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34 results for “gene tree discordance”
Complex models of sequence evolution improve fit, but not gene tree discordance, for tetrapod mitogenomes
<p>Variation in gene tree estimates is widely observed in empirical phylogenomic data and is often assumed to be the result of biological processes. However, a recent study using tetrapod mitochondrial genomes to control for biological sources of variation due to their haploid, uniparentally inherited, and non-recombining nature found that levels of discordance among mitochondrial gene trees were comparable to those found in studies that assume only biological sources of variation. Additionally, they found that several of the models of sequence evolution chosen to infer gene trees were doing an inadequate job of fitting the sequence data. These results indicated that significant amounts of gene tree discordance in empirical data may be due to poor fit of sequence evolution models and that more complex and biologically realistic models may be needed. To test how the fit of sequence evolution models relates to gene tree discordance, we analyzed the same mitochondrial datasets as the previous study using two additional, more complex models of sequence evolution that each model a different biologically realistic aspect of the evolutionary process: a covarion model to incorporate heterotachy, and a model partitioned model to incorporate variable evolutionary patterns by codon position. Our results show that both additional models fit the data better than the models used in the previous study, with the covarion being consistently and strongly preferred as tree size increases. However, even these more preferred models still inferred highly discordant mitochondrial gene trees, thus deepening the mystery around what we label the "Mito-Phylo Paradox" and leading us to ask whether the observed variation could be biological after all.</p>
Data from: Whole genomes reveal evolutionary relationships and mechanisms underlying gene-tree discordance in Neodiprion sawflies
<p>Rapidly evolving taxa are excellent models for understanding the mechanisms that give rise to biodiversity. However, developing an accurate historical framework for comparative analysis of such lineages remains a challenge due to ubiquitous incomplete lineage sorting and introgression. Here, we use a whole-genome alignment, multiple locus-sampling strategies, and locus-based and SNP-based species-tree methods to infer a species tree for eastern North American <em>Neodiprion</em> species, a clade of pine-feeding sawflies (Order: Hymenopteran; Family: Diprionidae). We recovered a well-supported species tree that—except for three uncertain relationships—is robust to different strategies for analyzing whole-genome data. Despite this consistency, underlying gene-tree discordance is high. To understand this discordance, we use multiple regression to model topological discordance as a function of several genomic features. We find that gene-tree discordance tends to be higher in regions of the genome that may be more prone to gene-tree estimation error, as indicated by a lower density of parsimony-informative sites, a higher density of genes, a higher average pairwise genetic distance, and gene trees with lower average bootstrap support. Also, contrary to the expectation that discordance via incomplete lineage sorting is reduced in low-recombination regions of the genome, we find a <em>negative</em> correlation between recombination rate and topological discordance. We offer potential explanations for this pattern and hypothesize that it may be unique to lineages that have diverged with gene flow. Our analysis also reveals an unexpected discordance hotspot on Chromosome 1, which contains several genes potentially involved in mitochondrial-nuclear interactions and produces a gene-tree that resembles a highly discordant mitochondrial tree. Based on these observations, we hypothesize that our genome-wide scan for topological discordance has identified a nuclear locus involved in a mito-nuclear incompatibility. Together, these results demonstrate how phylogenomic analysis coupled with high-quality, annotated genomes can generate novel hypotheses about the mechanisms that drive divergence and produce variable genealogical histories across genomes.</p>
Data for: Resolving marine–freshwater transitions by diatoms through a fog of gene tree discordance
<p>Despite the obstacles facing marine colonists, most lineages of aquatic organisms have colonized and diversified in freshwaters repeatedly. These transitions can trigger rapid morphological or physiological change and, on longer timescales, lead to increased rates of speciation and extinction. Diatoms are a lineage of ancestrally marine microalgae that have diversified throughout freshwater habitats worldwide. We generated a phylogenomic dataset of genomes and transcriptomes for 59 diatom taxa to resolve freshwater transitions in one lineage, the Thalassiosirales. Although most parts of the species tree were consistently resolved with strong support, we had difficulties resolving a Paleocene radiation, which affected the placement of one freshwater lineage. This and other parts of the tree were characterized by high levels of gene tree discordance caused by incomplete lineage sorting and low phylogenetic signal. Despite differences in species trees inferred from concatenation versus summary methods and codons versus amino acids, traditional methods of ancestral state reconstruction supported six transitions into freshwaters, two of which led to subsequent species diversification. Evidence from gene trees, protein alignments, and diatom life history together suggest that habitat transitions were largely the product of homoplasy rather than hemiplasy, a condition where transitions occur on branches in gene trees not shared with the species tree. Nevertheless, we identified a small set of putatively hemiplasious genes, many of which have been associated with shifts to low salinity, indicating that hemiplasy played a small but potentially important role in freshwater adaptation. Accounting for differences in evolutionary outcomes, in which some taxa became locked into freshwaters while others were able to return to the ocean or become salinity generalists, might help further distinguish different sources of adaptive mutation in freshwater diatoms.</p>
Gene tree discord, simplex plots, and statistical tests under the coalescent
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Data for: Resolving marine–freshwater transitions by diatoms through a fog of gene tree discordance
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Data from: Whole genomes reveal evolutionary relationships and mechanisms underlying gene-tree discordance in Neodiprion sawflies
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Complex models of sequence evolution improve fit, but not gene tree discordance, for tetrapod mitogenomes
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Disentangling sources of gene tree discordance in phylogenomic datasets: testing ancient hybridizations in Amaranthaceae s.l.
<p>Gene tree discordance in large genomic datasets 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 dataset 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.</p>
Data from: Phylogenomics reveals ancient gene tree discordance in the amphibian Tree of Life
<p>Molecular phylogenies have yielded strong support for many parts of the amphibian Tree of Life, but poor support for the resolution of deeper nodes, including relationships among families and orders. To clarify these relationships, we provide a phylogenomic perspective on amphibian relationships by developing a taxon-specific Anchored Hybrid Enrichment protocol targeting hundreds of conserved exons which are effective across the class. After obtaining data from 220 loci for 286 species (representing 94% of the families and 44% of the genera), we estimate a phylogeny for extant amphibians and identify gene tree–species tree conflict across the deepest branches of the amphibian phylogeny. We perform locus-by-locus genealogical interrogation of alternative topological hypotheses for amphibian monophyly, focusing on interordinal relationships. We find that phylogenetic signal deep in the amphibian phylogeny varies greatly across loci in a manner that is consistent with incomplete lineage sorting in the ancestral lineage of extant amphibians. Our results overwhelmingly support amphibian monophyly and a sister relationship between frogs and salamanders, consistent with the Batrachia hypothesis. Species tree analyses converge on a small set of topological hypotheses for the relationships among extant amphibian families. These results clarify several contentious portions of the amphibian Tree of Life, which in conjunction with a set of vetted fossil calibrations, support a surprisingly younger timescale for crown and ordinal amphibian diversification than previously reported. More broadly, our study provides insight into the sources, magnitudes, and heterogeneity of support across loci in phylogenomic data sets.</p>
Phylogenomic analyses in Phrymaceae reveal extensive gene tree discordance in relationships among major clades
<p>• 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.</p> <p>• 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.</p> <p>• 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.</p> <p>• 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.</p>
Dataset for: Smith et al., Phylogenomic analysis of the parrots of the world distinguishes artifactual from biological sources of gene tree discordance
<p>Gene tree discordance is expected in phylogenomic trees and biological processes are often invoked to explain it. However, heterogeneous levels of phylogenetic signal among individuals within datasets may cause artifactual sources of topological discordance. We examined how the information content in tips and subclades impacts topological discordance in the parrots (Order: Psittaciformes), a diverse and highly threatened clade of nearly 400 species. Using ultraconserved elements from 96% of the clade's species-level diversity, we estimated concatenated and species trees for 382 ingroup taxa. We found that discordance among tree topologies was most common at nodes dating between the late Miocene and Pliocene, and often at the taxonomic level of genus. Accordingly, we used two metrics to characterize information content in tips and assess the degree to which conflict between trees was being driven by lower quality samples. Most instances of topological conflict and non-monophyletic genera in the species tree could be objectively identified using these metrics. For subclades still discordant after tip-based filtering, we used a machine learning approach to determine whether phylogenetic signal or noise was the more important predictor of metrics supporting the alternative topologies. We found that when signal favored one of the topologies, noise was the most important variable in poorly performing models that favored the alternative topology. In sum, we show that artifactual sources of gene tree discordance, which are likely a common phenomenon in many datasets, can be distinguished from biological sources by quantifying the information content in each tip and modeling which factors support each topology.</p>
Data from: Sources of gene tree discordance and their implications for systematics and evolution of a megadiverse Australian plant radiation (subtribe Hakeinae, Proteaceae)
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Data from: Whole-genomes illuminate the drivers of gene tree discordance and the tempo of tinamou diversification (Aves: Tinamidae)
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Phylogenomic analyses in Phrymaceae reveal extensive gene tree discordance in relationships among major clades
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Data from: Phylogenomics reveals ancient gene tree discordance in the amphibian Tree of Life
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Dataset for: Smith et al., Phylogenomic analysis of the parrots of the world distinguishes artifactual from biological sources of gene tree discordance
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Disentangling sources of gene tree discordance in phylogenomic datasets: testing ancient hybridizations in Amaranthaceae s.l.
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Data from: Genomic data resolves gene tree discordance in spiderhunters (Nectariniidae, Arachnothera)
Reduced representation genomic sequencing methods efficiently gather sequence data from thousands of loci throughout the genome. These data can be used to test previous phylogenetic hypotheses produced from limited numbers of mitochondrial and nuclear loci that often reveal intriguing, but conflicting results. In this paper, we use phylogenomic data to revisit recent molecular phylogenetic work that clarified many taxonomic relationships within spiderhunters, but also questioned monophyly of this distinctive genus of sunbirds (AVES: Nectariniidae; Arachnothera). DNA sequence data were produced by target-capture sequencing of ultraconserved elements (UCEs) to infer the evolutionary history of 11 species of Arachnothera and six outgroups, including the Purple-naped Sunbird (Hypogramma hypogrammicum), which previous work suggested might lie within Arachnothera. Although we recovered many different gene tree topologies, concatenated and coalescent methods of analysis converged on a species tree that strongly supports the monophyly of Arachnothera, with Hypogramma as its sister taxon.
Dataset from: Resolving marine–freshwater transitions by diatoms through a fog of gene tree discordance
<p>This repository contains the datasets, code, and results for:</p> <p>Roberts et al. Resolving marine-freshwater transitions by diatoms through a fog of gene tree discordance.</p> <p>CONTACT INFORMATION:</p> <p>Andrew J. Alverson<br> University of Arkansas<br> aja [at] uark [dot] edu</p> <p>Wade R. Roberts<br> University of Arkansas<br> wader [at] uark [dot] edu</p> <p>TAXON LABEL INFORMATION:</p> <p>Genomes have strain ID before genus_species (e.g., CCMP332_Cyclotella_cryptica)<br> Transcriptomes have genus_species before strain ID (e.g., Cyclotella_nana_AJA048-54)</p> <p><br> DATA AND DIRECTORY OVERVIEW:</p> <p>Voucher images of diatom strains collected:</p> <ul> <li>voucher-images.tgz</li> </ul> <p>OrthoFinder output:</p> <ul> <li>orthofinder.zip</li> </ul> <p>Predicted proteomes and coding sequences for each strain:</p> <ul> <li>proteomes.zip</li> <li>coding-sequences.zip</li> </ul> <p>Workflow for phylogenomic dataset assembly and species tree analyses:</p> <ul> <li>phylogenomic-workflow.html</li> <li>phylogenomic-workflow.md</li> <li>phylogenomic-workflow.pdf</li> </ul> <p>Fasta files, alignments, and gene trees for each ortholog:</p> <ul> <li>datasets.zip</li> </ul> <p>Concatenated alignments, partition models, and estimated species trees:</p> <ul> <li>species-trees.zip</li> <li>species-trees.nexus</li> </ul> <p>Analyses results and code to plot figures:</p> <ul> <li>analyses-and-plots.zip</li> </ul> <p>Additional scripts and miscellaneous files:</p> <ul> <li>scripts-and-misc.zip</li> </ul> <p>Supplemental Materials for publication:</p> <ul> <li>supplemental-materials.zip</li> </ul> <p> </p>
Data from: Extensive gene tree discordance and hemiplasy shaped the genomes of North American columnar cacti
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