Exploring the second intermediate hosts and morphology of human- and cat-specific Opisthorchis viverrini-like populations

Infection by the zoonotic fish-borne trematode, Opisthorchis viverrini, remains a crucial health issue in Thailand and neighboring countries. Recently, molecular analysis revealed two populations of putative O. viverrini: one found primarily in human hosts ("human-specific" population) and the other primarily in cats ("cat-specific" population). It is unclear how the infective stages (metacercariae) of these different populations circulate among definitive and reservoir hosts in nature. To gain an insight into this, mitochondrial cox1 and nad1 gene sequences of metacercariae from fish intermediate hosts were examined. None of 192 metacercariae from cyprinid fish in Lao PDR and Thailand had sequences typical of "cat-specific" O. viverrini, suggesting that cyprinid fish are not the main second intermediate hosts of this population. Interestingly, all 20 O. viverrini-like metacercariae from snakehead fish (Channa striata) shared 99.51% to 100% sequence identity with eggs from cats naturally infected in a previous study. Hence, we propose a modification of the known transmission dynamics of O. viverrini: consumption of metacercariae within snakehead fish provides another pathway for cats and (occasionally) humans to acquire infection. We also performed morphological comparisons of eggs, metacercariae, and adult flukes (raised in hamsters) of both Opisthorchis populations. The "cat-specific" population has eggs that are narrower and adults that are shorter and wider than in the human-specific population. The metacercaria of the "cat-specific" population is elliptical, while that of the "human-specific" population is oval, occasionally rounded. Our results confirmed that O. viverrini-like metacercariae from snakehead fish are the infective stages of the "cat-specific" fluke. This provides a new insight into the dissemination and transmission of each population in the second intermediate host. The identity of the cat-specific population is discussed.

Unravelling the maternal evolutionary history of the African leopard (Panthera pardus pardus)

The African leopard (Panthera pardus pardus) has lost a significant proportion of its historical range, notably in north-western Africa and South Africa. Recent studies have explored the genetic diversity and population structure of African leopards across the continent. A notable genetic observation is the presence of two divergent mitochondrial lineages, PAR-I and PAR-II. Both lineages appeared to be distributed widely, with PAR-II frequently found in southern Africa. Until now, no study has attempted to date the emergence of either lineage, assess haplotype distribution, or explore their evolutionary histories in any detail. To investigate these underappreciated questions, we compiled the largest and most geographically representative leopard data set of the mitochondrial NADH-5 gene to date. We combined samples (n = 33) collected in an altitudinal transect across the Mpumalanga province of South Africa, where two populations of leopard are known to be in genetic contact, with previously published sequences of African leopard (n = 211). We estimate that the maternal PAR-I and PAR-II lineages diverged approximately 0.7051 (0.4477-0.9632) million years ago (Ma). Through spatial and demographic analyses, we show that while PAR-I underwent a mid-Pleistocene population expansion resulting in several closely related haplotypes with little geographic structure across much of its range, PAR-II remained at constant size and may even have declined slightly in the last 0.1 Ma. The higher genetic drift experienced within PAR-II drove a greater degree of structure with little haplotype sharing and unique haplotypes in central Africa, the Cape, KwaZulu-Natal and the South African Highveld. The phylogeographic structure of PAR-II, with its increasing frequency southward and its exclusive occurrence in south-eastern South Africa, suggests that this lineage may have been isolated in South Africa during the mid-Pleistocene. This hypothesis is supported by historical changes in paleoclimate that promoted intense aridification around the Limpopo Basin between 1.0-0.6 Ma, potentially reducing gene flow and promoting genetic drift. Interestingly, we ascertained that the two nuclear DNA populations identified by a previous study as East and West Mpumalanga correspond to PAR-I and PAR-II, respectively, and that they have come into secondary contact in the Lowveld region of South Africa. Our results suggest a subdivision of African leopard mtDNA into two clades, with one occurring almost exclusively in South Africa, and we identify the potential environmental drivers of this observed structure. We caution that our results are based on a single mtDNA locus, but it nevertheless provides a hypothesis that can be further tested with a dense sample of nuclear DNA data, preferably whole genomes. If our interpretation holds true, it would provide the first genetic explanation for the smaller observed size of leopards at the southernmost end of their range in Africa.

Population Genetics of Culex tritaeniorhynchus (Diptera: Culicidae) in Türkiye

PURPOSE

Mosquitoes are important vectors of pathogens that can affect humans and animals. Culex tritaeniorhynchus is an important vector of arboviruses such as Japanese encephalitis virus, West Nile virus among various human and animal communities. These diseases are of major public health concern and can have huge economic and health burdens in prevalent countries. Although populations of this important mosquito species have been detected in the Mediterranean and Aegean regions of Türkiye; little is known about its population structure. Our study is to examine the population genetics and genetic composition of Cx. tritaeniorhynchus mosquitoes collected from several localities using cytochrome oxidase subunit I (COI) and the NADH dehydrogenase subunit 5 genes (ND5). This is the first extensive study of Cx. tritaeniorhynchus in the mainland Türkiye with sampling spanning many of provinces.

METHODS

In this study, DNA extraction, amplification of mitochondrial COI and ND5 genes and population genetic analyses were performed on ten geographic populations of Culex tritaeniorhynchus in the Aegean and Mediterranean region of Türkiye.

RESULTS

Between 2019 and 2020, 96 samples were collected from 10 geographic populations in the Aegean and Mediterranean regions; they were molecularly analyzed and 139 sequences (50 sequence for COI and 89 sequence for ND5) were used to determine the population structure and genetic diversity. For ND5 gene region, the samples produced 24 haplotypes derived from 15 variable sites and for COI gene region, 43 haplotypes were derived from 17 variable sites. The haplotype for both gene regions was higher than nucleotide diversity. Haplotype phylogeny revealed two groups present in all populations. AMOVA test results show that the geographical populations were the same for all gene regions. Results suggest that Cx. tritaeniorhynchus is a native population in Türkiye, the species is progressing towards speciation and there is no genetic differentiation between provinces and regions.

CONCLUSION

This study provides useful information on the molecular identifcation and genetic diversity of Cx. tritaeniorhynchus; these results are important to improve mosquito control programs.

The role of interaction between vitamin D and VDR FokI gene polymorphism (rs2228570) in sleep quality of adults

To evaluate association of vitamin D with sleep quality in adults and the influence of VDR-gene polymorphism FokI (rs2228570;A > G). Cross-sectional population-based study in adults, conducted in Brazil. The outcome was sleep-quality, evaluated by the Pittsburgh Sleep Quality Index. Vitamin D was determined by indirect electrochemiluminescence and classified as deficiency (VDD), 25(OH)D < 20 ng/mL in a healthy population or 25(OH)D < 30 ng/mL for groups at risk for VDD. FokI polymorphism in the VDR-gene was genotyped by qPCR and classified as homozygous wild (FF or AA), heterozygous (Ff or AG), or homozygous mutant (ff or GG). Multivariate logistic analysis was used to estimate the association between vitamin D and FokI polymorphism with sleep-quality. In a total of 1674 individuals evaluated, 53.6% had poor-sleep-quality, 31.5% had VDD, and the genotype frequency of the FokI polymorphism was 9.9% FF, 44.6% Ff, and 45.5% ff. In multivariate analysis, individuals with VDD had 1.51 times the chance of poor-sleep-quality, and individuals with the ff genotype had 1.49 times the chance of poor-sleep-quality (OR:1.49;95%CI:1.05-2.12) when compared to individuals with the FF or Ff genotype. In the combined analysis, individuals with VDD and ff genotype had more chance of poor-sleep-quality than individuals with sufficient vitamin D and genotype Ff or FF (OR:2.19;95%CI:1.27-3.76). Our data suggest that VDD and VDR FokI gene polymorphism are associated with poor-sleep-quality, and combining the two factors increases the chance of poor-sleep-quality compared to separate groups.

Population dataset for 23 Y-STR in the Merkit clan form Kazakh population

This study presents a comprehensive analysis of 23 Y-STR data for the Merkit clan, a subgroup within the Kerey tribe of the Kazakh people. A total of 64 complete haplotypes were generated using the PowerPlex Y23 System. The data obtained using 23 Y-STR markers has been submitted to the Y Chromosome Haplotype Reference Database (YHRD) at yhrd.org, which will significantly enhance the forensic database for the Kazakh population in Kazakhstan. The research focuses on the distribution of haplotypes within the clan and their genealogical lines, which were visualized using a Median-joining network and Multidimensional scaling plot. The study identifies four distinct haplogroup clusters, revealing important insights into the genetic makeup and historical lineage of the Merkits. This dataset not only enriches our understanding of Kazakh genetic structure but also holds significant value for anthropological and population genetic research, as well as for forensic genetics. This work bridges a notable gap in genetic research on the Merkit clan, contributing to a deeper understanding of Central Asian nomadic tribes.

An overload of missense variants in the OTOG gene may drive a higher prevalence of familial Meniere disease in the European population

Meniere disease is a complex inner ear disorder with significant familial aggregation. A differential prevalence of familial MD (FMD) has been reported, being 9-10% in Europeans compared to 6% in East Asians. A broad genetic heterogeneity in FMD has been described, OTOG being the most common mutated gene, with a compound heterozygous recessive inheritance. We hypothesize that an OTOG-related founder effect may explain the higher prevalence of FMD in the European population. Therefore, the present study aimed to compare the allele frequency (AF) and distribution of OTOG rare variants across different populations. For this purpose, the coding regions with high constraint (low density of rare variants) were retrieved in the OTOG coding sequence in Non-Finnish European (NFE).. Missense variants (AF < 0.01) were selected from a 100 FMD patient cohort, and their population AF was annotated using gnomAD v2.1. A linkage analysis was performed, and odds ratios were calculated to compare AF between NFE and other populations. Thirteen rare missense variants were observed in 13 FMD patients, with 2 variants (rs61978648 and rs61736002) shared by 5 individuals and another variant (rs117315845) shared by two individuals. The results confirm the observed enrichment of OTOG rare missense variants in FMD. Furthermore, eight variants were enriched in the NFE population, and six of them were in constrained regions. Structural modeling predicts five missense variants that could alter the otogelin stability. We conclude that several variants reported in FMD are in constraint regions, and they may have a founder effect and explain the burden of FMD in the European population.

Performance and characterization of 94 identity-informative SNPs in Northern Han Chinese using ForenSeq ™ DNA signature prep kit

Target and flanking region (FR) variation at 94 identity-informative SNPs (iSNPs) are investigated in 635 Northern Han Chinese using the ForenSeq DNA Signature Prep Kit on the MiSeq FGx Forensic Genomics System. The dataset presents the following performance characteristics (average values): ≥60% bases with a quality score of 20 or higher (%≥ Q20); >700 × of depth of coverage (DoC) from both Sample Details Reports and Flanking Region Reports; >80% of effective reads; ≥60% of allele coverage ratio (ACR); and ≥70% of inter-locus balance, while some stable low-performance characteristics are also observed: low DoC at rs1736442, rs1031825, rs7041158, rs338882, rs2920816, rs1493232, rs719366, and rs2342747; high noise at rs891700; and imbalanced ACR at rs6955448 and rs338882. The average amplicon length is 69 bp, suitable for detecting degraded samples. Bioinformatic concordance achieves 99.99% between the ForenSeq Universal Analysis Software (UAS) and the Integrative Genomic Viewer (IGV) inspection. Discordance results from flanking region deletions of rs10776839, rs8078417, rs2831700, and rs1454361. Due to FR variants within amplicons detected by massively parallel sequencing (MPS), the increases in the number of unique alleles, effective alleles (Ae), and observed heterozygosity (Hobs) are 46.81%, 4.51%, and 3.29%, respectively. Twelve FR variants are first reported to dbSNP, such as rs1252699848, rs1665500714, rs1771121532, rs2097285015, rs1851671415, rs2045669877, rs2046758811, rs2044248635, rs1251308240, rs1968822112, rs1981638299, and rs1341756746. All 94 iSNPs from target and amplicon data are in Hardy-Weinberg equilibrium (HWE) and independent within autosomes. As expected, forensic parameters from the amplicon data increase significantly on the combined power of discrimination (CPD = 1 - 3.9876 × 10-38) and the combined power of exclusion (CPE = 1 - 6.6690 × 10-8). Additionally, the power of the system effectiveness (CPD = 1 - 6.7054 × 10-72 and CPE = 1 - 4.4719 × 10-20) with sequence-based 27 autosomal STRs and 94 iSNP amplicons in combination is substantially improved compared to one type of marker alone. In conclusion, we have established a traditional length-based and current sequence-based reference database with 58 STRs and 94 iSNPs in the Northern Han Chinese population. We hope these data can serve as a solid reference and foundation for forensic practice.

The Poultry Red Mite, Dermanyssus gallinae, travels far but not frequently, and takes up permanent residence on farms

Management of Dermanyssus gallinae, a cosmopolitan hematophagous mite responsible for damage in layer poultry farming, is hampered by a lack of knowledge of its spatio-temporal population dynamics. Previous studies have shown that the circulation of this pest between farms is of strictly anthropogenic origin, that a mitochondrial haplogroup has been expanding on European farms since the beginning of the 21st century and that its local population growth may be particularly rapid. To refine our understanding of how D. gallinae spreads within and among farms, we characterized the genetic structure of mite populations at different spatial scales and sought to identify the main factors interrupting gene flow between poultry houses and between mitochondrial haplogroups. To this end, we selected and validated the first set of nuclear microsatellite markers for D. gallinae and sequenced a region of the CO1-encoding mitochondrial gene in a subsample of microsatellite-genotyped mites. We also tested certain conditions required for effective contamination of a poultry house through field experimentation, and conducted a survey of practices during poultry transfers. Our results confirm the role of poultry transport in the dissemination of mite populations, but the frequency of effective contamination after the introduction of contaminated material into poultry houses seems lower than expected. The high persistence of mites on farms, even during periods when poultry houses are empty and cleaned, and the very large number of nodes in the logistic network (large number of companies supplying pullets or transporting animals) undoubtedly explain the very high prevalence on farms. Substantial genetic diversity was measured in farm populations, probably as a result of the mite's known haplodiploid mode of sexual reproduction, coupled with the dense logistic network. The possibility of the occasional occurrence of asexual reproduction in this sexually reproducing mite was also revealed in our analyses, which could explain the extreme aggressiveness of its demographic dynamics under certain conditions.

Fitness difference between two synonymous mutations of Phytophthora infestans ATP6 gene

BACKGROUND

Sequence variation produced by mutation provides the ultimate source of natural selection for species adaptation. Unlike nonsynonymous mutation, synonymous mutations are generally considered to be selectively neutral but accumulating evidence suggests they also contribute to species adaptation by regulating the flow of genetic information and the development of functional traits. In this study, we analysed sequence characteristics of ATP6, a housekeeping gene from 139 Phytophthora infestans isolates, and compared the fitness components including metabolic rate, temperature sensitivity, aggressiveness, and fungicide tolerance among synonymous mutations.

RESULTS

We found that the housekeeping gene exhibited low genetic variation and was represented by two major synonymous mutants at similar frequency (0.496 and 0.468, respectively). The two synonymous mutants were generated by a single nucleotide substitution but differed significantly in fitness as well as temperature-mediated spatial distribution and expression. The synonymous mutant ending in AT was more common in cold regions and was more expressed at lower experimental temperature than the synonymous mutant ending in GC and vice versa.

CONCLUSION

Our results are consistent with the argument that synonymous mutations can modulate the adaptive evolution of species including pathogens and have important implications for sustainable disease management, especially under climate change.

Genetic diversities in wild and cultivated populations of the two closely-related medical plants species, Tripterygium Wilfordii and T. Hypoglaucum (Celastraceae)

BACKGROUND

The sustainable supply of medicinal plants is important, and cultivating and domesticating them has been suggested as an optimal strategy. However, this can lead to a loss of genetic diversity. Tripterygium wilfordii Hook. f. is a medicinal plant commonly used in traditional Chinese medicine, but its wild populations are dwindling due to excessive harvesting. To protect the species and meet the increasing demand, it is urgent to cultivate it on a large scale. However, distinguishing between T. wilfordii and T. hypoglaucum, two similar species with different medicinal properties, is challenging. Therefore, it is crucial to understand the genetic diversity and population structure of these species for their sustainable utilization.

RESULTS

In this study, we investigated the genetic diversity and population structure of the two traditional medicinal semiwoody vines plant species, Tripterygium wilfordii and T. hypoglaucum, including wild and cultivated populations using chloroplast DNA (cpDNA) sequences and microsatellite loci. Our results indicated that the two species maintain a high level of genetic divergence, indicating possible genetic bases for the different contents of bioactive compounds of the two species. T. wilfordii showed lower genetic diversity and less subdivided population structures of both markers than T. hypoglaucum. The potential factors in shaping these interesting differences might be differentiated pollen-to-seed migration rates, interbreeding, and history of population divergence. Analyses of cpDNA and microsatellite loci supported that the two species are genetically distinct entities. In addition, a significant reduction of genetic diversity was observed for cultivated populations of the two species, which mainly resulted from the small initial population size and propagated vegetative practice during their cultivation.

CONCLUSION

Our findings indicate significant genetic divergence between T. wilfordii and T. hypoglaucum. The genetic diversity and population structure analyses provide important insights into the sustainable cultivation and utilization of these medicinal plants. Accurate identification and conservation efforts are necessary for both species to ensure the safety and effectiveness of crude drug use. Our study also highlighted the importance of combined analyses of different DNA markers in addressing population genetics of medicinal plants because of the contrasts of inheritance and rates of gene flow. Large-scale cultivation programs should consider preserving genetic diversity to enhance the long-term sustainability of T. wilfordii and T. hypoglaucum. Our study proposed that some populations showed higher genetic diversity and distinctness, which can be considered with priority for conservation and as the sources for future breeding and genetic improvement.

Neutral diversity in experimental metapopulations

New automated and high-throughput methods allow the manipulation and selection of numerous bacterial populations. In this manuscript we are interested in the neutral diversity patterns that emerge from such a setup in which many bacterial populations are grown in parallel serial transfers, in some cases with population-wide extinction and splitting events. We model bacterial growth by a birth-death process and use the theory of coalescent point processes. We show that there is a dilution factor that optimises the expected amount of neutral diversity for a given number of cycles, and study the power law behaviour of the mutation frequency spectrum for different experimental regimes. We also explore how neutral variation diverges between two recently split populations by establishing a new formula for the expected number of shared and private mutations. Finally, we show the interest of such a setup to select a phenotype of interest that requires multiple mutations.

Demographic inference for spatially heterogeneous populations using long shared haplotypes

We introduce a modified spatial Λ-Fleming-Viot process to model the ancestry of individuals in a population occupying a continuous spatial habitat divided into two areas by a sharp discontinuity of the dispersal rate and effective population density. We derive an analytical formula for the expected number of shared haplotype segments between two individuals depending on their sampling locations. This formula involves the transition density of a skew diffusion which appears as a scaling limit of the ancestral lineages of individuals in this model. We then show that this formula can be used to infer the dispersal parameters and the effective population density of both regions, using a composite likelihood approach, and we demonstrate the efficiency of this method on a range of simulated data sets.

On the feasibility of malaria hypothesis

In 1954, Allison proposed that hemoglobin S (HbS) gene causes protection against fatal malaria. This would explain the high HbS gene frequency observed in certain regions hyperendemic for malaria, so-called "malaria hypothesis". This in silico study was conducted to examine the feasibility of the hypothesis under more realistic initial conditions, where a mutant gene with heterozygous advantage against malaria (e.g., HbS) was introduced in a group of Neolithic hunter-gatherers who decided to start agriculture nearby water where malaria killed a proportion of population. The tribe population size, number of children born to each woman in each generation, mortality from malaria and sickle cell disease, the protection factor provided by the gene carriers against malaria, the probability of mating between the members of the parent and offspring populations, population growth, and increased fertility in women heterozygous for HbS, were also considered. For effectively confer protection against malaria within the shortest possible period, the mutation needs to be happened in a small population. For a large population, the process would take around 100 generations (~ 2500 years) or more to provide an effective protection. Even then, the probability that the new gene could survive and propagate to future generations is about 35%. Conventional population genetics equations with differential or difference equations, give totally incorrect estimates of the gene frequency in small populations; discrete mathematics should be used, instead. After introduction of the advantageous mutation, the gene frequency increased until a steady state value. This value is far less than the gene frequency reported in certain tribes of Africa. It seems that the malaria hypothesis, per se, could not explain such a high observed gene frequency, unless HbS is associated with lower mortality from other causes too.

High genetic diversity of the himalayan marmot relative to plague outbreaks in the Qinghai-Tibet Plateau, China

Plague, as an ancient zoonotic disease caused by Yersinia pestis, has brought great disasters. The natural plague focus of Marmota himalayana in the Qinghai-Tibet Plateau is the largest, which has been constantly active and the leading source of human plague in China for decades. Understanding the population genetics of M. himalayana and relating that information to the biogeographic distribution of Yersinia pestis and plague outbreaks are greatly beneficial for the knowledge of plague spillover and arecrucial for pandemic prevention. In the present research, we assessed the population genetics of M. himalayana. We carried out a comparative study of plague outbreaks and the population genetics of M. himalayana on the Qinghai-Tibet Plateau. We found that M. himalayana populations are divided into two main clusters located in the south and north of the Qinghai-Tibet Plateau. Fourteen DFR genomovars of Y. pestis were found and exhibited a significant region-specific distribution. Additionally, the increased genetic diversity of plague hosts is positively associated with human plague outbreaks. This insight gained can improve our understanding of biodiversity for pathogen spillover and provide municipally directed targets for One Health surveillance development, which will be an informative next step toward increased monitoring of M. himalayana dynamics.

Phase-type distributions in mathematical population genetics: An emerging framework

A phase-type distribution is the time to absorption in a continuous- or discrete-time Markov chain. Phase-type distributions can be used as a general framework to calculate key properties of the standard coalescent model and many of its extensions. Here, the 'phases' in the phase-type distribution correspond to states in the ancestral process. For example, the time to the most recent common ancestor and the total branch length are phase-type distributed. Furthermore, the site frequency spectrum follows a multivariate discrete phase-type distribution and the joint distribution of total branch lengths in the two-locus coalescent-with-recombination model is multivariate phase-type distributed. In general, phase-type distributions provide a powerful mathematical framework for coalescent theory because they are analytically tractable using matrix manipulations. The purpose of this review is to explain the phase-type theory and demonstrate how the theory can be applied to derive basic properties of coalescent models. These properties can then be used to obtain insight into the ancestral process, or they can be applied for statistical inference. In particular, we show the relation between classical first-step analysis of coalescent models and phase-type calculations. We also show how reward transformations in phase-type theory lead to easy calculation of covariances and correlation coefficients between e.g. tree height, tree length, external branch length, and internal branch length. Furthermore, we discuss how these quantities can be used for statistical inference based on estimating equations. Providing an alternative to previous work based on the Laplace transform, we derive likelihoods for small-size coalescent trees based on phase-type theory. Overall, our main aim is to demonstrate that phase-type distributions provide a convenient general set of tools to understand aspects of coalescent models that are otherwise difficult to derive. Throughout the review, we emphasize the versatility of the phase-type framework, which is also illustrated by our accompanying R-code. All our analyses and figures can be reproduced from code available on GitHub.

Parasite and genetic diversity of big-scale sand smelt (Atherina boyeri Risso, 1810) populations in their natural and expansion ranges in Ukraine

The big-scale sand smelt (Atherina boyeri) is an Atlanto-Mediterranean amphidromous fish species found within the Black Sea. Here, we assess differences in the parasite fauna of big-scale sand smelt populations from their natural range in the northwestern Black Sea and from their expansion range in the Lower and Middle River Dnipro. In addition, we undertook a microsatellite analysis to assess the genetic similarity of fish from the different locations. We found that the parasite community of fish in their natural range was wider than that from their expansion range. While the Gulf of Odesa was most distant from all other localities by parasite community composition and the Dnipro Reservoir was characterised by an absence of parasites (newest and most distant expansion locality), only fish from the Danube Delta showed a significant genetic difference. Our results suggest that the parasite community of big-scale sand smelt is primarily influenced by environmental factors, such as habitat type, water salinity and/or prey composition. Both microsatellite analysis and parasite community species composition (e.g. the presence of the marine Telosentis exiguus in the Kakhovka Reservoir and freshwater Raphidascaris sp. in the Gulf of Odesa) confirmed that populations in the River Dnipro reservoirs had, at some time, been connected with native marine populations, thus also confirming the species' amphidromous nature.

Mathematical constraints on a family of biodiversity measures via connections with Rényi entropy

The Hill numbers are statistics for biodiversity measurement in ecological studies, closely related to the Rényi and Shannon entropies from information theory. Recent developments in the mathematics of diversity in the setting of population genetics have produced mathematical constraints that characterize how standard measures depend on the highest-frequency class in a discrete probability distribution. Here, we apply these constraints to diversity statistics in ecology, focusing on the Hill numbers and the Rényi and Shannon entropies. The mathematical bounds can shift perspectives on the diversities of communities, in that when upper and lower bounds on Hill numbers are evaluated in a classic butterfly example, Hill numbers that are initially larger in one community switch positions-so that associated normalized Hill numbers are instead smaller than those of the other community. The new bounds hence add to the tools available for interpreting a commonly used family of statistics for ecological data.

Genome-based tools for onchocerciasis elimination: utility of the mitochondrial genome for delineating Onchocerca volvulus transmission zones

National programs in Africa have expanded their objectives from control of onchocerciasis (river blindness) as a public health problem to elimination of parasite transmission, motivated by the reduction of Onchocerca volvulus infection prevalence in many African meso- and hyperendemic areas due to mass drug administration of ivermectin (MDAi). Given the large, contiguous hypo-, meso-, and hyperendemic areas, sustainable elimination of onchocerciasis in sub-Saharan Africa requires delineation of geographic boundaries for parasite transmission zones, so that programs can consider the risk of parasite re-introduction through vector or human migration from areas with ongoing transmission when making decisions to stop MDAi. We propose that transmission zone boundaries can be delineated by characterising the parasite genetic population structure within and between potential zones. We analysed whole mitochondrial genome sequences of 189 O. volvulus adults to determine the pattern of genetic similarity across three West African countries: Ghana, Mali, and Côte d'Ivoire. Population genetic structure indicates that parasites from villages near the Pru, Daka, and Black Volta rivers in central Ghana belong to one parasite population, indicating that the assumption that river basins constitute individual transmission zones is not supported by the data. Parasites from Mali and Côte d'Ivoire are genetically distinct from those from Ghana. This research provides the basis for developing tools for elimination programs to delineate transmission zones, to estimate the risk of parasite re-introduction via vector or human movement when intervention is stopped in one area while transmission is ongoing in others, to identify the origin of infections detected post-treatment cessation, and to investigate whether persisting prevalence despite ongoing interventions in one area is due to parasites imported from others.

Lack of pollinators selects for increased selfing, restricted gene flow and resource allocation in the rare Mediterranean sage Salvia brachyodon

Range contraction and habitat fragmentation can cause biodiversity loss by creating conditions that directly or indirectly affect the survival of plant populations. Fragmented habitats can alter pollinator guilds and impact their behavior, which may result in pollen/pollinator limitation and selection for increased selfing as a mechanism for reproductive assurance. We used Salvia brachyodon, a narrowly distributed and endangered sage from eastern Adriatic, to test the consequences of range contraction and habitat fragmentation. Molecular data indicate a severe and relatively recent species range reduction. While one population is reproductively almost completely isolated, moderate gene flow has been detected between the remaining two populations. The high pollen-to-ovule ratio and the results of controlled hand pollination indicate that S. brachyodon has a mixed mating system. Quantitative and qualitative differences in the community and behaviour of flower visitors resulted in limited pollination services in one population where no effective pollinator other than pollen and nectar robbers were observed. In this population, self-pollination predominated over cross-pollination. Various environmental factors, in which plant-pollinator interactions play a pivotal role, have likely created selection pressures that have led to genetic and phenotypic differentiation and different resource allocation strategies among populations.

Reconstruct recent multi-population migration history by using identical-by-descent sharing

Identical-by-descent (IBD) is a fundamental genomic characteristic in population genetics and has been widely used for population history reconstruction. However, limited by the nature of IBD, which could only capture the relationship between two individuals/haplotypes, existing IBD-based history inference is constrained to two populations. In this study, we propose a novel framework by leveraging IBD sharing in multi-population and develop a method, MatrixIBD, to reconstruct recent multi-population migration history. Specifically, we employ the structured coalescent theory to precisely model the genealogical process and then estimate the IBD sharing across multiple populations. Within our model, we establish a theoretical connection between migration history and IBD sharing. Our method is rigorously evaluated through simulations, revealing its remarkable accuracy and robustness. Furthermore, we apply MatrixIBD to Central and South Asia in the Human Genome Diversity Project and successfully reconstruct the recent migration history of three closely related populations in South Asia. By taking into account the IBD sharing across multiple populations simultaneously, MatrixIBD enables us to attain clearer and more comprehensive insights into the history of regions characterized by complex migration dynamics. This approach provides a holistic perspective on intricate patterns embedded within the recent population migration history.

Fasta2Structure: a user-friendly tool for converting multiple aligned FASTA files to STRUCTURE format

BACKGROUND

The STRUCTURE software has gained popularity as a tool for population structure and genetic analysis. Nevertheless, formatting data to meet STRUCTURE's specific requirements can be daunting and susceptible to errors, especially when handling multilocus data. This article highlights the creation of a graphical user interface (GUI) application tailored to streamline the process of converting multiple sequence alignments into a single, cohesive file that is compatible with the STRUCTURE software.

RESULTS

The application has been developed utilizing Tkinter for the GUI and Biopython for handling FASTA files. This program processes the files, pinpoints variable sites, and converts the sequences into a binary format. Subsequently, the sequences are concatenated and presented within the graphical interface's text area, enabling users to review and confirm the results. Furthermore, the program stores the concatenated results in a file, delivering a ready-to-use input for the STRUCTURE software.

CONCLUSION

This application offers an efficient and dependable solution for transforming multiple aligned FASTA files into a concatenated binary format file, which is compatible with the STRUCTURE software. With its user-friendly graphical interface and error-reduction approach, this tool proves invaluable for researchers engaged in population structure and genetic analysis.

Climatic and soil characteristics account for the genetic structure of the invasive cactus moth Cactoblastis cactorum, in its native range in Argentina

Background

Knowledge of the physical and environmental conditions that may limit the migration of invasive species is crucial to assess the potential for expansion outside their native ranges. The cactus moth, Cactoblastis cactorum, is native to South America (Argentina, Paraguay, Uruguay and Brazil) and has been introduced and invaded the Caribbean and southern United States, among other regions. In North America there is an ongoing process of range expansion threatening cacti biodiversity of the genus Opuntia and the commercial profits of domesticated Opuntia ficus-indica.

Methods

To further understand what influences the distribution and genetic structure of this otherwise important threat to native and managed ecosystems, in the present study we combined ecological niche modeling and population genetic analyses to identify potential environmental barriers in the native region of Argentina. Samples were collected on the host with the wider distribution range, O. ficus-indica.

Results

Significant genetic structure was detected using 10 nuclear microsatellites and 24 sampling sites. At least six genetic groups delimited by mountain ranges, salt flats and wetlands were mainly located to the west of the Dry Chaco ecoregion. Niche modeling supports that this region has high environmental suitability where the upper soil temperature and humidity, soil carbon content and precipitation were the main environmental factors that explain the presence of the moth. Environmental filters such as the upper soil layer may be critical for pupal survival and consequently for the establishment of populations in new habitats, whereas the presence of available hosts is a necessary conditions for insect survival, upper soil and climatic characteristics will determine the opportunities for a successful establishment.

Genetic diversity and natural selection of apical membrane antigen-1 (ama-1) in Cameroonian Plasmodium falciparum isolates

Antigenic variation associated with genetic diversity in global Plasmodium falciparum apical membrane antigen-1 (PfAMA-1) is a major impediment to designing an effective malaria vaccine. Here, we report the first study on genetic diversity and natural selection of the Pfama-1 gene in P. falciparum isolates from Cameroon. A total of 328 P. falciparum positive samples collected during 2016 and 2019 from five localities of Cameroon were analysed. The ectodomain coding fragment of Pfama-1 gene was amplified for polymorphism profiling and natural selection analysis. A total of 108 distinct haplotypes were found in 203 P. falciparum isolates with considerable nucleotide diversity (π = 0.016) and haplotype diversity (Hd = 0.976). Most amino acid substitutions detected were scattered in ectodomain-I and few specific mutations viz P145L, K148Q, K462I, L463F, N471K, S482L, E537G, K546R and I547F were seen only in Cameroonian isolates. A tendency of natural selection towards positive diversifying selection was observed (Taj-D = 2.058). Five positively selected codon sites (P145L, S283L, Q308E/K, P330S and I547F) were identified, which overlapped with predicted B-cell epitopes and red blood cell (RBC) binding sites, suggesting their potential implication in host immune pressure and parasite-RBC binding complex modulation. The Cameroonian P. falciparum populations indicated a moderate level of genetic differentiation when compared with global sequences, with few exceptions from Vietnam and Venezuela. Our findings provide baseline data on existing Pfama-1 gene polymorphisms in Cameroonian field isolates, which will be useful information for malaria vaccine design.

Genetic diversity and forensic statistical support for the 12 X-STR markers in the Malaysian Indian population using Qiagen Investigator® Argus X-12 QS kit

X-chromosome short tandem repeats (X-STRs) are useful for human identification, especially in complex kinship scenarios. Since forensic statistical parameters vary among populations and the X-STRs population data for the diverse population of Peninsular Malaysia's are unavailable, this attempt for Indians (n = 201) appears forensically relevant to support the 12 X-STRs markers' evidential value for human identification in Malaysia. The Qiagen Investigator® Argus X-12 QS kit showed that DXS10135 was the most polymorphic locus with high genetic diversity, polymorphism information richness, heterozygosity, and exclusion power. Based on allele frequencies, the strength of discrimination and mean exclusion chance (MECKrüger, MECKishida, MECDesmarais, and MECDesmaraisDuo) values for the Malaysian Indians were ≥0.999997790686228. As for haplotype frequencies, the overall discrimination power and mean exclusion probability (MECKrüger, MECKishida, MECDesmarais, and MECDesmaraisDuo) were ≥0.9999984801951. The genetic distance, neighbor-joining phylogenetic tree, and principal component analysis also supported the evidential value of the 12 X-STRs markers for forensic practical caseworks in Malaysia.

Co-occurrence of dual lineages within Simulium (Gomphostilbia) atratum De Meijere in the Indonesian Archipelago along Wallace's Line

Mitochondrial cytochrome c oxidase subunit I (COI) sequences were utilized to infer the population genetic structure of Simulium (Gomphostilbia) atratum De Meijere, an endemic simulid species to Indonesia. Both median-joining haplotype network and maximum-likelihood tree revealed two genetic lineages (A and B) within the species, with an overlap distribution in Lombok, which is situated along Wallace's line. Genetic differentiation and gene flow with varying frequencies (FST = 0.02-0.967; Nm = 0.01-10.58) were observed between populations of S. (G.) atratum, of which population pairs of different lineages showed high genetic differentiation. Notably, the high genetic distance of up to 5.92 % observed within S. (G.) atratum in Lombok was attributed to the existence of two genetically distinct lineages. The co-occurrence of distinct lineages in Lombok indicated that Wallace's line did not act as faunistic border for S. (G.) atratum in the present study. Moreover, both lineages also exhibited unimodal distributions and negative values of neutrality tests, suggesting a pattern of population expansion. The expansion and divergence time estimation suggested that the two lineages of S. (G.) atratum diverged and expanded during the Pleistocene era in Indonesia.

Gene drives for the extinction of wild metapopulations

Population-suppressing gene drives may be capable of extinguishing wild populations, with proposed applications in conservation, agriculture, and public health. However, unintended and potentially disastrous consequences of release of drive-engineered individuals are extremely difficult to predict. We propose a model for the dynamics of a sex ratio-biasing drive, and using simulations, we show that failure of the suppression drive is often a natural outcome due to stochastic and spatial effects. We further demonstrate rock-paper-scissors dynamics among wild-type, drive-infected, and extinct populations that can persist for arbitrarily long times. Gene drive-mediated extinction of wild populations entails critical complications that lurk far beyond the reach of laboratory-based studies. Our findings help in addressing these challenges.

Genetic approaches reveal a healthy population and an unexpectedly recent origin for an isolated desert spring fish

Foskett Spring in Oregon's desert harbors a historically threatened population of Western Speckled Dace (Rhinichthys klamathensis). Though recently delisted, the dace's recruitment depends upon regular removal of encroaching vegetation. Previous studies assumed that Foskett Dace separated from others in the Warner Valley about 10,000 years ago, thereby framing an enigma about the population's surprising ability to persist for so long in a tiny habitat easily overrun by plants. To investigate that persistence and the effectiveness of interventions to augment population size, we assessed genetic diversity among daces inhabiting Foskett Spring, a refuge at Dace Spring, and three nearby streams. Analysis revealed a robust effective population size (Ne) of nearly 5000 within Foskett Spring, though Ne in the Dace Spring refuge is just 10% of that value. Heterozygosity is slightly lower than expected based on random mating at all five sites, indicating mild inbreeding, but not at a level of concern. These results confirm the genetic health of Foskett Dace. Unexpectedly, genetic differentiation reveals closer similarity between Foskett Dace and a newly discovered population from Nevada's Coleman Creek than between Foskett Dace and dace elsewhere in Oregon. Demographic modeling inferred Coleman Creek as the ancestral source of Foskett Dace fewer than 1000 years ago, much more recently than previously suspected and possibly coincident with the arrival of large herbivores whose grazing may have maintained open water suitable for reproduction. These results solve the enigma of persistence by greatly shortening the duration over which Foskett Dace have inhabited their isolated spring.

Contamination acts as a genotype-dependent barrier to gene flow, causing genetic erosion and fine-grained population subdivision in Mussels from the Strait of Istanbul

This study provides evidence of fine-grained genetic structuring in Mediterranean mussels (Mytilus galloprovincialis) from the Strait of Istanbul, caused by barriers to gene flow via contaminant-mediated selection. In this study, mitochondrial D-loop sequences were analyzed in mussels from 8 localities, all less than 30 kilometers apart, with differing contaminant loads. The results were: 1) Intra-population genetic differentiation (ΦST) between sites with high and low contaminant loads was high (up to 0.459), even at distances of only a few kilometers. 2) Genetic diversity was negatively correlated with the contaminant load ("genetic erosion"). 3) There was evidence of selection, based on haplotype frequencies and neutrality tests (Tajima's D), with purifying selection at the most contaminated site and balancing selection at the least contaminated. 4) Genetic distance was not correlated with geographic distance (no isolation-by-distance), but was correlated with contaminant load at each site. 5) Population dendrograms and Bayesian estimators of migration indicated that gene flow between sites was affected by contamination. For the dendrograms of the sampling sites, the clades clustered according to contaminant load more than geographic distance. Overall, these results suggest that 1) contamination may serve as a genotype-dependent dispersal barrier (i.e., contamination may not affect total number of migrants, just the relative proportions of the haplotypes in the established immigrants), leading strong population differentiation over short distances, and 2) genetic erosion may occur by a combination of selection and altered patterns of haplotype-specific gene flow. These effects may be more pronounced in the Strait of Istanbul than in other locations because of the riverine nature and strong, uni-directional current of the strait.

Rare-variant and polygenic analyses of amyotrophic lateral sclerosis in the French-Canadian genome

PURPOSE

The genetic etiology of amyotrophic lateral sclerosis (ALS) includes few rare, large-effect variants and potentially many common, small-effect variants per case. The genetic risk liability for ALS might require a threshold comprised of a certain amount of variants. Here, we tested the degree to which risk for ALS was affected by rare variants in ALS genes, polygenic risk score, or both.

METHODS

335 ALS cases and 356 controls from Québec, Canada were concurrently tested by microarray genotyping and targeted sequencing of ALS genes known at the time of study inception. ALS genome-wide association studies summary statistics were used to estimate an ALS polygenic risk score (PRS). Cases and controls were subdivided into rare-variant heterozygotes and non-heterozygotes.

RESULTS

Risk for ALS was significantly associated with PRS and rare variants independently in a logistic regression model. Although ALS PRS predicted a small amount of ALS risk overall, the effect was most pronounced between ALS cases and controls that were not heterozygous for a rare variant in the ALS genes surveyed.

CONCLUSION

Both PRS and rare variants in ALS genes impact risk for ALS. PRS for ALS is most informative when rare variants are not observed in ALS genes.

Validating a Mitochondrial Sweep Accompanying the Rapid Spread of a Maternally Inherited Symbiont

Maternally inherited symbiotic bacteria that interfere with the reproduction of their hosts can contribute to selective sweeps of mitochondrial haplotypes through hitch-hiking or coordinate inheritance of cytoplasmic bacteria and host mitochondria. The sweep will be manifested by genetic variations of mitochondrial genomic DNA of symbiont-infected hosts relative to their uninfected counterparts. In particular, at the population level, infected specimens will show a reduced mitochondrial DNA polymorphism compared to that in the nuclear DNA. This may challenge the use of mitochondrial DNA sequences as neutral genetic markers, as the mitochondrial patterns will reflect the evolutionary history of parasitism, rather than the sole evolutionary history of the host. Here, I describe a detailed step-by-step procedure to infer the occurrence and timing of symbiont-induced mitochondrial sweeps in host species.

Using two self-developed InDel panels to explore forensic traits and ancestral components in the Hui group

To address the challenges faced by forensic examiners in degraded DNA analysis, we have developed two different panels for various forensic applications, encompassing an AIM-InDel panel for ancestry inference and a Multi-InDel panel for individual identification, respectively. Herein, the efficiencies of these two panels were tested in the Chinese Hui group. By calculating forensic parameters and simulating family relationships, we verified that the Multi-InDel panel could be an effective tool for individual identification, paternity testing, and could assist in kinship identification in the Hui group. For full siblings, the true positive rate of kinship discrimination was 96.553%, when the threshold of log10LR was 1. The cumulative probability of matching as well as cumulative probability of exclusion were 3.8117 × 10-26 and 0.999999722, respectively. Meanwhile, we found that the AIM-InDel panel was effective for bio-geographic ancestry inference, with the vast majority of loci contributing significantly to distinguish East Asian, African, and European populations. By studying the population structure of the Hui ethnic minority, the genetic distance to the Beijing Han population was the closest among the 26 reference populations, which was similar to previous reports. In summary, we have developed two panels which can be effectively applied to the Hui group for individual identification, parentage testing and bio-geographic ancestry inference.

Estimation of population specific values of theta for sequence-based STR profiles

We describe the estimation of θ (theta) values from autosomal STR sequencing data for five metapopulations. The data were compiled from 20 publications and included 39 datasets comprising a total of 7005 samples. The estimates are suitable for use within the calculation of match probabilities in forensic casework. We also have constructed a phylogenetic tree using this data that aligns with our understanding of human evolution.

Genetic diversity and population structure of farmed and wild Nile tilapia (Oreochromis niloticus) in Uganda: The potential for aquaculture selection and breeding programs

Nile tilapia is one of the most important aquaculture species globally, providing high-quality animal protein for human nutrition and a source of income to sustain the livelihoods of many people in low- and middle-income countries. This species is native to Africa and nowadays farmed throughout the world. However, the genetic makeup of its native populations remains poorly characterized. Additionally, there has been important introgression and movement of farmed (as well as wild) strains connected to tilapia aquaculture in Africa, yet the relationship between wild and farmed populations is unknown in most of the continent. Genetic characterization of the species in Africa has the potential to support the conservation of the species as well as supporting selective breeding to improve the indigenous strains for sustainable and profitable aquaculture production. In the current study, a total of 382 fish were used to investigate the genetic structure, diversity, and ancestry within and between Ugandan Nile tilapia populations from three major lakes including Lake Albert (L. Albert), Lake Kyoga (L. Kyoga) and Lake Victoria (L. Victoria), and 10 hatchery farms located in the catchment regions of these lakes. Our results showed clear genetic structure of the fish sourced from the lakes, with L. Kyoga and L. Albert populations showing higher genetic similarity. We also observed noticeable genetic structure among farmed populations, with most of them being genetically similar to L. Albert and L. Kyoga fish. Admixture results showed a higher (2.55-52.75%) contribution of L. Albert / L. Kyoga stocks to Uganda's farmed fish than the stock from L. Victoria (2.12-28.02%). We observed relatively high genetic diversity across both wild and farmed populations, but some farms had sizable numbers of highly inbred fish, raising concerns about management practices. In addition, we identified a genomic region on chromosome 5, harbouring the key innate immune gene BPI and the key growth gene GHRH, putatively under selection in the Ugandan Nile tilapia population. This region overlaps with the genomic region previously identified to be associated with growth rate in farmed Nile tilapia.

The effect of environmental factors on the genetic differentiation of Cucurbita ficifolia populations based on whole-genome resequencing

BACKGROUND

Cucurbita ficifolia is one of the squash species most resistant to fungal pathogens, and has especially high resistance to melon Fusarium wilt. This species is therefore an important germplasm resource for the breeding of squash and melon cultivars.

RESULTS

Whole-genome resequencing of 223 individuals from 32 populations in Yunnan Province, the main cucurbit production area in China, was performed and 3,855,120 single-nucleotide polymorphisms (SNPs) and 1,361,000 InDels were obtained. SNP analysis suggested that levels of genetic diversity in C. ficifolia were high, but that different populations showed no significant genetic differentiation or geographical structure, and that individual C. ficifolia plants with fruit rinds of a similar color did not form independent clusters. A Mantel test conducted in combination with geographical distance and environmental factors suggested that genetic distance was not correlated with geographical distance, but had a significant correlation with environmental distance. Further associations between the genetic data and five environmental factors were analyzed using whole-genome association analysis. SNPs associated with each environmental factor were investigated and genes 250 kb upstream and downstream from associated SNPs were annotated. Overall, 15 marker-trait-associated SNPs (MTAs) and 293 genes under environmental selection were identified. The identified genes were involved in cell membrane lipid metabolism, macromolecular complexes, catalytic activity and other related aspects. Ecological niche modeling was used to simulate the distribution of C. ficifolia across time, from the present and into the future. We found that the area suitable for C. ficifolia changed with the changing climate in different periods.

CONCLUSIONS

Resequencing of the C. ficifolia accessions has allowed identification of genetic markers, such as SNPs and InDels. The SNPs identified in this study suggest that environmental factors mediated the formation of the population structure of C. ficifolia in China. These SNPs and Indels might also contribute to the variation in important pathways of genes for important agronomic traits such as yield, disease resistance and stress tolerance. Moreover, the genome resequencing data and the genetic markers identified from 223 accessions provide insight into the genetic variation of the C. ficifolia germplasm and will facilitate a broad range of genetic studies.

Microsatellites reveal divergence in population genetic diversity, and structure of osyris lanceolata (santalaceae) in Uganda and Kenya

BACKGROUND

Osyris lanceolata (Hochst. & Steud.) (Santalaceae) is a multipurpose plant highly valued culturally and economically in Africa. However, O. lanceolata populations have rapidly dwindled in East Africa due to overexploitation and this is believed to cause further consequences on the species' genetic diversity and structure within the region. Information regarding a species' genetic diversity and structure is necessary for conservation but this is currently lacking for O. lanceolata in Uganda and Kenya. Lack of adequate scientific data hinders conservation efforts hence threatening the species survival and livelihoods. This study investigated patterns in genetic diversity and structure of O. lanceolata in Uganda and Kenya. Ten polymorphic microsatellite loci were used to genotype 210 individuals: 96 from Ugandan and 114 from Kenyan populations.

RESULTS

All populations were highly polymorphic (80-100% polymorphism). A genetic differentiation was found between Kenyan and Ugandan populations. The highest genetic differentiation was among individuals and the least among populations. The Kenyan populations showed higher genetic diversity than Ugandan populations. The Ugandan populations showed more marker deviations from Hardy-Weinberg equilibrium and inbreeding coefficient. Two populations showed evidence of going through a recent bottleneck. There was significant genetic differentiation and structuring at higher K values into larger clusters and observed admixture between populations. The populations were significantly isolated by altitude as opposed to distance and climatic variables. Main barriers were associated with altitude differences. The data supports the idea of long-distance gene-flow between high altitude populations in both countries.

CONCLUSION

The divergence in genetic structure suggests unrecognised taxonomic units within O. lanceolata which are characteristic to lower altitudes and higher altitudes including most Kenyan populations with divergent evolutionary patterns. Geographical barriers and environmental gradients could have influenced this genetic divergence, and such patterns may escalate the species microevolutionary processes into full allopatric speciation. Further investigations into the species' genetic admixture and emerging taxonomic units are necessary to guide conservation strategies in the region.

Genomic DNA extraction optimization and validation for genome sequencing using the marine gastropod Kellet's whelk

Next-generation sequencing technologies, such as Nanopore MinION, Illumina Hiseq and Novaseq, and PacBio Sequel II, hold immense potential for advancing genomic research on non-model organisms, including the vast majority of marine species. However, application of these technologies to marine invertebrate species is often impeded by challenges in extracting and purifying their genomic DNA due to high polysaccharide content and other secondary metabolites. In this study, we help resolve this issue by developing and testing DNA extraction protocols for Kellet's whelk (Kelletia kelletii), a subtidal gastropod with ecological and commercial importance, by comparing four DNA extraction methods commonly used in marine invertebrate studies. In our comparison of extraction methods, the Salting Out protocol was the least expensive, produced the highest DNA yields, produced consistent high DNA quality, and had low toxicity. We validated the protocol using an independent set of tissue samples, then applied it to extract high-molecular-weight (HMW) DNA from over three thousand Kellet's whelk tissue samples. The protocol demonstrated scalability and, with added clean-up, suitability for RAD-seq, GT-seq, as well as whole genome sequencing using both long read (ONT MinION) and short read (Illumina NovaSeq) sequencing platforms. Our findings offer a robust and versatile DNA extraction and clean-up protocol for supporting genomic research on non-model marine organisms, to help mediate the under-representation of invertebrates in genomic studies.

Characterization and population genetics of Haemonchus contortus in Merino sheep in Lesotho

Haemonchus contortus is the most pathogenic and economically restrictive gastrointestinal nematode in the small ruminant industry globally. Morbidity, poor cross-bodily state, and mortality of sheep in Lesotho suggest the presence of H. contortus. The present study investigated the morphological, molecular, and population genetics of H. contortus third-stage larvae infecting sheep in four ecological zones (EZ) of Lesotho. Coprocultures were prepared for larval morphological identification and PCR determination. Larvae were identified morphologically as 100% H. contortus. The Second Internal Transcribed Spacer (ITS-2) gene of the ribosomal DNA of H. contortus isolates in the present study revealed nucleotide homology ranging from 97 to 100% when compared with selected GenBank reference sequences. Pairwise evolutionary divergence among H. contortus isolates was low, with 0.01318 recorded as the highest in the present study. Five haplotypes resulted from 14 Lesotho sequences. Haplotype diversity and nucleotide diversity were 0.76923 and 0.00590, respectively. Genetic differentiation among isolates was low but not statistically significant. An analysis of molecular variance revealed that most molecular variation was distributed within topographic populations at 94.79% (FST = 0.05206, p > 0.05) and 5.21% among populations. There was high gene flow and no definite population genetic structure among Lesotho isolates.

[Race as Global Data Stream: Anthropological Research in 20th Century Hamburg as a Vantage Point for a Data History of Racialization]

This article explores anthropological research conducted in Hamburg during the 20th century and demonstrates how historically specific discourse networks (Aufschreibesysteme) shaped concepts of race and their subsequent use in politics. To this end, this study examines three paradigms within the history of German anthropology in terms of their underlying inscription technique: physical anthropology/loose-leaf collection, "Erblehre"/card index, and population genetics/electronic data processing. By outlining a data history of racialization, this article avoids the ontological pitfalls of recent debates about the category of race.

Utility of wastewater genomic surveillance compared to clinical surveillance to track the spread of the SARS-CoV-2 Omicron variant across England

The world has moved into a new stage of managing the SARS-CoV-2 pandemic with minimal restrictions and reduced testing in the population, leading to reduced genomic surveillance of virus variants in individuals. Wastewater-based epidemiology (WBE) can provide an alternative means of tracking virus variants in the population but decision-makers require confidence that it can be applied to a national scale and is comparable to individual testing data. We analysed 19,911 samples from 524 wastewater sites across England at least twice a week between November 2021 and February 2022, capturing sewage from >70% of the English population. We used amplicon-based sequencing and the phylogeny based de-mixing tool Freyja to estimate SARS-CoV-2 variant frequencies and compared these to the variant dynamics observed in individual testing data from clinical and community settings. We show that wastewater data can reconstruct the spread of the Omicron variant across England since November 2021 in close detail and aligns closely with epidemiological estimates from individual testing data. We also show the temporal and spatial spread of Omicron within London. Our wastewater data further reliably track the transition between Omicron subvariants BA1 and BA2 in February 2022 at regional and national levels. Our demonstration that WBE can track the fast-paced dynamics of SARS-CoV-2 variant frequencies at a national scale and closely match individual testing data in time shows that WBE can reliably fill the monitoring gap left by reduced individual testing in a more affordable way.

Insights on Pinna nobilis population genetic structure in the Aegean and Ionian Sea

The fan mussel Pinna nobilis Linnaeus, 1758 is an endemic species of the Mediterranean Sea, protected by international agreements. It is one of the largest bivalves in the world, playing an important role in the benthic communities; yet it has been recently characterized as Critically Endangered by the IUCN, due to mass mortality events. In this context, the assessment of the genetic variation of the remaining P. nobilis populations and the evaluation of connectivity among them are crucial elements for the conservation of the species. For this purpose, samples were collected from six regions of the Eastern Mediterranean Sea; the Islands of Karpathos, Lesvos and Crete; the Chalkidiki and Attica Peninsulas; and the Amvrakikos Gulf. Sampling was performed either by collecting tissue from the individuals or by using a non-invasive method, i.e., by scraping the inside of their shells aiming to collect their mucus and thus avoid stress induction to them. Conventional molecular techniques with the use of the COI and 16S rRNA mitochondrial markers were selected for the depiction of the intra-population genetic variability. The analyses included 104 samples from the present study and publicly available sequences of individuals across the whole Mediterranean Sea. The results of this work (a) suggest the use of eDNA as an efficient sampling method for protected bivalves and (b) shed light to the genetic structure of P. nobilis population in the Eastern Mediterranean; this latter knowledge might prove to be fundamental for the species conservation and hence the ecosystem resilience. The haplotype analyses reinforced the evidence that there is a certain degree of connectivity among the distinct regions of the Mediterranean; yet there is evidence of population distinction within the basin, namely between the Western and the Eastern basins. The combination of both genetic markers in the same analysis along with the inclusion of a large number of individuals produced more robust results, revealing a group of haplotypes being present only in the Eastern Mediterranean and providing insights for the species' most suitable conservation management.

Genome-wide expression QTL mapping reveals the highly dynamic regulatory landscape of a major wheat pathogen

BACKGROUND

In agricultural ecosystems, outbreaks of diseases are frequent and pose a significant threat to food security. A successful pathogen undergoes a complex and well-timed sequence of regulatory changes to avoid detection by the host immune system; hence, well-tuned gene regulation is essential for survival. However, the extent to which the regulatory polymorphisms in a pathogen population provide an adaptive advantage is poorly understood.

RESULTS

We used Zymoseptoria tritici, one of the most important pathogens of wheat, to generate a genome-wide map of regulatory polymorphism governing gene expression. We investigated genome-wide transcription levels of 146 strains grown under nutrient starvation and performed expression quantitative trait loci (eQTL) mapping. We identified cis-eQTLs for 65.3% of all genes and the majority of all eQTL loci are within 2kb upstream and downstream of the transcription start site (TSS). We also show that polymorphism in different gene elements contributes disproportionally to gene expression variation. Investigating regulatory polymorphism in gene categories, we found an enrichment of regulatory variants for genes predicted to be important for fungal pathogenesis but with comparatively low effect size, suggesting a separate layer of gene regulation involving epigenetics. We also show that previously reported trait-associated SNPs in pathogen populations are frequently cis-regulatory variants of neighboring genes with implications for the trait architecture.

CONCLUSIONS

Overall, our study provides extensive evidence that single populations segregate large-scale regulatory variation and are likely to fuel rapid adaptation to resistant hosts and environmental change.

Population structure of pygmy (Kogia breviceps) and dwarf (Kogia sima) sperm whales in the Southern Hemisphere may reflect foraging ecology and dispersal patterns

Little is known about the biology of pygmy (Kogia breviceps) and dwarf (K. sima) sperm whales as these animals are difficult to observe in the wild. However, both species strand frequently along the South African, Australian and New Zealand coastlines, providing samples for these otherwise inaccessible species. The use of DNA samples from tissue and DNA extracted from historical material, such as teeth and bone, allowed a first analysis of the population structure of both species in the Southern Hemisphere. A 279 base pair consensus region of the mitochondrial cytochrome b gene was sequenced for 96 K. breviceps (53 tissue and 43 teeth or bone samples) and 29 K. sima (3 tissue and 26 teeth or bone samples), and 26 and 12 unique haplotypes were identified, respectively. K. breviceps showed a higher nucleotide diversity of 0.82% compared to 0.40% in K. sima. Significant genetic differentiation was detected in the Southern Hemisphere between K. breviceps from South Africa and New Zealand (ФST = 0.042, p < 0.05). Mitochondrial control region sequences (505 bp) were available for 44 individuals (41 K. breviceps and 3 K. sima) for comparative purposes. A comprehensive global phylogenetic analysis (maternal lineage) of our sequences together with all available Kogia mtDNA sequences largely supported previously published phylogenetic findings, but highlighted some changed inferences about oceanic divergences within both species. The higher nucleotide diversity and low population differentiation observed in K. breviceps may result from its broad foraging ecology and wide distribution, which may indicate a more opportunistic feeding behaviour and tolerance towards a larger range of water temperatures than K. sima.

Unveiling the genetic landscape of high-altitude adaptive ethnic groups with polymorphic markers: Implications of comprehensive forensic appraisals and population genetic investigations

Background

Deletion/insertion polymorphisms (DIPs), a novel class of biomarker, have been widely utilized in forensic areas for individual identification, paternity tests, and ancestral origin inference due to its applicability to degraded samples and low mutation rates. Despite the availability of a well-established commercial kit, the Investigator® DIPplex kit (Qiagen), certain loci exhibit limited levels of polymorphisms in East Asian populations, particularly in Chinese populations.

Objective

This dissertation seeks to undertake a comprehensive evaluation about the forensic efficiency of a self-developed multiplex amplification system in high-altitude adaptive ethnic groups of China. Healthy unrelated Tibetan individuals residing in Tibet Autonomous Region and Qinghai Province were genotyped using previously reported 43 deletion/insertion polymorphism loci. Forensic statistical analyses including allele frequencies and forensic parameters were conducted in the two Tibetan groups, and the genetic relatedness of the studied groups with reference populations from the 1000 Genomes Project Phase 3 were investigated.

Results

Forensic statistical results showed that the polymorphism information content values of the 43 deletion/insertion polymorphism loci in the two Tibetan groups exceeded 0.35. Moreover, the combined power of discrimination using the 43 deletion/insertion polymorphism loci was calculated to be 0.9999999999999999984 in the Qinghai Tibetan group and 0.9999999999999999921 in the Tibet Tibetan group. The cumulative power of exclusion using the 43 deletion/insertion polymorphism loci was calculated to be 0.999782512 in the Qinghai Tibetan group and 0.999886205 in the Tibet Tibetan group. Analysis of population genetics demonstrated that the two studied Tibetan groups shared close genetic relationships with East Asia populations.

Conclusion

The set of 43 deletion/insertion polymorphism loci exhibited remarkable forensic efficacy, rendering it a promising tool for forensic practice. Population genetic analyses indicated that the two Tibetan groups had closer genetic affinities to East Asian populations.

A forensic population database of autosomal STR and X-STR markers in the Qiang ethnic minority of China

The Qiang ethnic group is one of the oldest ethnic groups in China and is the most active ethnic group among all the populations along the Tibetan-Yi corridor. They have had a profound impact nationally and internationally. The paternal and maternal genetic feature of the Qiang ethnic group has been revealed, leaving the question of the genetic characteristics from autosomes and X chromosome not answered. The aim of this study was to explore the potential of 36 A-STR (Microreader™ 36A ID System) and 19 X-STR (Microreader™ 19X System) for application in the Qiang population and to elucidate their genetic diversity in southwest China. The cumulative probability of exclusion (CPE) for autosomal STRs is 1-1.3814 × 10-15 and the mean paternity exclusion chance (MEC) for X-STRs is 1-1.7323 × 10-6. Forensic parameters suggest that the STRs analyzed here are well-suited for forensic applications. The results of phylogenetic, interpopulation differentiation, and principal coordinates analysis (PCoA) indicate that the Qiang people have extensive connections with ethnic minorities in China, supporting the view that the Qiang people are the oldest group in the entire Sino-Tibetan language family. The Qiang appeared genetically more associated with most ethnic groups in China, especially the Han. The calculation of random matching probability (RMP) was improved by Fst correction of allele frequencies to make RMP more accurate and reasonable. This study can fill in the gaps in the Qiang STR reference database, providing valuable frequency data for forensic applications and evidence for the Qiang's genetic pattern as an important ancestral position in the Sino-Tibetan populations.

Intraspecific microdiversity and ecological drivers of lactic acid bacteria in naturally fermented milk ecosystem

Traditional fermented milks are produced by inoculating technique, which selects well-adapted microorganisms that have been passed on through generations. Few reports have used naturally fermented milks as model ecosystems to investigate the mechanism of formation of intra-species microbial diversity. Here, we isolated and whole-genome-sequenced a total of 717 lactic acid bacterial isolates obtained from 12 independent naturally fermented milks collect from 12 regions across five countries. We further analyzed the within-sample intra-species phylogenies of 214 Lactobacillus helveticus isolates, 97 Lactococcus lactis subsp. lactis isolates, and 325 Lactobacillus delbrueckii subsp. bulgaricus isolates. We observed a high degree of intra-species genomic and functional gene diversity within-/between-sample(s). Single nucleotide polymorphism-based phylogenetic reconstruction revealed great within-sample intra-species heterogeneity, evolving from multiple lineages. Further phylogenetic reconstruction (presence-absence gene profile) revealed within-sample inter-clade functional diversity (based on carbohydrate-active enzyme- and peptidase-encoding genes) in all three investigated species/subspecies. By identifying and mapping clade-specific genes of intra-sample clades of the three species/subspecies to the respective fermented milk metagenome, we found extensive potential inter-/intra-species horizontal gene transfer events. Finally, the microbial composition of the samples is closely linked to the nucleotide diversity of the respective species/subspecies. Overall, our results contribute to the conservation of lactic acid bacteria resources, providing ecological insights into the microbial ecosystem of naturally fermented dairy products.

The composition of piRNA clusters in Drosophila melanogaster deviates from expectations under the trap model

BACKGROUND

It is widely assumed that the invasion of a transposable element (TE) in mammals and invertebrates is stopped when a copy of the TE jumps into a piRNA cluster (i.e., the trap model). However, recent works, which for example showed that deletion of three major piRNA clusters has no effect on TE activity, cast doubt on the trap model.

RESULTS

Here, we test the trap model from a population genetics perspective. Our simulations show that the composition of regions that act as transposon traps (i.e., potentially piRNA clusters) ought to deviate from regions that have no effect on TE activity. We investigated TEs in five Drosophila melanogaster strains using three complementary approaches to test whether the composition of piRNA clusters matches these expectations. We found that the abundance of TE families inside and outside of piRNA clusters is highly correlated, although this is not expected under the trap model. Furthermore, the distribution of the number of TE insertions in piRNA clusters is also much broader than expected.

CONCLUSIONS

We found that the observed composition of piRNA clusters is not in agreement with expectations under the simple trap model. Dispersed piRNA producing TE insertions and temporal as well as spatial heterogeneity of piRNA clusters may account for these deviations.

disperseNN2: a neural network for estimating dispersal distance from georeferenced polymorphism data

Spatial genetic variation is shaped in part by an organism's dispersal ability. We present a deep learning tool, disperseNN2, for estimating the mean per-generation dispersal distance from georeferenced polymorphism data. Our neural network performs feature extraction on pairs of genotypes, and uses the geographic information that comes with each sample. These attributes led disperseNN2 to outperform a state-of-the-art deep learning method that does not use explicit spatial information: the mean relative absolute error was reduced by 33% and 48% using sample sizes of 10 and 100 individuals, respectively. disperseNN2 is particularly useful for non-model organisms or systems with sparse genomic resources, as it uses unphased, single nucleotide polymorphisms as its input. The software is open source and available from https://github.com/kr-colab/disperseNN2 , with documentation located at https://dispersenn2.readthedocs.io/en/latest/ .

Studies on genetic diversity, gene flow and landscape genetic in Avicennia marina: Spatial PCA, Random Forest, and phylogeography approaches

Mangrove forests grow in coastal areas, lagoons, estuaries, and deltas and form the main vegetation in tidal and saline wetlands. Due to the mankind activities and also changes in climate, these forests face degradations and probably extinction in some areas. Avicennia marina is one of the most distributed mangrove species throughout the world. The populations of A. marina occur in a limited region in southern parts of Iran. Very few genetic and spatial analyses are available on these plants from our country. Therefore, the present study was planned to provide detailed information on Avicennia marina populations with regard to genetic diversity, gene flow versus genetic isolation, effects of spatial variables on connectivity and structuring the genetic content of trees populations and also identifying adaptive genetic regions in respond too spatial variables. We used SCoT molecular markers for genetic analyses and utilized different computational approaches for population genetics and landscapes analyses. The results of present study showed a low to moderate genetic diversity in the studied populations and presence of significant Fst values among them. Genetic fragmentation was also observed within each province studied. A limited gene flow was noticed among neighboring populations within a particular province. One population was almost completely isolated from the gene flow with other populations and had peculiar genetic content.Spatial PCA analysis revealed both significant global and local genetic structuring in the studied populations. Spatial variables like humidity, longitude and altitude were the most important spatial features affecting genetic structure in these populations.

Mitochondrial sequence data reveal population structure within Pustulosa pustulosa

Unionid mussels are among the most imperiled group of organisms in North America, and Pustulosa pustulosa is a freshwater species with a relatively wide latitudinal distribution that extends from southern Ontario, Canada, to Texas, USA. Considerable morphological and geographic variation in the genus Pustulosa (formerly Cyclonaias) has led to uncertainty over species boundaries, and recent studies have suggested revisions to species-level classifications by synonymizing C. aurea, C. houstonensis, C. mortoni, and C. refulgens with C. pustulosa (currently P. pustulosa). Owing to its wide range and shallow phylogenetic differentiation, we analyzed individuals of P. pustulosa using mitochondrial DNA sequence data under a population genetics framework. We included 496 individuals, which were comprised of 166 samples collected during this study and 330 additional sequences retrieved from GenBank. Pairwise ΦST measures based on ND1 data suggested there may be up to five major geographic groups present within P. pustulosa. Genetic differentiation between regions within Texas was higher compared to populations from the Mississippi and Great Lakes populations, which may reflect differences in historical connectivity. Mitochondrial sequence data also revealed varying demographic histories for each major group suggesting each geographic region has also experienced differential population dynamics in the past. Future surveys should consider exploring variation within species after phylogeographic delimitation has been performed. In this study, we begin to address this need for freshwater mussels via the P. pustulosa system.

Genomic insights into selection for heterozygous alleles and woody traits in Populus tomentosa

Heterozygous alleles are widespread in outcrossing and clonally propagated woody plants. The variation in heterozygosity that underlies population adaptive evolution and phenotypic variation, however, remains largely unknown. Here, we describe a de novo chromosome-level genome assembly of Populus tomentosa, an economic and ecologically important native tree in northern China. By resequencing 302 natural accessions, we determined that the South subpopulation (Pop_S) encompasses the ancestral strains of P. tomentosa, while the Northwest subpopulation (Pop_NW) and Northeast subpopulation (Pop_NE) experienced different selection pressures during population evolution, resulting in significant population differentiation and a decrease in the extent of heterozygosity. Analysis of heterozygous selective sweep regions (HSSR) suggested that selection for lower heterozygosity contributed to the local adaptation of P. tomentosa by dwindling gene expression and genetic load in the Pop_NW and Pop_NE subpopulations. Genome-wide association studies (GWAS) revealed that 88 single nucleotide polymorphisms (SNPs) within 63 genes are associated with nine wood composition traits. Among them, the selection for the homozygous AA allele in PtoARF8 is associated with reductions in cellulose and hemicellulose contents by attenuating PtoARF8 expression, and the increase in lignin content is attributable to the selection for decreases in exon heterozygosity in PtoLOX3 during adaptive evolution of natural populations. This study provides novel insights into allelic variations in heterozygosity associated with adaptive evolution of P. tomentosa in response to the local environment and identifies a series of key genes for wood component traits, thereby facilitating genomic-based breeding of important traits in perennial woody plants.