Neural Architecture for Question Answering Using a Knowledge Graph and Web Corpus

In Web search, entity-seeking queries often trigger a special Question Answering (QA) system. It may use a parser to interpret the question to a structured query, execute that on a knowledge graph (KG), and return direct entity responses. QA systems based on precise parsing tend to be brittle: minor syntax variations may dramatically change the response. Moreover, KG coverage is patchy. At the other extreme, a large corpus may provide broader coverage, but in an unstructured, unreliable form. We present AQQUCN, a QA system that gracefully combines KG and corpus evidence. AQQUCN accepts a broad spectrum of query syntax, between well-formed questions to short `telegraphic' keyword sequences. In the face of inherent query ambiguities, AQQUCN aggregates signals from KGs and large corpora to directly rank KG entities, rather than commit to one semantic interpretation of the query. AQQUCN models the ideal interpretation as an unobservable or latent variable. Interpretations and candidate entity responses are scored as pairs, by combining signals from multiple convolutional networks that operate collectively on the query, KG and corpus. On four public query workloads, amounting to over 8,000 queries with diverse query syntax, we see 5--16% absolute improvement in mean average precision (MAP), compared to the entity ranking performance of recent systems. Our system is also competitive at entity set retrieval, almost doubling F1 scores for challenging short queries.Comment: Accepted to Information Retrieval Journa

An evaluation of the PCR-RFLP technique to aid molecular-based monitoring of felids and canids in India

<p>Abstract</p> <p>Background</p> <p>The order Carnivora is well represented in India, with 58 of the 250 species found globally, occurring here. However, small carnivores figure very poorly in research and conservation policies in India. This is mainly due to the dearth of tested and standardized techniques that are both cost effective and conducive to small carnivore studies in the field. In this paper we present a non-invasive genetic technique standardized for the study of Indian felids and canids with the use of PCR amplification and restriction enzyme digestion of scat collected in the field.</p> <p>Findings</p> <p>Using existing sequences of felids and canids from GenBank, we designed primers from the 16S rRNA region of the mitochondrial genome and tested these on ten species of felids and five canids. We selected restriction enzymes that would cut the selected region differentially for various species within each family. We produced a restriction digestion profile for the potential differentiation of species based on fragment patterns. To test our technique, we used felid PCR primers on scats collected from various habitats in India, representing varied environmental conditions. Amplification success with field collected scats was 52%, while 86% of the products used for restriction digestion could be accurately assigned to species. We verified this through sequencing. A comparison of costs across the various techniques currently used for scat assignment showed that this technique was the most practical and cost effective.</p> <p>Conclusions</p> <p>The species-specific key developed in this paper provides a means for detailed investigations in the future that focus on elusive carnivores in India and this approach provides a model for other studies in areas of Asia where many small carnivores co-occur.</p

Estimation of genetically effective breeding numbers using a rejection algorithm approach

Polygynous mating results in nonrandom sampling of the adult male gamete pool in each generation, thereby increasing the rate of genetic drift. In principle, genetic paternity analysis can be used to infer the effective number of breeding males (Nebm). However, this requires genetic data from an exhaustive sample of candidate males. Here we describe a new approach to estimate Nebm using a rejection algorithm in association with three statistics: Euclidean distance between the frequency distributions of maternally and paternally inherited alleles, average number of paternally inherited alleles and average gene diversity of paternally inherited alleles. We quantify the relationship between these statistics and Nebm using an individual-based simulation model in which the male mating system varied continuously between random mating and extreme polygyny. We evaluate this method using genetic data from a natural population of highly polygynous fruit bats (Cynopterous sphinx). Using data in the form of mother–offspring genotypes, we demonstrate that estimates of Nebm are very similar to independent estimates based on a direct paternity analysis that included data on candidate males. Our method also permits an evaluation of uncertainty in estimates of Nebm and thus facilitates inferences about the mating system from genetic data. Finally, we investigate the sensitivity of our method to sample size, model assumptions, adult population size and the mating system. These analyses demonstrate that the rejection algorithm provides accurate estimates of Nebm across a broad range of demographic scenarios, except when the true Nebm is high

Ancient geographical gaps and paleo-climate shape the Phylogeography of an endemic bird in the sky islands of Southern India

Background Sky islands, formed by the highest reaches of mountain tracts physically isolated from one another, represent one of the biodiversity-rich regions of the world. Comparative studies of geographically isolated populations on such islands can provide valuable insights into the biogeography and evolution of species on these islands. The Western Ghats mountains of southern India form a sky island system, where the relationship between the island structure and the evolution of its species remains virtually unknown despite a few population genetic studies. Methods and Principal Findings We investigated how ancient geographic gaps and glacial cycles have partitioned genetic variation in modern populations of a threatened endemic bird, the White-bellied Shortwing Brachypteryx major, across the montane Shola forests on these islands and also inferred its evolutionary history. We used Bayesian and maximum likelihood-based phylogenetic and population-genetic analyses on data from three mitochondrial markers and one nuclear marker (totally 2594 bp) obtained from 33 White-bellied Shortwing individuals across five islands. Genetic differentiation between populations of the species correlated with the locations of deep valleys in the Western Ghats but not with geographical distance between these populations. All populations revealed demographic histories consistent with population founding and expansion during the Last Glacial Maximum. Given the level of genetic differentiation north and south of the Palghat Gap, we suggest that these populations be considered two different taxonomic species. Conclusions and Significance Our results show that the physiography and paleo-climate of this region historically resulted in multiple glacial refugia that may have subsequently driven the evolutionary history and current population structure of this bird. The first avian genetic study from this biodiversity hotspot, our results provide insights into processes that may have impacted the speciation and evolution of the endemic fauna of this region

Mixed Fortunes: Ancient Expansion and Recent Decline in Population Size of a Subtropical Montane Primate, the Arunachal Macaque Macaca munzala

Quaternary glacial oscillations are known to have caused population size fluctuations in many temperate species. Species from subtropical and tropical regions are, however, considerably less studied, despite representing most of the biodiversity hotspots in the world including many highly threatened by anthropogenic activities such as hunting. These regions, consequently, pose a significant knowledge gap in terms of how their fauna have typically responded to past climatic changes. We studied an endangered primate, the Arunachal macaque Macaca munzala, from the subtropical southern edge of the Tibetan plateau, a part of the Eastern Himalaya biodiversity hotspot, also known to be highly threatened due to rampant hunting. We employed a 534 bp-long mitochondrial DNA sequence and 22 autosomal microsatellite loci to investigate the factors that have potentially shaped the demographic history of the species. Analysing the genetic data with traditional statistical methods and advance Bayesian inferential approaches, we demonstrate a limited effect of past glacial fluctuations on the demographic history of the species before the last glacial maximum, approximately 20,000 years ago. This was, however, immediately followed by a significant population expansion possibly due to warmer climatic conditions, approximately 15,000 years ago. These changes may thus represent an apparent balance between that displayed by the relatively climatically stable tropics and those of the more severe, temperate environments of the past. This study also draws attention to the possibility that a cold-tolerant species like the Arunachal macaque, which could withstand historical climate fluctuations and grow once the climate became conducive, may actually be extremely vulnerable to anthropogenic exploitation, as is perhaps indicated by its Holocene ca. 30-fold population decline, approximately 3,500 years ago. Our study thus provides a quantitative appraisal of these demographically important events, emphasising the ability to potentially infer the occurrence of two separate historical events from contemporary genetic data

Non-sister Sri Lankan White-eyes (genus Zosterops) are a Result of Independent Colonizations

Co-occurrence of closely related taxa on islands could be attributed to sympatric speciation or multiple colonization. Sympatric speciation is considered to be rare in small islands, however multiple colonizations are known to be common in both oceanic and continental islands. In this study we investigated the phylogenetic relatedness and means of origin of the two sympatrically co-occurring Zosterops white-eyes, the endemic Zosterops ceylonensis and its widespread regional congener Z. palpebrosus, in the island of Sri Lanka. Sri Lanka is a continental island in the Indian continental shelf of the Northern Indian Ocean. Our multivariate morphometric analyses confirmed the phenotypic distinctness of the two species. Maximum Likelihood and Bayesian phylogenetic analyses with ~2000bp from two mitochondrial (ND2 and ND3) and one nuclear (TGF) gene indicated that they are phylogenetically distinct, and not sister to each other. The two subspecies of the peninsula India; Z. p. egregius of Sri Lanka and India and Z. p. nilgiriensis of Western Ghats (India) clustered within the Z. palpebrosus clade having a common ancestor. In contrast, the divergence of the endemic Z. ceylonensis appears to be much deeper and is basal to the other Zosterops white-eyes. Therefore we conclude that the two Zosterops species originated in the island through independent colonizations from different ancestral lineages, and not through island speciation or multiple colonization from the same continental ancestral population. Despite high endemism, Sri Lankan biodiversity is long considered to be a subset of southern India. This study on a speciose group with high dispersal ability and rapid diversification rate provide evidence for the contribution of multiple colonizations in shaping Sri Lanka’s biodiversity. It also highlights the complex biogeographic patterns of the South Asian region, reflected even in highly vagile groups such as birds

A panel of microsatellites to individually identify leopards and its application to leopard monitoring in human dominated landscapes

<p>Abstract</p> <p>Background</p> <p>Leopards are the most widely distributed of the large cats, ranging from Africa to the Russian Far East. Because of habitat fragmentation, high human population densities and the inherent adaptability of this species, they now occupy landscapes close to human settlements. As a result, they are the most common species involved in human wildlife conflict in India, necessitating their monitoring. However, their elusive nature makes such monitoring difficult. Recent advances in DNA methods along with non-invasive sampling techniques can be used to monitor populations and individuals across large landscapes including human dominated ones. In this paper, we describe a DNA-based method for leopard individual identification where we used fecal DNA samples to obtain genetic material. Further, we apply our methods to non-invasive samples collected in a human-dominated landscape to estimate the minimum number of leopards in this human-leopard conflict area in Western India.</p> <p>Results</p> <p>In this study, 25 of the 29 tested cross-specific microsatellite markers showed positive amplification in 37 wild-caught leopards. These loci revealed varied levels of polymorphism (four-12 alleles) and heterozygosity (0.05-0.79). Combining data on amplification success (including non-invasive samples) and locus specific polymorphisms, we showed that eight loci provide a sibling probability of identity of 0.0005, suggesting that this panel can be used to discriminate individuals in the wild. When this microsatellite panel was applied to fecal samples collected from a human-dominated landscape, we identified 7 individuals, with a sibling probability of identity of 0.001. Amplification success of field collected scats was up to 72%, and genotype error ranged from 0-7.4%.</p> <p>Conclusion</p> <p>Our results demonstrated that the selected panel of eight microsatellite loci can conclusively identify leopards from various kinds of biological samples. Our methods can be used to monitor leopards over small and large landscapes to assess population trends, as well as could be tested for population assignment in forensic applications.</p

The Critically Endangered Forest Owlet Heteroglaux Blewitti is Nested Within the Currently Recognized Athene Clade: A Century-Old Debate Addressed

Range-restricted species generally have specific niche requirements and may often have unique evolutionary histories. Unfortunately, many of these species severely lack basic research, resulting in poor conservation strategies. The phylogenetic relationship of the Critically Endangered Forest Owlet Heteroglaux blewitti has been the subject of a century-old debate. The current classifications based on non-phylogenetic comparisons of morphology place the small owls of Asia into three genera, namely, Athene, Glaucidium, and Heteroglaux. Based on morphological and anatomical data, H. blewitti has been alternatively hypothesized to belong within Athene, Glaucidium, or its own monotypic genus Heteroglaux. To test these competing hypotheses, we sequenced six loci (~4300 bp data) and performed phylogenetic analyses of owlets. Mitochondrial and nuclear trees were not congruent in their placement of H. blewitti. However, both mitochondrial and nuclear combined datasets showed strong statistical support with high maximum likelihood bootstrap (\u3e/ = 90) and Bayesian posterior probability values (\u3e/ = 0.98) for H. blewitti being nested in the currently recognized Athene group, but not sister to Indian A. brama. The divergence of H. blewitti from its sister taxa was between 4.3 and 5.7 Ma coinciding with a period of drastic climatic changes in the Indian subcontinent. This study presented the first genetic analysis of H. blewitti, a Critically Endangered species, and addressed the long debate on the relationships of the Athene-Heteroglaux-Glaucidium complex. We recommend further studies with more data and complete taxon sampling to understand the biogeography of Indian Athene species