Identification of ancestry informative marker (AIM) panels to assess hybridisation between feral and domestic sheep

Hybridisation of wild populations with their domestic counterparts can lead to the loss of wildtype genetic integrity, outbreeding depression, and loss of adaptive features. The Mediterranean island of Sardinia hosts one of the last extant autochthonous European mouflon (Ovis aries musimon) populations. Although conservation policies, including reintroduction plans, have been enforced to preserve Sardinian mouflon, crossbreeding with domestic sheep has been documented. We identified panels of single nucleotide polymorphisms (SNPs) that could act as ancestry informative markers able to assess admixture in feral x domestic sheep hybrids. The medium-density SNP array genotyping data of Sardinian mouflon and domestic sheep (O. aries aries) showing pure ancestry were used as references. We applied a two-step selection algorithm to this data consisting of preselection via Principal Component Analysis followed by a supervised machine learning classification method based on random forest to develop SNP panels of various sizes. We generated ancestry informative marker (AIM) panels and tested their ability to assess admixture in mouflon x domestic sheep hybrids both in simulated and real populations of known ancestry proportions. All the AIM panels recorded high correlations with the ancestry proportion computed using the full medium-density SNP array. The AIM panels proposed here may be used by conservation practitioners as diagnostic tools to exclude hybrids from reintroduction plans and improve conservation strategies for mouflon populations

Molecular characterization of the Montecristo feral goats in the Mediterranean context

The Montecristo wild goat is an endangered feral population occurring on the homonymous island in the Tuscan Archipelago since a long time. The origins of Montecristo goats are still debated, with authors dating their introduction either back to Neolithic times or between the 6th and 13th century of the Common Era. To investigate the evolutionary history and relationships of this population we assembled a 50K SNP dataset including 55 Mediterranean breeds and two nuclei of Montecristo goats sampled on the island and from an ex situ conservation project on the Italian mainland, respectively. Diversity levels, gene flow, population structure and relationships were assessed through multiple approaches. The insular population scored the lowest values of both observed and expected heterozygosity, highlighting reduced genetic variation, while the ex situ nucleus highlighted a less severe reduction. Multivariate statistics, Neighbour-network and population structure analyses clearly separated the insular nucleus from all other breeds, but also the two Montecristo populations from each other. Treemix software analysis pinpointed possible genetic inputs received by the two Montecristo goat nuclei from different sources, while Runs Of Homozygosity (ROHs) indicated an ancient bottleneck/founder effect in the insular population and recent inbreeding in the ex situ one. Overall, our results suggest that Montecristo goats experienced several demographic fluctuations combined with admixture events over time, and highlighted a noticeable differentiation between the two nuclei. This evidence can serve as a starting point to implement marker-assisted conservation plans for the endangered Montecristo feral goat

Efficient Symmetry Reduction and the Use of State Symmetries for Symbolic Model Checking

One technique to reduce the state-space explosion problem in temporal logic model checking is symmetry reduction. The combination of symmetry reduction and symbolic model checking by using BDDs suffered a long time from the prohibitively large BDD for the orbit relation. Dynamic symmetry reduction calculates representatives of equivalence classes of states dynamically and thus avoids the construction of the orbit relation. In this paper, we present a new efficient model checking algorithm based on dynamic symmetry reduction. Our experiments show that the algorithm is very fast and allows the verification of larger systems. We additionally implemented the use of state symmetries for symbolic symmetry reduction. To our knowledge we are the first who investigated state symmetries in combination with BDD based symbolic model checking

Parallelizing Deadlock Resolution in Symbolic Synthesis of Distributed Programs

Previous work has shown that there are two major complexity barriers in the synthesis of fault-tolerant distributed programs: (1) generation of fault-span, the set of states reachable in the presence of faults, and (2) resolving deadlock states, from where the program has no outgoing transitions. Of these, the former closely resembles with model checking and, hence, techniques for efficient verification are directly applicable to it. Hence, we focus on expediting the latter with the use of multi-core technology. We present two approaches for parallelization by considering different design choices. The first approach is based on the computation of equivalence classes of program transitions (called group computation) that are needed due to the issue of distribution (i.e., inability of processes to atomically read and write all program variables). We show that in most cases the speedup of this approach is close to the ideal speedup and in some cases it is superlinear. The second approach uses traditional technique of partitioning deadlock states among multiple threads. However, our experiments show that the speedup for this approach is small. Consequently, our analysis demonstrates that a simple approach of parallelizing the group computation is likely to be the effective method for using multi-core computing in the context of deadlock resolution

The SNP-Based Profiling of Montecristo Feral Goat Populations Reveals a History of Isolation, Bottlenecks, and the Effects of Management

The Montecristo wild goat is an endangered feral population that has been on the homony-mous island in the Tuscan Archipelago since ancient times. The origins of Montecristo goats are still debated, with authors dating their introduction either back to Neolithic times or between the 6th and 13th century of the Common Era. To investigate the evolutionary history and relationships of this population we assembled a 50K SNP dataset including 55 Mediterranean breeds and two nuclei of Montecristo goats sampled on the island and from an ex situ conservation project. Diversity levels, gene flow, population structure, and genetic relationships were assessed through multiple approaches. The insular population scored the lowest values of both observed and expected heterozygosity, high-lighting reduced genetic variation, while the ex situ nucleus highlighted a less severe reduction. Multivariate statistics, network, and population structure analyses clearly separated the insular nucleus from all other breeds, including the population of Montecristo goats from the mainland. Moreover, admixture and gene flow analyses pinpointed possible genetic inputs received by the two Montecristo goat nuclei from different sources, while Runs of Homozygosity (ROHs) indicated an ancient bottleneck/founder effect in the insular population and recent extensive inbreeding in the ex situ one. Overall, our results suggest that Montecristo goats experienced several demographic fluctuations combined with admixture events over time and highlighted a noticeable differentiation between the two nuclei

Runs of homozygosity in the Italian goat breeds: impact of management practices in low-input systems

Background: Climate and farming systems, several of which are considered as low-input agricultural systems, vary between goat populations from Northern and Southern Italy and have led to different management practices. These processes have impacted genome shaping in terms of inbreeding and regions under selection and resulted in differences between the northern and southern populations. Both inbreeding and signatures of selection can be pinpointed by the analysis of runs of homozygosity (ROH), which provides useful information to assist the management of this species in different rural areas. Results: We analyzed the ROH distribution and inbreeding (FROH) in 902 goats from the Italian Goat Consortium2 dataset. We evaluated the differences in individual ROH number and length between goat breeds from Northern (NRD) and Central-southern (CSD) Italy. Then, we identified the signatures of selection that differentiate these two groups using three methods: ROH, ΔROH, and averaged FST. ROH analyses showed that some Italian goat breeds have a lower inbreeding coefficient, which is attributable to their management and history. ROH are longer in breeds that are undergoing non-optimal management or with small population size. In several small breeds, the ROH length classes are balanced, reflecting more accurate mating planning. The differences in climate and management between the NRD and CSD groups have resulted in different ROH lengths and numbers: the NRD populations bred in isolated valleys present more and shorter ROH segments, while the CSD populations have fewer and longer ROH, which is likely due to the fact that they have undergone more admixture events during the horizontal transhumance practice followed by a more recent standardization. We identified four genes within signatures of selection on chromosome 11 related to fertility in the NRD group, and 23 genes on chromosomes 5 and 6 related to growth in the CSD group. Finally, we identified 17 genes on chromosome 12 related to environmental adaptation and body size with high homozygosity in both groups. Conclusions: These results show how different management practices have impacted the level of genomic inbreeding in two Italian goat groups and could be useful to assist management in a low-input system while safeguarding the diversity of small populations

Is there a best Büchi automaton for explicit model checking?

LTL to Büchi automata (BA) translators are traditionally optimized to produce automata with a small number of states or a small number of non-deterministic states. In this paper, we search for properties of Büchi automata that really influence the performance of explicit model checkers. We do that by manual analysis of several automata and by experiments with common LTL-to-BA translators and realistic verification tasks. As a result of these experiences, we gain a better insight into the characteristics of automata that work well with Spin.Překladače LTL na Büchiho automaty jsou obvykle optimalizovány tak, aby produkovaly automaty s co nejmenším počtem stavů, či s co nejmenším počtem nedeterministických stavů. V této publikaci hledáme vlastnosti Büchiho automatů, které skutečně ovlivňují výkon nástrojů pro explicitní metodu ověřování modelu (model checking). A to pomocí manuální analýzy několika automatů a experimenty s běžnými překladače LTL na automaty a realistickými verifikačními úlohami. Výsledkem těchto experimentů je lepší porozumění charakteristik automatů, které jsou dobré pro model checker Spin