Mitochondrial dna diversity of crossbanded barb Puntioplites bulu (Bleeker, 1851) from natural populations in peninsular Malaysia

Puntoplites bulu is a freshwater Cyprinidae and widely distributed in Southeast Asia. It has attracted considerable interest due to high demand and price. However, an apparent decline in its distribution and abundance is observed and this is due to several factors, such as habitat degradation, pollution, and overfishing. Intraspecific variation of P.bulu from three major rivers in Peninsular Malaysia were determined based on genetic divergence by using mtDNA Cyt b. Two distinct genetic lineages were apparent viz Central West and East Peninsular Malaysia with natural barriers (the Titiwangsa Range) acted as natural dividers between these two lineages. Alternatively, the close genetic relation and haplotype sharing that were observed between Perak and Kelantan populations could be due to human translocations. Further, haplotype sharing between Kelantan and Pahang populations revealed the migration ability of P. bulu through ancient connectivity. These findings provide an important base study for initiating a selective breeding program

Fast and robust identity-by-descent inference with the templated positional Burrows-Wheeler transform

Estimating the genomic location and length of identical-by-descent (IBD) segments among individuals is a crucial step in many genetic analyses. However, the exponential growth in the size of biobank and direct-to-consumer (DTC) genetic data sets makes accurate IBD inference a significant computational challenge. Here we present the templated positional Burrows-Wheeler transform (TPBWT) to make fast IBD estimates robust to genotype and phasing errors. Using haplotype data simulated over pedigrees with realistic genotyping and phasing errors we show that the TPBWT outperforms other state-of-the-art IBD inference algorithms in terms of speed and accuracy. For each phase-aware method, we explore the false positive and false negative rates of inferring IBD by segment length and characterize the types of error commonly found. Our results highlight the fragility of most phased IBD inference methods; the accuracy of IBD estimates can be highly sensitive to the quality of haplotype phasing. Additionally we compare the performance of the TPBWT against a widely used phase-free IBD inference approach that is robust to phasing errors. We introduce both in-sample and out-of-sample TPBWT-based IBD inference algorithms and demonstrate their computational efficiency on massive-scale datasets with millions of samples. Furthermore we describe the binary file format for TPBWT-compressed haplotypes that results in fast and efficient out-of-sample IBD computes against very large cohort panels. Finally, we demonstrate the utility of the TPBWT in a brief empirical analysis exploring geographic patterns of haplotype sharing within Mexico. Hierarchical clustering of IBD shared across regions within Mexico reveals geographically structured haplotype sharing and a strong signal of isolation by distance. Our software implementation of the TPBWT is freely available for non-commercial use in the code repository https://github.com/23andMe/phasedibd.

A DNA barcode library for ground beetles of Germany: the genus Pterostichus Bonelli, 1810 and allied taxa (Insecta, Coleoptera, Carabidae)

Species of the ground beetle genus Pterostichus Bonelli, 1810 are some of the most common carabids in Europe. This publication provides a first comprehensive DNA barcode library for this genus and allied taxa including Abax Bonelli, 1810, Molops Bonelli, 1810, Poecilus Bonelli, 1810, and Stomis Clairville, 1806 for Germany and Central Europe in general. DNA barcodes were analyzed from 609 individuals that represent 51 species, including sequences from previous studies as well as more than 198 newly generated sequences. The results showed a 1:1 correspondence between BIN and traditionally recognized species for 44 species (86%), whereas two (4%) species were characterized by two BINs. Three BINs were found for one species (2%), while one BIN for two species was revealed for two species pairs (8%). Low interspecific distances with maximum pairwise K2P values below 2.2% were found for four species pairs. Haplotype sharing was found for two closely related species pairs: Pterostichus adstrictus Eschscholtz, 1823/Pterostichus oblongopunctatus (Fabricius, 1787) and Pterostichus nigrita Paykull, 1790/Pterostichus rhaeticus Heer, 1837. In contrast to this, high intraspecific sequence divergences with values above 2.2% were shown for three species (Molops piceus (Panzer, 1793), Pterostichus panzeri (Panzer, 1805), Pterostichus strenuus (Panzer, 1793)). Summarizing the results, the present DNA barcode library does not only allow the identification of most of the analyzed species, but also provides valuable information for alpha-taxonomy as well as for ecological and evolutionary research. This library represents another step in building a comprehensive DNA barcode library of ground beetles as part of modern biodiversity research.

The Rise of the GRN C157KfsX97 Mutation in Southern Italy: Going Back to the Fall of the Western Roman Empire

Background: Frontotemporal lobar degeneration (FTLD) designates a group of neurodegenerative diseases with remarkable clinical, pathological, and genetic heterogeneity. Mutations in progranulin gene (GRN) are among the most common causes of familial FTLD. The GRN C157KfsX97 mutation is the most frequent mutation occurring in Southern Italy and has been already described in a previous work. Objective: In this study, we reported on additional cases carrying the same mutation and performed a genetic study on the whole cohort, aiming at demonstrating the existence of a founder effect and estimating the age of this mutation. Methods/Results: Based on the haplotype sharing analysis, a founder effect was highly probable, while the age of the mutation, estimated by means of DMLE+ software, resulted in a range between 52 and 82 generations, with the highest frequency at about 62 generations, 1,550 years ago. Conclusion: This is the first study that reports the age estimation of the most recent common ancestor for the GRN C157KfsX97 mutation recurring in Southern Italy. Mutation dating in a geographically restricted population may be useful in order to plan genetic counseling and screening programs in the field of public health.

Evidence of introgression in endemic frogs from the campo rupestre contradicts the reduced hybridization hypothesis

The campo rupestre ecosystem is considered an old, climatically buffered, infertile landscape. As a consequence, long-term isolation is thought to have played an important role in the diversification of its biota. Here, we tested for hybridization between two endemic leaf frogs from the campo rupestre. We used sequence markers and coalescent models to verify haplotype sharing between the species, to test the existence and direction of gene flow, and to reconstruct the spatiotemporal dynamics of gene flow. Additionally, ecological niche modelling (ENM) was used to assess for potential co-occurrence by overlapping the climatic niche of these species since the middle Pleistocene. We found haplotype sharing and/or lack of differentiation in four nuclear fragments, one of them associated with introgression. The coalescent models support introgressive hybridization unidirectionally from Pithecopus megacephalus to P. ayeaye, occurring ~300 kya. ENM corroborates this scenario, revealing areas of potential environmental niche overlap for the species at about 787 kya. These results contradict the expectation of reduced hybridization, while ENM suggests climatic fluctuation rather than stability for the two species. The reduced hybridization hypothesis needs to be further investigated because our results suggest that it may have unrealistic premises at least for animals.

Evaluation of the genetic diversity of six Chinese indigenous chickens

Objective: The extensive breeding of commercial chickens has led to a sharp decrease in the resources of many indigenous chickens, especially the indigenous chickens in the southeastern coastal region, which are on the verge of extinction, and the indigenous chickens in the northwestern region of China, which are also at risk. However, there are few reports on the evaluation of genetic diversity and conservation of genetic resources of indigenous chickens in remote areas in the Northwest of China.Methods: In the present study, the genetic diversity and phylogenetic relationship of six indigenous chickens from different regions were studied based on variation in mitochondrial DNA control region (D-loop), and the degree of introgression from commercial breeds into these chickens was determined by the amount of haplotype sharing between indigenous and commercial breeds.Results: Twenty-five polymorphic sites and 25 haplotypes were detected in 206 individuals. Principal component analysis showed that the Jingning chicken had the highest genetic diversity among the six indigenous chickens. According to the degree of introgression, the six indigenous breeds may be involved in haplotype sharing with commercial breeds, and the introgression from commercial chickens into the Haidong chicken is the most serious.Conclusion: The genetic uniqueness of indigenous chickens has been eroded, so it is necessary to consider the protection of their genetic resources. Phylogenetic analysis suggests that the six indigenous chickens have two major matrilineal origins: one from Yunnan or its surrounding areas in China and the other from the Indian subcontinent.

Fast and robust identity-by-descent inference with the templated positional Burrows-Wheeler transform

Estimating the genomic location and length of identical-by-descent (IBD) segments among individuals is a crucial step in many genetic analyses. However, the exponential growth in the size of biobank and direct-to-consumer (DTC) genetic data sets makes accurate IBD inference a significant computational challenge. Here we present the templated positional Burrows-Wheeler transform (TPBWT) to make fast IBD estimates robust to genotype and phasing errors. Using haplotype data simulated over pedigrees with realistic genotyping and phasing errors we show that the TPBWT outperforms other state-of-the-art IBD inference algorithms in terms of speed and accuracy. For each phase-aware method, we explore the false positive and false negative rates of inferring IBD by segment length and characterize the types of error commonly found. Our results highlight the fragility of most phased IBD inference methods; the accuracy of IBD estimates can be highly sensitive to the quality of haplotype phasing. Additionally we compare the performance of the TPBWT against a widely used phase-free IBD inference approach that is robust to phasing errors. We introduce both in-sample and out-of-sample TPBWT-based IBD inference algorithms and demonstrate their computational efficiency on massive-scale datasets with millions of samples. Furthermore we describe the binary file format for TPBWT-compressed haplotypes that results in fast and efficient out-of-sample IBD computes against very large cohort panels. Finally, we demonstrate the utility of the TPBWT in a brief empirical analysis exploring geographic patterns of haplotype sharing within Mexico. Hierarchical clustering of IBD shared across regions within Mexico reveals geographically structured haplotype sharing and a strong signal of isolation by distance. Our software implementation of the TPBWT is freely available for non-commercial use in the code repository https://github.com/23andMe/phasedibd.

A rapid, accurate approach to inferring pedigrees in endogamous populations

Accurate reconstruction of pedigrees from genetic data remains a challenging problem. Pedigree inference algorithms are often trained only on urban European-descent families, which are comparatively ‘outbred’ compared to many other global populations. Relationship categories can be difficult to distinguish (e.g. half-sibships versus avuncular) without external information. Furthermore, published software cannot accommodate endogamous populations where there may be reticulations within a pedigree or elevated haplotype sharing. We design a simple, rapid algorithm which initially uses only high-confidence first degree relationships to seed a machine learning step based on the number of identical by descent segments. Additionally, we define a new statistic to polarize individuals to ancestor versus descendant generation. We test our approach in a sample of 700 individuals from northern Namibia, sampled from an endogamous population. Due to a culture of concurrent relationships in this population, there is a high proportion of half-sibships. We accurately identify first through third degree relationships for all categories, including half-sibships, half-avuncular-ships etc. We further validate our approach in the Barbados Asthma Genetics Study (BAGS) dataset. Accurate reconstruction of pedigrees holds promise for tracing allele frequency trajectories, improved phasing and other population genomic questions.

845. Children with Clinical Plasmodium falciparum Infection Have Increased Sharing of Haplotypes with Household Members as well as Temporally Proximal, Symptomatic Peers

Background Falciparum malaria transmission has failed to decline in proportion to control efforts in certain regions such as Bungoma county, western Kenya. One proposed strategy to eradicate malaria is ring testing and treatment; however, it remains unknown whether infections spread locally or if asymptomatically infected household members are a risk factor for clinical disease. Methods From April 2013 to June 2014, we enrolled 442 cases (RDT+ children hospitalized with malaria) and 442 matched controls; all household members of cases and controls were also enrolled and tested, of which 13.6% (n = 608/4449) were RDT+. From each RDT+ participant, parasite gDNA was PCR-amplified at both Pf circumsporozoite protein (csp) and apical membrane antigen 1 (ama1) loci, amplicons sequenced on an Illumina Miseq, and haplotypes inferred using dada2. Results We identified 120 csp and 180 ama1 unique haplotypes (Figure 1). We evaluated the genetic distance between infected individuals using three novel indices: sharing of parasite haplotypes on binary and proportional scales and the L1 norm. Case children median [IQR] binary/proportional sharing of both csp and ama1 haplotypes was significantly increased with members of their origin household (e.g., csp binary sharing: origin = 50.3 [0–87.5] vs. similar household = 0 [0–50.3]; P = 0.01; Wilcoxon sign-rank test), indicating that cases are more likely to share haplotype-identical parasites with members of their own household (Figure 2). We also computed population-level haplotype sharing indices for all pairs of case children and observed no association between genetic relatedness and geographic distance. In contrast, we identified a strong inverse relationship between haplotype sharing and temporal distance, which we exploited to identify the molecular signature of an outbreak (Figure 3). Conclusion Overall, these findings suggest that, although haplotype sharing is more common within households, temporal rather than geographic proximity predicts parasite genetic similarity. The observation that identical haplotype combinations are found nearly simultaneously across the study area implies that ring testing approaches may not effectively reduce transmission. Disclosures All Authors: No reported Disclosures.