DOI: 10.5061/dryad.kkwh70s9q
title: Data for: Genomic signals of local adaptation across climatically heterogenous habitats in an invasive tropical fruit fly (Bactrocera tryoni)

description: Local adaptation plays a key role in the successful establishment of pest
 populations in new environments by enabling them to tolerate novel biotic
 and abiotic conditions experienced outside their native range. However,
 the genomic underpinnings of such adaptive responses remain unclear,
 especially for agriculturally important pests. We investigated population
 genomic signatures in the tropical/subtropical Queensland fruit fly,
 Bactrocera tryoni, which has an expanded range encompassing temperate and
 arid zones in Australia, and tropical zones in the Pacific Islands. Using
 reduced representation sequencing data from 28 populations, we detected
 allele frequency shifts associated with the native/invasive status of
 populations and identified environmental factors that have likely driven
 population differentiation. We also determined that precipitation,
 temperature, and geographic variables explain allelic shifts across the
 distribution range of B. tryoni. We found spatial heterogeneity in
 signatures of local adaptation across various climatic conditions in
 invaded areas. Specifically, disjunct invasive populations in the tropical
 Pacific Islands and arid zones of Australia were characterised by multiple
 significantly differentiated single nucleotide polymorphisms (SNPs), some
 of which were associated with genes with well-understood function in
 environmental stress (e.g., heat and desiccation) response. However,
 invasive populations in southeast Australian temperate zones showed higher
 gene flow with the native range and lacked a strong local adaptive signal.
 These results suggest that population connectivity with the native range
 has differentially affected local adaptive patterns in different invasive
 populations. Overall, our findings provide insights into the evolutionary
 underpinnings of invasion success of an important horticultural pest in
 climatically distinct environments.
description: # Data for: Genomic signals of local adaptation across climatically
 heterogenous habitats in an invasive tropical fruit fly (*Bactrocera
 tryoni*)
 [https://doi.org/10.5061/dryad.kkwh70s9q](https://doi.org/10.5061/dryad.kkwh70s9q) ## Description of the data and file structure 1\. bioclim\_minus2\.txt: Six uncorrelated bioclimatic variables \(BIO3: Isothermality; BIO5: Max Temperature of Warmest Month \- deg C; BIO8: Mean Temperature of Wettest Quarter \- deg C; BIO9: Mean Temperature of Driest Quarter \- deg C; BIO12: Annual Precipitation \- mm; BIO19: Precipitation of Coldest Quarter \- mm\) for all populations excluding Mareeba and Weipa used as input file for the GF analysis\. 2\. BayPass\_input\.geno: BayPass input file in geno format for all 28 populations\. 3\. BayPass\_nativevsAliceSprings\.ecotype: BayPass ecotype file for contrasting native populations vs\. Alice Springs\. 4\. BayPass\_nativevsExpanded\.ecotype: BayPass ecotype file for contrasting native populations vs\. southern expanded populations\. 5\. BayPass\_nativevsPacificIslands\.ecotype: BayPass ecotype file for contrasting native populations vs\. Tahiti and Loyalty islands\. 6\. BayPass\_nativevsPooled\.ecotype: BayPass ecotype file for contrasting native populations vs\. all invasive populations\. 7\. bialSNP\_MAF05\_geno\_LDdecayInput\.vcf: VCF containing SNPs filtered for biallelic markers with minimum allele frequency \(MAF\) of 0\.05 and missing data but not for linkage disequilibrium \(LD\)\. This VCF was used for LD decay analysis\. 8\. conStruct\_coordinates\_latlon\.txt: Coordinates of 301 samples in latitude and longitude format used in the conStruct analysis\. 9\. conStruct\_distances\.txt: Matrix of pairwise geographic distances between each individual used in the conStruct analysis\. 10\. conStruct\_input: Matrix of allele frequencies created using the structure2conStruct function of the R package conStruct\. 11\. EEMS\.coord: Coordinates of 301 samples used in EEMS analysis\. 12\. EEMS\.diffs: Genetic dissimilarity matrix created using the bed2diffs\_v1 R function\, used as the input file for EEMS analysis\. 13\. EEMS\.outer: Enclosed habitat polygon created using the Google Maps API v3 tool\, used for EEMS analysis\. 14\. EEMS\_params\_chain1\.ini: Parameters for the EEMS analysis\. 15\. FinalFiltered\_301samples\.vcf: Final VCF containing SNPs filtered for biallelic markers\, MAF\, missing data\, and LD\. 16\. pop\_alleleFreq\_minus2\.txt: Population allele frequencies \(excluding Mareeba and Weipa\) used as input file for the GF analysis\. 17\. population\_map\_301samples\.txt: Population information for samples\. 18\. sNMF\_input\.geno: sNMF input file\. ## Sharing/Access information No new genomic data was generated as part of this study. Raw DartSeq data was derived from the following source: * Popa-Báez Á-D, Catullo R, Lee SF, Yeap HL, Mourant RG, Frommer M, et al. (2020). Genome-wide patterns of differentiation over space and time in the Queensland fruit fly. Sci Rep 10: 10788. ## Code/Software Related scripts are available at GitHub: https://github.com/Elahep/B.tryoni\_PopGenomics