DOI: 10.5061/dryad.98sf7m0g3
title: Data from: Low coverage genomic data resolve the population divergence and gene flow history of an Australian rain forest fig wasp

description: Population divergence and gene flow are key processes in evolution and
 ecology. Model-based analysis of genome-wide datasets allows
 discrimination between alternative scenarios for these processes even in
 non-model taxa. We used two complementary approaches (one based on the
 blockwise site frequency spectrum (bSFS), the second on the Pairwise
 Sequentially Markovian Coalescent (PSMC)) to infer the divergence history
 of a fig wasp, Pleistodontes nigriventris. Pleistodontes nigriventris and
 its fig tree mutualist Ficus watkinsiana are restricted to rain forest
 patches along the eastern coast of Australia, and are separated into
 northern and southern populations by two dry forest corridors (the
 Burdekin and St. Lawrence Gaps). We generated whole genome sequence data
 for two haploid males per population and used the bSFS approach to infer
 the timing of divergence between northern and southern populations of P.
 nigriventris, and to discriminate between alternative isolation with
 migration (IM) and instantaneous admixture (ADM) models of post divergence
 gene flow. Pleistodontes nigriventris has low genetic diversity (π =
 0.0008), to our knowledge one of the lowest estimates reported for a
 sexually reproducing arthropod. We find strongest support for an ADM model
 in which the two populations diverged ca. 196kya in the late Pleistocene,
 with almost 25% of northern lineages introduced from the south during an
 admixture event ca. 57kya. This divergence history is highly concordant
 with individual population demographies inferred from each pair of haploid
 males using PSMC. Our analysis illustrates the inferences possible with
 genome-level data for small population samples of tiny, non-model
 organisms and adds to a growing body of knowledge on the population
 structure of Australian rain forest taxa.
description: Full methods and additional data summaries (including sampling
 locations and assembly summary metrics) and all cited references are
 provided in the Molecular Ecology Journal version of this paper, and also
 on BioRxiv (BIORXIV/2020/959205). The short read data and assembly for
 this analysis are deposted in the European Nucleotide Archive, Study
 PRJEB35527, available from
 https://www.ebi.ac.uk/ena/browser/view/PRJEB35527 The
 associated files are scripts and a Mathematica notebook and scripts used
 for demographic analysis using variants in genome-wide sampling of
 sequence blocks in an Australian fig wasp, Pleistodontes
 nigriventris.
description: This folder contains: -
 Cooper_et_al_SI.nb<br> the mathematica notebook used for the
 blockwise analyses presented in Cooper et al 2020 -
 FW_POL_387_mathematica_ready_output.txt<br> the blockwise summary
 used as input for the mathematica Cooper_et_al_SI.nb -
 Lohse_et_al2016_File_S1_Overview and definitions_20_11_2018.nb<br>
 the automation used to derive expressions for the generating function used
 in Cooper_et_al_SI - twoEADnRXTsimpSortλx2N.m,
 twoEADnRXTsimpSortλy2N.m, twoEnRXTsimpλxSort.m,
 twoEnRXTsimpλySort.m<br> the expressions for the generating function
 used in Cooper_et_al_SI -
 block_cutter_vcf_contig_pos_LC.py<br> the python script used to
 generate the FW_POL_387_mathematica_ready_output.txt (from the .vcf and
 bed file of Callable loci) 
 - Block_Cutter_VCF_LC_Commands.sh