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38 results for “phylogenomic conflict”
Investigating sources of conflict in deep phylogenomics of vetigastropod snails
<p><span><span><span><span><span><span><span><span><span><span><span>Phylogenetic analyses may suffer from multiple sources of error leading to conflict between genes and methods of inference. The evolutionary history of the mollusc clade Vetigastropoda makes them susceptible to these conflicts, their higher level phylogeny remaining largely unresolved. Originating over 350 million years ago, vetigastropods were the dominant marine snails in the Paleozoic. Multiple extinction events and new radiations have resulted in both very long and very short branches and a large extant diversity of over 4000 species. This is the perfect setting of a hard phylogenetic question in which sources of conflict can be explored. We present 41 new transcriptomes across the diversity of vetigastropods (62 terminals total), and provide the first genomic-scale phylogeny for the group. We find that deep divergences differ from previous studies in which long branch attraction was likely pervasive. Robust results leading to changes in taxonomy include the paraphyly of the order Lepetellida and the family Tegulidae. Tectinae <b>subfam. nov.</b> is designated for the clade comprising <i>Tectus</i>, <i>Cittarium</i> and <i>Rochia</i>. For two early divergences, topologies disagreed between concatenated analyses using site heterogeneous models <i>vs.</i> concatenated partitioned analyses and summary coalescent methods. We investigated rate and composition heterogeneity among genes, as well as missing data by locus and by taxon, none of which had an impact on the inferred topologies. We also found no evidence for ancient introgression throughout the phylogeny. We further tested whether uninformative genes and over-partitioning were responsible for this discordance by evaluating the phylogenetic signal of individual genes using likelihood mapping, and by analyzing the most informative genes with a full multispecies coalescent model. We find that most genes are not informative at the two conflicting nodes, but neither this nor gene-wise partitioning are the cause of discordant results. New method implementations that simultaneously integrate amino acid profile mixture models and the multispecies coalescent might be necessary to resolve these and other recalcitrant nodes in the Tree of Life.</span></span></span></span></span></span></span></span></span></span></span></p>
Data for: Ancient rapid radiation explains most conflicts among gene trees and well-supported phylogenomic trees of nostocalean cyanobacteria
<p>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 datasets 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 datasets. 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. 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 datasets from previous studies. Our findings highlight the important role of rapid radiations as a potential cause of strongly conflicting phylogenetic relationships when using phylogenomic datasets 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.</p>
Phylogenomics and Intergenomic Conflict in a Challenging Orchid Clade (Calypsoinae): Monophyly of Corallorhiza, Paraphyly of Oreorchis, and Resurrection of Kitigorchis
<p>Dataset S1: Concatenated nuclear sequence capture data (Angiosperms353) for Calypsoinae. This nexus file contains a partition block, which can be used to plit the data into individual alignments (in R, Trifusion, SequenceMatrix, etc.).</p> <p>Dataset S2: Concatenated nuclear sequence capture data (Angiosperms353) for Calypsoinae without partition block.</p> <p>Dataset S3: Concatenated mitochondrial sequence data for Calypsoinae.</p> <p>Dataset S4: Concatenated plastid gene sequence data for Calypsoinae.</p> <p> </p>
Investigating sources of conflict in deep phylogenomics of vetigastropod snails
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Data for: Ancient rapid radiation explains most conflicts among gene trees and well-supported phylogenomic trees of nostocalean cyanobacteria
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Exploration of plastid phylogenomic conflict yields new insights into the deep relationships of Leguminosae
<p>Phylogenomic analyses have helped resolve many recalcitrant relationships in the angiosperm tree of life, yet phylogenetic resolution of the backbone of the Leguminosae, one of the largest and most economically and ecologically important families, remains poor due to generally limited molecular data and incomplete taxon sampling of previous studies. Here, we resolve many of the Leguminosae's thorniest nodes through comprehensive analysis of plastome-scale data using multiple modified coding and noncoding datasets of 187 species representing almost all major clades of the family. Additionally, we thoroughly characterize conflicting phylogenomic signal across the plastome in light of the family's complex history of plastome evolution. Most analyses produced largely congruent topologies with strong statistical support, and provided strong support for resolution of some long-controversial deep relationships among the early diverging lineages of the subfamilies Caesalpinioideae and Papilionoideae. The robust phylogenetic backbone reconstructed in this study establishes a framework for future studies on legume classification, evolution, and diversification. However, conflicting phylogenetic signal was detected and quantified at several key nodes that prevents the confident resolution of these nodes using plastome data alone.</p>
Data from: Phylogenomics and topological conflicts in the tribe Anthospermeae (Rubiaceae)
<p>Genome skimming (shallow whole-genome sequencing) offers time- and cost-efficient production of large amounts of DNA data that can be used to address unsolved evolutionary questions. Here we address phylogenetic relationships and topological incongruence in the tribe Anthospermeae (Rubiaceae), using phylogenomic data from the mitochondrion, the nuclear ribosomal cistron, and the plastome. All three genomic compartments resolve relationships in the Anthospermeae; the tribe is monophyletic and consists of three major subclades. Carpacoce Sond. is sister to the remaining clade, which comprises an African subclade and a Pacific subclade. Most results, from all three genomic compartments, are statistically well-supported; however, not fully consistent. Intergenomic topological incongruence is most notable in the Pacific subclade but present also in the African subclade. Hybridization and introgression followed by organelle capture may explain these conflicts but other processes, such as incomplete lineage sorting (ILS), can yield similar patterns and cannot be ruled out based on the results. Whereas the null hypothesis of congruence among all sequenced loci in the individual genomes could not be rejected for nuclear and mitochondrial data, it was rejected for plastid data. Phylogenetic analyses of three subsets of plastid loci identified using hierarchical likelihood ratio test demonstrated statistically supported intragenomic topological incongruence. Given that plastid genes are thought to be fully linked, this result is surprising and may suggest modelling or sampling error. However, biological processes such as biparental inheritance and inter-plastome recombination have been reported and may be responsible for the observed intragenomic incongruence. Mitochondrial insertions into the plastome are rarely documented in angiosperms. Our results indicate that a mitochondrial insertion event in the plastid trnSGGA-rps4 IGS region occurred in the common ancestor of the Pacific clade of Anthospermeae. Exclusion/inclusion of this locus in phylogenetic analyses had strong impact on topological results in the Pacific clade.</p>
Signal, Uncertainty, and Conflict in Phylogenomic Data for a Diverse Lineage of Microbial Eukaryotes (Diatoms, Bacillariophyta)
<p>This data depository contains analysis results from Parks, Wickett, and Alverson 2017 (Signal, Uncertainty, and Conflict in Phylogenomic Data for a Diverse Lineage of Microbial Eukaryotes (Diatoms, Bacillariophyta) (Mol. Biol. Evol. doi:10.1093/molbev/msx268)), and is made freely available to the research community.</p> <p>The file and subfolders here are as follows:</p> <p>gene_alignments<br> - contains compressed (tarred and gzipped) folders with all gene alignments at 0.2, 0.5 and 0.8 alignment column occupancy cutoffs. In each folder, there are also text files listing which gene alignments fall under which taxon occupancy subsetting strategy (i.e., 10-20% taxon occupancy, 40-60% taxon occupancy, 80-100% taxon occupancy, etc).</p> <p>gene_trees<br> - contains all (compressed) gene trees (bootstrapped versions, 100 bootstrap pseudo-replicates)) used in Astral analyses for each alignment column occupancy cutoff (0.2, 0.5, 0.8); nodes with less than 33% bootstrap support are collapsed.</p> <p>hmms.mafft_aligned<br> - contains (compressed) hmm specifications for each major diatom morphotype (radial and polar centrics, araphid and raphid pennates) from the 0.2 alignment column occupancy subset of the data. A summary of the sampling scheme and the hmm results/counts are also available in HMM_sampling.docx.</p> <p>mmetsp_nuclear_transcriptome_assemblies<br> - these are the compressed nuclear transcriptome assemblies that were done in-house (i.e., mostly MMETSP samples). Assemblies do not include organellar or rDNA loci.</p> <p>species_trees<br> - contains (compressed) species trees for all phylogenetic strategies and alignment column occupancy cutoff/data subset strategies.</p> <p>Suppl_1.MMETSP_basic_summaries.xlsx<br> - this an identical file to Parks, Wickett and Alverson 2017 supplementary file 1. This file contains taxon, strain and SRA information for all assembled taxa, and a variety of assembly metric information.</p> <p> </p>
Phylogenomic conflict analyses in the apple genus Malus s.l. reveal widespread hybridization and allopolyploidy driving diversification, with insights into the complex biogeographic history in the Northern Hemisphere
<p>Phylogenomic evidence from an increasing number of studies has demonstrated that different data sets and analytical approaches often reconstruct strongly supported but conflicting relationships. In this study, 785 single-copy nuclear genes and 75 complete plastomes were used to infer the phylogenetic relationships and estimate the historical biogeography of the apple genus <em>Malus</em> sensu lato, an economically important lineage disjunctly distributed in the Northern Hemisphere and involved in known and suspected hybridization and allopolyploidy events. The nuclear phylogeny recovered the monophyly of <em>Malus</em> s.l. (including <em>Docynia</em>); however, the genus was supported to be biphyletic in the plastid phylogeny. An ancient chloroplast capture event in the Eocene in western North America best explains the cytonuclear discordance. Our conflict analysis demonstrated that ILS, hybridization, and allopolyploidy could explain the widespread nuclear gene tree discordance. One deep hybridization event (<em>Malus doumeri)</em> and one recent event (<em>Malus</em> coronaria) were detected in <em>Malus</em> s.l. Furthermore, our historical biogeographic analysis integrating living and fossil data supported a widespread East Asian-western North American origin of <em>Malus</em> s.l. in the Eocene, followed by several extinction and dispersal events in the Northern Hemisphere. We also propose a general workflow for assessing phylogenomic discordance and biogeographic analysis using deep genome skimming datasets.</p>
Phylogenomics reveals patterns ancient hybridization and differential diversification that contribute to phylogenetic conflict in willows, poplars, and close relatives
<p>Despite the economic, ecological, and scientific importance of the genera <em>Salix</em> L. (willows) and <em>Populus</em> L. (poplars, cottonwoods, and aspens) Salicaceae, we know little about the sources of differences in species diversity between the genera and of the phylogenetic conflict that often confounds estimating phylogenetic trees. <em>Salix</em> subgenera and sections, in particular, have been difficult to classify, with one recent attempt termed a 'spectacular failure' due to a speculated radiation of the subgenera <em>Vetrix</em> and <em>Chamaetia</em>. Here we use targeted sequence capture to understand the evolutionary history of this portion of the Salicaceae plant family. Our phylogenetic hypothesis was based on 787 gene regions and identified extensive phylogenetic conflict among genes. Our analysis supported some previously described subgeneric relationships and confirmed polyphyly of others. Using an f<sub>branch</sub> analysis we identified several cases of hybridization in deep branches of the phylogeny, which likely contributed to discordance among gene trees. In addition, we identified a rapid increase in diversification rate near the origination of the <em>Vetrix</em>-<em>Chamaetia</em> clade in <em>Salix</em>. This region of the tree coincided with several nodes that lacked strong statistical support, indicating a possible increase in incomplete lineage sorting due to rapid diversification. The extraordinary level of both recent and ancient hybridization in both <em>Salix</em> and <em>Populus</em> have played important roles in the diversification and diversity in these two genera.</p>
Exploration of plastid phylogenomic conflict yields new insights into the deep relationships of Leguminosae
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Phylogenomic conflict analyses in the apple genus Malus s.l. reveal widespread hybridization and allopolyploidy driving diversification, with insights into the complex biogeographic history in the Northern Hemisphere
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Data from: Why do phylogenomic data sets yield conflicting trees? Data type influences the avian tree of life more than taxon sampling
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Inconsistent performance of multi-type genomic data in phylogenomics of neuropteridan insects, with solutions toward conflicting results
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Phylogenomics reveals patterns ancient hybridization and differential diversification that contribute to phylogenetic conflict in willows, poplars, and close relatives
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Data from: Phylogenomics and topological conflicts in the tribe Anthospermeae (Rubiaceae)
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Data from: Verbalizing phylogenomic conflict: representation of node congruence across competing reconstructions of the neoavian explosion
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Phylogenetic conflicts, combinability, and deep phylogenomics in plants
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Nuclear phylogenomic analyses of asterids conflict with plastome trees and support novel relationships among major lineages
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Phylogenomic analysis of brachyuran crabs using transcriptome data reveals possible sources of conflicting phylogenetic relationships within the group
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