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Phylogenetic conflicts, combinability, and deep phylogenomics in plants

https://doi.org/10.1101/371930

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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1002/ajb2.1064openalex-snapshot

A matter of phylogenetic scale: Distinguishing incomplete lineage sorting from lateral gene transfer as the cause of gene tree discord in recent versus deep diversification histories

inferredcites →https://doi.org/10.1002/ajb2.1069openalex-snapshot

From cacti to carnivores: Improved phylotranscriptomic sampling and hierarchical homology inference provide further insight into the evolution of Caryophyllales

inferredcites →https://doi.org/10.1007/978-1-4612-1694-0_15openalex-snapshot

Information Theory and an Extension of the Maximum Likelihood Principle

inferredcites →https://doi.org/10.1016/0025-5564(81)90043-2openalex-snapshot

Comparison of phylogenetic trees

inferredcites →https://doi.org/10.1016/0169-5347(96)10006-9openalex-snapshot

Combining data in phylogenetic analysis

inferredcites →https://doi.org/10.1016/j.cub.2017.02.031openalex-snapshot

A Large and Consistent Phylogenomic Dataset Supports Sponges as the Sister Group to All Other Animals

inferredcites →https://doi.org/10.1016/j.cub.2018.01.063openalex-snapshot

The Interrelationships of Land Plants and the Nature of the Ancestral Embryophyte

inferredcites →https://doi.org/10.1016/j.ympev.2015.07.018openalex-snapshot

The gene tree delusion

inferredcites →https://doi.org/10.1016/j.ympev.2015.10.027openalex-snapshot

Implementing and testing the multispecies coalescent model: A valuable paradigm for phylogenomics

inferredcites →https://doi.org/10.1038/nature06614openalex-snapshot

Broad phylogenomic sampling improves resolution of the animal tree of life

inferredcites →https://doi.org/10.1038/nature09014openalex-snapshot

A formal test of the theory of universal common ancestry

inferredcites →https://doi.org/10.1038/ncomms16047openalex-snapshot

The ancestral flower of angiosperms and its early diversification

inferredcites →https://doi.org/10.1038/nmeth.4285openalex-snapshot

ModelFinder: fast model selection for accurate phylogenetic estimates

inferredcites →https://doi.org/10.1038/s41559-017-0126openalex-snapshot

Contentious relationships in phylogenomic studies can be driven by a handful of genes

inferredcites →https://doi.org/10.1038/s41559-017-0331-3openalex-snapshot

Ctenophore relationships and their placement as the sister group to all other animals

inferredcites →https://doi.org/10.1071/sb9900021openalex-snapshot

Trees from sequences: panacea or pandora's box?

inferredcites →https://doi.org/10.1073/pnas.0603335103openalex-snapshot

The deepest divergences in land plants inferred from phylogenomic evidence

inferredcites →https://doi.org/10.1073/pnas.0607004104openalex-snapshot

High-resolution species trees without concatenation

inferredcites →https://doi.org/10.1073/pnas.1213498109openalex-snapshot

Hornwort pyrenoids, carbon-concentrating structures, evolved and were lost at least five times during the last 100 million years

inferredcites →https://doi.org/10.1073/pnas.1323926111openalex-snapshot

Phylotranscriptomic analysis of the origin and early diversification of land plants

inferredcites →https://doi.org/10.1073/pnas.97.8.4086openalex-snapshot

Seed plant phylogeny inferred from all three plant genomes: Monophyly of extant gymnosperms and origin of Gnetales from conifers

inferredcites →https://doi.org/10.1073/pnas.97.8.4092openalex-snapshot

Phylogeny of seed plants based on all three genomic compartments: Extant gymnosperms are monophyletic and Gnetales' closest relatives are conifers

inferredcites →https://doi.org/10.1080/10635150801910436openalex-snapshot

Testing Congruence in Phylogenomic Analysis

inferredcites →https://doi.org/10.1093/bioinformatics/btl474openalex-snapshot

GARD: a genetic algorithm for recombination detection

inferredcites →https://doi.org/10.1093/bioinformatics/btl505openalex-snapshot

TimeTree: a public knowledge-base of divergence times among organisms

inferredcites →https://doi.org/10.1093/bioinformatics/btu033openalex-snapshot

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

inferredcites →https://doi.org/10.1093/bioinformatics/btu462openalex-snapshot

ASTRAL: genome-scale coalescent-based species tree estimation

inferredcites →https://doi.org/10.1093/bioinformatics/btx063openalex-snapshot

Phyx: phylogenetic tools for unix

inferredcites →https://doi.org/10.1093/gbe/evr013openalex-snapshot

Detecting Phylogenetic Breakpoints and Discordance from Genome-Wide Alignments for Species Tree Reconstruction

inferredcites →https://doi.org/10.1093/molbev/msl051openalex-snapshot

Automated Phylogenetic Detection of Recombination Using a Genetic Algorithm

inferredcites →https://doi.org/10.1093/molbev/msl170openalex-snapshot

Bayesian Estimation of Concordance among Gene Trees

inferredcites →https://doi.org/10.1093/molbev/msp098openalex-snapshot

INDELible: A Flexible Simulator of Biological Sequence Evolution

inferredcites →https://doi.org/10.1093/molbev/mss020openalex-snapshot

PartitionFinder: Combined Selection of Partitioning Schemes and Substitution Models for Phylogenetic Analyses

inferredcites →https://doi.org/10.1093/molbev/msu245openalex-snapshot

Orthology Inference in Nonmodel Organisms Using Transcriptomes and Low-Coverage Genomes: Improving Accuracy and Matrix Occupancy for Phylogenomics

inferredcites →https://doi.org/10.1093/molbev/msu300openalex-snapshot

IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies

inferredcites →https://doi.org/10.1093/molbev/msv037openalex-snapshot

Tree of Life Reveals Clock-Like Speciation and Diversification

inferredcites →https://doi.org/10.1093/molbev/msw260openalex-snapshot

PartitionFinder 2: New Methods for Selecting Partitioned Models of Evolution for Molecular and Morphological Phylogenetic Analyses

inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a025813openalex-snapshot

Can three incongruence tests predict when data should be combined?

inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a026176openalex-snapshot

Gnetum and the Angiosperms: Molecular Evidence that Their Shared Morphological Characters Are Convergent, Rather than Homologous

inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a026192openalex-snapshot

Molecular phylogenetic analysis among bryophytes and tracheophytes based on combined data of plastid coded genes and the 18S rRNA gene

inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a026201openalex-snapshot

Multiple Comparisons of Log-Likelihoods with Applications to Phylogenetic Inference

inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a026290openalex-snapshot

Multigene Phylogeny of Land Plants with Special Reference to Bryophytes and the Earliest Land Plants

inferredcites →https://doi.org/10.1093/sysbio/38.1.7openalex-snapshot

A Concern for Evidence and a Phylogenetic Hypothesis of Relationships among Epicrates (Boidae, Serpentes)

inferredcites →https://doi.org/10.1093/sysbio/46.3.523openalex-snapshot

Gene Trees in Species Trees

inferredcites →https://doi.org/10.1093/sysbio/syp031openalex-snapshot

Estimating Species Phylogenies Using Coalescence Times among Sequences

inferredcites →https://doi.org/10.1093/sysbio/syq010openalex-snapshot

New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0

inferredcites →https://doi.org/10.1093/sysbio/syt109openalex-snapshot

Conflicting Phylogenies for Early Land Plants are Caused by Composition Biases among Synonymous Substitutions

inferredcites →https://doi.org/10.1093/sysbio/syu055openalex-snapshot

Coalescent versus Concatenation Methods and the Placement of Amborella as Sister to Water Lilies

inferredcites →https://doi.org/10.1093/sysbio/syv041openalex-snapshot

Can We Identify Genes with Increased Phylogenetic Reliability?

inferredcites →https://doi.org/10.1093/sysbio/syv059openalex-snapshot

Selecting Question-Specific Genes to Reduce Incongruence in Phylogenomics: A Case Study of Jawed Vertebrate Backbone Phylogeny

inferredcites →https://doi.org/10.1093/sysbio/syw101openalex-snapshot

Bayes factors unmask highly variable information content, bias, and extreme influence in phylogenomic analyses

inferredcites →https://doi.org/10.1093/sysbio/syx097openalex-snapshot

Information Criteria for Comparing Partition Schemes

inferredcites →https://doi.org/10.1093/sysbio/syy015openalex-snapshot

Inferring Phylogenetic Networks Using PhyloNet

inferredcites →https://doi.org/10.1093/sysbio/syy043openalex-snapshot

Analyzing Contentious Relationships and Outlier Genes in Phylogenomics

inferredcites →https://doi.org/10.1093/sysbio/syz007openalex-snapshot

Assessing Combinability of Phylogenomic Data Using Bayes Factors

inferredcites →https://doi.org/10.1101/gr.141978.112openalex-snapshot

Genome-scale coestimation of species and gene trees

inferredcites →https://doi.org/10.1111/j.1558-5646.2008.00549.xopenalex-snapshot

IS A NEW AND GENERAL THEORY OF MOLECULAR SYSTEMATICS EMERGING?

inferredcites →https://doi.org/10.1126/science.1248229openalex-snapshot

A Promiscuous Intermediate Underlies the Evolution of LEAFY DNA Binding Specificity

inferredcites →https://doi.org/10.1126/science.1250463openalex-snapshot

Statistical binning enables an accurate coalescent-based estimation of the avian tree

inferredcites →https://doi.org/10.1126/science.1253451openalex-snapshot

Whole-genome analyses resolve early branches in the tree of life of modern birds

inferredcites →https://doi.org/10.1186/1471-2148-10-321openalex-snapshot

Complete plastome sequences of Equisetum arvense and Isoetes flaccida: implications for phylogeny and plastid genome evolution of early land plant lineages

inferredcites →https://doi.org/10.1186/s12862-015-0423-0openalex-snapshot

Analysis of phylogenomic datasets reveals conflict, concordance, and gene duplications with examples from animals and plants

inferredcites →https://doi.org/10.1186/s12864-016-3407-6openalex-snapshot

Bacterial whole genome-based phylogeny: construction of a new benchmarking dataset and assessment of some existing methods

inferredcites →https://doi.org/10.1214/aos/1176344136openalex-snapshot

Estimating the Dimension of a Model

inferredcites →https://doi.org/10.1371/journal.pgen.1005896openalex-snapshot

Inferring Phylogenetic Networks with Maximum Pseudolikelihood under Incomplete Lineage Sorting

inferredcites →https://doi.org/10.1371/journal.pone.0197433openalex-snapshot

So many genes, so little time: A practical approach to divergence-time estimation in the genomic era

inferredcites →https://doi.org/10.1534/g3.116.034744openalex-snapshot

Reconstructing the Backbone of the Saccharomycotina Yeast Phylogeny Using Genome-Scale Data

inferredcites →https://doi.org/10.1666/0094-8373(2004)030<0082:dadani>2.0.co;2openalex-snapshot

Dark and disturbed: a new image of early angiosperm ecology

inferredcites →https://doi.org/10.3732/ajb.1700083openalex-snapshot

Widespread paleopolyploidy, gene tree conflict, and recalcitrant relationships among the carnivorous Caryophyllales

inferredcites →https://doi.org/10.7287/peerj.preprints.3489v1openalex-snapshot

Cause of gene tree discord? Distinguishing incomplete lineage sorting and lateral gene transfer in phylogenetics

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.1101/2020.03.27.012237openalex-snapshot

When species trees disagree: an approach consistent with the coalescent that quantifies phylogenomic support for contentious relationships

inferred← citeshttps://doi.org/10.1101/816967openalex-snapshot

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

inferred← citeshttps://doi.org/10.7717/peerj.7747openalex-snapshot

Characterizing gene tree conflict in plastome-inferred phylogenies

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