Whole-genome sequencing projects are increasingly populating the tree of life and characterizing biodiversity1–4. Sparse taxon sampling has previously been proposed to confound phylogenetic inference5, and captures only a fraction of the genomic diversity. Here we report a substantial step towards the dense representation of avian phylogenetic and molecular diversity, by analysing 363 genomes from 92.4% of bird families—including 267 newly sequenced genomes produced for phase II of the Bird 10,000 Genomes (B10K) Project. We use this comparative genome dataset in combination with a pipeline that leverages a reference-free whole-genome alignment to identify orthologous regions in greater numbers than has previously been possible and to recognize genomic novelties in particular bird lineages. The densely sampled alignment provides a single-base-pair map of selection, has more than doubled the fraction of bases that are confidently predicted to be under conservation and reveals extensive patterns of weak selection in predominantly non-coding DNA. Our results demonstrate that increasing the diversity of genomes used in comparative studies can reveal more shared and lineage-specific variation, and improve the investigation of genomic characteristics. We anticipate that this genomic resource will offer new perspectives on evolutionary processes in cross-species comparative analyses and assist in efforts to conserve species.

The Angora goat populations in Argentina (AR), France (FR) and South Africa (SA) have been kept geographically and genetically distinct. Due to country-specific selection and breeding strategies, there is a need to characterize the populations on a genetic level. In this study we analysed genetic variability of Angora goats from three distinct geographical regions using the standardized 50k Goat SNP Chip. A total of 104 goats (AR: 30; FR: 26; SA: 48) were genotyped. Heterozygosity values as well as inbreeding coefficients across all autosomes per population were calculated. Diversity, as measured by expected heterozygosity (HE) ranged from 0.371 in the SA population to 0.397 in the AR population. The SA goats were the only population with a positive average inbreeding coefficient value of 0.009. After merging the three datasets, standard QC and LD-pruning, 15 105 SNPs remained for further analyses. Principal component and clustering analyses were used to visualize individual relationships within and between populations. All SA Angora goats were separated from the others and formed a well-defined, unique cluster, while outliers were identified in the FR and AR breeds. Apparent admixture between the AR and FR populations was observed, while both these populations showed signs of having some common ancestry with the SA goats. LD averaged over adjacent loci within the three populations per chromosome were calculated. The highest LD values estimated across populations were observed in the shorter intervals across populations. The Ne for the Angora breed was estimated to be 149 animals ten generations ago indicating a declining trend. Results confirmed that geographic isolation and different selection strategies caused genetic distinctiveness between the populations.

The Nguni cattle breed is a landrace breed adapted to different ecological regions of South Africa. A number of ecotypes are recognised based on phenotype within the breed, but it is not known if they are genetically distinct. In this study molecular characterization was performed on Makhathini (MAK), Pedi (PED), Shangaan (SHA) and Venda (VEN) Nguni cattle ecotypes. Two Nguni cattle populations, not kept as separate ecotypes, from University of Fort Hare (UFH) and Agricultural Research Council Loskop South farm (LOS) were also included. Genotypic data was generated for 189 unrelated Nguni cattle selected based on pedigree records using 22 microsatellite markers. The expected heterozygosity values varied from 69% (UFH) to 72% PED with a mean number of alleles ranging from 6.0 to 6.9. The F ST estimate demonstrated that 4.8% of the total genetic variation was due to the genetic differentiation between the populations and 92.2% accounted for differences within the populations. The genetic distances and structure analysis revealed the closest relationship between MAK, PEDI and SHA ecotypes, followed by SHA and VEN. The UFH population clustered with the MAK ecotype, indicating that they are more genetically similar, while the LOS cattle grouped as a distinct cluster. Results suggest that the genetic differentiation between the PED and SHA ecotypes is low and can be regarded as one ecotype based on 2 limited genetic differences. The results of this study can be applied as a point of reference for further genetic studies towards conservation of Nguni cattle ecotypes.

The Namaqua Afrikaner is an endangered sheep breed indigenous to South Africa, primarily used in smallholder farming systems. Genetic characterisation is essential for the breed's conservation and utilization. In this study a genetic characterisation was performed on 144 Namaqua Afrikaner sheep kept at the Karakul Experimental Station (KES), Carnarvon Experimental Station (CES) and a private farm Welgeluk (WGK) using 22 microsatellite markers. The mean number of alleles observed was low (3.7 for KES, 3.9 for CES, 4.2 for WGK). Expected Heterozygosity values across loci ranged between 46% for WGK, 48% for KES and 55% for CES, indicating low to moderate genetic variation. The AMOVA analyses revealed that 89.5% of the genetic variation was due to differences within populations. The population structure confirmed the differentiation of three clusters with high relationships between the CES and WGK populations. In the population structure comparison with Pedi and SA Mutton Merino sheep, limited hybridization between the Namaqua Afrikaner sheep and both of these breeds were observed. The results of this study will serve as a reference for genetic management and conservation of Namaqua Afrikaner sheep.

Goats (Capra aegagrus hircus) have not been a prioritized livestock species with regards to molecular research. The genetic characterization of commercial South African (SA) goat breeds should contribute to improving the management of available animal genetic resources. The aim of this study was to investigate genetic diversity within and among SA commercial goat breeds utilizing the 50k goat beadchip. 88 goats originating from four breeds (dairy: British Alpine, Saanen, Toggenburg; fibre: Angora) were genotyped with the goat SNP50 beadchip. Average MAF values ranged from 0.25 for the Angora to 0.29 for the Saanen, with 46 983 and 50 368 polymorphic SNPs obtained for the respective breeds. Observed heterozygosity values ranged from 0.365 for the Angora to 0.431 for the Toggenburg breed. Linkage disequilibrium (LD) estimation revealed average r 2 values of 0.12 and 0.15 for dairy and fibre breeds, respectively. LD decay was shown to occur after a distance interval of 20-40kb and 40-60kb for dairy and Angora breeds, respectively. Principal component analysis (PCA) produced clusters corresponding to the different production types (dairy and fibre). The Angora, British Alpine and Saanen breeds showed high proportions of membership to respective inferred ancestral populations with ADMIXTURE (97%, 84% and 92%, respectively). The results obtained in this study indicated genetic uniformity within dairy and fibre goats due to productionspecific trait selection. Sufficient levels of genetic variation was, however, observed to allow genetic progress for SA commercial goat breeds pending the improved management of these goat genetic resources.