DOI: 10.5061/dryad.sj548
title: Data from: Genome-wide insights into population structure and genetic history of Tunisian local cattle using the Illumina BovineSNP50 Beadchip

description: Background: Tunisian local cattle populations are at risk of extinction as
 they were massively crossed with imported breeds. Preservation of
 indigenous livestock populations is important because each of them
 comprises a unique set of genes resulting from a local environment-driven
 selection that occurred over hundreds of years. The diversity and genetic
 structure of Tunisian local cattle populations are poorly understood.
 However, such information is crucial to the conservation and sustainable
 use of genetic resources. In addition, comparing the genomic structure of
 population sets from different parts of the world could help yield insight
 into their origin and history. In the present study, we provide a detailed
 assessment of the population structure of the three Tunisian local cattle
 populations using various methods, and we highlight their origin and
 history by investigating approximately ~38,000 SNPs in a broad panel of
 878 individuals from 37 worldwide cattle breeds representative of African,
 European and indicine populations. Results: Our study revealed a low level
 of divergence and high genetic diversity in Tunisian local cattle
 reflecting low levels of genetic drift. A Comparison with the worldwide
 cattle panel pinpointed the admixed origin of the genome of the three
 Tunisian populations with the two main European and African ancestries.
 Our results were in agreement with previous historical and archaeological
 reports about the past gene flow that existed between North African and
 South European breeds, in particular with Iberian cattle. We also detected
 a low-level indicine introgression in the three Tunisian populations and
 we inferred that indicine ancestry was inherited via African ancestors.
 Conclusions: Our results represent the first study providing genetic
 evidence about the origin and history of Tunisian local cattle. The
 information provided by the fine-scale genetic characterization of our
 study will enhance the establishment of a national conservation strategy
 for these populations. These results may enable the identification of
 genetic variants involved in adaptation to harsh environmental conditions.
description: Ben-Jemaa_data_2015.tarUnrooted Neighbor-joining treeNeighbor-joining tree relating the 877 individuals from the 37 bovine populations. The phylogenetic tree was computed using 38597 SNPs. The genetic distance between each pair of individuals was estimated from the number of loci for which they differ.Unrooted_NJ_tree.pdfNeighborNet graph based on Nei genetic distanceNeighborNet graph based on Nei genetic distance of 37 bovine populations. Breeds belonging to one of the three types :African, European and Zebu, were grouped together. Sets of parallel edges (reticulations) on the NeighborNet graph observed between populations indicate past hybridization events.Population_NeighborNet_graph.pdfMaximum likelihood tree with no migration eventsMaximum likelihood tree inferred from a subset of 13 cattle populations when no migration edges were fit. Nelore breed (NEL) was set as a rooting outgroup. The scale bar shows 10 times the average standard error of the estimated entries in the sample covariance matrix.ML_Tree_No_migration_events.pdfMaximum likelihood tree with eight migration eventsMaximum likelihood phylogenetic network inferred from a subset of 13 populations. Migration events (modeled as arrows) were added sequentially up to eight migrations. Migration arrows are colored according to their weight. The scale bar shows 10 times the average standard error of the estimated entries in the sample covariance matrix.ML_tree_8_migration_events.pdf