees ◽  
Network Analyses ◽  
Gene Tree Discordance ◽  
Close Relatives

Premise of the study: 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 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 cloudogram, and carried out phylogenetic network analyses using PhyloNet and HyDe. We searched for whole genome duplication (WGD) events using chromosome numbers, synonymous distance, and gene duplication events. Key results: Most gene trees support the monophyly of Phrymaceae and each of its tribes. Most gene trees also support the tribe Mimuleae being sister to Phrymeae + Diplaceae + Leucocarpeae, with extensive gene tree discordance among the latter three. Despite the discordance, polyphyly of Mimulus s.l. is strongly supported, and no particular reticulation event among the Phrymaceae tribes is well supported. Reticulation likely occurred among Erythranthe bicolor and close relatives. No ancient WGD event 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 genome-scale data do not always fully "resolve" phylogenetic relationships. They present rich opportunities to investigate reticulate evolution, and gene and genome evolution involved in lineage diversification and adaptation.

Dissecting incongruence between concatenation- and quartet-based approaches in phylogenomic data

2021 ◽  
Author(s):  
Xing-Xing Shen ◽  
Jacob L Steenwyk ◽  
Antonis Rokas
Keyword(s):  
Incomplete Lineage Sorting ◽  
Phylogenetic Signal ◽  
Estimation Error ◽  
Gene Tree ◽  
Data Matrix ◽  
Species Trees ◽  
Likelihood Score ◽  
Log Likelihood ◽  
The Difference ◽  
Gene Tree Discordance

Abstract Topological conflict or incongruence is widespread in phylogenomic data. Concatenation- and coalescent-based approaches often result in incongruent topologies, but the causes of this conflict can be difficult to characterize. We examined incongruence stemming from conflict between likelihood-based signal (quantified by the difference in gene-wise log likelihood score or ΔGLS) and quartet-based topological signal (quantified by the difference in gene-wise quartet score or ΔGQS) for every gene in three phylogenomic studies in animals, fungi, and plants, which were chosen because their concatenation-based IQ-TREE (T1) and quartet-based ASTRAL (T2) phylogenies are known to produce eight conflicting internal branches (bipartitions). By comparing the types of phylogenetic signal for all genes in these three data matrices, we found that 30% - 36% of genes in each data matrix are inconsistent, that is, each of these genes has higher log likelihood score for T1 versus T2 (i.e., ΔGLS >0) whereas its T1 topology has lower quartet score than its T2 topology (i.e., ΔGQS <0) or vice versa. Comparison of inconsistent and consistent genes using a variety of metrics (e.g., evolutionary rate, gene tree topology, distribution of branch lengths, hidden paralogy, and gene tree discordance) showed that inconsistent genes are more likely to recover neither T1 nor T2 and have higher levels of gene tree discordance than consistent genes. Simulation analyses demonstrate that removal of inconsistent genes from datasets with low levels of incomplete lineage sorting (ILS) and low and medium levels of gene tree estimation error (GTEE) reduced incongruence and increased accuracy. In contrast, removal of inconsistent genes from datasets with medium and high ILS levels and high GTEE levels eliminated or extensively reduced incongruence, but the resulting congruent species phylogenies were not always topologically identical to the true species trees.

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