---
res:
  bibo_abstract:
  - 'Genome-scale diversity data are increasingly available in a variety of biological
    systems, and can be used to reconstruct the past evolutionary history of species
    divergence. However, extracting the full demographic information from these data
    is not trivial, and requires inferential methods that account for the diversity
    of coalescent histories throughout the genome. Here, we evaluate the potential
    and limitations of one such approach. We reexamine a well-known system of mussel
    sister species, using the joint site frequency spectrum (jSFS) of synonymousmutations
    computed either fromexome capture or RNA-seq, in an Approximate Bayesian Computation
    (ABC) framework. We first assess the best sampling strategy (number of: individuals,
    loci, and bins in the jSFS), and show that model selection is robust to variation
    in the number of individuals and loci. In contrast, different binning choices
    when summarizing the jSFS, strongly affect the results: including classes of low
    and high frequency shared polymorphisms can more effectively reveal recent migration
    events. We then take advantage of the flexibility of ABC to compare more realistic
    models of speciation, including variation in migration rates through time (i.e.,
    periodic connectivity) and across genes (i.e., genome-wide heterogeneity in migration
    rates). We show that these models were consistently selected as the most probable,
    suggesting that mussels have experienced a complex history of gene flow during
    divergence and that the species boundary is semi-permeable. Our work provides
    a comprehensive evaluation of ABC demographic inference in mussels based on the
    coding jSFS, and supplies guidelines for employing different sequencing techniques
    and sampling strategies. We emphasize, perhaps surprisingly, that inferences are
    less limited by the volume of data, than by the way in which they are analyzed.@eng'
  bibo_authorlist:
  - foaf_Person:
      foaf_givenName: Christelle
      foaf_name: Fraisse, Christelle
      foaf_surname: Fraisse
      foaf_workInfoHomepage: http://www.librecat.org/personId=32DF5794-F248-11E8-B48F-1D18A9856A87
    orcid: 0000-0001-8441-5075
  - foaf_Person:
      foaf_givenName: Camille
      foaf_name: Roux, Camille
      foaf_surname: Roux
  - foaf_Person:
      foaf_givenName: Pierre
      foaf_name: Gagnaire, Pierre
      foaf_surname: Gagnaire
  - foaf_Person:
      foaf_givenName: Jonathan
      foaf_name: Romiguier, Jonathan
      foaf_surname: Romiguier
  - foaf_Person:
      foaf_givenName: Nicolas
      foaf_name: Faivre, Nicolas
      foaf_surname: Faivre
  - foaf_Person:
      foaf_givenName: John
      foaf_name: Welch, John
      foaf_surname: Welch
  - foaf_Person:
      foaf_givenName: Nicolas
      foaf_name: Bierne, Nicolas
      foaf_surname: Bierne
  bibo_doi: 10.7717/peerj.5198
  bibo_issue: '7'
  bibo_volume: 2018
  dct_date: 2018^xs_gYear
  dct_identifier:
  - UT:000440484800002
  dct_language: eng
  dct_publisher: PeerJ@
  dct_title: 'The divergence history of European blue mussel species reconstructed
    from Approximate Bayesian Computation: The effects of sequencing techniques and
    sampling strategies@'
...