Estimates Of Relatedness Research Articles

PATRIOT: A Pipeline for Tracing Identity-by-Descent for Chromosome Segments to Improve Genomic Prediction in Self-Pollinating Crop Species.

The lowering genotyping cost is ushering in a wider interest and adoption of genomic prediction and selection in plant breeding programs worldwide. However, improper conflation of historical and recent linkage disequilibrium between markers and genes restricts high accuracy of genomic prediction (GP). Multiple ancestors may share a common haplotype surrounding a gene, without sharing the same allele of that gene. This prevents parsing out genetic effects associated with the underlying allele of that gene among the set of ancestral haplotypes. We present “Parental Allele Tracing, Recombination Identification, and Optimal predicTion” (i.e., PATRIOT) approach that utilizes marker data to allow for a rapid identification of lines carrying specific alleles, increases the accuracy of genomic relatedness and diversity estimates, and improves genomic prediction. Leveraging identity-by-descent relationships, PATRIOT showed an improvement in GP accuracy by 16.6% relative to the traditional rrBLUP method. This approach will help to increase the rate of genetic gain and allow available information to be more effectively utilized within breeding programs.

Pseudomonas Phage MD8: Genetic Mosaicism and Challenges of Taxonomic Classification of Lambdoid Bacteriophages.

Pseudomonas phage MD8 is a temperate phage isolated from the freshwater lake Baikal. The organisation of the MD8 genome resembles the genomes of lambdoid bacteriophages. However, MD8 gene and protein sequences have little in common with classified representatives of lambda-like phages. Analysis of phage genomes revealed a group of other Pseudomonas phages related to phage MD8 and the genomic layout of MD8-like phages indicated extensive gene exchange involving even the most conservative proteins and leading to a high degree of genomic mosaicism. Multiple horizontal transfers and mosaicism of the genome of MD8, related phages and other λ-like phages raise questions about the principles of taxonomic classification of the representatives of this voluminous phage group. Comparison and analysis of various bioinformatic approaches applied to λ-like phage genomes demonstrated different efficiency and contradictory results in the estimation of genomic similarity and relatedness. However, we were able to make suggestions for the possible origin of the MD8 genome and the basic principles for the taxonomic classification of lambdoid phages. The group comprising 26 MD8-related phages was proposed to classify as two close genera belonging to a big family of λ-like phages.

Genetic diversity and structure in Arizona pronghorn following conservation efforts

AbstractArizona pronghorn (Antilocapra americana) population numbers have declined over the last century due to unregulated‐harvest, population fragmentation, urban expansion, and habitat loss. Captive breeding, reintroductions, and translocations have helped to curb decline and boost population numbers of the endangered Sonoran subspecies (A. a. sonoriensis). To assess the effect of on‐going management actions on the Sonoran subspecies, we collected multi‐locus genotype data and performed tests of genetic differentiation and population structure in comparison to the non‐endangered American subspecies (A. a. americana). We provide updated estimates of genetic diversity and relatedness to serve as a benchmark for future management toward further recovery of Sonoran pronghorn. Management actions have upheld distinction between the two subspecies in Arizona and stemmed further genetic diversity loss while avoiding an increase in inbreeding within the captive‐bred Sonoran population.

Genetic diversity and relatedness inferred from microsatellite loci as a tool for broodstock management of fine flounder Paralichthys adspersus

Paralichthys adspersus is a native species from the Pacific coast of South America that is of great economic importance for Peruvian aquaculture. Even though establishing sustainable farming depends on avoiding irreversible damage to the population gene pool due to processes such as inbreeding, studies focusing on genetically characterizing farmed stocks are yet to be documented. By using ten microsatellite loci on captive and wild individuals of P. adspersus, we successfully characterized the only commercial broodstock of this species in Peru by means of determining the genetic diversity and inferring relatedness. Although most microsatellite loci showed deviations from Hardy-Weinberg equilibrium, the genetic diversity levels in the commercial broodstock were considered healthy compared to those obtained for a wild population, with an average number of alleles of 17.40, an effective number of alleles of 9.14, and an observed and expected heterozygosity of 0.49 and 0.87. No significant differences between the broodstock and the wild population in terms of genetic diversity were observed. The fixation index and analysis of molecular variance also indicated a low rate of differentiation between both populations. In relatedness estimation, the analysis based on five method-of-moment estimators and a maximum-likelihood estimator showed the category “unrelated” as being the most probable relationship among the individuals within the commercial broodstock. Our findings reveal the conservation of genetic diversity in this population and outline potential breeding strategies that hatchery managers could use to minimize the loss of genetic diversity and long-term inbreeding. This could help establish proper genetic management in captive populations of P. adspersus and should apply to other captive stocks where pedigree information is lacking.

The Use of “Genotyping-by-Sequencing” to Recover Shared Genealogy in Genetically Diverse Eucalyptus Populations

The recovery of genealogy in both natural and captive populations is critical for any decision in the management of genetic resources. It allows for the estimation of genetic parameters such as heritability and genetic correlations, as well as defining an optimal mating design that maintains a large effective population size. We utilised “genotyping-by-sequencing” (GBS) in combination with bioinformatics tools developed specifically for GBS data to recover genetic relatedness, with a focus on parent-offspring relationships in a Eucalyptus nitens breeding population as well as recognition of individuals representing other Eucalyptus species and putative hybrids. We found a clear advantage on using tools specifically designed for data of highly variable sequencing quality when recovering genetic relatedness. The parent-offspring relatedness showed a significant response to data filtering from 0.05 to 0.3 when the standard approach (G1) was used, while it oscillated around 0.4 when the specifically designed method (G5) was implemented. Additionally, comparisons with commonly used tools demonstrated vulnerability of the relatedness estimates to incorrect imputation of missing data when shallow sequencing information and genetically distant individuals are present in the population. In turn, these biased imputed genotypes negatively affected the estimation of genetic relatedness between parents and offspring. Careful filtering for both genetic outliers and shallowly sequenced markers led to improvements in estimations of genetic relatedness. Alternatively, a method that avoided missing data imputation and took sequence depth into consideration improved the accuracy of parent-offspring relationship coefficients where sequencing data quality was highly variable.

Toward Unifying Evolutionary Ecology and Genomics to Understand Positive Plant-Plant Interactions Within Wild Species.

In a local environment, plant networks include interactions among individuals of different species and among genotypes of the same species. While interspecific interactions are recognized as main drivers of plant community patterns, intraspecific interactions have recently gained attention in explaining plant community dynamics. However, an overview of intraspecific genotype-by-genotype interaction patterns within wild plant species is still missing. From the literature, we identified 91 experiments that were mainly designed to investigate the presence of positive interactions based on two contrasting hypotheses. Kin selection theory predicts partisan help given to a genealogical relative. The rationale behind this hypothesis relies on kin/non-kin recognition, with the positive outcome of kin cooperation substantiating it. On the other hand, the elbow-room hypothesis supports intraspecific niche partitioning leading to positive outcome when genetically distant genotypes interact. Positive diversity-productivity relationship rationalizes this hypothesis, notably with the outcome of overyielding. We found that both these hypotheses have been highly supported in experimental studies despite their opposite predictions between the extent of genetic relatedness among neighbors and the level of positive interactions. Interestingly, we identified a highly significant effect of breeding system, with a high proportion of selfing species associated with the presence of kin cooperation. Nonetheless, we identified several shortcomings regardless of the species considered, such as the lack of a reliable estimate of genetic relatedness among genotypes and ecological characterization of the natural habitats from which genotypes were collected, thereby impeding the identification of selective drivers of positive interactions. We therefore propose a framework combining evolutionary ecology and genomics to establish the eco-genomic landscape of positive GxG interactions in wild plant species.

Parentage Analysis in Giant Grouper (Epinephelus lanceolatus) Using Microsatellite and SNP Markers from Genotyping-by-Sequencing Data.

Pedigree information is necessary for the maintenance of diversity for wild and captive populations. Accurate pedigree is determined by molecular marker-based parentage analysis, which may be influenced by the polymorphism and number of markers, integrity of samples, relatedness of parents, or different analysis programs. Here, we described the first development of 208 single nucleotide polymorphisms (SNPs) and 11 microsatellites for giant grouper (Epinephelus lanceolatus) taking advantage of Genotyping-by-sequencing (GBS), and compared the power of SNPs and microsatellites for parentage and relatedness analysis, based on a mixed family composed of 4 candidate females, 4 candidate males and 289 offspring. CERVUS, PAPA and COLONY were used for mutually verification. We found that SNPs had a better potential for relatedness estimation, exclusion of non-parentage and individual identification than microsatellites, and > 98% accuracy of parentage assignment could be achieved by 100 polymorphic SNPs (MAF cut-off < 0.4) or 10 polymorphic microsatellites (mean Ho = 0.821, mean PIC = 0.651). This study provides a reference for the development of molecular markers for parentage analysis taking advantage of next-generation sequencing, and contributes to the molecular breeding, fishery management and population conservation.

NGSremix: a software tool for estimating pairwise relatedness between admixed individuals from next-generation sequencing data.

Estimation of relatedness between pairs of individuals is important in many genetic research areas. When estimating relatedness, it is important to account for admixture if this is present. However, the methods that can account for admixture are all based on genotype data as input, which is a problem for low-depth next-generation sequencing (NGS) data from which genotypes are called with high uncertainty. Here, we present a software tool, NGSremix, for maximum likelihood estimation of relatedness between pairs of admixed individuals from low-depth NGS data, which takes the uncertainty of the genotypes into account via genotype likelihoods. Using both simulated and real NGS data for admixed individuals with an average depth of 4x or below we show that our method works well and clearly outperforms all the commonly used state-of-the-art relatedness estimation methods PLINK, KING, relateAdmix, and ngsRelate that all perform quite poorly. Hence, NGSremix is a useful new tool for estimating relatedness in admixed populations from low-depth NGS data. NGSremix is implemented in C/C++ in a multi-threaded software and is freely available on Github https://github.com/KHanghoj/NGSremix.

Population structure and genetic diversity of the Pee Dee cotton breeding program.

Accelerated marker-assisted selection and genomic selection breeding systems require genotyping data to select the best parents for combining beneficial traits. Since 1935, the Pee Dee (PD) cotton germplasm enhancement program has developed an important genetic resource for upland cotton (Gossypium hirsutum L.), contributing alleles for improved fiber quality, agronomic performance, and genetic diversity. To date, a detailed genetic survey of the program's eight historical breeding cycles has yet to be undertaken. The objectives of this study were to evaluate genetic diversity across and within-breeding groups, examine population structure, and contextualize these findings relative to the global upland cotton gene pool. The CottonSNP63K array was used to identify 17,441 polymorphic markers in a panel of 114 diverse PD genotypes. A subset of 4597 markers was selected to decrease marker density bias. Identity-by-state pairwise distance varied substantially, ranging from 0.55 to 0.97. Pedigree-based estimates of relatedness were not very predictive of observed genetic similarities. Few rare alleles were present, with 99.1% of SNP alleles appearing within the first four breeding cycles. Population structure analysis with principal component analysis, discriminant analysis of principal components, fastSTRUCTURE, and a phylogenetic approach revealed an admixed population with moderate substructure. A small core collection (n &lt; 20) captured 99% of the program's allelic diversity. Allele frequency analysis indicated potential selection signatures associated with stress resistance and fiber cell growth. The results of this study will steer future utilization of the program's germplasm resources and aid in combining program-specific beneficial alleles and maintaining genetic diversity.

Population structure and relatedness estimates in a Mexican sample.

Population stratification (PS) is a confounding factor in genome-wide association studies (GWASs) and also an interesting process itself. Latin American populations have mixed genetic ancestry, which may account for PS. We have analyzed the relatedness, by means of the identity-by-descent (IBD) estimations, in a sample of 1805 individuals and 1.006.703 autosomal mutations from a case-control study of colorectal cancer in Mexico. When using the recommended protocol for quality control assessment, 402 should have been removed due to relatedness. Our purpose was to analyze this value in the context of an admixed population. For that aim, we reanalyzed the sample using two software designed for admixed populations, obtaining estimates of 110 and 70 related individuals to remove. The results showed that the first estimation of relatedness was an effect of the higher Native American contribution in part of the data samples, being a confounding factor for IBD estimations. We conclude in the importance of considering PS and genetic ancestry in order to avoid spurious results, not only in GWAS but also in relatedness analysis.

Strandings provide insight into social group structure of Atlantic white‐sided dolphins

AbstractAtlantic white‐sided dolphins (Lagenorhynchus acutus) are highly social odontocetes with a poorly understood tendency to mass strand. With limited capacity to study social ecology in the open ocean, mass strandings provide an opportunity to improve our understanding of group structure. Our study of 32 mass stranding events that occurred on Cape Cod, Massachusetts, between 1999 and 2009 identifies aspects of social ecology that vary across the year. A greater number of mass stranding events occurred outside of the breeding season and there was evidence of age‐structuring during the breeding season. We find generally low average intragroup pairwise relatedness assessed across eight microsatellite loci in a subset of 16 mass stranding events. Mass stranded groups do not show higher than expected relatedness when compared to a baseline estimate derived from single‐stranded individuals. Overall, our integration of genetic estimates of relatedness with data on sex and maturity‐class from stranded specimens suggests that Atlantic white‐sided dolphins fall near the more fluid end of the continuum from short‐term, highly fluid social associations to long‐term, stable groups represented among the odontocetes. Despite their tendency to mass strand, stable, kin‐based associations are not a defining feature of social group structure in this species.

Kin structure and roost fidelity in greater noctule bats

Roost fidelity is an important aspect of mammalian biology. Studying the mechanisms underlying philopatry can help us understand a species’ energetic requirements, ecological constraints and social organisation. Temperate bat species notably exhibit a high degree of female philopatry considering their size, resulting in maternity colonies segregated at the mitochondrial level. We focus on the greater noctule, Nyctalus lasiopterus, to study this behaviour in more depth. We make use of microsatellite data for 11 markers across 84 individuals residing in Maria Luisa Park in Seville, Spain. At the time of sampling this urban park boasted the highest number of bats of any known colony of this species, among which three social groups were observed to segregate spatially. We studied the distribution of pairs of individuals across filial relationship categories and relatedness estimates relative to the social group of each individual. This analysis was complemented by information on roost-use frequency among a subset of genotyped bats. We found no significant relationship between roost use and genetic distance, but there was evidence that more closely related bats are more likely to be found in the same social group. Mother-daughter pairs shared the same group more often than expected, as did pairs of individuals of relatedness above 0.43. We discuss the implications of these results in terms of the behavioural ecology of temperate bats and for conservation efforts aimed at preserving them.

Moving far, staying close: red fox dispersal patterns revealed by SNP genotyping

The genetic structure of a population can provide important insights into animal movements at varying geographical scales. Individual and social behaviors, such as philopatry and dispersal, affect patterns of relatedness, age and sex structure, shaping the local genetic structure of populations. However, these fine scale patterns may not be detected within broader population genetic structure. Using SNP genotyping for pairwise relatedness estimates, we investigated the spatial and genetic structuring of 141 red foxes within south-central Sweden at two scales. First, we looked at broad scale population structuring among red foxes at the regional level. We then estimated pairwise relatedness values to evaluate the spatial and genetic structure of male, female and mixed sex pairs for patterns of philopatry and dispersal at a more localized scale. We found limited genetic differentiation at the regional scale. However, local investigations revealed patterns of female philopatry and male biased dispersal. There were significant differences in pairwise geographic distances between highly related same sex pairs with the average distance between related males, 37.8 km, being six times farther than that of related females, averaging 6.3 km. In summary, the low levels of genetic differentiation found in this study illustrates the mobility and dispersal ability of red foxes across scales. However, relatedness plays a strong role in the spatial organization of red foxes locally, ultimately contributing to male biased dispersal patterns.

Pedigree reconstruction and distant pairwise relatedness estimation from genome sequence data: A demonstration in a population of rhesus macaques (Macaca mulatta).

A primary challenge in the analysis of free‐ranging animal populations is the accurate estimation of relatedness among individuals. Many aspects of population analysis rely on knowledge of relatedness patterns, including socioecology, demography, heritability and gene mapping analyses, wildlife conservation and the management of breeding colonies. Methods for determining relatedness using genome‐wide data have improved our ability to determine kinship and reconstruct pedigrees in humans. However, methods for reconstructing complex pedigree structures and estimating distant relatedness (beyond third‐degree) have not been widely applied to other species. We sequenced the genomes of 150 male rhesus macaques from the Tulane National Primate Research Center colony to estimate pairwise relatedness, reconstruct closely related pedigrees, estimate more distant relationships and augment colony records. Methods for determining relatedness developed for human genetic data were applied and evaluated in the analysis of nonhuman primates, including identity‐by‐descent‐based methods for pedigree reconstruction and shared segment‐based inference of more distant relatedness. We compared the genotype‐based pedigrees and estimated relationships to available colony pedigree records and found high concordance (95.5% agreement) between expected and identified relationships for close relatives. In addition, we detected distant relationships not captured in colony records, including some as distant as twelfth‐degree. Furthermore, while deep sequence coverage is preferable, we show that this approach can also provide valuable information when only low‐coverage (5×) sequence data is available. Our findings demonstrate the value of these methods for determination of relatedness in various animal populations, with diverse applications to conservation biology, evolutionary and ecological research and biomedical studies.

Estimation of Molecular Pairwise Relatedness in Autopolyploid Crops.

A suitable pairwise relatedness estimation is key to genetic studies. Several methods are proposed to compute relatedness in autopolyploids based on molecular data. However, unlike diploids, autopolyploids still need further studies considering scenarios with many linked molecular markers with known dosage. In this study, we provide guidelines for plant geneticists and breeders to access trustworthy pairwise relatedness estimates. To this end, we simulated populations considering different ploidy levels, meiotic pairings patterns, number of loci and alleles, and inbreeding levels. Analysis were performed to access the accuracy of distinct methods and to demonstrate the usefulness of molecular marker in practical situations. Overall, our results suggest that at least 100 effective biallelic molecular markers are required to have good pairwise relatedness estimation if methods based on correlation is used. For this number of loci, current methods based on multiallelic markers show lower performance than biallelic ones. To estimate relatedness in cases of inbreeding or close relationships (as parent-offspring, full-sibs, or half-sibs) is more challenging. Methods to estimate pairwise relatedness based on molecular markers, for different ploidy levels or pedigrees were implemented in the AGHmatrix R package.

Identity-by-descent with uncertainty characterises connectivity of Plasmodium falciparum populations on the Colombian-Pacific coast.

Characterising connectivity between geographically separated biological populations is a common goal in many fields. Recent approaches to understanding connectivity between malaria parasite populations, with implications for disease control efforts, have used estimates of relatedness based on identity-by-descent (IBD). However, uncertainty around estimated relatedness has not been accounted for. IBD-based relatedness estimates with uncertainty were computed for pairs of monoclonal Plasmodium falciparum samples collected from five cities on the Colombian-Pacific coast where long-term clonal propagation of P. falciparum is frequent. The cities include two official ports, Buenaventura and Tumaco, that are separated geographically but connected by frequent marine traffic. Fractions of highly-related sample pairs (whose classification using a threshold accounts for uncertainty) were greater within cities versus between. However, based on both highly-related fractions and on a threshold-free approach (Wasserstein distances between parasite populations) connectivity between Buenaventura and Tumaco was disproportionally high. Buenaventura-Tumaco connectivity was consistent with transmission events involving parasites from five clonal components (groups of statistically indistinguishable parasites identified under a graph theoretic framework). To conclude, P. falciparum population connectivity on the Colombian-Pacific coast abides by accessibility not isolation-by-distance, potentially implicating marine traffic in malaria transmission with opportunities for targeted intervention. Further investigations are required to test this hypothesis. For the first time in malaria epidemiology (and to our knowledge in ecological and epidemiological studies more generally), we account for uncertainty around estimated relatedness (an important consideration for studies that plan to use genotype versus whole genome sequence data to estimate IBD-based relatedness); we also use threshold-free methods to compare parasite populations and identify clonal components. Threshold-free methods are especially important in analyses of malaria parasites and other recombining organisms with mixed mating systems where thresholds do not have clear interpretation (e.g. due to clonal propagation) and thus undermine the cross-comparison of studies.

Precise natal homing and an estimate of age at sexual maturity in hawksbill turtles

AbstractThe geographic specificity of natal philopatry (how precisely breeding individuals return to their natal origins) influences breeding biology, genetic diversity and habitat range, and therefore has important implications for species resiliency and management. Also, the age at which individuals reach sexual maturity and enter the breeding population is a vital parameter for demographic analyses. Empirical research on philopatry and maturation, however, is challenging for long‐lived animals that are difficult to observe, such as marine turtles that have complex oceanic life histories. Regional natal philopatry is well established for marine turtles, but the geographic specificity of philopatry is unclear. Similarly, estimates of age at maturity vary widely, and direct evidence is lacking. Here, we targeted these information gaps by assessing kinship among 256 females from Antigua’s Jumby Bay (JB) hawksbill turtle rookery, a population with demonstrated nest‐site fidelity and neophyte assimilation. We estimated mother–daughter and full sibling relationships with a maximum‐likelihood full‐pedigree reconstruction approach, incorporating genotypic (12 microsatellites), maternal genealogy (mitochondrial DNA) and age structure (long‐term mark–recapture) data. We validated relationships with parentage assignment and pairwise relatedness estimators. Fourteen veteran nesters were the mothers of 42 younger nesters, and 94 nesters formed 35 full sibships. Time between the first nesting records of mothers and their daughters indicated maximum time to maturity as short as 14 years in Caribbean hawksbills. Thirteen of the 14 mothers showed consistently high fidelity to JB for two decades, providing compelling evidence that 41 of these daughters originated from JB nests and returned to this 1‐km‐long natal site to breed. Rookeries with strongly philopatric individuals might have limited colonization potential and be at a disadvantage in the event of habitat loss. This study demonstrates the utility of long‐term mark–recapture data in kinship analyses for answering questions relevant to endangered species conservation.

Democratizing Sequencing for Infection Control: A Scalable, Automated Pipeline for WGS Analysis for Outbreak Detection

Background: Whole-genome sequencing (WGS) is well established as a high-resolution method for measuring bacterial relatedness to better understand infection transmission in cases of healthcare-associated infections (HAIs). However, sequencing is still rarely used in HAI investigations due to a lack of access to computational analysis platforms with actionable turnaround times. Single-nucleotide polymorphism (SNP) analysis is typically used to determine bacterial relatedness. However, SNP-based methods often require a suite of bioinformatics tools that can be difficult to use and interpret without the expertise of a trained computational biologist. These obstacles become more significant in the case of prospective, real-time surveillance of HAIs, which can require the analysis of a large number of isolates. To enable the use of WGS for proactive determination of infection outbreaks, a rapid, automated method that can scale to large data sets is needed. Methods: Here, we demonstrate the capabilities of ksim, a novel automated algorithm to determine the clonality of bacterial samples using WGS. ksim measures the number of shared kmers (genomic subsequences of length k) between bacterial samples to determine their relatedness. ksim also filters out accessory genomic regions, such as plasmids, that can confound genetic relatedness estimates. We benchmarked the accuracy and speed of ksim relative to an SNP-based pipeline on simulated data sets (with sequencing reads generated in silico) and on 9 clinical-cluster data sets (6 publicly available and 3 real-time data sets from Massachusetts General Hospital [MGH]). We also used ksim to determine the relatedness of &gt;5,000 historical clinical bacterial isolates from MGH, collected between 2015 and 2019. Results: ksim first preprocesses raw sequencing data to generate a common data structure, after which it computes the genomic distance between bacterial samples in ∼0.2 seconds in simple cases and in ∼4 seconds in complex cases when accessory genome filtering is required. In simulations across 5 species, ksim determined clonality (defined as &lt;40 SNPs) with high accuracy (sensitivity, 99.7% and specificity, 99.6%). ksim performance on 9 clinical HAI data sets demonstrated its sensitivity (99.4%) and specificity (90.8%) compared to an SNP-based pipeline. ksim efficiently analyzed &gt;5,000 clinical samples from MGH and found previously unidentified transmission clusters. Conclusions:ksim shows promise for rapid clonality determination in HAI outbreaks and has the potential to scale to tens of thousands of samples. This method could enable infection control teams to use WGS for prospective outbreak detection via an automated computational pipeline without the need for specialized computational biology training.Funding: Day Zero Diagnostics and the NIH provided Funding: for this study.Disclosures: Mohamad Sater reports salary from Day Zero Diagnostics.

Bridging Semantic Gaps between Natural Languages and APIs with Word Embedding

Developers increasingly rely on text matching tools to analyze the relation between natural language words and APIs. However, semantic gaps, namely textual mismatches between words and APIs, negatively affect these tools. Previous studies have transformed words or APIs into low-dimensional vectors for matching; however, inaccurate results were obtained due to the failure of modeling words and APIs simultaneously. To resolve this problem, two main challenges are to be addressed: the acquisition of massive words and APIs for mining and the alignment of words and APIs for modeling. Therefore, this study proposes Word2API to effectively estimate relatedness of words and APIs. Word2API collects millions of commonly used words and APIs from code repositories to address the acquisition challenge. Then, a shuffling strategy is used to transform related words and APIs into tuples to address the alignment challenge. Using these tuples, Word2API models words and APIs simultaneously. Word2API outperforms baselines by 10-49.6 percent of relatedness estimation in terms of precision and NDCG. Word2API is also effective on solving typical software tasks, e.g., query expansion and API documents linking. A simple system with Word2API-expanded queries recommends up to 21.4 percent more related APIs for developers. Meanwhile, Word2API improves comparison algorithms by 7.9-17.4 percent in linking questions in Question&Answer communities to API documents.

Beaver genetic surveillance in Britain

Founder genetic composition can affect reintroduction success, especially as the number of animals released tends to be small and therefore less genetically diverse than their source populations. Numerous translocations and reinforcements of beavers, Castor fiber, have occurred with little regard to geographic and/or genetic origin. Beaver reintroduction to Britain has been haphazard and currently disjointed populations of varying status exist – from sanctioned wild releases, unlicensed populations and naturalistic enclosed projects. This study investigated the genetic composition of two originally unofficially released beaver populations in Britain - Tayside, east Scotland, and River Otter, Devon, to provide data to support decision on their future management. From both wild populations (n = 34Tayside, n = 9Devon) all were confirmed as Eurasian beaver. The vast majority, origin was likely assignable to Germany and the mixed founder population of Bavaria. Eighty-two percent of the Tayside individuals examined at 275 loci were at least as closely related as first cousins, with pairwise estimates of relatedness at 26 loci indicated that the Devon beavers were more closely related on average. So far there is no evidence to suggest that beavers are failing to adapt to the British environment despite their reduced genetic founder based, however attention to genetic augmentation and longer-term management of genetic diversity should be factored into comprehensive restoration plans for the species across Britain. Many recent reintroductions are relying on serial founder events from an already limited founder base and that is counter to best practice in reintroduction planning.