Biology subjects

Browett, S.

Publications and source records attributed to Browett, S..

3 recordsLinked to original sources

bioRxiv2019

A Population Genomics Analysis of the Native Irish Galway Sheep Breed

The Galway sheep population is the only native Irish sheep breed and represents an important livestock genetic resource, which is currently categorised as \"at-risk\". In the present study, comparative population genomics analyses of Galway sheep and other sheep populations of European origin were used to investigate the microevolution and recent genetic history of the breed. These analyses support the hypothesis that British Leicester sheep were used in the formation of the Galway breed and suggest more recent gene flow from the Suffolk sheep breed. When compared to conventional and endangered breeds, the Galway breed was intermediate in effective population size, genomic inbreeding and runs of homozygosity. This indicates that, although the Galway breed is declining, it is still relatively genetically diverse and that conservation and management plans informed by genomic information may aid its recovery. The Galway breed also exhibited distinct genomic signatures of artificial or natural selection when compared to other breeds, which highlighted candidate genes that may be involved in meat and wool production.

genomics↗

bioRxiv2019

Fishing for mammals: landscape-level monitoring of terrestrial and semi-aquatic communities using eDNA from lotic ecosystems

O_LIEnvironmental DNA (eDNA) metabarcoding has revolutionised biomonitoring in both marine and freshwater ecosystems. However, for semi-aquatic and terrestrial animals, the application of this technique remains relatively untested.\nC_LIO_LIWe first assess the efficiency of eDNA metabarcoding in detecting semi-aquatic and terrestrial mammals in natural lotic ecosystems in the UK by comparing sequence data recovered from water and sediment samples to the mammalian communities expected from historical data. Secondly, we evaluate the detection efficiency of eDNA samples compared to multiple conventional non-invasive survey methods (latrine surveys and camera trapping) using occupancy modelling.\nC_LIO_LIeDNA metabarcoding detected a large proportion of the expected mammalian community within each area. Common species in the areas were detected at the majority of sites. Several key species of conservation concern in the UK were detected by eDNA in areas where authenticated records do not currently exist, but potential false positives were also identified for several non-native species.\nC_LIO_LIWater-based eDNA samples provided comparable results to conventional survey methods in per unit of survey effort for three species (water vole, field vole, and red deer) using occupancy models. The comparison between survey effort to reach a detection probability of [≥]0.95 revealed that 3-6 water replicates would be equivalent to 3-5 latrine surveys and 5-30 weeks of single camera deployment, depending on the species.\nC_LIO_LISynthesis and Applications. eDNA metabarcoding represents an extremely promising tool for monitoring mammals, allowing for the detection of multiple species simultaneously, and provides comparable results to widely-used conventional survey methods. eDNA from freshwater systems delivers a terrestrial dividend by detecting both semi-aquatic and terrestrial mammalian communities, and provides a basis for future monitoring at a landscape level over larger spatial and temporal scales (i.e. long-term monitoring at national levels).\nC_LI

ecology↗

bioRxiv2017

Genomic characterisation and conservation genetics of the indigenous Irish Kerry cattle breed

Kerry cattle are an endangered landrace heritage breed of cultural importance to Ireland. In the present study we have used genome-wide SNP data (Illumina(R) BovineSNP50 array) to evaluate genomic diversity within the Kerry cattle population and between Kerry cattle and other European cattle breeds. Visualisation of patterns of genetic differentiation and gene flow among cattle breeds using phylogenetic trees with ancestry graphs highlighted, in particular, historical gene flow from the British Shorthorn breed into the ancestral population of modern Kerry cattle. Principal component analysis (PCA) and genetic clustering emphasised the genetic distinctiveness of Kerry cattle relative to comparator British and European cattle breeds. Modelling of genetic effective population size (Ne) revealed a demographic trend of diminishing Ne over time and that recent estimated Ne values for the Kerry breed may be less than the threshold for sustainable genetic conservation. In addition, analysis of genome-wide autozygosity (FROH) showed that genomic inbreeding has increased significantly during the 20 years between 1992 and 2012. Finally, signatures of selection revealed genomic regions subject to natural and artificial selection as Kerry cattle adapted to the climate, physical geography and agro-ecology of southwest Ireland.\n\nNote 1: This is an Associate Editor (D.E.M) Inaugural Article submission to Frontiers in Genetics: Livestock Genomics\n\nNote 2: British English language style preferred for publication of this article.

genomics↗