DOI: 10.5061/dryad.jm63xsjk5
title: Revisiting the multispecies coalescent model fit with an example from a complete molecular phylogeny of the Liolaemus wiegmannii species group (Squamata: Liolaemidae)

description: 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 L.
 anomalus group is inferred as the closest to the L. wiegmannii group when
 gene flow is incorporated via a Multispecies Network Coalescent model, and
 a reticulation, suggesting historical gene flow between the L. wiegmannii
 and L. montanus groups is inferred, which has not been previously
 reported. We argue that there are at least three sources of discrepancy
 between the literature and the node ages estimated in our study: the use
 of strict molecular clocks without statistical justification, misplaced
 fossil calibrations, and the estimation of coalescent times instead of
 species divergence times. We encouraged systematists to routinely test the
 fit of the MSC model when estimating species trees using sequence-based
 markers, and to follow a phylogenetic network approach when both this test
 is significant and when historical gene flow is considered one plausible
 source of the departure from the MSC model.
description: 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 <em>Liolaemus wiegmannii
 </em>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 <em>Liolaemus montanus</em> section of the
 <em>Eulaemus</em> subgenus of <em>Liolaemus</em>
 (Squamata: Liolaemidae), including all the known species/lineages of the
 <em>Liolaemus wiegmannii</em> 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 at https://github.com/arleyc/P2C2M2 and https://www.beast2.org/path-sampling/, respectively. Phylogenetic networks inference were made using a maximum pseudolikelihood approach implemented in PhyloNet 3.8.2. Networks were inferred based on Bayesian gene trees, allowing the number of reticulations (h) from 0 to 6. The nexus control file supplied in this dataset will replicate a 10 runs inference for h=2, which was the number of reticulations chosen based on a loglikelihood criteria. Alternative networks for h values different than 2 can be replicated by replacing this parameter value from the control file provided here.
description: # 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, with 10 % of burnin and using the Maximum clade credibility tree
 and Median heights options. * XML files to estimate trees for run P2C2M2
 were manually edited to BEAST 2 to save branch rate information into the
 gene trees. The XML example for running a Marginal Likelihood Estimation
 for a given gene tree-molecular clock combination was also manually
 edited, in order to run the Path Sampling analysis of the Model Selection
 package of BEAST 2 ( see
 [https://www.beast2.org/path-sampling/](https://www.beast2.org/path-sampling/) for general instructions in XML edition to run this analysis). * A control nexus file with the specifications of the maximum pseudolikelihood phylogenetic network analysis of PhyloNet 3.8.2, considering 2 reticulation events in the net, is also provided here. This file also contains the 14 gene/partition trees used for estimate the phylogenetic network. The output of this run includes estimated networks with branch information, their associated logLikelihood, and a phylogenetic Network in Dendroscope format. Runs for infer networks with different numbers of reticulations can be replicated by replacing the argument h of the PhyloNet script (which is 2 in this case). ### Data and file overview **DNA alignments in nexus format:** * `12S.nex` * `A1D.nex` * `A4B.nex` * `A9C.nex` * `A12D.nex` * `CMOS.nex` * `CYTB.nex` * `DMXL.nex` * `DNAH3.nex` * `EXPH5.nex` * `KIF24.nex` * `MXRA5.nex` * `ND4.nex` * `PNN.nex` * `PRLR.nex` * `SNCAIP.nex` **XML files for species tree estimation and divergence times**: * `2logBF.xml`: XML for estimating the species tree under the preferred combination of clock models. * `Strict.xml`: XML for estimating the species tree under a strict clock for all loci/partitions. * `RLC.xml`: XML for estimating the species tree under a Random Local Clock (RLC) for those loci in which the strict clock was rejected (based on Bayes factors). **Species trees under alternative clock model settings**: * `species_2logBF.tree`: Species tree of the *Liolaemus montanus* section of *Eulaemus* inferred under the preferred combination of molecular clock models (based on Bayes factors). * `species_Strict.tree`: Species tree of the *Liolaemus montanus* section of *Eulaemus* inferred under a strict molecular clock model for all loci/partitions. * `species_RLC.tree`: Species tree of the *Liolaemus montanus* section of *Eulaemus* inferred under a Random Local Clock (RLC) for those loci in which the strict clock was rejected (based on Bayes factors). **XML files to generate the P2C2M2's input species and gene trees files (see also [[https://github.com/arleyc/P2C2M2](https://github.com/arleyc/P2C2M2)] for instructions on how to run P2C2M2)**: * `2logBF_P2C2M2.xml`: XML for generating the input species and gene trees files under the preferred combination of clock models. * `Strict_P2C2M2.xml`: XML for generating the input species and gene trees files under a strict clock for all loci/partitions. **XML example to run a Marginal Likelihood Estimation (MLE) for a particular molecular clock model using the Path Sampling method of the Model Selection package of BEAST 2**: * `Strict_KIF24_MLE.xml`: In this example, the analysis will estimate the marginal likelihood of the Strict Molecular Clock model for the KIF24 loci. **PhyloNet nexus control files, outputs, and XML to infer gene trees**: * `Eulaemus_MPL_h2.nex`: This control file have all the specifications and input data (gene trees) to infer the 2 reticulations phylogenetic network in PhyloNet 3.8.2, using a maximum pseudolikelihood (MPL) approach. Replacing the number of reticulations (h) with values between 0 and 6 will generate the rest of the networks inferred in our original study. * `Phylonet_h2_10runs.out`: This is the resulting output of the complete run specified in the control file described above. The file contains inferred networks considering 2 reticulations, branch information included in the nets, and output in Dendroscope format, and the logLikelihood for each estimated topology. * `h2_network_dendroscope`: The preferred phylogenetic network (based on logLikelihood values) for the *Liolaemus montanus* section of *Eulaemus*. * `Gene_Trees_Net.xml`: XML for estimating the gene trees used for the species phylogenetic network inference in PhyloNet 3.8.2.