Genome-wide Single Nucleotide Polymorphism Research Articles

Maternal and Parent-of-Origin Gene–Environment Effects on the Etiology of Orofacial Clefting

Background/Objectives: We investigated maternal and parent-of-origin (PoO) gene-environment interaction effects on the risk of nonsyndromic orofacial clefts for two maternal environmental factors: periconceptional smoking and folic acid supplementation. Methods: Genome-wide single nucleotide polymorphisms (SNPs) genotypes and TopMed-imputed genotypes were obtained for case-parent triads from the EUROCRAN and ITALCLEFT studies. Candidate regions were selected around target SNPs from a previous genome-wide association study, resulting in 12 (726 SNPs) and 11 regions (730 SNPs) for maternal and PoO effects, respectively. Log-linear models were used to analyze 404 case-parent triads and 40 case-parent dyads. p-values were combined across regions. Results: None of the interactions reached statistical significance after correction for the number of regions tested. Nominally significant (pooled p-values < 0.05) interactions pointed to regions in or close to genes LRRC7 (maternal gene-folate interaction), NCKAP5 (PoO-smoking interaction), and IFT43 and GPATCH2L (PoO-folate interaction). Conclusions: Our results suggested that the genetic effects in or around these genes were heightened under periconceptional exposure to tobacco or no folic acid supplementation. The involvement of these genes in orofacial cleft development, in conjunction with environmental exposures, should be further studied.

Genome-wide study suggests inheritance of personality traits in Toy Poodles and Miniature Dachshunds.

Domestic dogs exhibit significant diversity in both morphology and personality. Recent studies focusing on large-breed dogs reported the contribution of genetic factors to personality. However, the genetic influence in small-breed dogs remains unexplored. In the present study, we investigated the personality of two small-breed dogs using a questionnaire and genome-wide single-nucleotide polymorphism data obtained from 301 Toy Poodles and 183 Miniature Dachshunds using the Illumina CanineHD 230K SNP BeadChip. The factor analysis conducted on a questionnaire consisting of 39 items identified seven factors. Among the seven personality factors, 'activeness' in Toy Poodles and 'human-directed sociability' in Miniature Dachshunds had an estimated heritability of 0.425 (SE = 0.311) and 0.514 (SE = 0.355), respectively. In addition, genome-wide association study suggested that two genomic regions possibly affect personality. The dog breeds focused on in this study are most popular in Japan, thus their information is in high demand.

Successive cycles of allopatric differentiation and secondary contact shape phylogeographical structure in an Indo-West Pacific reef fish

Abstract Geographical barriers and sea-level fluctuations have significantly influenced the population genetic structure and evolutionary history of Indo-West Pacific (IWP) reef species. This study examines these effects in Abudefduf septemfasciatus (banded sergeant), a widely distributed egg-brooding IWP damselfish. Using 4700 genome-wide single nucleotide polymorphisms obtained from double-digest restriction site-associated DNA sequencing and a 1638-bp mitochondrial gene fragment from 106 samples across six IWP locations, we identified two main genetic clusters: one in the Indian Ocean and another in the Pacific Ocean. Within the Pacific, two distinct subclusters were detected, with overlapping ranges in Taiwan. Demographic analysis of the dataset using two-population genetic models in ∂a∂I, based on diffusion approximation, revealed asymmetric gene flow, with stronger migration from the Indian Ocean to the Pacific. Recurrent episodes of isolation and secondary contact during Pleistocene glacial cycles further shaped these genetic patterns. Our findings provide new insights into the complex phylogeography and evolutionary dynamics of banded sergeants, contributing to a broader understanding of how historical environmental changes have driven the diversification of IWP reef fishes.

High-throughput analysis of microbiomes in a meat processing facility: are food processing facilities an establishment niche for persisting bacterial communities?

BackgroundMicrobial spoilage in meat impedes the development of sustainable food systems. However, our understanding of the origin of spoilage microbes is limited. Here, we describe a detailed longitudinal study that assesses the microbial dynamics in a meat processing facility using high-throughput culture-dependent and culture-independent approaches to reveal the diversity, dispersal, persistence, and biofilm formation of spoilage-associated microbes.ResultsCulture-dependent and culture-independent approaches revealed a large diversity of microbes within the meat facility, including 74 undescribed bacterial taxa and multiple spoilage-associated microbes. Ten out of 10 reconstituted microbial communities formed biofilms, and the biofilm biomass was generally higher at 4 °C than at 25 °C. Isolates obtained at different sampling times or from different sampling sites that differed in fewer than 10 genome-wide single-nucleotide polymorphisms were considered the same (persistent) strains. Strains of Carnobacterium maltaromaticum and Rahnella rivi persisted over a period of 6 months across sampling sites and time, stemming from floor drains in the cooler room. Meat isolates of Carnobacterium divergens, Rahnella inusitata, and Serratia proteamaculans originated from food contact and non-food contact environments of the packaging area.ConclusionsCulture-dependent isolation, complemented by culture-independent analyses, is essential to fully uncover the microbial diversity in food processing facilities. Microbial populations permanently resided within the meat processing facility, serving as a source of transmission of spoilage microbes. The ability of these microbes to coexist and form biofilms facilitates their persistence. Our data together with prior data on persistence of Listeria monocytogenes indicates that microbial persistence in food processing facilities is the rule rather than an exception.-75cynRBG-ecg4-DNt8vX5Video

A two-sample bidirectional Mendelian randomization analysis between telomere length and hyperthyroidism.

hyperthyroidism characterized by low thyrotropin, highlighting complications and risks, including cardiac issues, osteoporosis, adverse pregnancy outcomes, unintentional weight loss, and increased mortality associated with untreated hyperthyroidism. However, the casual association between telomere length (TL) and hyperthyroidism remains unclear. We aim to explore the casual relationship between TL and hyperthyroidism. A two-sample bidirectional Mendelian randomization (MR) analysis employed the inverse variance weighted (IVW) method, supplemented by additional approaches such as Weighted Median (WM), and MR Egger. The summary statistics for TL were derived from the UK Biobank, comprising 472,174 individuals, while the data for hyperthyroidism were sourced from the GWAS Catalog and the FinnGen database, encompassing cohorts of 460,499 and 173,938 individuals, respectively. Utilizing 139 genome-wide significant single nucleotide polymorphisms (SNPs) as instrumental variables (IVs) for TL, forward MR analyses indicated a negative causal effect of TL on hyperthyroidism. The risk of hyperthyroidism decreased as genetically predicted TL increased by one standard deviation, as determined by the IVW form GWAS Catalog (OR:0.659,95%CI: 0.541-0.802, p <0.001) and IVW from FinnGen(OR:0.634, 95%CI: 0.479-0.840, p = 0.001). Other MR methods exhibited a consistent trend in the impact of TL on hyperthyroidism. Reverse MR analysis suggested no causal association between TL and hyperthyroidism (p > 0.05). Sensitivity analyses confirmed the robustness of these results, suggesting minimal susceptibility to confounding factors and bias. The finding that longer telomeres reduce hyperthyroidism risk highlights the need to validate hyperthyroidism's impact on telomere length, offering valuable insights for prevention and treatment.

APCAD Part 2: A Novel Method for Detection of Meiotic Aneuploidy in Preimplantation Embryos

Background/Objectives: Preimplantation genetic testing methods to detect aneuploidy (PGT-A) based on genomewide single nucleotide polymorphism (SNP) data were scarce and did not meet our needs. Methods: Hence, we developed a novel method for this purpose. After the raw B-allele frequency (rBAF) values of Single Nucleotide Polymorfisms (SNPs) are obtained from a sample of interest with SNP array, the BAF values for specific categories of SNPs (cBAF) are visualized separately. Results: The analysis of the cBAF, rBAF and Log2R profiles enables to distinguish all common types of chromosomal abnormalities without haplotyping. This was demonstrated by reanalyzing data from 359 embryos which had previously been analyzed with Karyomapping. We identified additional underrepresented maternal haplotypes in five samples that we could not detect with Karyomapping. In addition, we identified all chromosomes with meiotic-origin copy number gains (both parental homolog (BPH)) (n = 70) and all chromosomes with a non-mosaic copy number loss larger than 5 Mb (n = 93) that had been detected with Karyomapping. Conclusions: We conclude that the proposed method can be used to reliably detect meiotic-origin aneuploidy without haplotyping and, hence without the need for a phasing reference.

Breaking the Hybrid Myth of Paphiopedilum wenshanense: Double Bifurcated Divergence Followed by Adaptive Introgression Formed a Morphological Intermediate.

Species with intermediate phenotypes are usually hypothesised to have originated from hybrid speciation. However, other mechanisms, such as double bifurcated speciation with introgression may create the same phenotypes. Clarifying the underlying process generating the observed intermediate morphology is important for conservation efforts, as it provides insights into the species' evolutionary background and adaptability. Here, we utilised genome-wide single nucleotide polymorphism data to test evolutionary history models for Paphiopedilum wenshanense Z. J. Liu & J. Yong Zhang, an orchid species that is widely considered to be a hybrid with intermediate morphology of other two closely related species, P. concolor Pfitzer and P. bellatulum Pfitzer, distributed in Indochina. Our results rejected the hybrid speciation hypothesis and ascribed the intermediate floral phenotypes of P. wenshanese to introgression from P. concolor after it diverged from P. bellatulum during the last glacial maximum. Excluding the geographic covariate, the current genetic mixing rate of P. wenshanense from P. concolor is stronger in the south part of its range and is associated with precipitation in the early summer, indicating that population divergence in P. wenshanense is being driven by adaptive introgression. These genetic patterns also correspond to the observed floral variation across P. wenshaense populations. The introgression from P. concolor, along with the intermediate and varying floral morphologies, may expand the ecological opportunities for P. wenshanense, providing an explanation for why high genetic diversity has been maintained despite a high level of inbreeding and small census population size. Our study provides a framework for future research to investigate the characteristics and underlying mechanisms of intermediate morphologies in general.

The Genetic Architecture of Local Adaptation and Reproductive Character Displacement in Scutiger boulengeri Complex (Anura: Megophryidae).

Speciation is a continuous process driven by barriers to gene flow. Based on genome-wide SNPs (single nucleotide polymorphisms) of 190 toads from 31 sampling sites of Scutiger boulengeri complex, we found evidence for monophyly which represented a continuous speciation process of at least six lineages in S. boulengeri, which radiated and exhibited varying degrees of divergence and gene flow. The SNP-based phylogenetic tree was largely discordant with the multilocus mitochondrial tree (i.e., S. mammatus and S. glandulatus nested in the lineages of S. boulengeri) published before. The Min Mountains (MM) and Qinghai-Tibet Plateau (QTP) lineages differ fundamentally in habitat (i.e., elevation) and morphology (i.e., SVL), we detected signatures of potential high-altitude and cold adaptation genes in QTP (vs. MM). We found the evidence of reproductive trait disparity (i.e., SVL and nuptial pads) is key to promoting sympatric rather than allopatric species pairs. In addition, we identified selection signals for genes related to sympatric character displacement, genes linked to obesity-related traits, nuptial spines morphology and enlarged chest nuptial pads in S. mammatus (vs. QTP group of S. boulengeri). Our study provided new insight and paradigm for a varied speciation pattern from local adaptation of allopatry to sympatric character displacement in the S. boulengeri complex.

Circumpolar and Regional Seascape Drivers of Genomic Variation in a Southern Ocean Octopus.

Understanding how ecological, environmental and geographic features influence population genetic patterns provides crucial insights into a species' evolutionary history, as well as their vulnerability or resilience under climate change. In the Southern Ocean, population genetic variation is influenced across multiple spatial scales ranging from circum-Antarctic, which encompasses the entire continent, to regional, with varying levels of geographic separation. However, comprehensive analyses testing the relative importance of different environmental and geographic variables on genomic variation across these scales are generally lacking in the Southern Ocean. Here, we examine genome-wide single nucleotide polymorphisms of the Southern Ocean octopus Pareledone turqueti across the Scotia Sea and the Antarctic continental shelf, at depths between 102 and 1342 m, throughout most of this species' range. The circumpolar distribution of P. turqueti is biogeographically structured with a clear signature of isolation-by-geographical distance, but with long-distance genetic connectivity also detected between East and West Antarctica. Genomic variation of P. turqueti was also associated with bottom water temperature at a circumpolar scale, driven by a genotype-temperature association with the warmer sub-Antarctic Shag Rocks and South Georgia. Within the Scotia Sea, geographic distance, oxygen and fine-scale isolation-by-water depth were apparent drivers of genomic variation at regional scales. Putative positive selection of haemocyanin (oxygen transport protein), calcium ion transport and genes linked to RNA modification, detected within the Scotia Sea, suggest physiological adaptation to the regional sharp temperature gradient (~0-+2°C). Overall, we identified seascape drivers of genomic variation in the Southern Ocean at circumpolar and regional scales in P. turqueti and contextualised the role of environmental adaptations in the Southern Ocean.

Genetic diversity and population structure analysis of 418 tomato cultivars based on single nucleotide polymorphism markers.

Tomato (Solanum lycopersicum) is a highly valuable fruit crop. However, due to the lack of scientific and accurate variety identification methods and unified national standards, production management is scattered and non-standard, resulting in mixed varieties. This poses considerable difficulties for the cataloging and preservation of germplasm resources as well as the identification, promotion, and application of new tomato varieties. To better understand the genetic diversity and population structure of representative tomato varieties, we collected 418 tomato varieties from the past 20 years and analyzed them using genome-wide single nucleotide polymorphism (SNP) markers. We initially assessed the population structure, genetic relationships, and genetic profiles of the 418 tomato germplasm resources utilizing simplified genome sequencing techniques. A total of 3,374,929 filtered SNPs were obtained and distributed across 12 chromosomes. Based on these SNP loci, the 418 tomatoes samples were divided into six subgroups. The population structure and genetic relationships among existing tomato germplasm resources were determined using principal component analysis, population structure analysis, and phylogenetic tree analysis. Rigorous selection criteria identified 15 additional high-quality DNA fingerprints from 50 validated SNP loci, effectively enabling the identification of the 418 tomato varieties, which were successfully converted into KASP (Kompetitive Allele Specific PCR) markers. This study represents the first comprehensive investigation assessing the diversity and population structure of a large collection of tomato varieties. Overall, it marks a considerable advancement in understanding the genetic makeup of tomato populations. The results broadened our understanding of the diversity, phylogeny, and population structure of tomato germplasm resources. Furthermore, this study provides a scientific basis and reference data for future analysis of genetic diversity, species identification, property rights disputes, and molecular breeding in tomatoes.

Multigenerational hybridisation results in heterosis and facilitates adaptive introgression, with no evidence of outbreeding depression in a pair of marine gastropods.

Anthropogenic environmental changes continue to threaten species globally. For example, translocation of species has caused unintentional hybridisation, which has contributed to species declines. On the other hand, hybridisation can be used to increase the evolutionary potential of species vulnerable to rapid environmental change, although the benefits of mixing genetically divergent lineages do not come without risks to individual fitness and the long-term viability of populations. Here, we use a combination of genome-wide Single Nucleotide Polymorphism (SNP) markers, mitochondrial DNA sequencing and measurements of growth rate to determine the genetic consequences of hybridisation between two congeneric marine gastropods across 27 years (~18 generations). Multigeneration hybridisation resulted from the introduction of the intertidal periwinkle Bembicium vittatum (a direct developer) into the native range of its congener Bembicium auratum (a species with planktotrophic larval dispersal). Despite significant genetic divergence between the species, we found no direct evidence of outbreeding depression in the admixed population. Instead, we found evidence for heterosis, which dissipated over time. After an initial lag, the frequency of introduced B. vittatum alleles declined dramatically in the hybrid population. However, a few B. vittatum alleles (3.18%) increased significantly in frequency against the overall trend, providing evidence of adaptive introgression. In the context of hybridisation as a conservation management tool, our results provide some evidence of the potential benefits that can be gained, and suggest that the costs due to outbreeding depression can be small.

Investigation of introgressive hybridization in endangered Sinohyriopsis mussels (Mollusca: Unionidae) using genome-wide data in Japan

Anthropogenic hybridization is a global phenomenon and a major concern in conservation biology. Sinohyriopsis schlegelii (Mollusca: Bivalvia: Unionidae), native to Lake Biwa in Japan, is considered endangered because of its hybridization with an introduced Chinese species, S. cumingii. Although previous research suggested hybridization among Sinohyriopsis mussels, the research has failed to (1) evaluate the prevalence of hybrids, (2) predict the genetic consequences for populations containing hybrids, and (3) genetically assess a population devoid of hybrids. This study aimed to fill the knowledge gaps. We collected samples from all persistent populations in Lake Biwa, Lake Kasumigaura, and Lake Anenuma (the latter two populations were introduced from Lake Biwa) and analyzed genome-wide single nucleotide polymorphisms (SNPs) data. Our findings demonstrate that hybrids are prevalent in Lake Biwa and Lake Kasumigaura but absent in Lake Anenuma. The proportion of S. cumingii ancestry increased over the past 20 years, indicating that the genetic material of S. schlegelii may diminish further in the future. Moreover, the S. schlegelii population in Lake Anenuma shared genetic similarities with the pre-hybridization population of Lake Biwa. Although the Lake Anenuma population exhibited lower genetic diversity, no signs of inbreeding were observed. Overall, the Lake Anenuma population remains the only genetically pure S. schlegelii population, but its low genetic diversity indicates a reduced adaptive potential to environmental changes. This study provides valuable insights into the current genetic status of S. schlegelii, ultimately informing conservation efforts for this critically endangered species.

Genome-wide scans for signatures of selection in North African sheep reveals differentially selected regions between fat- and thin-tailed breeds.

North Africa counts several sheep breeds that can be categorized as fat- and thin-tailed. The former are well adapted to dryland environments. In this study, we used 50K genome-wide single nucleotide polymorphism profiles from 462 animals representing nine fat-tailed and 13 thin-tailed sheep breeds across North Africa to localize genomic regions putatively under differential selective pressures between the two types of breeds. We observed genetic clines from east to west and from north to south. The east-west cline separates the fat- and thin-tailed breeds, with the exception of the fat-tailed Algerian Barbarine, which is closely related to a genetically homogeneous cluster of Moroccan and Algerian thin-tailed breeds. Using a combination of three extended haplotype homozygosity tests, we detected seven candidate regions under divergent selection between fat- and thin-tailed sheep. The strongest selection signals reside on chromosomes 1 and 13, with the latter spanning the BMP2 gene, known to be associated with the fat-tail phenotype. Overall, the candidate regions under selection in fat-tailed sheep overlap with genes associated with adaptation to desert-like environments including adipogenesis, as well as heat and drought tolerance. Our results confirm previously reported candidate genes known to be a target of fat-tail selection in sheep but also reveal novel candidate genes specifically under selection in North African populations.

Populations of Latvia and Lithuania in the context of some Indo-European and non-Indo-European speaking populations of Europe and India: insights from genetic structure analysis.

The aim of this study was to investigate the relationship among Lithuanian, Latvian, Indian, and some other populations through a genome-wide data analysis of single nucleotide polymorphisms (SNPs). Limited data of Baltic populations were mostly compared with geographically closer modern and ancient populations in the past, but no previous investigation has explored their genetic relationships with distant populations, like the ones of India, in detail. To address this, we collected and merged genome-wide SNP data from diverse publicly available sources to create a comprehensive dataset with a substantial sample size especially from Lithuanians and Latvians. Principal component analysis (PCA) and admixture analysis methods were employed to assess the genetic structure and relationship among the populations under investigation. Additionally, we estimated an effective population size (Ne) and divergence time to shed light on potential past events between the Baltic and Indian populations. To gain a broader perspective, we also incorporated ancient and modern populations from different continents into our analyses. Our findings revealed that the Balts, unsurprisingly, have a closer genetic affinity with individuals from Indian population who speak Indo-European languages, compared to other Indian linguistic groups (such as speakers of Dravidian, Austroasiatic, and Sino-Tibetan languages). However, when compared to other populations from the European continent, which also speak Indo-European and some Uralic languages, the Balts did not exhibit a stronger resemblance to Indo-European-speaking Indians. In conclusion, this study provides an overview of the genetic relationship and structure of the populations investigated, along with insights into their divergence times.

Allergic diseases and T2DM: a bidirectional multivariable Mendelian randomization study and mediation analysis

Background Clinical studies involving observation have uncovered a mutual relationship between allergic disorders and diabetes, yet the precise causal link remains undetermined. Methods We conducted two-sample bidirectional Mendelian randomization analyses using single nucleotide polymorphisms (SNPs) associated with allergic conditions (asthma, allergic rhinitis, atopic dermatitis) from genome-wide studies and SNPs related to type 2 diabetes from FinnGen. Initially, we evaluated the causal link between allergic disorders and type 2 diabetes through a univariate Mendelian randomization study, incorporating inverse variance weighting, MR-Egger, and the weighted median estimator. To address potential confounding, we employed multivariate Mendelian randomization. Finally, we validated mediators influencing the correlation between asthma and type 2 diabetes. Results The Inverse variance weighted method showed that asthma genetically increased the risk of type 2 diabetes [Asthma-type 2 diabetes: β(95%CI)＝0.892 (0.152–1.632), p = 0.018]. Allergic rhinitis and type 2 diabetes exhibit a mutual protective effect: β(95% CI)＝−1.333 (−2.617 to −0.049), p = 0.042; type 2 diabetes-Allergic rhinitis: β(95%CI)＝−0.002 (−0.004 to −0.000), p = 0.018. The Multivariable Mendelian randomization study results showed that after excluding confounding factors, asthma still demonstrates statistical significance in relation to type 2 diabetes. Through mediation analysis, it was discovered that lung function and the percentage of monocytes in leukocytes exert an inhibitory effect on the mediation between asthma and type 2 diabetes. Conclusion The Multivariable Mendelian randomization study indicates asthma as a risk factor for type 2 diabetes. Lung function, and the percentage of monocytes in leukocytes, play an inhibitory role in asthma and type 2 diabetes mediating effects.

Phylogenomic analyses of hamsters (Cricetinae) inferred from GBS data and mitochondrial genomes

Accurate species delimitation and identification is crucial for species conservation, providing a foundation for studies on evolutionary biology, ecology, and essentially all biological disciplines. The subfamily Cricetinae (Cricetidae, Rodentia), known as hamsters, is widely distributed in the Palearctic region. At present, there are nine genera and 18 species of hamsters are recognized worldwide, although the taxonomic status of certain taxa remains unclear. In this study, we collected 146 hamster specimens representing 14 species and generated new mitochondrial genomes and nuclear genome-wide single nucleotide polymorphisms (SNPs) to explore their relationships among these hamsters using multiple species delimitation approaches. Results showed: (1) strong phylogenetic support for the classification of Urocricetus, Nothocricetulus, and Cansumys as separate genera; (2) Urocricetus contained two separate species, U. kamensis and U. lama, with U. alticola and U. tibetanus considered synonyms of U. lama; (3) U. kamensis and U. lama are separated by the Nujiang River, with the matching divergence time suggesting that the formation of the river was the primary evolutionary factor driving the species differentiation, and (4) genetic differentiation occurred within the Tscherskia genus, which included two cryptic species.

From phylogenomics to breeding: Can universal target capture probes be used in the development of SNP markers for kinship analysis?

Leveraging DNA markers, particularly single-nucleotide polymorphisms (SNPs), in parentage analysis, sib-ship reconstruction, and genomic relatedness analysis can enhance plant breeding efficiency. However, the limited availability of genomic information, confined to the most commonly used species, hinders the broader application of SNPs in species of lower economic interest (e.g., most tree species). We explored the possibility of using universal target capture probes, namely Angiosperms353, to identify SNPs and assess their effectiveness in genomic relatedness analysis. We tested the approach in 11 tree species, six of which had a half-sib family structure. Variants were called within species, and genomic relatedness analysis was conducted in species with two or more families. Scalability via amplicon sequencing was tested by designing primers and testing them in silico. Adequate SNPs for relatedness analysis were identified in all species. Relatedness values from Angiosperms353-based SNPs highly correlated with those from thousands of genome-wide DArTseq SNPs in Cordia africana, one of the species with a family structure. The in silico performance of designed primers demonstrated the potential for scaling up via amplicon sequencing. Utilizing universal target capture probes for SNP identification can help overcome the limitations of genomic information availability, thereby enhancing the application of genomic markers in breeding plant species with lower economic interest.

Enhanced adaptive permutation test with negative binomial distribution in genome-wide omics datasets.

The permutation test has been widely used to provide the p-values of statistical tests when the standard test statistics do not follow parametric null distributions. However, the permutation test may require huge numbers of iterations, especially when the detection of very small p-values is required for multiple testing adjustments in the analysis of datasets with a large number of features. To overcome this computational burden, we suggest a novel enhanced adaptive permutation test that estimates p-values using the negative binomial (NB) distribution. By the method, the number of permutations are differently determined for individual features according to their potential significance. In detail, the permutation procedure stops, when test statistics from the permuted dataset exceed the observed statistics from the original dataset by a predefined number of times. We showed that this procedure reduced the number of permutations especially when there were many insignificant features. For significant features, we enhanced the reduction with Stouffer's method after splitting datasets. From the simulation study, we found that the enhanced adaptive permutation test dramatically reduced the number of permutations while keeping the precision of the permutation p-value within a small range, when compared to the ordinary permutation test. In real data analysis, we applied the enhanced adaptive permutation test to a genome-wide single nucleotide polymorphism (SNP) dataset of 327,872 features. We found the analysis with the enhanced adaptive permutation took a feasible time for genome-wide omics datasets, and successfully identified features of highly significant p-values with reasonable confidence intervals.

Tracking the North American Asian Longhorned Beetle Invasion With Genomics.

Biological invasions pose significant threats to ecological and economic stability, with invasive pests like the Asian longhorned beetle (Anoplophora glabripennis Motschulsky, ALB) causing substantial damage to forest ecosystems. Effective pest management relies on comprehensive knowledge of the insect's biology and invasion history. This study uses genomics to address these knowledge gaps and inform existing biosurveillance frameworks. We used 2768 genome-wide single nucleotide polymorphisms to compare invasive A. glabripennis populations in North America, using genomic variation to trace their sources of invasion and spread patterns, thereby refining our understanding of this species' invasion history. We found that most North American A. glabripennis infestations were distinct, resulting from multiple independent introductions from the native range. Following their introduction, all invasive populations experienced a genetic bottleneck which was followed by a population expansion, with a few also showing secondary spread to satellite infestations. Our study provides a foundation for a genome-based biosurveillance tool that can be used to clarify the origin of intercepted individuals, allowing regulatory agencies to strengthen biosecurity measures against this invasive beetle.

Strong Small-Scale Differentiation but No Cryptic Species Within the Two Isopod Species Asellus aquaticus and Proasellus coxalis in a Restored Urban River System (Emscher, Germany).

Worldwide, humans have strongly altered river networks. Key changes resulted in modified hydromorphology, poor habitat quality and availability, migration barriers, and pollution. Restoration measures aim at mitigating anthropogenic stressors and at restoring connectivity, but the biological success of these measures is not guaranteed. Analyzing genetic diversity and metapopulation structure of target species in the river network with genetic markers can help to understand recolonization processes and to identify persisting gene flow barriers. Here, we studied the population genetic structure of the two pollution-tolerant detritivorous isopod species, Asellus aquaticus and Proasellus coxalis, in the former heavily degraded and polluted, but now mostly restored Emscher catchment in Germany. For both species, we analyzed mitochondrial cytochrome c oxidase I (COI) gene sequences and nuclear genome-wide single nucleotide polymorphism (SNP) data. Surprisingly, we found a strong metapopulation structure for both species with several isolated populations on a small-scale of few kilometers, but a still high genetic diversity, especially in the COI gene. For both taxa, potentially cryptic species are known, but our SNP data showed that the mitochondrial lineages represent only one species, each, in the study area. This highlights the importance of integrating high-resolution nuclear markers into species identification because species diversity may otherwise be overestimated. While we could identify some migration barriers and find indications for passive dispersal by birds or humans, these factors could not fully explain the local metapopulation structure, suggesting that also other drivers, such as isolation by adaptation, priority effects, or biotic interactions, play a role in shaping the population genetic structure.