@article{8928,
  abstract     = {Domestication is a human‐induced selection process that imprints the genomes of domesticated populations over a short evolutionary time scale and that occurs in a given demographic context. Reconstructing historical gene flow, effective population size changes and their timing is therefore of fundamental interest to understand how plant demography and human selection jointly shape genomic divergence during domestication. Yet, the comparison under a single statistical framework of independent domestication histories across different crop species has been little evaluated so far. Thus, it is unclear whether domestication leads to convergent demographic changes that similarly affect crop genomes. To address this question, we used existing and new transcriptome data on three crop species of Solanaceae (eggplant, pepper and tomato), together with their close wild relatives. We fitted twelve demographic models of increasing complexity on the unfolded joint allele frequency spectrum for each wild/crop pair, and we found evidence for both shared and species‐specific demographic processes between species. A convergent history of domestication with gene flow was inferred for all three species, along with evidence of strong reduction in the effective population size during the cultivation stage of tomato and pepper. The absence of any reduction in size of the crop in eggplant stands out from the classical view of the domestication process; as does the existence of a “protracted period” of management before cultivation. Our results also suggest divergent management strategies of modern cultivars among species as their current demography substantially differs. Finally, the timing of domestication is species‐specific and supported by the few historical records available.},
  author       = {Arnoux, Stéphanie and Fraisse, Christelle and Sauvage, Christopher},
  issn         = {14209101},
  journal      = {Journal of Evolutionary Biology},
  number       = {2},
  pages        = {270--283},
  publisher    = {Wiley},
  title        = {{Genomic inference of complex domestication histories in three Solanaceae species}},
  doi          = {10.1111/jeb.13723},
  volume       = {34},
  year         = {2021},
}

@article{9168,
  abstract     = {Interspecific crossing experiments have shown that sex chromosomes play a major role in reproductive isolation between many pairs of species. However, their ability to act as reproductive barriers, which hamper interspecific genetic exchange, has rarely been evaluated quantitatively compared to Autosomes. This genome-wide limitation of gene flow is essential for understanding the complete separation of species, and thus speciation. Here, we develop a mainland-island model of secondary contact between hybridizing species of an XY (or ZW) sexual system. We obtain theoretical predictions for the frequency of introgressed alleles, and the strength of the barrier to neutral gene flow for the two types of chromosomes carrying multiple interspecific barrier loci. Theoretical predictions are obtained for scenarios where introgressed alleles are rare. We show that the same analytical expressions apply for sex chromosomes and autosomes, but with different sex-averaged effective parameters. The specific features of sex chromosomes (hemizygosity and absence of recombination in the heterogametic sex) lead to reduced levels of introgression on the X (or Z) compared to autosomes. This effect can be enhanced by certain types of sex-biased forces, but it remains overall small (except when alleles causing incompatibilities are recessive). We discuss these predictions in the light of empirical data comprising model-based tests of introgression and cline surveys in various biological systems.},
  author       = {Fraisse, Christelle and Sachdeva, Himani},
  issn         = {1943-2631},
  journal      = {Genetics},
  number       = {2},
  publisher    = {Genetics Society of America},
  title        = {{The rates of introgression and barriers to genetic exchange between hybridizing species: Sex chromosomes vs autosomes}},
  doi          = {10.1093/genetics/iyaa025},
  volume       = {217},
  year         = {2021},
}

@article{6856,
  abstract     = {Plant mating systems play a key role in structuring genetic variation both within and between species. In hybrid zones, the outcomes and dynamics of hybridization are usually interpreted as the balance between gene flow and selection against hybrids. Yet, mating systems can introduce selective forces that alter these expectations; with diverse outcomes for the level and direction of gene flow depending on variation in outcrossing and whether the mating systems of the species pair are the same or divergent. We present a survey of hybridization in 133 species pairs from 41 plant families and examine how patterns of hybridization vary with mating system. We examine if hybrid zone mode, level of gene flow, asymmetries in gene flow and the frequency of reproductive isolating barriers vary in relation to mating system/s of the species pair. We combine these results with a simulation model and examples from the literature to address two general themes: (i) the two‐way interaction between introgression and the evolution of reproductive systems, and (ii) how mating system can facilitate or restrict interspecific gene flow. We conclude that examining mating system with hybridization provides unique opportunities to understand divergence and the processes underlying reproductive isolation.},
  author       = {Pickup, Melinda and Barton, Nicholas H and Brandvain, Yaniv and Fraisse, Christelle and Yakimowski, Sarah and Dixit, Tanmay and Lexer, Christian and Cereghetti, Eva and Field, David},
  issn         = {1469-8137},
  journal      = {New Phytologist},
  number       = {3},
  pages        = {1035--1047},
  publisher    = {Wiley},
  title        = {{Mating system variation in hybrid zones: Facilitation, barriers and asymmetries to gene flow}},
  doi          = {10.1111/nph.16180},
  volume       = {224},
  year         = {2019},
}