Revisiting the multispecies coalescent model fit with an example from a complete molecular phylogeny of the Liolaemus wiegmannii species group (Squamata: Liolaemidae)

Departures from the Multispecies Coalescent (MSC) assumptions could cause artefactual topologies and node heights estimates, and therefore, trees inferred without MSC model fit testing could potentially misrepresent an accurate approximation of the evolutionary history of a group. The current implementation of the MSC model testing for non-genomic level molecular markers cannot process trees estimated from BEAST 2, limiting its application for large datasets of sequence-based markers. Here we recode functions of the R package P2C2M to assess model fit to the MSC and apply this new implementation, which we named P2C2M2, to test the MSC model in a 16-loci dataset of 42 lizard species focused on the Liolaemus wiegmannii group. We found strong evidence of model departures in several loci, possibly due to historical gene flow, which could also be causing an unexpected position of the L. wiegmannii group within the L. montanus section of Eulaemus, when hybridization is not accounted for. The ..., Details on data collection and analysis can be found in the Material and Methods section of the article: Revisiting the problem of Multispecies Coalescent Model fit with an example from a complete molecular phylogeny of the Liolaemus wiegmannii species group (Squamata: Liolaemidae)
In general, the primary data available here includes DNA sequence data for 16 loci (13 nuclear loci and 3 mitochondrial) generated by Sanger sequencing. Species sampled for this dataset were focused on members of the Liolaemus montanus section of the Eulaemus subgenus of Liolaemus (Squamata: Liolaemidae), including all the known species/lineages of the Liolaemus wiegmannii group. These alignments comprise both published data from GenBank and originally generated sequences for this study.
Several XML files for replicating BEAST 2 runs are also included. XML files for infer input trees to run P2C2M2, and XML for marginal likelihood estimates were manually edited. Instructions on these editions can be found..., , # Revisiting the multispecies coalescent model fit with an example from a complete molecular phylogeny of the Liolaemus wiegmannii species group (Squamata: Liolaemidae)

[Access this dataset on Dryad](http://dx.doi.org/10.5061/dryad.jm63xsjk5)

**General information of the Dataset**

* Sequence alignments of this Dataset were generated via Sanger sequencing and include originally generated sequences for this study, as well as published data available in GenBank.
* Taxonomic Sampling was focused in the *Liolaemus montanus* section of the *Eulaemus* subgenus of *Liolaemus* (Squamata: Liolaemidae), but members of the *L. lineomaculatus* section and *Liolaemus sensu stricto* are also included.
* XML for replicating the BEAST 2 run for Species Trees estimates under different molecular clock model settings are included, as well as their respective resulting tree files after a 500 million MCMC length run. These tree files were annotated via the treeannotator Software distributed with BEAST,...,