Data from: Low coverage genomic data resolve the population divergence and gene flow history of an Australian rain forest fig wasp
Data files
Jul 07, 2020 version files 13.33 MB
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block_cutter_vcf_contig_pos_LC.py
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Block_Cutter_VCF_LC_Commands.sh
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Cooper_et_al_SI.nb
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Cooper_et_al_SI.pdf
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FW_POL_387_mathematica_ready_output.txt
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Lohse_et_al2016_File_S1_Overview_and_definitions_20_11_2018.nb
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README.txt
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twoEADnRXTsimpSortλx2N.m
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twoEADnRXTsimpSortλy2N.m
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twoEnRXTsimpλxSort.m
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twoEnRXTsimpλySort.m
Abstract
Methods
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.
Usage notes
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