scholarly journals Gene-tree reconciliation with MUL-trees to resolve polyploidy events

2016 ◽  
Author(s):  
Gregg W.C. Thomas ◽  
S. Hussain Ather ◽  
Matthew W. Hahn
Keyword(s):  
Parental Species ◽  
Gene Tree ◽  
Gene Duplications ◽  
Gene Trees ◽  
Tree Reconciliation ◽  
Labeled Trees ◽  
Yeast Data ◽  
Huge Impact ◽  
History Of ◽  
Gene Tree Reconciliation

AbstractPolyploidy can have a huge impact on the evolution of species, and it is a common occurrence, especially in plants. The two types of polyploids - autopolyploids and allopolyploids - differ in the level of divergence between the genes that are brought together in the new polyploid lineage. Because allopolyploids are formed via hybridization, the homoeologous copies of genes within them are at least as divergent as orthologs in the parental species that came together to form them. This means that common methods for estimating the parental lineages of allopolyploidy events are not accurate, and can lead to incorrect inferences about the number of gene duplications and losses. Here, we have adapted an algorithm for topology-based gene-tree reconciliation to work with multi-labeled trees (MUL-trees). By definition, MUL-trees have some tips with identical labels, which makes them a natural representation of the genomes of polyploids. Using this new reconciliation algorithm we can: accurately place allopolyploidy events on a phylogeny, identify the parental lineages that hybridized to form allopolyploids, distinguish between allo-, auto-, and (in most cases) no polyploidy, and correctly count the number of duplications and losses in a set of gene trees. We validate our method using gene trees simulated with and without polyploidy, and revisit the history of polyploidy in data from the clades including both baker’s yeast and bread wheat. Our re-analysis of the yeast data confirms the allopolyploid origin and parental lineages previously identified for this group. The method presented here should find wide use in the growing number of genomes from species with a history of polyploidy.

scholarly journals Gene-Tree Reconciliation with MUL-Trees to Resolve Polyploidy Events

2017 ◽  
Vol 66 (6) ◽  
pp. 1007-1018 ◽  
Author(s):  
Gregg W C Thomas ◽  
S Hussain Ather ◽  
Matthew W Hahn
Keyword(s):  
Parental Species ◽  
Gene Tree ◽  
Gene Duplications ◽  
Gene Trees ◽  
Tree Reconciliation ◽  
Labeled Trees ◽  
Yeast Data ◽  
Huge Impact ◽  
History Of ◽  
Gene Tree Reconciliation

Abstract Polyploidy can have a huge impact on the evolution of species, and it is a common occurrence, especially in plants. The two types of polyploids—autopolyploids and allopolyploids—differ in the level of divergence between the genes that are brought together in the new polyploid lineage. Because allopolyploids are formed via hybridization, the homoeologous copies of genes within them are at least as divergent as orthologs in the parental species that came together to form them. This means that common methods for estimating the parental lineages of allopolyploidy events are not accurate, and can lead to incorrect inferences about the number of gene duplications and losses. Here, we have adapted an algorithm for topology-based gene-tree reconciliation to work with multi-labeled trees (MUL-trees). By definition, MUL-trees have some tips with identical labels, which makes them a natural representation of the genomes of polyploids. Using this new reconciliation algorithm we can: accurately place allopolyploidy events on a phylogeny, identify the parental lineages that hybridized to form allopolyploids, distinguish between allo-, auto-, and (in most cases) no polyploidy, and correctly count the number of duplications and losses in a set of gene trees. We validate our method using gene trees simulated with and without polyploidy, and revisit the history of polyploidy in data from the clades including both baker’s yeast and bread wheat. Our re-analysis of the yeast data confirms the allopolyploid origin and parental lineages previously identified for this group. The method presented here should find wide use in the growing number of genomes from species with a history of polyploidy. [Polyploidy; reconciliation; whole-genome duplication.]

scholarly journals Evolinc: a comparative transcriptomics and genomics pipeline for quickly identifying sequence conserved lincRNAs for functional analysis

2017 ◽  
Author(s):  
Andrew D. L. Nelson ◽  
Upendra K. Devisetty ◽  
Kyle Palos ◽  
Asher K. Haug-Baltzell ◽  
Eric Lyons ◽  
...  
Keyword(s):  
Functional Analysis ◽  
Differential Expression Analysis ◽  
Gene Tree ◽  
Gene Trees ◽  
Tree Reconciliation ◽  
Origin And Evolution ◽  
Duplication Events ◽  
History Of ◽  
Human Telomerase ◽  
Gain Loss

AbstractLong intergenic non-coding RNAs (lincRNAs) are an abundant and functionally diverse class of eukaryotic transcripts. Reported lincRNA repertoires in mammals vary, but are commonly in the thousands to tens of thousands of transcripts, covering ~90% of the genome. In addition to elucidating function, there is particular interest in understanding the origin and evolution of lincRNAs. Aside from mammals, lincRNA populations have been sparsely sampled, precluding evolutionary analyses focused on lincRNA emergence and persistence. Here we present Evolinc, a two-module pipeline designed to facilitate lincRNA discovery and characterize aspects of lincRNA evolution. The first module (Evolinc-I) is a lincRNA identification workflow that also facilitates downstream differential expression analysis and genome browser visualization of identified lincRNAs. The second module (Evolinc-II) is a genomic and transcriptomic comparative analyses workflow that determines the phylogenetic depth to which a lincRNA locus is conserved within a user-defined group of related species. Evolinc-II builds families of homologous lincRNA loci, aligns constituent sequences, infers gene trees, and then uses gene tree / species tree reconciliation to reconstruct evolutionary processes such as gain, loss, or duplication of the locus. Here we demonstrate that Evolinc-I is agnostic to target organism by validating against previously annotated Arabidopsis and human lincRNA data. Using Evolinc-II, we examine ways in which conservation can rapidly be used to winnow down large lincRNA datasets to a small set of candidates for functional analysis. Finally, we show how Evolinc-II can be used to recover the evolutionary history of a known lincRNA, the human telomerase RNA (TERC). The analyses revealed unexpected duplication events as well as the loss and subsequent acquisition of a novel TERC locus in the lineage leading to mice and rats. The Evolinc pipeline is currently integrated in CyVerse’s Discovery Environment and is free to use by researchers.

scholarly journals Terraces in Gene Tree Reconciliation-Based Species Tree Inference

2020 ◽  
Author(s):  
Michael J. Sanderson ◽  
Michelle M. McMahon ◽  
Mike Steel
Keyword(s):  
Incomplete Lineage Sorting ◽  
Gene Tree ◽  
Solution Space ◽  
Species Tree ◽  
Gene Trees ◽  
Species Trees ◽  
Lineage Sorting ◽  
Data Set ◽  
Tree Reconciliation ◽  
The Impact

AbstractTerraces in phylogenetic tree space are sets of trees with identical optimality scores for a given data set, arising from missing data. These were first described for multilocus phylogenetic data sets in the context of maximum parsimony inference and maximum likelihood inference under certain model assumptions. Here we show how the mathematical properties that lead to terraces extend to gene tree - species tree problems in which the gene trees are incomplete. Inference of species trees from either sets of gene family trees subject to duplication and loss, or allele trees subject to incomplete lineage sorting, can exhibit terraces in their solution space. First, we show conditions that lead to a new kind of terrace, which stems from subtree operations that appear in reconciliation problems for incomplete trees. Then we characterize when terraces of both types can occur when the optimality criterion for tree search is based on duplication, loss or deep coalescence scores. Finally, we examine the impact of assumptions about the causes of losses: whether they are due to imperfect sampling or true evolutionary deletion.

scholarly journals Primate phylogenomics uncovers multiple rapid radiations and ancient interspecific introgression

2020 ◽  
Author(s):  
Dan Vanderpool ◽  
Bui Quang Minh ◽  
Robert Lanfear ◽  
Daniel Hughes ◽  
Shwetha Murali ◽  
...  
Keyword(s):  
World Monkey ◽  
Gene Tree ◽  
Species Tree ◽  
Molecular Dating ◽  
Macaca Nemestrina ◽  
Gene Trees ◽  
Individual Gene ◽  
Black And White ◽  
Fossil Evidence ◽  
History Of

AbstractOur understanding of the evolutionary history of primates is undergoing continual revision due to ongoing genome sequencing efforts. Bolstered by growing fossil evidence, these data have led to increased acceptance of once controversial hypotheses regarding phylogenetic relationships, hybridization and introgression, and the biogeographical history of primate groups. Among these findings is a pattern of recent introgression between species within all major primate groups examined to date, though little is known about introgression deeper in time. To address this and other phylogenetic questions, here we present new reference genome assemblies for three Old World Monkey species: Colobus angolensis ssp. palliatus (the black and white colobus), Macaca nemestrina (southern pig-tailed macaque), and Mandrillus leucophaeus (the drill). We combine these data with 23 additional primate genomes to estimate both the species tree and individual gene trees using thousands of loci. While our species tree is largely consistent with previous phylogenetic hypotheses, the gene trees reveal high levels of genealogical discordance associated with multiple primate radiations. We use strongly asymmetric patterns of gene tree discordance around specific branches to identify multiple instances of introgression between ancestral primate lineages. In addition, we exploit recent fossil evidence to perform fossil-calibrated molecular dating analyses across the tree. Taken together, our genome-wide data help to resolve multiple contentious sets of relationships among primates, while also providing insight into the biological processes and technical artifacts that led to the disagreements in the first place.

scholarly journals Ultra-Conserved Elements and morphology reciprocally illuminate conflicting phylogenetic hypotheses in Chalcididae (Hymenoptera, Chalcidoidea)

2019 ◽  
Author(s):  
Astrid Cruaud ◽  
Gérard Delvare ◽  
Sabine Nidelet ◽  
Laure Sauné ◽  
Sujeevan Ratnasingham ◽  
...  
Keyword(s):  
Gene Tree ◽  
Gc Content ◽  
Careful Analysis ◽  
Divergent Evolution ◽  
Joint Analysis ◽  
Tree Reconciliation ◽  
Representative Sampling ◽  
The Family ◽  
Molecular Phylogenetic ◽  
Gene Tree Reconciliation

ABSTRACTRecent technical advances combined with novel computational approaches promised the acceleration of our understanding of the tree of life. However, when it comes to hyperdiverse and poorly known groups of invertebrates, studies are still scarce. As published phylogenies will be rarely challenged by future taxonomists, careful attention must be paid to potential analytical bias. We present the first molecular phylogenetic hypothesis for the family Chalcididae, an emblematic group of parasitoid wasps, with a representative sampling (144 ingroups and 7 outgroups) that covers all described subfamilies and tribes and 82% of the known genera. Analyses of 538 Ultra-Conserved Elements (UCEs) with supermatrix (RAxML and IQTREE) and gene-tree reconciliation approaches (ASTRAL, ASTRID) resulted in highly supported topologies in overall agreement with morphology but reveal conflicting topologies for some of the deepest nodes. To resolve these conflicts, we explored the phylogenetic tree space with clustering and gene genealogy interrogation methods, analyzed marker and taxon properties that could bias inferences and performed a thorough morphological analysis (130 characters encoded for 40 taxa representative of the diversity). This joint analysis reveals that UCEs enable attainment of resolution between ancestry and convergent /divergent evolution when morphology is not informative enough, but also shows that a systematic exploration of bias with different analytical methods and a careful analysis of morphological features is required to prevent publication of artefactual results. We highlight a GC-content bias for ML approaches, an artefactual mid-point rooting of the ASTRAL tree and a deleterious effect of high percentage of missing data on gene tree reconciliation methods. Based on the results we propose a new classification of the family into eight subfamilies and 10 tribes that lay the foundation for future studies on the evolutionary history of Chalcididae.

scholarly journals Isometric gene tree reconciliation revisited

2017 ◽  
Vol 12 (1) ◽  
Author(s):  
Broňa Brejová ◽  
Askar Gafurov ◽  
Dana Pardubská ◽  
Michal Sabo ◽  
Tomáš Vinař
Keyword(s):  
Gene Tree ◽  
Tree Reconciliation ◽  
Gene Tree Reconciliation

scholarly journals Ancient and recent introgression shape the evolutionary history of pollinator adaptation and speciation in a model monkeyflower radiation (Mimulus section Erythranthe)

PLoS Genetics ◽  
2021 ◽  
Vol 17 (2) ◽  
pp. e1009095
Author(s):  
Thomas C. Nelson ◽  
Angela M. Stathos ◽  
Daniel D. Vanderpool ◽  
Findley R. Finseth ◽  
Yao-wu Yuan ◽  
...  
Keyword(s):  
Evolutionary History ◽  
Gene Tree ◽  
Nuclear Gene ◽  
Evolutionary Genetics ◽  
Species Tree ◽  
Pollination Syndrome ◽  
Gene Trees ◽  
Genome Wide ◽  
Hummingbird Pollination ◽  
History Of

Inferences about past processes of adaptation and speciation require a gene-scale and genome-wide understanding of the evolutionary history of diverging taxa. In this study, we use genome-wide capture of nuclear gene sequences, plus skimming of organellar sequences, to investigate the phylogenomics of monkeyflowers in Mimulus section Erythranthe (27 accessions from seven species). Taxa within Erythranthe, particularly the parapatric and putatively sister species M. lewisii (bee-pollinated) and M. cardinalis (hummingbird-pollinated), have been a model system for investigating the ecological genetics of speciation and adaptation for over five decades. Across >8000 nuclear loci, multiple methods resolve a predominant species tree in which M. cardinalis groups with other hummingbird-pollinated taxa (37% of gene trees), rather than being sister to M. lewisii (32% of gene trees). We independently corroborate a single evolution of hummingbird pollination syndrome in Erythranthe by demonstrating functional redundancy in genetic complementation tests of floral traits in hybrids; together, these analyses overturn a textbook case of pollination-syndrome convergence. Strong asymmetries in allele-sharing (Patterson’s D-statistic and related tests) indicate that gene-tree discordance reflects ancient and recent introgression rather than incomplete lineage sorting. Consistent with abundant introgression blurring the history of divergence, low-recombination and adaptation-associated regions support the new species tree, while high-recombination regions generate phylogenetic evidence for sister status for M. lewisii and M. cardinalis. Population-level sampling of core taxa also revealed two instances of chloroplast capture, with Sierran M. lewisii and Southern Californian M. parishii each carrying organelle genomes nested within respective sympatric M. cardinalis clades. A recent organellar transfer from M. cardinalis, an outcrosser where selfish cytonuclear dynamics are more likely, may account for the unexpected cytoplasmic male sterility effects of selfer M. parishii organelles in hybrids with M. lewisii. Overall, our phylogenomic results reveal extensive reticulation throughout the evolutionary history of a classic monkeyflower radiation, suggesting that natural selection (re-)assembles and maintains species-diagnostic traits and barriers in the face of gene flow. Our findings further underline the challenges, even in reproductively isolated species, in distinguishing re-use of adaptive alleles from true convergence and emphasize the value of a phylogenomic framework for reconstructing the evolutionary genetics of adaptation and speciation.

scholarly journals Phylogenomic Analyses Of 2,786 Genes In 158 Lineages Support a Root of The Eukaryotic Tree of Life Between Opisthokonts (Animals, Fungi and Their Microbial Relatives) and All Other Lineages

2021 ◽  
Author(s):  
Mario A Ceron Romero ◽  
Miguel M Fonseca ◽  
Leonardo de Oliveira Martins ◽  
David Posada ◽  
Laura A Katz
Keyword(s):  
Tree Species ◽  
High Throughput Sequencing ◽  
Single Gene ◽  
Gene Tree ◽  
Gene Families ◽  
Species Tree ◽  
Tree Of Life ◽  
Gene Duplications ◽  
Tree Reconciliation ◽  
Phylogenomic Analyses

Advances in phylogenetics and high throughput sequencing have allowed the reconstruction of deep phylogenetic relationships in the evolution of eukaryotes. Yet, the root of the eukaryotic tree of life remains elusive. The most popular hypothesis in textbooks and reviews is a root between Unikonta (Opisthokonta + Amoebozoa) and Bikonta (all other eukaryotes), which emerged from analyses of a single gene fusion. Subsequent highly cited studies based on concatenation of genes supported this hypothesis with some variations or proposed a root within Excavata. However, concatenation of genes neither considers phylogenetically informative events (i.e. gene duplications and losses), nor provides an estimate of the root. A more recent study using gene tree / species tree reconciliation methods suggested the root lies between Opisthokonta and all other eukaryotes, but only including 59 taxa and 20 genes. Here we apply a gene tree / species tree reconciliation approach to a gene-rich and taxon rich dataset (i.e. 2,786 gene families from two sets of 158 diverse eukaryotic lineages) to assess the root, and we iterate each analysis 100 times to quantify tree space uncertainty. We estimate a root between Fungi and all other eukaryotes, or between Opisthokonta and all other eukaryotes, and reject alternative roots from the literature. Based on further analysis of genome size we propose Opisthokonta + others as the most likely root.

scholarly journals A consensus phylogenomic approach highlights paleopolyploid and rapid radiation in the history of Ericales

2019 ◽  
Author(s):  
Drew A. Larson ◽  
Joseph F. Walker ◽  
Oscar M. Vargas ◽  
Stephen A. Smith
Keyword(s):  
Gene Tree ◽  
Gene Duplications ◽  
Species Relationships ◽  
Rapid Radiation ◽  
Genome Duplications ◽  
Tree Inference ◽  
History Of ◽  
Rapid Diversification ◽  
Clustering Approach ◽  
Edge Based

ABSTRACTPremise of studyLarge genomic datasets offer the promise of resolving historically recalcitrant species relationships. However, different methodologies can yield conflicting results, especially when clades have experienced ancient, rapid diversification. Here, we analyzed the ancient radiation of Ericales and explored sources of uncertainty related to species tree inference, conflicting gene tree signal, and the inferred placement of gene and genome duplications.MethodsWe used a hierarchical clustering approach, with tree-based homology and orthology detection, to generate six filtered phylogenomic matrices consisting of data from 97 transcriptomes and genomes. Support for species relationships was inferred from multiple lines of evidence including shared gene duplications, gene tree conflict, gene-wise edge-based analyses, concatenation, and coalescent-based methods and is summarized in a consensus framework.Key ResultsOur consensus approach supported a topology largely concordant with previous studies, but suggests that the data are not capable of resolving several ancient relationships due to lack of informative characters, sensitivity to methodology, and extensive gene tree conflict correlated with paleopolyploidy. We found evidence of a whole genome duplication before the radiation of all or most ericalean families and demonstrate that tree topology and heterogeneous evolutionary rates impact the inferred placement of genome duplications.ConclusionsOur approach provides a novel hypothesis regarding the history of Ericales and confidently resolves most nodes. We demonstrate that a series of ancient divergences are unresolvable with these data. Whether paleopolyploidy is a major source of the observed phylogenetic conflict warrants further investigation.

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