10.5061/DRYAD.98SF7M0G3
Stone, Graham
0000-0002-2737-696X
University of Edinburgh
Cooper, Lisa
University of Edinburgh
Bunnefeld, Lynsey
University of Stirling
Hearn, Jack
Liverpool School of Tropical Medicine
Cook, James
Western Sydney University
Lohse, Konrad
University of Edinburgh
Data from: Low coverage genomic data resolve the population divergence and
gene flow history of an Australian rain forest fig wasp
Dryad
dataset
2020
Ficus
Pleistodontes
Natural Environment Research Council
https://ror.org/02b5d8509
NE/J010499
2020-07-07T00:00:00Z
2020-07-07T00:00:00Z
en
https://doi.org/10.1111/mec.15523
13331068 bytes
4
CC0 1.0 Universal (CC0 1.0) Public Domain Dedication
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.
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.
This folder contains: - Cooper_et_al_SI.nb the mathematica notebook used
for the blockwise analyses presented in Cooper et al 2020 -
FW_POL_387_mathematica_ready_output.txt 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 the
automation used to derive expressions for the generating function used in
Cooper_et_al_SI - twoEADnRXTsimpSortλx2N.m, twoEADnRXTsimpSortλy2N.m,
twoEnRXTsimpλxSort.m, twoEnRXTsimpλySort.m the expressions for the
generating function used in Cooper_et_al_SI -
block_cutter_vcf_contig_pos_LC.py 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