DOI: 10.5061/dryad.sf5j2bf
title: Data from: Combining landscape genomics and ecological modelling to investigate local adaptation of indigenous Ugandan cattle to East Coast fever

description: East Coast fever (ECF) is a fatal sickness affecting cattle populations of
 eastern, central, and southern Africa. The disease is transmitted by the
 tick Rhipicephalus appendiculatus, and caused by the protozoan Theileria
 parva parva, which invades host lymphocytes and promotes their clonal
 expansion. Importantly, indigenous cattle show tolerance to infection in
 ECF-endemically stable areas. Here, the putative genetic bases underlying
 ECF-tolerance were investigated using molecular data and epidemiological
 information from 823 indigenous cattle from Uganda. Vector distribution
 and host infection risk were estimated over the study area and
 subsequently tested as triggers of local adaptation by means of landscape
 genomics analysis. We identified 41 and seven candidate adaptive loci for
 tick resistance and infection tolerance, respectively. Among the genes
 associated with the candidate adaptive loci are PRKG1 and SLA2. PRKG1 was
 already described as associated with tick resistance in indigenous South
 African cattle, due to its role into inflammatory response. SLA2 is part
 of the regulatory pathways involved into lymphocytes’ proliferation.
 Additionally, local ancestry analysis suggested the zebuine origin of the
 genomic region candidate for tick resistance.
description: Landscape genomics
 datasetRaw landscape genomics
 dataset in ped/map format is provided. Instructions and ancillary files
 are provided to obtain the clean dataset described in the main
 text.Population structure
 datasetRaw population structure
 dataset in ped/map format is provided. Instructions and ancillary files
 are provided to obtain the clean dataset described in the main
 text.Rhipicephalus
 appendiculatus distribution modelData and analyses (R
 code) used to obtain the discussed Rhipicephalus appendiculatus model are
 provided. README information is provided in the
 archive.Syncerus caffer
 distribution modelData and analyses (R
 code) used to obtain the discussed Syncerus caffer model are provided.
 README information is provided in the archive.Theileria parva parva
 infection risk modelData and analyses (R
 code) used to obtain the discussed Theileria parva parva infection risk
 model are provided. README information is provided in the
 archive.Landscape genomics
 analysis input files - K3 correction - R. appendiculatus association
 studySamβada input files of
 the genotype-environment association study involving: 1) R. appendiculatus
 occurrence probability and 2) population structure predictors derived from
 the three-cluster solution of the ADMIXTURE analysis.Landscape genomics
 analysis input files - K4 correction - R. appendiculatus association
 studySamβada inputs files of
 the genotype-environment association study involving: 1) R. appendiculatus
 occurrence probability and 2) population structure predictors derived from
 the four-cluster solution of the ADMIXTURE analysis.Landscape genomics
 analysis input files - K16 correction - R. appendiculatus association
 studySamβada input files of
 the genotype-environment association study involving: 1) R. appendiculatus
 occurrence probability and 2) population structure predictors derived from
 the sixteen-cluster solution of the ADMIXTURE analysis.Landscape genomics
 analysis input files - K3 correction - T. parva parva association
 studySamβada input file of
 the genotype-environment association study involving: 1) T. parva parva
 infection risk and 2) population structure predictors derived from the
 three-cluster solution of the ADMIXTURE analysis.Landscape genomics
 analysis input files - K4 correction - T. parva parva association
 studySamβada input files of
 the genotype-environment association study involving: 1) T. parva parva
 infection risk and 2) population structure predictors derived from the
 four-cluster solution of the ADMIXTURE analysis.Landscape genomics
 analysis input files - K16 correction - T. parva parva association
 studySamβada input files of
 the genotype-environment association study involving: 1) T. parva parva
 infection risk and 2) population structure predictors derived from the
 sixteen-cluster solution of the ADMIXTURE analysis.Hereford vs. Lohani test
 - Target pop. UgandaLocal ancestry results
 for the comparison Hereford vs. Lohani are provided together with the R
 code used for beta regression analysis. Pipeline is explained in the
 README file within the archive.Hereford vs. Tharparkar
 test - Target pop. UgandaLocal ancestry results
 for the comparison Hereford vs. Tharparkar are provided together with the
 R code used for beta regression analysis. Pipeline is explained in the
 README file within the archive.Muturu vs. Lohani test -
 Target pop. UgandaLocal ancestry results
 for the comparison Muturu vs. Lohani are provided together with the R code
 used for beta regression analysis. Pipeline is explained in the README
 file within the archive.Muturu vs. Tharparkar
 test - Target pop. UgandaLocal ancestry results
 for the comparison Muturu vs. Tharparkar are provided together with the R
 code used for beta regression analysis. Pipeline is explained in the
 README file within the archive.NDVI -
 eaststm01-03Normalized Difference
 Vegetation Index (NDVI) from the MODIS collection 5 (C5) data (see S1 Text
 for explanation). Average NDVI values in East Africa in the time span
 2001-2010. Data are composed by 72 ten-day overlapping periods
 (composites), which were distributed in twelve files (eaststm_XX). Here:
 eaststm01, eaststm02, eaststm03eaststm01-03.7zNDVI - eaststm04-06Normalized Difference Vegetation Index (NDVI) from the MODIS collection 5 (C5) data (see S1 Text for explanation). Average NDVI values in East Africa in the time span 2001-2010. Data are composed by 72 ten-day overlapping periods (composites), which were distributed in twelve files (eaststm_XX). Here: eaststm04, eaststm05, eaststm06eaststm04-06.7zNDVI - eaststm07-09Normalized Difference Vegetation Index (NDVI) from the MODIS collection 5 (C5) data (see S1 Text for explanation). Average NDVI values in East Africa in the time span 2001-2010. Data are composed by 72 ten-day overlapping periods (composites), which were distributed in twelve files (eaststm_XX). Here: eaststm07, eaststm08, eaststm09eaststm07-09.7zNDVI - eaststm10-12Normalized Difference Vegetation Index (NDVI) from the MODIS collection 5 (C5) data (see S1 Text for explanation). Average NDVI values in East Africa in the time span 2001-2010. Data are composed by 72 ten-day overlapping periods (composites), which were distributed in twelve files (eaststm_XX). Here: eaststm10, eaststm11, eaststm12eaststm10-12.7zSupplementary Figure 4Additional ADMIXTURE analysis: results.