DOI: 10.5061/dryad.rfj6q57hk
title: Data from: Geographic and seasonal variation of the for gene reveal signatures of local adaptation in Drosophila melanogaster

description: In the early 1980s, the observation that Drosophila melanogaster larvae
 differed in their foraging behavior laid the foundation for the work that
 would later lead to the discovery of the foraging gene (for) and its
 associated foraging phenotypes, rover and sitter. Since then, the
 molecular characterization of the for gene and our understanding
 of the mechanisms that maintain its phenotypic variants in the laboratory
 have progressed enormously. However, the significance and dynamics of such
 variation are yet to be investigated in nature. With the advent of
 next-generation sequencing, it is now possible to identify loci underlying
 adaptation of populations in response to environmental variation. Here, I
 present results of a genotype-environment association analysis that
 quantifies variation at the for gene among samples of D. melanogaster
 structured across space and time. These samples consist of published
 genomes of adult flies collected worldwide, and at least twice per site of
 collection (during spring and fall). Both an analysis of genetic
 differentiation based on Fst values, and an analysis of population
 structure revealed an east-west gradient in allele frequency. This
 gradient may be the result of spatially varying selection driven by the
 seasonality of precipitation. These results support the hypothesis that
 different patterns of gene flow as expected under models of isolation by
 distance and potentially isolation by environment are driving genetic
 differentiation among populations. Overall, this study is essential for
 understanding the mechanisms underlying the evolution of foraging behavior
 in D. melanogaster.
description: # Geographic and seasonal variation of the for gene reveal signatures of
 local adaptation in *Drosophila melanogaster* Author: Dylan Padilla Date:
 2023-12-12 GENERAL INFORMATION 1. Title of Dataset: Data from: Geographic
 and seasonal variation of the for gene reveal signatures of local
 adaptation in *Drosophila melanogaster* 2. Author Information A. Principal
 Investigator Contact Information Name: Dylan J. Padilla Perez Institution:
 Arizona State University Address: School of Life Sciences Email:
 DATA & FILE OVERVIEW 1. Description of
 datasets The data used in this study represent a subset of a dataset
 assembled by the Drosophila Genome Nexus project (DGN), the European
 Drosophila Population Genomics Consortium (DrosEU), and the Real Time
 Evolution Consortium (DrosRTEC). This dataset is known as the Drosophila
 Evolution over Space and Time (DEST), and it is coupled with environmental
 metadata. File List: File 1 Name: samps_10Nov2020.xlx (please convert this
 file from .xlsx to .csv) Description: Environmental metadata, including
 the coordinates and bioclimatic variables recorded at the collection site
 of each pooled sample. NAs indicate missing values. Column header include
 the following variables: sampleId: identification number of the sample.
 locality: name of the locality of collection. country: name of the country
 of collection. city: name of the city of collection. collectionDate: date
 of collection. lat: latitude. long: longitude. season: either spring or
 fall. type: sequence type (e.g., pooled sequence). continent: continent of
 collection. set: entity in charge of collecting the sample. For example,
 the Drosophila Genome Nexus project (DGN), the European Drosophila
 Population Genomics Consortium (DrosEU), or the Real Time Evolution
 Consortium (DrosRTEC). nFlies: number of flies. SRA_accession: accession
 number. SRA_experiment: experiment number. Model: sequencing technology.
 collector: name of researcher who collected the sample. sampleType: where
 the sample comes from (e.g., wild). year: year of collection. yday: day of
 the year when the sample was collected. stationId: name of the station
 where the sample was collected. estimate of the frequencies of 7
 cosmopolitan inversion polymorphisms: In(2L)t, In(2R)Ns, In(3L)P, In(3R)C,
 In(3R)K, In(3R)Mo, In(3R)Payne. sex: either male of female. The metadata
 table also includes climatic variables available at WorldClim v2. Of all
 the variables included in the metadata table, only BIO15 precipitation
 seasonality (coefficient of variation), and BIO4 temperature seasonality
 (standard deviation*100) were used in the study. File 2 Name:
 dest.all.PoolSNP.001.50.10Nov2020.ann.gds Description: Genomic Data
 Structure (GDS) file containing information on variant ID, sample ID,
 Position, Allele frequency, Chromosome number, Effective coverage, and
 gene annotations. NAs indicate missing values. File 3 Name:
 gl_geno.snmfProject Description: Estimates of admixture proportion
 (Admixture analysis). File 4 Name: wc2.1_30s_bio Description: WorldClim v2
 environmental variables. In the study, only BIO15 precipitation
 seasonality (coefficient of variation), and BIO4 temperature seasonality
 (standard deviation*100) were used. File 5 Name: npp-geotiff Description:
 Data on Net Primary Production (NPP) measured in units of elemental carbon
 from the NASA Socioeconomic Data and Applications Center. File 6 Name:
 MMRR.R Description: R script for 'MMRR' function that performs
 Multiple Matrix Regression with Randomization analysis. File 7 Name:
 fly.pv1.prec.chr2.RData Description: p-value estimates from
 genotype-environment association analysis for chromosome 2L (seasonality
 of precipitation). File 8 Name: fly.pv1.temp.chr2.RData Description:
 p-value estimates from genotype-environment association analysis for
 chromosome 2L (seasonality of temperature). File 9 Name:
 fly.pv1.npp.chr2.RData Description: p-value estimates from
 genotype-environment association analysis for chromosome 2L (net primary
 production-NPP). File 10 Name: snppca_chr2.RData Description: Result of
 Principal component analysis for chromosome 2L samples. File 11 Name:
 index.html Description: Workflow of the analyses containing instructions
 on how to use the files outlined above. SHARING/ACCESS INFORMATION 1.
 Links to other publicly accessible locations of the data:
 ,
 , , . 2. Was data derived from another source? Yes. The data set used in our study is a subset of a large data base compiled by Kapun et al, 2021. SESSION INFORMATION Instrument- or software-specific information needed to interpret the data: I performed all the analyses using the free software R 4.2.2 (2022-10-31) Running under: macOS Catalina 10.15.7.