Science Advances

Supplementary Materials

The PDF file includes:

  • Text S1. Jointly inferring phylogenetic relationships and hybridization events
  • Text S2. Determination of possible hybridization scenarios
  • Text S3. Inferring multiple hybridizations in four-taxon scenarios (quartet method)
  • Text S4. Application of the quartet method
  • Text S5. Pattern of hybridization indices along chromosomes
  • Fig. S1. Geographic distribution of the 13 diploid Aegilops/Triticum species.
  • Fig. S2.1. Distribution of hybridization indices for triplets composed of two individuals of the same focal species and a third individual from another species.
  • Fig. S2.2. Distribution of hybridization indices for triplets composed of two individuals from two sister species and a third one.
  • Fig. S2.3. Distribution of hybridization indices for triplets composed of two species belonging to sister clades within the D lineage and a third species.
  • Fig. S2.4. Sitopsis species as potential hybrids between species of the D clade and either Ae. mutica or Ae. speltoides.
  • Fig. S2.5. An example where successive hybridization events lead to apparent contradiction in hybrid triplets.
  • Fig. S3.1. The 10 informative site patterns with four species and mutations polarized with an outgroup.
  • Fig. S3.2. Notations for symmetric and asymmetric coalescent gene trees with four sequences.
  • Fig. S3.3. Decomposition of a hybridization network with two reticulations.
  • Fig. S3.4. Example of scenario parameterization.
  • Fig. S3.5. Possible gene trees embedded in a four-taxon species tree.
  • Fig. S3.6. Possible gene trees embedded in a four-taxon network tree as drawn on fig. S3.3C.
  • Fig. S4.1. Tested scenarios for the origin of the D clade.
  • Fig. S4.2. Tested scenarios for hybridization within the D clade.
  • Fig. S5.1. Distribution of the mean hybridization index for (A, Ae. mutica, and D) triplets (proportion of Ae. mutica in D) across 10-Mb concatenations.
  • Fig. S5.2. Distribution of the mean hybridization index and CI for (A, Ae. mutica, and D) triplets (proportion of Ae. mutica in D) along chromosomes.
  • Fig. S5.3. Simulation of the distribution of the hybridization index with mean size of genomic blocs from 5 to 50 Mb.
  • Fig. S5.4. Simulation of the distribution of the hybridization index with mean size of genomic blocs of 10 Mb and with 10 to 200 rearrangements per chromosome (500 Mb).
  • Table S1. List of accessions used in the study.
  • Table S2. Number of contigs (size, >250 bp) per individual trancriptome.
  • Table S3.1. Expected numbers of site patterns for symmetric taxon trees.
  • Table S3.2. Expected numbers of site patterns for asymmetric taxon trees.
  • Table S3.3. Expected numbers of site patterns for one-reticulation networks.
  • Table S4.1. Count numbers for the 10 informative site patterns with the different combinations of species from the A and D clade.
  • Table S4.2. AIC of the different scenarios with zero, one, or two reticulations.
  • Table S4.3. ML estimates of the parameters for the best model (M 4) for the 10 combinations of A and D species.
  • Table S4.4. Count numbers for the 10 informative site patterns with either Ae. comosa or Ae. uniaristata as a potential parent.
  • Table S4.5. AIC of the different scenarios with zero, one, or two reticulations.

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Other Supplementary Material for this manuscript includes the following:

  • Data file S1 (.nb format). This Mathematica notebook file contains two main parts: (i) the detailed derivation of the different equations presented in text S3 and (ii) the implementation of the likelihood method presented in text S3 (quartet method) and its application to the dataset.

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