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Rapid morphological divergence following a human-mediated introduction: The role of drift and directional selection

Citation

Sendell-Price, Ashley; Clegg, Kriste (2020), Rapid morphological divergence following a human-mediated introduction: The role of drift and directional selection, Dryad, Dataset, https://doi.org/10.5061/dryad.7d7wm37rm

Abstract

Theory predicts that when populations are established by few individuals, random founder effects can facilitate rapid phenotypic divergence even in the absence of selective processes. However, empirical evidence from historically documented colonisations suggest that, in most cases, drift alone is not sufficient to explain the rate of morphological divergence. Here, using the human-mediated introduction of the silvereye (Zosterops lateralis) to French Polynesia, which represents a potentially extreme example of population founding, we reassess the potential for morphological shifts to arise via drift alone. Despite only 80 years of separation from their New Zealand ancestors, French Polynesian silvereyes displayed significant changes in body and bill size and shape, most of which could be accounted for by drift, without the need to invoke selection. However, signatures of selection at genes previously identified as candidates for bill size and body shape differences in a range of bird species, also suggests a role for selective processes in driving morphological shifts within this population. Twenty-four SNPs in our RAD-Seq dataset were also found to be strongly associated with phenotypic variation. Hence, even under population founding extremes, when it is difficult to reject drift as the sole mechanism based on rate tests of phenotypic shifts, the additional role of divergent natural selection in novel environments can be revealed at the level of the genome.

Usage Notes

This dataset contains VCF files, morphological data and custom scripts required to repeat analyses conducted in Sendell-Price et al. (in press). Rapid morphological divergence following a human-mediated introduction: The role of drift and directional selection. Heredity. 

ZLat_Orientated_SNZ_FP_FullFiltered_63849SNPs.vcf
Full dataset VCF file (63,849 SNPs) mapped to the Zosterops lateralis melanops reference genome.

ZLat_Orientated_SNZ_FP_LD_Filtered_5414SNPs.vcf
SNP dataset filtered to remove one of every pair of SNPs with r2 > 0 within 100kb sliding windows and SNPs with missing data. This VCF file was used for admixture analysis. 

ZLat_Orientated_SNZ_FP_MaxMissingZero_LD_Filtered_1587SNPs.vcf
SNP dataset filtered to remove one of every pair of SNPs with r2 > 0 within 100kb sliding windows and SNPs with missing data. This VCF file was used when producing SFS for demographic analysis.

GWAS
The following files were used when preforming GWAS in GEMMA. 

  • SNZ_FP_75indv.bbgeno.gz
  • SNZ_FP_75indv.pheno
  • ZF_Pos_Map.txt
  • gemma_bslmm.sh - script to perform analyses
  • gemma_relmatrix.sh - script to produce relatedness matrix

Pairwise_VCFs
Contains VCF files used for outlier detection using PCAdapt. Each VCF contains samples from the New Zealand population plus one French Polynesian island. VCF files have been re-ordered relative to the zebra finch genome (based on output from satsuma synteny). 

Reorder_VCF
Custom scripts (plus required files) used to re-order VCF files into zebra finch chromosomes. 

Calculating_Landes_Statistic.xlsx
Excel spreadsheet containing morphological data for French Polynesian and New Zealand silvereyes. Also contains calculations of Lande’s statistic Ne* for each morphological trait.

Fastsimcoal
The following directory contains scripts and SFS required to repreform demopgraphic inference using fastsimcoal. This directory contains two sub-directories (1 per model tested).

  • Files ending .tpl - describe the model to be tested
  • Files ending .est - details prior estimates for parameters
  • Files ending .obs - 2D site frequency spectra
  • Launch_PointEstimate_Runs.sh - script used to run fastsimcoal for given model. 

 

Funding

Natural Environment Research Council

Genetics Society