Screening and selection of 21 novel microhaplotype markers for ancestry inference in ten Chinese Subpopulations

Genetic findings suggested that ethnolinguistically diverse populations in China harbor differentiated genetic structure and complex evolutionary admixture history, which provide the genetic basis and theoretical foundation for forensic biogeographical ancestry inference (BGAI). Forensic assays for BGAI among intracontinental eastern Eurasians were previously conducted mainly based on the SNPs or InDels. Microhaplotypes, as a set of closely linked SNPs within 200 base pairs, possess the advantages of both STR and SNP and have great potential in forensic ancestry inference. However, the developed forensic assay based on the ancestry informative microhaplotypes in the BGAI remained to be comprehensively explored, especially in China with enriching genetic diversity. Here, we described a new BGAI panel based on 21 novel identified ancestry informative microhaplotypes that focused on dissected finer-scale ancestry composition of Chinese populations. We initially screened all possible microhaplotypes with high Fst values among five East Asian populations and finally employed 21 candidate microhaplotypes in two multiplex SNaPshot assays. Forensic amplification efficiency and statistically/physically phased haplotypes of the 21 microhaplotypes were validated using both SNaPshot and massively parallel sequencing (MPS) platforms. Followingly, we validated the efficiency of these microhaplotypes for BGAI in 764 individuals from ten Chinese populations. Fine-scale ancestry source and ancestry proportion estimated by the principal component analysis (PCA), multidimensional scaling (MDS), phylogenetic tree and model-based STRUCTURE among worldwide populations and East Asians showed that our customized panel could provide a higher discrimination resolution in both continental population stratification and East Asian regional substructure. East Asian populations could be further classified into linguistically/geographically different intracontinental subpopulations (Tibeto-Burman, Tai-Kadai and others). Finally, we obtained a higher estimated accuracy using training and tested datasets in the microhaplotype-based panel than traditional SNP-based panels. Generally, the above results demonstrated that this microhaplotype panel was robust and suitable for forensic BGAI in Chinese populations, which not only provided a high discriminatory power for continental populations but also discriminated East Asians into linguistically restricted subpopulations.

Intraspecies Genomic Divergence of a Fig Wasp Species Is Due to Geographical Barrier and Adaptation

Understanding how intraspecies divergence results in speciation has great importance for our knowledge of evolutionary biology. Here we applied population genomics approaches to a fig wasp species (Valisia javana complex sp 1) to reveal its intraspecies differentiation and the underlying evolutionary dynamics. With re-sequencing data, we prove the Hainan Island population (DA) of sp1 genetically differ from the continental ones, then reveal the differed divergence pattern. DA has reduced SNP diversity but a higher proportion of population-specific structural variations (SVs), implying a restricted gene exchange. Based on SNPs, 32 differentiated islands containing 204 genes were detected, along with 1,532 population-specific SVs of DA overlapping 4,141 genes. The gene ontology (GO) enrichment analysis performed on differentiated islands linked to three significant GO terms on a basic metabolism process, with most of the genes failing to enrich. In contrast, population-specific SVs contributed more to the adaptation than the SNPs by linking to 59 terms that are crucial for wasp speciation, such as host reorganization and development regulation. In addition, the generalized dissimilarity modeling confirms the importance of environment difference on the genetic divergence within sp1. Hence, we assume the genetic divergence between DA and the continent due to not only the strait as a geographic barrier, but also adaptation. We reconstruct the demographic history within sp1. DA shares a similar population history with the nearby continental population, suggesting an incomplete divergence. Summarily, our results reveal how geographic barriers and adaptation both influence the genetic divergence at population-level, thereby increasing our knowledge on the potential speciation of non-model organisms.

The role of long non-coding RNAs in the regulation of pancreatic beta cell identity

Type 2 diabetes (T2D) is a widespread disease affecting millions in every continental population. Pancreatic β-cells are central to the regulation of circulating glucose, but failure in the maintenance of their mass and/or functional identity leads to T2D. Long non-coding RNAs (lncRNAs) represent a relatively understudied class of transcripts which growing evidence implicates in diabetes pathogenesis. T2D-associated single nucleotide polymorphisms (SNPs) have been identified in lncRNA loci, although these appear to function primarily through regulating β-cell proliferation. In the last decade, over 1100 lncRNAs have been catalogued in islets and the roles of a few have been further investigated, definitively linking them to β-cell function. These studies show that lncRNAs can be developmentally regulated and show highly tissue-specific expression. lncRNAs regulate neighbouring β-cell-specific transcription factor expression, with knockdown or overexpression of lncRNAs impacting a network of other key genes and pathways. Finally, gene expression analysis in studies of diabetic models have uncovered a number of lncRNAs with roles in β-cell function. A deeper understanding of these lncRNA roles in maintaining β-cell identity, and its deterioration, is required to fully appreciate the β-cell molecular network and to advance novel diabetes treatments.

Profiling variable-number tandem repeat variation across populations using repeat-pangenome graphs

Variable number tandem repeats (VNTRs) are composed of consecutive repetitive DNA with hypervariable repeat count and composition. They include protein coding sequences and associations with clinical disorders. It has been difficult to incorporate VNTR analysis in disease studies that use short-read sequencing because the traditional approach of mapping to the human reference is less effective for repetitive and divergent sequences. In this work, we solve VNTR mapping for short reads with a repeat-pangenome graph (RPGG), a data structure that encodes both the population diversity and repeat structure of VNTR loci from multiple haplotype-resolved assemblies. We develop software to build a RPGG, and use the RPGG to estimate VNTR composition with short reads. We use this to discover VNTRs with length stratified by continental population, and expression quantitative trait loci, indicating that RPGG analysis of VNTRs will be critical for future studies of diversity and disease.

The Colorado River Delta and California’s Central Valley are critical regions for many migrating North American landbirds

Migration is an important component of some species full annual cycle. California’s Central Valley and the Colorado River Delta provide important riparian and wetland habitats for migrating waterbirds in the arid west of North America, but little is known about whether these locations are important at the population level to migrating landbirds. We used eBird Status and Trends abundance data to quantify the importance of the Central Valley and Colorado River Delta to landbirds by estimating the proportion of the breeding population of 112 species that use each site during migration. We found that ~17 million landbirds use the Colorado River Delta in the spring and ~14 million in the fall. Across 4 study regions in the Central Valley, up to ~65 million landbirds migrate through in the spring and up to ~48 million in the fall. In the spring and fall, respectively, up to 37 and up to 30 species had at least 1% of their continental population migrate through the study regions. We also quantified the spatial concentration of each species across latitudinal transects to determine the extent to which study regions were acting as migratory bottlenecks. Landbird abundances were spatially concentrated in study regions 29.4% of all migration weeks, indicating that each study region acts as a migratory bottleneck. This application of eBird data is a powerful approach to quantifying the importance of sites to migrating birds. Our results provide evidence of population-level importance of the Central Valley and Colorado River Delta for many migratory landbirds.

“A Thousand Mounds”: Original Sites of Ancient Japan and Korea (Materials for Educational Course “Archaeology of Foreign Asia”)

Purpose. The term kofungun is used in Japan for the mounded tomb groups of the Kofun Period (3rd – 4th centuries), which corresponds to the concept of a burial mound complex. Packed tumuli clusters or senzuka-type burial mound groups are located mainly in the central part of Honshu Island. Similar burial grounds are also known in the South of the Korean Peninsula. This theme is associated with the importance that cultural contacts of island and continental population and their cultural traditions bring to the development of the region as a whole, and Japan and Korea separately. The aim of the research is to study groups of senzuka-type mounded burial groups in Japan and their analogies in Korea. Results. Packed tumuli clusters of Late Kofun are generally located in the center of Honshu Island. Common findings include sue and haji ware, armors and weapons, ornaments. Among the grave goods, a fairly noticeable number of items of Korean origin are found. Some parts of packed tumuli clusters are considered to belong to immigrant clans. Ceramic rice-cookers and Korean-type armors and weapons can often be found in such mounded tombs. Senzuka-type tumuli clusters found on the Korean Peninsula are located in the territory of the ancient Gaya state. The findings include hard ceramic pots, armors and weapons, ornaments, and so on. The Marisan tumuli cluster contains a special type of findings: some mounded tombs were decorated with ceramic figures similar to the Japanese haniwa. Conclusion. The appearance of large sized mounded tombs, surrounded by many small ones in the second half of the Kofun Period, may indicate the emergence of a broad social support of the ruling elite. The presence of items made on the territory of the Japanese islands using Korean technologies among the grave goods allows us to assume the resettlement of artisans from the Korean Peninsula to the Japanese islands. The materials of this research could be useful for students studying archaeology of East Asia.

REPRODUCTIVE ASPECTS OF THE PRAWN Macrobrachium amazonicum IN A CONTINENTAL POPULATION LIVING DOWNSTREAM OF A HYDROELECTRIC DAM

The migratory behavior of females of the freshwater prawn Macrobrachium amazonicum (Heller, 1862) can indicate a strategy that optimizes the population establishment. With this idea in mind, we evaluated the reproductive biology of M. amazonicum, hypothesizing that females were evenly distributed downstream of Hydroelectric Dam. Specimens were collected monthly for one year, from six sites of Rio Grande river. The specimens were sexed and measured (carapace length; CL). A total of 14,697 adults were captured, 2,864 males (AM), 11,082 non-breeding females (AF) and 751 breeding females (BF). The smallest BF had 3.8 mm CL. The distribution of demographic groups was assessed by a Principal Component Analysis (PCA), which explained 95.16% of the distribution over the collection sites. Breeding females were more abundant in the sites closest to the dam. This result can be explained by rainfall, which varied significantly throughout the year. As the breeding females migrated upstream toward the dam and were more abundant there, our hypothesis of homogeneous distribution was rejected. This behavior probably optimizes larval dispersion. The reproduction was continuous with peaks in the period preceding the maximum rainfall.

Managing incursions of Vespa velutina nigrithorax in the UK: an emerging threat to apiculture

Vespa velutina nigrithorax is an invasive species of hornet accidentally introduced into Europe in 2004. It feeds on invertebrates, including honey bees, and represents a threat to European apiculture. In 2016, the first nest of this hornet was detected and destroyed on mainland UK. A further 8 nests were discovered between 2016 and 2019. Nest dissection was performed on all nests together with microsatellite analyses of different life stages found in the nests to address the reproductive output and success of nests found in the UK. None of the nests had produced the next generation of queens. Follow-up monitoring in those regions detected no new nests in the following years. Diploid males were found in many UK nests, while microsatellite analysis showed that nests had low genetic diversity and the majority of queens had mated with one or two males. All UK nests derived from the European zone of secondary colonisation, rather than from the native range of the species. None of the nests discovered so far have been direct offspring of another UK nest. The evidence suggests that these nests were separate incursions from a continental population rather than belonging to a single established UK population of this pest.

Profiling variable-number tandem repeat variation across populations using repeat-pangenome graphs

Variable number tandem repeat sequences (VNTR) are composed of consecutive repeats of short segments of DNA with hypervariable repeat count and composition. They include protein coding sequences and associations with clinical disorders. It has been difficult to incorporate VNTR analysis in disease studies that use short-read sequencing because the traditional approach of mapping to the human reference is less effective for repetitive and divergent sequences. We solve VNTR mapping for short reads with a repeat-pangenome graph (RPGG), a data structure that encodes both the population diversity and repeat structure of VNTR loci from multiple haplotype-resolved assemblies. We developed software to build a RPGG, and use the RPGG to estimate VNTR composition with short reads. We used this to discover VNTRs with length stratified by continental population, and novel expression quantitative trait loci, indicating that RPGG analysis of VNTRs will be critical for future studies of diversity and disease.

Spatial and temporal variation in the migration of Ruddy-headed Goose in southern South America using satellite tagging

SummaryRuddy-headed Goose Chloephaga rubidiceps is the smallest of the five South American sheldgeese and has two separate populations: one sedentary, which resides in the Malvinas/Falkland Islands and one migratory that overwinters mainly in the Pampas region, Argentina and breeds in Southern Patagonia. The Ruddy-headed Goose’s continental population has decreased considerably, and recent estimates indicated that the population size is less than 800 individuals. In Argentina and Chile, this population is categorised as endangered. Understanding migration across vast landscapes is essential for the identification of factors affecting the survival of this endangered population and for the application of effective conservation measures. We aim to provide the first documentation of the complete migration cycle of Ruddy-headed Goose, and to analyse their annual migration in detail, including identification of stop-over, breeding and wintering sites, and to compare migration timing during spring and autumn migration. Adults were captured in the southern Pampas and equipped with solar satellite transmitters in 2015 and 2016. We analysed the influence of season (spring vs autumn migration) on the number and duration of stop-overs, distance travelled and overall migration speed using Generalized Linear Mixed Models. Our results showed that tracked geese used the eastern Patagonian route to reach their breeding grounds and take the same route after breeding. Spring migration was significantly faster than autumn migration, at least based on the number of days spent in their stop-overs. Stop-overs were closer to the final destination, either during spring and autumn migrations, though some of them were not used during subsequent migrations. Our migration cartography for Ruddy-headed Geese, together with the timing and location data, should be used to improve conservation efforts directed at this species and might contribute to the modification of the current status of ‘Least Concern’ under the IUCN criteria.