Investigating the footprint of post-domestication dispersal on the diversity of modern European, African and Asian goats.

BACKGROUND Goats were domesticated in the Fertile Crescent about 10,000 years before present (YBP) and subsequently spread across Eurasia and Africa. This dispersal is expected to generate a gradient of declining genetic diversity with increasing distance from the areas of early livestock management. Previous studies have reported the existence of such genetic cline in European goat populations, but they were based on a limited number of microsatellite markers. Here, we have analyzed data generated by the AdaptMap project and other studies. More specifically, we have used the geographic coordinates and estimates of the observed (Ho) and expected (He) heterozygosities of 1077 European, 1187 African and 617 Asian goats belonging to 38, 43 and 22 different breeds, respectively, to find out whether genetic diversity and distance to Ganj Dareh, a Neolithic settlement in western Iran for which evidence of an early management of domestic goats has been obtained, are significantly correlated. RESULTS Principal component and ADMIXTURE analyses revealed an incomplete regional differentiation of European breeds, but two genetic clusters representing Northern Europe and the British-Irish Isles were remarkably differentiated from the remaining European populations. In African breeds, we observed five main clusters: (1) North Africa, (2) West Africa, (3) East Africa, (4) South Africa, and (5) Madagascar. Regarding Asian breeds, three well differentiated West Asian, South Asian and East Asian groups were observed. For European and Asian goats, no strong evidence of significant correlations between Ho and He and distance to Ganj Dareh was found. In contrast, in African breeds we detected a significant gradient of diversity, which decreased with distance to Ganj Dareh. CONCLUSIONS The detection of a genetic cline associated with distance to the Ganj Dareh in African but not in European or Asian goat breeds might reflect differences in the post-domestication dispersal process and subsequent migratory movements associated with the management of caprine populations from these three continents

Capturing goats: documenting two hundred years of mitochondrial DNA diversity among goat populations from Britain and Ireland

The domestic goat (Capra hircus) plays a key role in global agriculture, being especially prized in regions of marginal pasture. However, the advent of industrialized breeding has seen a dramatic reduction in genetic diversity within commercial populations, while high extinction rates among feral herds have further depleted the reservoir of genetic variation available. Here, we present the first survey of whole mitochondrial genomic variation among the modern and historical goat populations of Britain and Ireland using a combination of mtDNA enrichment and high throughput sequencing. Fifteen historical taxidermy samples, representing the indigenous 'Old Goat' populations of the islands, were sequenced alongside five modern Irish dairy goats and four feral samples from endangered populations in western Ireland. Phylogenetic and network analyses of European mitochondrial variation revealed distinct groupings dominated by historical British and Irish samples, which demonstrate a degree of maternal genetic structure between the goats of insular and continental Europe. Several Irish modern feral samples also fall within these clusters, suggesting continuity between these dwindling populations and the ancestral 'Old Goats' of Ireland and Britain

Patterns of homozygosity in insular and continental goat breeds

Genetic isolation of breeds may result in a significant loss of diversity and have consequences on health and performance. In this study, we examined the effect of geographic isolation on caprine genetic diversity patterns by genotyping 480 individuals from 25 European and African breeds with the Goat SNP50 BeadChip and comparing patterns of homozygosity of insular and nearby continental breeds. Among the breeds analysed, number and total length of ROH varied considerably and depending on breeds, ROH could cover a substantial fraction of the genome (up to 1.6 Gb in Icelandic goats). When compared with their continental counterparts, goats from Iceland, Madagascar, La Palma and Ireland (Bilberry and Arran) displayed a significant increase in ROH coverage, ROH number and F values (P value < 0.05). Goats from Mediterranean islands represent a more complex case because certain populations displayed a significantly increased level of homozygosity (e.g. Girgentana) and others did not (e.g. Corse and Sarda). Correlations of number and total length of ROH for insular goat populations with the distance between islands and the nearest continental locations revealed an effect of extremely long distances on the patterns of homozygosity. These results indicate that the effects of insularization on the patterns of homozygosity are variable. Goats raised in Madagascar, Iceland, Ireland (Bilberry and Arran) and La Palma, show high levels of homozygosity, whereas those bred in Mediterranean islands display patterns of homozygosity that are similar to those found in continental populations. These results indicate that the diversity of insular goat populations is modulated by multiple factors such as geographic distribution, population size, demographic history, trading and breed management. The online version of this article (10.1186/s12711-018-0425-7) contains supplementary material, which is available to authorized users

Large-scale silicon quantum photonics implementing arbitrary two-qubit processing

Photonics is a promising platform for implementing universal quantum information processing. Its main challenges include precise control of massive circuits of linear optical components and effective implementation of entangling operations on photons. By using large-scale silicon photonic circuits to implement an extension of the linear combination of quantum operators scheme, we realize a fully programmable two-qubit quantum processor, enabling universal two-qubit quantum information processing in optics. The quantum processor is fabricated with mature CMOS-compatible processing and comprises more than 200 photonic components. We programmed the device to implement 98 different two-qubit unitary operations ( with an average quantum process fidelity of 93.2 +/- 4.5%), a two-qubit quantum approximate optimization algorithm, and efficient simulation of Szegedy directed quantum walks. This fosters further use of the linear-combination architecture with silicon photonics for future photonic quantum processors

Towards a Quantitative Model of Mobile Phone Usage Ireland – a Preliminary Study

Mobile phone networks were traditionally voice and SMS messaging networks which made them easy to quantify and model. More recently with the advent of broadband data connections and smart phones, mobile phone networks are being used for a wide range of purposes using ever more bandwidth. This paper utilises data provided by an Irish operator to provide an initial perspective on the current uses of mobile phone networks as a within Ireland. This work serves as a precursor to the development of a quantitative model of existing behaviour which in turn will help predict future requirements

Analysing Ireland’s Interurban Communication Network using Call Data Records

This work utilises data from an Irish mobile phone network to provide a preliminary, but novel, analysis of the interurban communication network between twenty five of the largest cities and towns in Ireland. An intuitive technique is applied to a mobile phone operator’s call detail records to identify the actual subscriber population of different urban areas with various penetration rates. Weighted communication links are generated between the urban centres based on spatial and temporal metrics of distance, and are examined for different times of the day and for different days of the week. These communication links are compared to the output of a standard gravity model in order to ascertain the latter’s ability to accurately represent Ireland’s interurban communication network. The results obtained are presented and discussed within

Towards a Quantitative Model of Mobile Phone Usage Ireland – a Preliminary Study

Mobile phone networks were traditionally voice and SMS messaging networks which made them easy to quantify and model. More recently with the advent of broadband data connections and smart phones, mobile phone networks are being used for a wide range of purposes using ever more bandwidth. This paper utilises data provided by an Irish operator to provide an initial perspective on the current uses of mobile phone networks as a within Ireland. This work serves as a precursor to the development of a quantitative model of existing behaviour which in turn will help predict future requirements

Inherent Fibrin Fiber Tension Propels Mechanisms of Network Clearance During Fibrinolysis

Proper wound healing necessitates both coagulation (the formation of a blood clot) and fibrinolysis (the dissolution of a blood clot). A thrombus resistant to clot dissolution can obstruct blood flow , leading to vascular pathologies. This study seeks to understand the mechanisms by which individual fibrin fibers , the main structural component of blood clots , are cleared from a local volume during fibrinolysis. We observed 2-D fibrin networks during lysis by plasmin , recording the clearance of each individual fiber. We found that , in addition to transverse cleavage of fibers , there were multiple other pathways by which clot dissolution occurred , including fiber bundling , buckling , and collapsing. These processes are all influenced by concentration of plasmin utilized in lysis. The network fiber density influenced the kinetics and distribution of these pathways. Individual cleavage events often resulted in large morphological changes in network structure , suggesting that the inherent tension in fibers played a role in fiber clearance. Using images before and after a cleavage event to measure fiber lengths , we estimated that fibers are strained ˆ¼23% beyond their equilibrium length during polymerization. To understand the role of fiber tension in fibrinolysis we modeled network clearance under differing amounts of fiber polymerized strain (prestrain). The comparison of experimental and model data indicated that fibrin tension enables 35% more network clearance due to network rearrangements after individual cleavage events than would occur if fibers polymerized in a non-tensed state. Our results highlight many characteristics and mechanisms of fibrin breakdown , which have implications on future fibrin studies , our understanding of the fibrinolytic process , and the development of thrombolytic therapies