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38 results for “phylogenomic conflict”
Data from: Congruence and conflict in the higher-level phylogenetics of squamate reptiles: an expanded phylogenomic perspective
<p>Genome-scale data have the potential to clarify phylogenetic relationships across the tree of life, but have also revealed extensive gene tree conflict. This seeming paradox, whereby larger datasets both increase statistical confidence and uncover significant discordance, suggests that understanding sources of conflict is important for accurate reconstruction of evolutionary history. We explore this paradox in squamate reptiles, the vertebrate clade comprising lizards, snakes, and amphisbaenians. We collected an average of 5103 loci for 91 species of squamates that span higher-level diversity within the clade, which we augmented with publicly available sequences for an additional 17 taxa. Using a locus-by-locus approach, we evaluated support for alternative topologies at 17 contentious nodes in the phylogeny. We identified shared properties of conflicting loci, finding that rate and compositional heterogeneity drives discordance between gene trees and species tree and that conflicting loci rarely overlap across contentious nodes. Finally, by comparing our tests of nodal conflict to previous phylogenomic studies, we confidently resolve nine of the 17 problematic nodes. We suggest this locus-by-locus and node-by-node approach can be used to build consensus on which topological resolutions remain uncertain in phylogenomic studies of other contentious groups.</p>
Data from: Conflicting phylogenomic signals reveal a pattern of reticulate evolution in a recent high-Andean diversification (Asteraceae: Astereae: Diplostephium)
High-throughput sequencing is helping biologists to overcome the difficulties of inferring the phylogenies of recently diverged taxa. The present study analyzes the phylogenetic signal of genomic regions with different inheritance patterns using genome skimming and ddRAD-seq in a species-rich Andean genus (Diplostephium) and its allies. We analyzed the complete nuclear ribosomal cistron, the complete chloroplast genome, a partial mitochondrial genome, and a nuclear-ddRAD matrix separately with phylogenetic methods. We applied several approaches to understand the causes of incongruence among datasets, including simulations and the detection of introgression using the D-statistic (ABBA-BABA test). We found significant incongruence among the nuclear, chloroplast, and mitochondrial phylogenies. The strong signal of hybridization found by simulations and the D-statistic among genera and inside the main clades of Diplostephium indicate reticulate evolution as a main cause of phylogenetic incongruence. Our results add evidence for a major role of reticulate evolution in events of rapid diversification. Hybridization and introgression confound chloroplast and mitochondrial phylogenies in relation to the species tree as a result of the uniparental inheritance of these genomic regions. Practical implications regarding the prevalence of hybridization are discussed in relation to the phylogenetic method.
Data from: Phylogenomic analyses resolve an ancient trichotomy at the base of Ischyropsalidoidea (Arachnida, Opiliones) despite high levels of gene tree conflict and unequal minority resolution frequencies
Phylogenetic resolution of ancient rapid radiations has remained problematic despite major advances in statistical approaches and DNA sequencing technologies. Here we report on a combined phylogenetic approach utilizing transcriptome data in conjunction with Sanger sequence data to investigate a tandem of ancient divergences in the harvestmen superfamily Ischyropsalidoidea (Arachnida, Opiliones, Dyspnoi). We rely on Sanger sequences to resolve nodes within and between closely related genera, and use RNA-seq data from a subset of taxa to resolve a short and ancient internal branch. We use several analytical approaches to explore this succession of ancient diversification events, including concatenated and coalescent-based analyses and maximum likelihood gene trees for each locus. We evaluate the robustness of phylogenetic inferences using a randomized locus sub-sampling approach, and find congruence across these methods despite considerable incongruence across gene trees. Incongruent gene trees are not recovered in frequencies expected from a simple multispecies coalescent model, and we reject incomplete lineage sorting as the sole contributor to gene tree conflict. Using these approaches we attain robust support for higher-level phylogenetic relationships within Ischyropsalidoidea.
Data from: Phylogenomics uncovers confidence and conflict in the rapid radiation of Australo-Papuan rodents
The estimation of robust and accurate measures of branch support has proven challenging in the era of phylogenomics. In datasets of potentially millions of sites, bootstrap support for bifurcating relationships around very short internal branches can be inappropriately inflated. Such over-estimation of branch support may be particularly problematic in rapid radiations, where phylogenetic signal is low and incomplete lineage sorting severe. Here, we explore this issue by comparing various branch support estimates under both concatenated and coalescent frameworks, in the recent radiation Australo-Papuan murine rodents (Muridae: Hydromyini). Using nucleotide sequence data from 1245 independent loci and several phylogenomic inference methods, we unequivocally resolve the majority of genus-level relationships within Hydromyini. However, at four nodes we recover inconsistency in branch support estimates both within and among concatenated and coalescent approaches. In most cases, concatenated likelihood approaches using standard fast bootstrap algorithms did not detect any uncertainty at these four nodes, regardless of partitioning strategy. However, we found this could be overcome with two-stage resampling, i.e. across genes and sites within genes (using -bsam GENESITE in IQtree). In addition, low confidence at recalcitrant nodes was recovered using UFBoot2, a recent revision to the bootstrap protocol in IQtree, but this depended on partitioning strategy. Summary coalescent approaches also failed to detect uncertainty under some circumstances. For each of four recalcitrant nodes, an equivalent (or close to equivalent) number of genes were in strong support (> 75% bootstrap) of both the primary and at least one alternative topological hypothesis, suggesting notable phylogenetic conflict among loci not detected using some standard branch support metrics. Recent debate has focused on the appropriateness of concatenated versus multi-genealogical approaches to resolving species relationships, but less so on accurately estimating uncertainty in large datasets. Our results demonstrate the importance of employing multiple approaches when assessing confidence, and highlight the need for greater attention to the development of robust measures of uncertainty in the era of phylogenomics.
Untying the Gordian Knot of plastid phylogenomic conflict: a case from ferns
<p>Phylogenomic studies based on plastid genome have resolved the recalcitrant relationships among various plants, yet the phylogeny of Dennstaedtiaceae at the taxonomic level remains unresolved due to conflicting plastid genes, limited molecular data and incomplete taxon sampling of previous studies. The present study generated 31 new plastid genomes of Dennstaedtiaceae (9 genera, 30 species) and combined 41 publicly available sequences of plastid genome (including 24 families, 26 genera, 41 species) to solve and explore the evolution of Dennstaedtiaceae. In order to minimize the impact of systematic errors on the resolution of phylogenetic inference, we applied six strategies to generate 30 datasets based on CDS, Spacer, and All datasets, and two tree inference methods (maximum-likelihood, ML; and multispecies coalescent, MSC) to comprehensively analyze the plastome-scale data. Besides, the phylogenetic signal among all loci was quantified for the controversial node using the ML framework, and the phylogenetic hypotheses among all datasets were tested. In the species tree based on different data sets and methods, obvious conflicts were detected at the base of the polypod ferns. Meanwhile, the topology of the "CDS-codon-align-rm3" (CDS removed the third codon) matrix was selected as the primary reference or summary tree due to its analysis results are consistent, and similar to the topological structure of the amino-acid matrix. The final phylogenetic tree supported Dennstaedtiaceae as the sister group to eupolypods, and<em> Dennstaedtia</em> (sen. lat.) can divided into smaller genera, which was also supported by geographical distribution and plastid structure. This robust reconstructed phylogenetic backbone established a framework for future studies on Dennstaedtiaceae classification, evolution and diversification. The present study suggests considering plastid phylogenomic conflict when using plastid genomes. From our results, reducing saturated genes or sites can effectively mitigate the tree conflicts of distantly related taxa. Moreover, amino acid sequences may verify the accuracy of nucleotide-based phylogeny.</p>
FIGURE 1 in Improved modelling of compositional heterogeneity reconciles phylogenomic conflicts among lacewings
FIGURE 1. Phylogram of Neuropterida relationships based on the CAT-GTR+G4 analysis of anchored hybrid enrichment (AHE) amino acid data. All branches have a support value of ≥ 0.93 Bayesian posterior probability (BPP) except those indicated by red dots (BPP <0.9). Abbreviations: Conio., Coniopterygoidea; Dilar., Dilaroidea; Ithon., Ithonoidea; Megal., Megaloptera; Psych., Psychopsoidea; Raphi., Raphidioptera. Superfamilial classification is adapted from Engel et al. (2018).
FIGURE 2 in Improved modelling of compositional heterogeneity reconciles phylogenomic conflicts among lacewings
FIGURE 2. Congruent interfamilial relationships of Neuropterida inferred from transcriptomic (left) and AHE (right) amino acid data respectively under the site-heterogeneous CAT-GTR+G4 model. All branches have a strong support (BPP> 0.93), except for the monophyly of Myrmeleontidae (only weakly supported in AHE nucleotide data under the CAT-GTR+G4 model). Note that the transcriptomic dataset has fewer and sparser familial sampling than the AHE data.
Data from: Phylogenomic analyses resolve an ancient trichotomy at the base of Ischyropsalidoidea (Arachnida, Opiliones) despite high levels of gene tree conflict and unequal minority resolution frequencies
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Data from: Congruence and conflict in the higher-level phylogenetics of squamate reptiles: an expanded phylogenomic perspective
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Data from: Phylogenomics uncovers confidence and conflict in the rapid radiation of Australo-Papuan rodents
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Data from: Conflicting phylogenomic signals reveal a pattern of reticulate evolution in a recent high-Andean diversification (Asteraceae: Astereae: Diplostephium)
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Untying the Gordian Knot of plastid phylogenomic conflict: a case from ferns
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A phylogenomic perspective on gene tree conflict and character evolution in Caprifoliaceae using target enrichment data, with Zabelioideae recognized as a new subfamily
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Data from: Resolving conflict in eutherian mammal phylogeny using phylogenomics and the multispecies coalescent model
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Data from: Phylogenomics of phrynosomatid lizards: conflicting signals from sequence capture versus restriction site associated DNA sequencing
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Data from: Phylogenomic interrogation of Arachnida reveals systemic conflicts in phylogenetic signal
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Data from: Analysis of phylogenomic datasets reveals conflict, concordance, and gene duplications with examples from animals and plants
Background: The use of transcriptomic and genomic datasets for phylogenetic reconstruction has become increasingly common as researchers attempt to resolve recalcitrant nodes with increasing amounts of data. The large size and complexity of these datasets introduce significant phylogenetic noise and conflict into subsequent analyses. The sources of conflict may include hybridization, incomplete lineage sorting, or horizontal gene transfer, and may vary across the phylogeny. For phylogenetic analysis, this noise and conflict has been accommodated in one of several ways: by binning gene regions into subsets to isolate consistent phylogenetic signal; by using gene-tree methods for reconstruction, where conflict is presumed to be explained by incomplete lineage sorting (ILS); or through concatenation, where noise is presumed to be the dominant source of conflict. The results provided herein emphasize that analysis of individual homologous gene regions can greatly improve our understanding of the underlying conflict within these datasets. Results: Here we examined two published transcriptomic datasets, the angiosperm group Caryophyllales and the aculeate Hymenoptera, for the presence of conflict, concordance, and gene duplications in individual homologs across the phylogeny. We found significant conflict throughout the phylogeny in both datasets and in particular along the backbone. While some nodes in each phylogeny showed patterns of conflict similar to what might be expected with ILS alone, the backbone nodes also exhibited low levels of phylogenetic signal. In addition, certain nodes, especially in the Caryophyllales, had highly elevated levels of strongly supported conflict that cannot be explained by ILS alone. Conclusion: This study demonstrates that phylogenetic signal is highly variable in phylogenomic data sampled across related species and poses challenges when conducting species tree analyses on large genomic and transcriptomic datasets. Further insight into the conflict and processes underlying these complex datasets is necessary to improve and develop adequate models for sequence analysis and downstream applications. To aid this effort, we developed the open source software phyparts (https://bitbucket.org/blackrim/phyparts), which calculates unique, conflicting, and concordant bipartitions, maps gene duplications, and outputs summary statistics such as internode certainy (ICA) scores and node-specific counts of gene duplications.
Data from: Analysis of phylogenomic datasets reveals conflict, concordance, and gene duplications with examples from animals and plants
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