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Homoploid hybridization signals due to ancestral subdivision: a case study on the D lineage in wheat

https://doi.org/10.1101/628685
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Outgoing claims: the papers this work cites, builds on, or argues with.

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An Introduction to Categorical Data Analysis
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Structural evolution of wheat chromosomes 4A, 5A, and 7B and its impact on recombination
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Don't forget the ancestral polymorphisms
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Hybrid speciation
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Draft genome of the wheat A-genome progenitor Triticum urartu
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Aegilops tauschii draft genome sequence reveals a gene repertoire for wheat adaptation
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Insights from genomes into the evolutionary importance and prevalence of hybridization in nature
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Genes encoding plastid acetyl-CoA carboxylase and 3-phosphoglycerate kinase of the Triticum / Aegilops complex and the evolutionary history of polyploid wheat
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Effect of ancient population structure on the degree of polymorphism shared between modern human populations and ancient hominins
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Variation in repeated nucleotide sequences sheds light on the phylogeny of the wheat B and G genomes.
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Rapid hybrid speciation in wild sunflowers
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SplitsTree: analyzing and visualizing evolutionary data.
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RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies
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Indel Reliability in Indel-Based Phylogenetic Inference
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Distinguishing Recent Admixture from Ancestral Population Structure
inferredcites →https://doi.org/10.1093/genetics/105.2.437openalex-snapshot
EVOLUTIONARY RELATIONSHIP OF DNA SEQUENCES IN FINITE POPULATIONS
inferredcites →https://doi.org/10.1093/molbev/msn172openalex-snapshot
Subdivision in an Ancestral Species Creates Asymmetry in Gene Trees
inferredcites →https://doi.org/10.1093/molbev/msr048openalex-snapshot
Testing for Ancient Admixture between Closely Related Populations
inferredcites →https://doi.org/10.1093/molbev/mss117openalex-snapshot
Ancient Structure in Africa Unlikely to Explain Neanderthal and Non-African Genetic Similarity
inferredcites →https://doi.org/10.1093/molbev/mst010openalex-snapshot
MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability
inferredcites →https://doi.org/10.1093/molbev/msu103openalex-snapshot
The Doubly Conditioned Frequency Spectrum Does Not Distinguish between Ancient Population Structure and Hybridization
inferredcites →https://doi.org/10.1093/oxfordjournals.jhered.a105590openalex-snapshot
THE ORIGIN OF TRITICUM SPELTA AND ITS FREE-THRESHING HEXAPLOID RELATIVES*
inferredcites →https://doi.org/10.1099/mgen.0.000056openalex-snapshot
SNP-sites: rapid efficient extraction of SNPs from multi-FASTA alignments
inferredcites →https://doi.org/10.1111/evo.12399openalex-snapshot
HOW COMMON IS HOMOPLOID HYBRID SPECIATION?
inferredcites →https://doi.org/10.1111/j.1420-9101.2012.02599.xopenalex-snapshot
Hybridization and speciation
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TESTING THE CONSTANT-RATE NEUTRAL ALLELE MODEL WITH PROTEIN SEQUENCE DATA
inferredcites →https://doi.org/10.1111/j.1558-5646.2007.00267.xopenalex-snapshot
THE RATE OF GENOME STABILIZATION IN HOMOPLOID HYBRID SPECIES
inferredcites →https://doi.org/10.1111/mec.13557openalex-snapshot
A genomic perspective on hybridization and speciation
inferredcites →https://doi.org/10.1111/nph.12931openalex-snapshot
The chloroplast view of the evolution of polyploid wheat
inferredcites →https://doi.org/10.1111/nph.13294openalex-snapshot
A re‐evaluation of the homoploid hybrid origin of A egilops tauschii, the donor of the wheat D‐subgenome
inferredcites →https://doi.org/10.1111/nph.13487openalex-snapshot
Chloroplast phylogeny of Triticum/Aegilops species is not incongruent with an ancient homoploid hybrid origin of the ancestor of the bread wheat D‐genome
inferredcites →https://doi.org/10.1111/nph.13563openalex-snapshot
Multiple rounds of ancient and recent hybridizations have occurred within the Aegilops–Triticum complex
inferredcites →https://doi.org/10.1111/nph.14113openalex-snapshot
Reconciling the evolutionary origin of bread wheat (Triticum aestivum)
inferredcites →https://doi.org/10.1111/tpj.13436openalex-snapshot
Towards a whole‐genome sequence for rye ( Secale cereale L.)
inferredcites →https://doi.org/10.1126/sciadv.aav9188openalex-snapshot
Pervasive hybridizations in the history of wheat relatives
inferredcites →https://doi.org/10.1126/science.1250092openalex-snapshot
Ancient hybridizations among the ancestral genomes of bread wheat
inferredcites →https://doi.org/10.1126/science.1251788openalex-snapshot
A chromosome-based draft sequence of the hexaploid bread wheat ( Triticum aestivum ) genome
inferredcites →https://doi.org/10.1139/g93-004openalex-snapshot
The evolution of polyploid wheats: identification of the A genome donor species
inferredcites →https://doi.org/10.1139/g94-125openalex-snapshot
Detection of interchromosomal translocations within the Triticeae by RFLP analysis
inferredcites →https://doi.org/10.1186/s41044-016-0019-8openalex-snapshot
PorthoMCL: Parallel orthology prediction using MCL for the realm of massive genome availability
inferredcites →https://doi.org/10.1371/journal.pcbi.1004812openalex-snapshot
Incomplete Lineage Sorting and Hybridization Statistics for Large-Scale Retroposon Insertion Data
inferredcites →https://doi.org/10.1371/journal.pgen.1002947openalex-snapshot
The Date of Interbreeding between Neandertals and Modern Humans
inferredcites →https://doi.org/10.1371/journal.pone.0079329openalex-snapshot
Sequence-Based Analysis of Translocations and Inversions in Bread Wheat (Triticum aestivum L.)
inferredcites →https://doi.org/10.1534/genetics.114.165548openalex-snapshot
Chromosomal Evolution and Patterns of Introgression inHelianthus
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