Data from: A likelihood-based comparison of population histories in a parasitoid guild

Little is known about the stability of trophic relationships in complex natural communities over evolutionary timescales. Here, we use sequence data from 18 nuclear loci to reconstruct and compare the intraspecific histories of major Pleistocene refugial populations in the Middle East, the Balkans and Iberia in a guild of four Chalcid parasitoids (Cecidostiba fungosa, C. semifascia, Hobbya stenonota and Mesopolobus amaenus) all attacking Cynipid oak galls. We develop a likelihood method to numerically estimate models of divergence between three populations from multilocus data. We investigate the power of this framework on simulated data, and - using triplet alignments of intronic loci - quantify the support for all possible divergence relationships between refugial populations in the four parasitoids. Although an East to West order of population divergence has highest support in all but one species, we cannot rule out alternative population tree topologies. Comparing the estimated times of population splits between species, we find that one species, M. amaenus, has a significantly older history than the rest of the guild and must have arrived in central Europe at least one glacial cycle prior to other guild members. This suggests that although all four species may share a common origin in the East, they expanded westwards into Europe at different times.

Lohse_2012_data.tar
The python scripts polarize.py and polarizeSumStat condense a file of multiple alignmnets (fasta format) into either a list of binary alignmnets (O=ancestral, 1=derived state) or a list summary statitsics (for details see Mathematica notebook Lohse_et_al 2012_Analysis). Both are simple text files which use Mathematica's list notation. The archive Lohse_2012_data.tar contains both the python scripts and the data files for each of the four parasitoid species. These are used as input for the likelihood analysis (see in Mathematica notebook Lohse_et_al 2012_Analysis).
Lohse_et_al_2012_Analysis
Mathematica notebook implementing the likelihood calculation. The summary files provided in Lohse_2012_data.tar are used as input.

Lohse, Konrad; Barton, Nick; Stone, Graham; Melika, George (2012). Data from: A likelihood-based comparison of population histories in a parasitoid guild [Dataset]. Dryad. https://doi.org/10.5061/dryad.0g0fs