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Bayesian phylogenetic analysis for diploid and allotetraploid species networks

https://doi.org/10.1101/129361
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What this work says

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

inferredcites →https://doi.org/10.1007/b11601500openalex-snapshot
Combinatorial Stochastic Processes
inferredcites →https://doi.org/10.1007/s00285-005-0365-zopenalex-snapshot
Phylogenetic networks from multi-labelled trees
inferredcites →https://doi.org/10.1016/0025-5564(81)90043-2openalex-snapshot
Comparison of phylogenetic trees
inferredcites →https://doi.org/10.1016/j.jtbi.2008.04.005openalex-snapshot
The conditioned reconstructed process
inferredcites →https://doi.org/10.1073/pnas.0913022107openalex-snapshot
Bayesian species delimitation using multilocus sequence data
inferredcites →https://doi.org/10.1093/bioinformatics/btp133openalex-snapshot
PADRE: a package for analyzing and displaying reticulate evolution
inferredcites →https://doi.org/10.1093/bioinformatics/btq548openalex-snapshot
HybridNET: a tool for constructing hybridization networks
inferredcites →https://doi.org/10.1093/biomet/82.4.711openalex-snapshot
Reversible Jump Markov Chain Monte Carlo Computation and Bayesian Model Determination
inferredcites →https://doi.org/10.1093/genetics/164.4.1645openalex-snapshot
Bayes Estimation of Species Divergence Times and Ancestral Population Sizes Using DNA Sequences From Multiple Loci
inferredcites →https://doi.org/10.1093/molbev/msl045openalex-snapshot
Reconstructing the Evolutionary History of Polyploids from Multilabeled Trees
inferredcites →https://doi.org/10.1093/molbev/msp274openalex-snapshot
Bayesian Inference of Species Trees from Multilocus Data
inferredcites →https://doi.org/10.1093/oso/9780198536932.001.0001openalex-snapshot
Poisson Processes
inferredcites →https://doi.org/10.1093/sysbio/syp055openalex-snapshot
Identifying Hybridization Events in the Presence of Coalescence via Model Selection
inferredcites →https://doi.org/10.1093/sysbio/syr096openalex-snapshot
Inferring Species Networks from Gene Trees in High-Polyploid North American and Hawaiian Violets (Viola, Violaceae)
inferredcites →https://doi.org/10.1093/sysbio/syt012openalex-snapshot
Statistical Inference of Allopolyploid Species Networks in the Presence of Incomplete Lineage Sorting
inferredcites →https://doi.org/10.1109/tcbb.2010.122openalex-snapshot
Metrics on Multilabeled Trees: Interrelationships and Diameter Bounds
inferredcites →https://doi.org/10.1109/tcbb.2011.137openalex-snapshot
Algorithms for Reticulate Networks of Multiple Phylogenetic Trees
inferredcites →https://doi.org/10.1111/j.0006-341x.1999.00001.xopenalex-snapshot
Bayesian Phylogenetic Inference via Markov Chain Monte Carlo Methods
inferredcites →https://doi.org/10.1111/nph.14111openalex-snapshot
Next‐generation polyploid phylogenetics: rapid resolution of hybrid polyploid complexes using PacBio single‐molecule sequencing
inferredcites →https://doi.org/10.1186/1471-2148-11-291openalex-snapshot
Estimating hybridization in the presence of coalescence using phylogenetic intraspecific sampling
inferredcites →https://doi.org/10.1186/1471-2148-9-216openalex-snapshot
Inferring polyploid phylogenies from multiply-labeled gene trees

What points at this work

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

inferred← citeshttps://doi.org/10.1016/j.micres.2019.01.004openalex-snapshot
Nodule-associated microbiome diversity in wild populations of Sulla coronaria reveals clues on the relative importance of culturable rhizobial symbionts and co-infecting endophytes
inferred← citeshttps://doi.org/10.1073/pnas.2410934122openalex-snapshot
Phylogenetic networks empower biodiversity research
inferred← citeshttps://doi.org/10.1093/g3journal/jkac182openalex-snapshot
Insights from the genomes of 4 diploid Camelina spp.
inferred← citeshttps://doi.org/10.1093/sysbio/syab081openalex-snapshot
Maximum Parsimony Inference of Phylogenetic Networks in the Presence of Polyploid Complexes
inferred← citeshttps://doi.org/10.1093/sysbio/syad009openalex-snapshot
Phylogenetic Analysis of Allotetraploid Species Using Polarized Genomic Sequences
inferred← citeshttps://doi.org/10.1093/sysbio/syae046openalex-snapshot
Complex but Clear Allopolyploid Pattern of Subtribe Tussilagininae (Asteraceae: Senecioneae) Revealed by Robust Phylogenomic Evidence, with Development of a Novel Homeolog-Sorting Pipeline
inferred← citeshttps://doi.org/10.1093/sysbio/syag045openalex-snapshot
Evolving View on Phylogenetic Networks
inferred← citeshttps://doi.org/10.1093/sysbio/syy024openalex-snapshot
Dating the Species Network: Allopolyploidy and Repetitive DNA Evolution in American Daisies (Melampodium sect. Melampodium, Asteraceae)
inferred← citeshttps://doi.org/10.1101/2021.08.23.455123openalex-snapshot
Insights from the genomes of four diploid Camelina spp.
inferred← citeshttps://doi.org/10.1101/2021.08.30.458250openalex-snapshot
Unraveling Phylogenetic Relationships, Reticulate Evolution, and Genome Composition of Polyploid Plant Complexes by Rad-Seq and Hyb-Seq
inferred← citeshttps://doi.org/10.1101/2023.08.08.552429openalex-snapshot
Efficient assembly of plant genomes: A case study with evolutionary implications in Ranunculus (Ranunculaceae)
inferred← citeshttps://doi.org/10.1111/2041-210x.14072openalex-snapshot
homologizer: Phylogenetic phasing of gene copies into polyploid subgenomes
inferred← citeshttps://doi.org/10.1111/nph.17105openalex-snapshot
Polyploid phylogenetics
inferred← citeshttps://doi.org/10.1111/nph.18284openalex-snapshot
Untying Gordian knots: unraveling reticulate polyploid plant evolution by genomic data using the large Ranunculus auricomus species complex
inferred← citeshttps://doi.org/10.1111/tpj.15650openalex-snapshot
Tracking the ancestry of known and ‘ghost’ homeologous subgenomes in model grass Brachypodium polyploids
inferred← citeshttps://doi.org/10.1111/tpj.70390openalex-snapshot
Assembling genomes of non‐model plants: A case study with evolutionary insights from Ranunculus (Ranunculaceae)
inferred← citeshttps://doi.org/10.1146/annurev-ecolsys-110316-022729openalex-snapshot
Phylogenetics of Allopolyploids
inferred← citeshttps://doi.org/10.1146/annurev-ecolsys-121415-032302openalex-snapshot
Integrating Networks, Phylogenomics, and Population Genomics for the Study of Polyploidy
inferred← citeshttps://doi.org/10.3389/fpls.2022.842842openalex-snapshot
Reticulate Evolution in the Western Mediterranean Mountain Ranges: The Case of the Leucanthemopsis Polyploid Complex
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