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Phase Resolution of Heterozygous Sites in Diploid Genomes is Important to Phylogenomic Analysis under the Multispecies Coalescent Model

https://doi.org/10.1093/sysbio/syab047
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Outgoing claims: the papers this work cites, builds on, or argues with.

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Sampling among haplotype resolutions in a coalescent-based genealogy sampler
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Allele phasing has minimal impact on phylogenetic reconstruction from targeted nuclear gene sequences in a case study of Artocarpus
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Evolution of Protein Molecules
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inferredcites →https://doi.org/10.1038/nrg2950openalex-snapshot
The importance of phase information for human genomics
inferredcites →https://doi.org/10.1038/nrg3054openalex-snapshot
Haplotype phasing: existing methods and new developments
inferredcites →https://doi.org/10.1038/s41587-020-0719-5openalex-snapshot
Fully phased human genome assembly without parental data using single-cell strand sequencing and long reads
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Haplotype-resolved genome analyses of a heterozygous diploid potato
inferredcites →https://doi.org/10.1038/s41592-020-01056-5openalex-snapshot
Haplotype-resolved de novo assembly using phased assembly graphs with hifiasm
inferredcites →https://doi.org/10.1073/pnas.0913022107openalex-snapshot
Bayesian species delimitation using multilocus sequence data
inferredcites →https://doi.org/10.1073/pnas.200348197openalex-snapshot
Worldwide DNA sequence variation in a 10-kilobase noncoding region on human chromosome 22
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Frequentist Properties of Bayesian Posterior Probabilities of Phylogenetic Trees Under Simple and Complex Substitution Models
inferredcites →https://doi.org/10.1080/10635150590945313openalex-snapshot
Branch-Length Prior Influences Bayesian Posterior Probability of Phylogeny
inferredcites →https://doi.org/10.1086/319501openalex-snapshot
A New Statistical Method for Haplotype Reconstruction from Population Data
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Bayesian Haplotype Inference for Multiple Linked Single-Nucleotide Polymorphisms
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A Comparison of Bayesian Methods for Haplotype Reconstruction from Population Genotype Data
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Inferring Phylogenies.
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A Fast and Flexible Statistical Model for Large-Scale Population Genotype Data: Applications to Inferring Missing Genotypes and Haplotypic Phase
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Computational Molecular Evolution
inferredcites →https://doi.org/10.1093/acprof:oso/9780199602605.001.0001openalex-snapshot
Molecular Evolution
inferredcites →https://doi.org/10.1093/bioinformatics/btaa605openalex-snapshot
PRANC: ML species tree estimation from the ranked gene trees under coalescence
inferredcites →https://doi.org/10.1093/czoolo/61.5.854openalex-snapshot
The BPP program for species tree estimation and species delimitation
inferredcites →https://doi.org/10.1093/genetics/105.2.437openalex-snapshot
EVOLUTIONARY RELATIONSHIP OF DNA SEQUENCES IN FINITE POPULATIONS
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A new method of inference of ancestral nucleotide and amino acid sequences.
inferredcites →https://doi.org/10.1093/genetics/158.3.1253openalex-snapshot
Human DNA Sequence Variation in a 6.6-kb Region Containing the Melanocortin 1 Receptor Promoter
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/msaa166openalex-snapshot
A Simulation Study to Examine the Information Content in Phylogenomic Data Sets under the Multispecies Coalescent Model
inferredcites →https://doi.org/10.1093/molbev/msab009openalex-snapshot
Complexity of the simplest species tree problem
inferredcites →https://doi.org/10.1093/molbev/msn148openalex-snapshot
Estimation of Hominoid Ancestral Population Sizes under Bayesian Coalescent Models Incorporating Mutation Rate Variation and Sequencing Errors
inferredcites →https://doi.org/10.1093/molbev/msu279openalex-snapshot
Unguided Species Delimitation Using DNA Sequence Data from Multiple Loci
inferredcites →https://doi.org/10.1093/molbev/msx126openalex-snapshot
StarBEAST2 Brings Faster Species Tree Inference and Accurate Estimates of Substitution Rates
inferredcites →https://doi.org/10.1093/molbev/msx277openalex-snapshot
Coalescent-Based Analyses of Genomic Sequence Data Provide a Robust Resolution of Phylogenetic Relationships among Major Groups of Gibbons
inferredcites →https://doi.org/10.1093/molbev/msx307openalex-snapshot
Bayesian Inference of Species Networks from Multilocus Sequence Data
inferredcites →https://doi.org/10.1093/molbev/msy147openalex-snapshot
Species Tree Inference with BPP Using Genomic Sequences and the Multispecies Coalescent
inferredcites →https://doi.org/10.1093/molbev/msz263openalex-snapshot
Optimizing Phylogenomics with Rapidly Evolving Long Exons: Comparison with Anchored Hybrid Enrichment and Ultraconserved Elements
inferredcites →https://doi.org/10.1093/molbev/msz296openalex-snapshot
A Bayesian Implementation of the Multispecies Coalescent Model with Introgression for Phylogenomic Analysis
inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a003795openalex-snapshot
Global Patterns of Human DNA Sequence Variation in a 10-kb Region on Chromosome 1
inferredcites →https://doi.org/10.1093/sysbio/syaa085openalex-snapshot
Diversification, Introgression, and Rampant Cytonuclear Discordance in Rocky Mountains Chipmunks (Sciuridae: Tamias)
inferredcites →https://doi.org/10.1093/sysbio/sys004openalex-snapshot
Ultraconserved Elements Anchor Thousands of Genetic Markers Spanning Multiple Evolutionary Timescales
inferredcites →https://doi.org/10.1093/sysbio/sys049openalex-snapshot
Anchored Hybrid Enrichment for Massively High-Throughput Phylogenomics
inferredcites →https://doi.org/10.1093/sysbio/syw092openalex-snapshot
Misconceptions on Missing Data in RAD-seq Phylogenetics with a Deep-scale Example from Flowering Plants
inferredcites →https://doi.org/10.1093/sysbio/syw119openalex-snapshot
Efficient Bayesian Species Tree Inference under the Multispecies Coalescent
inferredcites →https://doi.org/10.1093/sysbio/syx058openalex-snapshot
Conserved Nonexonic Elements: A Novel Class of Marker for Phylogenomics
inferredcites →https://doi.org/10.1093/sysbio/syx085openalex-snapshot
Coestimating Reticulate Phylogenies and Gene Trees from Multilocus Sequence Data
inferredcites →https://doi.org/10.1093/sysbio/syy039openalex-snapshot
Allele Phasing Greatly Improves the Phylogenetic Utility of Ultraconserved Elements
inferredcites →https://doi.org/10.1093/sysbio/syy051openalex-snapshot
The Spectre of Too Many Species
inferredcites →https://doi.org/10.1101/gr.074492.107openalex-snapshot
Velvet: Algorithms for de novo short read assembly using de Bruijn graphs
inferredcites →https://doi.org/10.1101/gr.089532.108openalex-snapshot
ABySS: A parallel assembler for short read sequence data
inferredcites →https://doi.org/10.1101/gr.214874.116openalex-snapshot
Direct determination of diploid genome sequences
inferredcites →https://doi.org/10.1111/j.1365-294x.2011.05411.xopenalex-snapshot
Speciation in the Rana chensinensis species complex and its relationship to the uplift of the Qinghai–Tibetan Plateau
inferredcites →https://doi.org/10.1111/j.1755-0998.2009.02732.xopenalex-snapshot
seqphase : a web tool for interconverting phase input/output files and fasta sequence alignments
inferredcites →https://doi.org/10.1146/annurev-ecolsys-110316-022645openalex-snapshot
The Utility of Single Nucleotide Polymorphism (SNP) Data in Phylogenetics
inferredcites →https://doi.org/10.1371/journal.pgen.1007308openalex-snapshot
Comparison of phasing strategies for whole human genomes

What points at this work

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

inferred← citeshttps://doi.org/10.1093/jmammal/gyaf010zenodo-depositor-declared
Coalescent-delimitation framework disentangles species boundaries within the Neotropical mouse-opossums subgenus Marmosops
inferred← citeshttps://doi.org/10.1007/978-1-0716-4836-0_4openalex-snapshot
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inferred← citeshttps://doi.org/10.1071/is22011openalex-snapshot
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inferred← citeshttps://doi.org/10.1093/molbev/msaf184openalex-snapshot
The Impact of Sequencing and Genotyping Errors on Bayesian Analysis of Genomic Data under the Multispecies Coalescent Model
inferred← citeshttps://doi.org/10.1093/sysbio/syac009openalex-snapshot
Full-Likelihood Genomic Analysis Clarifies a Complex History of Species Divergence and Introgression: The Example of the erato-sara Group of Heliconius Butterflies
inferred← citeshttps://doi.org/10.1093/sysbio/syac077openalex-snapshot
Power of Bayesian and Heuristic Tests to Detect Cross-Species Introgression with Reference to Gene Flow in the Tamias quadrivittatus Group of North American Chipmunks
inferred← citeshttps://doi.org/10.1093/sysbio/syad015openalex-snapshot
Estimation of species divergence times in presence of cross-species gene flow
inferred← citeshttps://doi.org/10.1093/sysbio/syad019openalex-snapshot
Complex Patterns of Diversification in the Gray Zone of Speciation: Model-Based Approaches Applied to Patagonian Liolaemid Lizards (Squamata: Liolaemus kingii clade)
inferred← citeshttps://doi.org/10.1093/sysbio/syae024openalex-snapshot
Benefits and Limits of Phasing Alleles for Network Inference of Allopolyploid Complexes
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Inference of Cross-Species Gene Flow Using Genomic Data Depends on the Methods: Case Study of Gene Flow in Drosophila
inferred← citeshttps://doi.org/10.1093/sysbio/syaf053openalex-snapshot
Selecting a Window Size for Phylogenomic Analyses of Whole Genome Alignments Using AIC
inferred← citeshttps://doi.org/10.1093/zoolinnean/zlag118openalex-snapshot
Integrative delimitation and demographic modelling uncover speciation with gene flow in Homonota geckos (Gekkota: Phyllodactylidae) from Argentina’s highlands
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Population-scale long-read DNA sequencing: peering under the hood of the new evolutionary genomics
inferred← citeshttps://doi.org/10.1101/2021.02.10.430600openalex-snapshot
Full-likelihood genomic analysis clarifies a complex history of species divergence and introgression: the example of the erato-sara group of Heliconius butterflies
inferred← citeshttps://doi.org/10.1101/2021.12.07.471567openalex-snapshot
Significant cross-species gene flow detected in the Tamias quadrivittatus group of North American chipmunks
inferred← citeshttps://doi.org/10.2139/ssrn.6170238openalex-snapshot
Genome-wide SNP data reveal population boundaries, gene flow, and diversification patterns in the Western Banded Gecko (Coleonyx variegatus)
inferred← citeshttps://doi.org/10.3390/ani13030471openalex-snapshot
Genome Evolution and the Future of Phylogenomics of Non-Avian Reptiles
inferred← citeshttps://doi.org/10.3390/genes15111404openalex-snapshot
OHDLF: A Method for Selecting Orthologous Genes for Phylogenetic Construction and Its Application in the Genus Camellia
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