Neutral Single Nucleotide Polymorphisms Research Articles

Habitat Quality and Water Availability Affect Genetic Connectivity of Platypus Across an Urban Landscape

ABSTRACTFreshwater ecosystems are among the most threatened globally. Understanding how environmental variables influence the gene flow of freshwater species can help identify landscape features requiring conservation management. We used landscape genetic resistance modelling to assess the influence of climate, topography and vegetation cover on genetic structure and gene flow in platypus (Ornithorhynchus anatinus) in an urban region of south‐east Queensland, Australia. Thirty DNA samples were genotyped using the DArTseq platform, and data were filtered to produce a panel of 5478 neutral single nucleotide polymorphism (SNP) markers. We used fastSTRUCTURE, partial redundancy analysis and maximum likelihood analyses to understand platypus genetic structure and landscape influences on gene flow. Between one and three genetic clusters were detected using fastSTRUCTURE. Partial redundancy analysis identified Topographic Wetness Index and antecedent rainfall as driving genetic differentiation between samples. A maximum likelihood population effects model suggested gene flow was spatially structured by Normalised Difference Vegetation Index at a fine scale (100 m) and antecedent rainfall at a landscape scale (1 km). Thus, less vegetated areas appear to restrict the gene flow of platypus in urban systems. Rainfall, vegetation cover and topographic wetness are also important for maintaining platypus gene flow across landscapes. Our research recommends conservation management through restoration of water flow and riverine vegetation to help maintain platypus connectivity and increase gene flow among populations.

Seascape Genomics of the Smooth Hammerhead Shark Sphyrna zygaena Reveals Regional Adaptive Clinal Variation.

Globally, hammerhead sharks have experienced severe declines owing to continued overexploitation and anthropogenic change. The smooth hammerhead shark Sphyrna zygaena remains understudied compared to other members of the family Sphyrnidae. Despite its vulnerable status, a comprehensive understanding of its genetic landscape remains lacking in many regions worldwide. The present study aimed to conduct a fine-scale genomic assessment of Sphyrna zygaena within the highly dynamic marine environment of South Africa's coastline, using thousands of single nucleotide polymorphisms (SNPs) derived from restriction site-associated DNA sequencing (3RAD). A combination of differentiation-based outlier detection methods and genotype-environment association (GEA) analysis was employed in Sphyrna zygaena. Subsequent assessments of putatively adaptive loci revealed a distinctive south to east genetic cline. Among these, notable correlations between adaptive variation and sea-surface dissolved oxygen and salinity were evident. Conversely, analysis of 111,243 neutral SNP markers revealed a lack of regional population differentiation, a finding that remained consistent across various analytical approaches. These results provide evidence for the presence of differential selection pressures within a limited spatial range, despite high gene flow implied by the selectively neutral dataset. This study offers notable insights regarding the potential impacts of genomic variation in response to fluctuating environmental conditions in the circumglobally distributed Sphyrna zygaena.

Genetic and Phenotypic Divergence in a Dung Beetle 50 Years After Its Introduction to Australia.

Species translocations are increasingly being used in conservation and for biological control. The success of a translocation can be strongly influenced by the evolutionary processes occurring during the early phase of the introduction and the subsequent spread to new regions. In this study, morphological variation and population genetic structure were assessed in the African dung beetle Digitonthophagus gazella, a species that was intentionally introduced to Australia for biological control in 1968 and subsequently spread widely across the northern part of the continent. A dataset based on 1594 neutral single nucleotide polymorphism (SNP) loci that were genotyped in 187 individuals from 12 sites revealed significant genetic divergences between sites (global F ST = 0.118) and provides evidence of restricted gene flow among established populations at small to moderate spatial scales (74-500 km). Geometric morphometric analyses revealed significant divergence among populations in the shape of the foretibia, a trait ecologically important for tunnelling in soil and dung. Moreover, phenotypic divergence in this trait for both sexes was significantly higher than genetic differentiation at selectively neutral loci (P ST > F ST), suggesting that directional selection is contributing to the phenotypic divergences among populations. Our study shows how population structure can establish quickly in an introduced species and highlights the importance of considering local adaptation when performing translocations on established populations.

The Range‐Wide Genetic Structure of a High‐Elevation Conifer Species, Subalpine Larch

ABSTRACTAimSubalpine larch is a long‐lived conifer with a restricted distribution at treeline in the mountains of western North America. Climate change is reducing the availability of this habitat and subalpine larch is unlikely to adapt to its changing environment due to its long generation time, relatively low levels of standing genetic variation and the high degree of habitat fragmentation across the species' range. This study seeks to elucidate the genetic structure of subalpine larch to inform future conservation and management efforts.LocationWestern North America.TaxonSubalpine larch (Larix lyallii Parl.).MethodsTissue was collected from high‐elevation populations across the entire species range. Restriction site associated DNA sequencing was used to generate single nucleotide polymorphism (SNP) data. Population genetic analyses identified genetic differentiation.ResultsClustering analyses performed using 751 neutral SNPs identified three genetically differentiated regions: the Cascade Range, the southern Rocky Mountains and the northern Rocky Mountains. AMOVA confirmed significant genetic differentiation among regions. A discriminant analysis of principal components and a dendrogram of Provesti's genetic distance both supported the hypothesis that genetically distinct lineages arose after dispersal from a single Pleistocene refugium. Significant isolation by distance (IBD) supported the key role of dispersal in shaping modern patterns of genetic variation in subalpine larch.Main ConclusionsPost‐Pleistocene dispersal resulted in genetic differentiation among groups of subalpine larch in the Cascade Range, the southern Rocky Mountains and the northern Rocky Mountains. These three regions should be prioritised for future management.

Fine-scale adaptive divergence and population genetic structure of Aedes aegypti in Metropolitan Manila, Philippines

BackgroundThe adaptive divergence of Aedes aegypti populations to heterogeneous environments can be a driving force behind the recent expansion of their habitat distribution and outbreaks of dengue disease in urbanized areas. In this study, we investigated the population genomics of Ae. aegypti at a regional scale in Metropolitan Manila, Philippines.MethodsWe used the Pool-Seq double digestion restriction-site association DNA sequencing (ddRAD-Seq) approach to generate a high number of single nucleotide polymorphisms (SNPs), with the aim to determine local adaptation and compare the population structure with 11 microsatellite markers. A total of 217 Ae. aegypti individuals from seven female and seven male populations collected from Metropolitan Manila were used in the assays.ResultsWe detected 65,473 SNPs across the populations, of which 76 were non-neutral SNPs. Of these non-neutral SNPs, the multivariate regression test associated 50 with eight landscape variables (e.g. open space, forest, etc.) and 29 with five climate variables (e.g. air temperature, humidity, etc.) (P-value range 0.005–0.045) in female and male populations separately. Male and female populations exhibited contrasting spatial divergence, with males exhibiting greater divergence than females, most likely reflecting the different dispersal abilities of male and female mosquitoes. In the comparative analysis of the same Ae. aegypti individuals, the pairwise FST values of 11 microsatellite markers were lower than those of the neutral SNPs, indicating that the neutral SNPs generated via pool ddRAD-Seq were more sensitive in terms of detecting genetic differences between populations at fine-spatial scales.ConclusionsOverall, our study demonstrates the utility of pool ddRAD-Seq for examining genetic differences in Ae. aegypti populations in areas at fine-spatial scales that could inform vector control programs such as Wolbachia-infected mosquito mass-release programs. This in turn would provide information on mosquito population dispersal patterns and the potential barriers to mosquito movement within and around the release area. In addition, the potential of environmental adaptability observed in Ae. aegypti could help population control efforts.Graphical

Seascapes Shaped the Local Adaptation and Population Structure of South China Coast Yellowfin Seabream (Acanthopagrus latus).

Understanding the genetic composition and regional adaptation of marine species under environmental heterogeneity and fishing pressure is crucial for responsible management. In order to understand the genetic diversity and adaptability of yellowfin seabream (Acanthopagrus latus) along southern China coast, this study was conducted a seascape genome analysis on yellowfin seabream from the ecologically diverse coast, spanning over 1600 km. A total of 92 yellowfin seabream individuals from 15 sites were performed whole-genome resequencing, and 4,383,564 high-quality single nucleotide polymorphisms (SNPs) were called. By conducting a genotype-environment association analysis, 29,951 adaptive and 4,328,299 neutral SNPs were identified. The yellowfin seabream exhibited two distinct population structures, despite high gene flow between sites. The seascape genome analysis revealed that genetic structure was influenced by a variety of factors including salinity gradients, habitat distance, and ocean currents. The frequency of allelic variation at the candidate loci changed with the salinity gradient. Annotation of these loci revealed that most of the genes are associated with osmoregulation, such as kcnab2a, kcnk5a, and slc47a1. These genes are significantly enriched in pathways associated with ion transport including G protein-coupled receptor activity, transmembrane signaling receptor activity, and transporter activity. Overall, our findings provide insights into how seascape heterogeneity affects adaptive evolution, while providing important information for regional management in yellowfin seabream populations.

The contribution of intraspecific variation to future climate responses of brown algae

AbstractIntraspecific variation, which may arise through the interplay between environmental heterogeneity and adaptive variation, has consequences for the resilience of species to climate change. Here, we revealed the levels of intraspecific genomic variation and its causes in a widespread brown alga (Sargassum horneri). Our datasets included both benthic and floating samples from 20 populations sampled along a latitudinal gradient in the Chinese marginal seas. We prepared two datasets: 1) 4628 filtered single nucleotide polymorphisms (SNPs) for all samples, and 2) 20,735 filtered SNPs for only benthic samples. We conducted genotype‐environment association analyses and outlier tests to identify adaptive loci for each dataset. Both neutral and adaptive SNPs revealed a deep genetic split between benthic populations in the North Yellow Sea (NYS) and East China Sea. Redundancy analysis demonstrated that temperature is a major factor driving adaptive divergence of benthic populations. Predictions of the lineage‐level species distribution model revealed severe habitat loss of S. horneri in the NYS and eastern coasts of Korea under RCP8.5 in the 2100 s; however, the low‐latitude boundary remained stable. Based on these results, we speculate that low‐latitude populations may have high resilience to global warming. The dispersal routes of floating samples were determined by coastal currents; however, restricted gene flow between regions was detected. Thus, we speculate that opportunities for the recovery of depleted populations through natural gene flow may be limited. This study highlights the importance of applying conservation strategies (e.g., assisted gene flow) to protect coastal species from local extinction in the future.

Species boundaries and conservation implications of Cinnamomum japonicum, an endangered plant in China

AbstractClear species boundaries are crucial for plans and actions on biodiversity conservation. However, morphological similarities among allied species can result in taxonomic difficulties, thus impeding conservation efforts. In China, Cinnamomum japonicum Siebold is a well‐known endangered plant, yet suffers from longstanding taxonomic issues. Here, we explicitly evaluate whether C. japonicum, C. chenii, and C. chekiangense are the same phylogenetic species on the basis of a multi‐individual sampling strategy. We identified three sets of low‐copy orthologous genes from 19 Lauraceae taxa for phylogenetic inferences. Both the concatenation and coalescent‐based phylogenies supported that C. chenii individuals were embedded in the C. japonicum clade, indicating these two taxa are conspecific. Meanwhile, C. chekiangense accessions formed a monophyly which was not sister to C. japonicum. This result, together with the morphological differences that the leaves of C. japonicum are glabrous with a faveolate pattern of venation while those of C. chekiangense have trichomes and inevident lateral veins, led us to consider both as two distinct species. Based on 17 728 neutral single nucleotide polymorphisms (SNPs), the ADMIXTURE analysis suggested that the Chinese C. japonicum populations in Zhoushan Archipelago (=C. chenii) were genetically differentiated from the Japanese and Korean ones. Furthermore, ecological niche modeling predicted that the present distribution area of Chinese C. japonicum is likely to be unsuitable under global warming scenarios. Together with its limited distribution and genetic uniqueness, we recommend that Chinese C. japonicum deserves conservation priorities.

Genetic Adaptation of Siberian Larch (Larix sibirica Ledeb.) to High Altitudes

Forest trees growing in high altitude conditions offer a convenient model for studying adaptation processes. They are subject to a whole range of adverse factors that are likely to cause local adaptation and related genetic changes. Siberian larch (Larix sibirica Ledeb.), whose distribution covers different altitudes, makes it possible to directly compare lowland with highland populations. This paper presents for the first time the results of studying the genetic differentiation of Siberian larch populations, presumably associated with adaptation to the altitudinal gradient of climatic conditions, based on a joint analysis of altitude and six other bioclimatic variables, together with a large number of genetic markers, single nucleotide polymorphisms (SNPs), obtained from double digest restriction-site-associated DNA sequencing (ddRADseq). In total, 25,143 SNPs were genotyped in 231 trees. In addition, a dataset of 761 supposedly selectively neutral SNPs was assembled by selecting SNPs located outside coding regions in the Siberian larch genome and mapped to different contigs. The analysis using four different methods (PCAdapt, LFMM, BayeScEnv and RDA) revealed 550 outlier SNPs, including 207 SNPs whose variation was significantly correlated with the variation of some of environmental factors and presumably associated with local adaptation, including 67 SNPs that correlated with altitude based on either LFMM or BayeScEnv and 23 SNPs based on both of them. Twenty SNPs were found in the coding regions of genes, and 16 of them represented non-synonymous nucleotide substitutions. They are located in genes involved in the processes of macromolecular cell metabolism and organic biosynthesis associated with reproduction and development, as well as organismal response to stress. Among these 20 SNPs, nine were possibly associated with altitude, but only one of them was identified as associated with altitude by all four methods used in the study, a nonsynonymous SNP in scaffold_31130 in position 28092, a gene encoding a cell membrane protein with uncertain function. Among the studied populations, at least two main groups (clusters), the Altai populations and all others, were significantly genetically different according to the admixture analysis based on any of the three SNP datasets as follows: 761 supposedly selectively neutral SNPs, all 25,143 SNPs and 550 adaptive SNPs. In general, according to the AMOVA results, genetic differentiation between transects or regions or between population samples was relatively low, although statistically significant, based on 761 neutral SNPs (FST = 0.036) and all 25,143 SNPs (FST = 0.017). Meanwhile, the differentiation based on 550 adaptive SNPs was much higher (FST = 0.218). The data showed a relatively weak but highly significant linear correlation between genetic and geographic distances (r = 0.206, p = 0.001).

Neutral vs. non-neutral genetic footprints of Plasmodium falciparum multiclonal infections.

At a time when effective tools for monitoring malaria control and eradication efforts are crucial, the increasing availability of molecular data motivates their application to epidemiology. The multiplicity of infection (MOI), defined as the number of genetically distinct parasite strains co-infecting a host, is one key epidemiological parameter for evaluating malaria interventions. Estimating MOI remains a challenge for high-transmission settings where individuals typically carry multiple co-occurring infections. Several quantitative approaches have been developed to estimate MOI, including two cost-effective ones relying on molecular data: i) THE REAL McCOIL method is based on putatively neutral single nucleotide polymorphism loci, and ii) the varcoding method is a fingerprinting approach that relies on the diversity and limited repertoire overlap of the var multigene family encoding the major Plasmodium falciparum blood-stage antigen PfEMP1 and is therefore under selection. In this study, we assess the robustness of the MOI estimates generated with these two approaches by simulating P. falciparum malaria dynamics under three transmission conditions using an extension of a previously developed stochastic agent-based model. We demonstrate that these approaches are complementary and best considered across distinct transmission intensities. While varcoding can underestimate MOI, it allows robust estimation, especially under high transmission where repertoire overlap is extremely limited from frequency-dependent selection. In contrast, THE REAL McCOIL often considerably overestimates MOI, but still provides reasonable estimates for low and moderate transmission. Regardless of transmission intensity, results for THE REAL McCOIL indicate that an inaccurate tail at high MOI values is generated, and that at high transmission, an apparently reasonable estimated MOI distribution can arise from some degree of compensation between overestimation and underestimation. As many countries pursue malaria elimination targets, defining the most suitable approach to estimate MOI based on sample size and local transmission intensity is highly recommended for monitoring the impact of intervention programs.

ГЕНОТИПІЧНА ТА ФЕНОТИПІЧНА ХАРАКТЕРИСТИКА СТІЙКОСТІ ДО АНТИМІКОБАКТЕРІАЛЬНИХ ПРЕПАРАТІВ 8 ШТАМІВ M. TUBERCULOSIS, ВИДІЛЕНИХ ВІД ХВОРИХ З ВПЕРШЕ ДІАГНОСТОВАНИМ ТУБЕРКУЛЬОЗОМ ЛЕГЕНЬ

The article presents the experience of whole-genome sequencing of M. tuberculosis (MBT) strains. Materials and methods. 8 MBT isolates were tested. The strains were obtained from patients with newly detected pulmonary tuberculosis (NDPTB). Critical concentrations of anti-mycobacterial drugs (AMBD): H; R; E; Z; Lfx; Mfx; Am; cm; Lzd; Bdq; Dlm and Cfz were determined using the BACTEC MGIT system. Sequencing of MBT strains was performed on Illumina MiSeq equipment at the laboratory of microbiology and biochemistry of the National Institute of phthisiology and pulmonology (NIPP). The obtained whole-genome sequences of MBT strains were deposited in fastq files and analyzed using the PhyResSE program (https://bioinf.fz-borstel.de/mchips/phyresse/) with the bioanalytical solution package. The panel of this package includes gene targets involved in the development of MBT to AMBP. Phylogenetic information and a certain spoligotype make it possible to obtain neutral single nucleotide polymorphisms. The genetic profile of the drug was performed according to the WHO mutation catalog (https://www.who.int/publications/i/item/9789240028173). The results. The dominant in Ukraine Beijing genotype was represented by 7 strains. The non-beijing group included 1 strain: Ural. 7 MBT strains belonged to the Beijing family, Lineage 2 phylogenetic line with the same spoligotype indices. The analysis of mutations according to the “Catalogue of mutations of the M. tuberculosis complex and their association with drug resistance”, WHO, 2021, allowed all detected mutations to be divided into categories - associated with resistance, associated with resistance - intermediate, not associated with resistance, with uncertain significance. Comparison of the resistance profile with the corresponding genotype showed that isolates, belonging to the Beijing genotype, usually carried MDR/pre-XDR mutations. Comparison of the resistance profile with the corresponding genotype showed that isolates belonging to the Beijing genotype usually carried MDR/pre-XDR mutations. All MBT strains with resistance to R had mutations found in the rpoB gene. The canonical amino acid substitution of rpoB S450L, associated with a high level of resistance to R with a non-significant decrease in the viability of the strains, was identified in 6 isolates. Another clinically significant mutation in rpoB (S435Y) was found in 2 cases and only in representatives of the Beijing family. Mutations of the categories: not associated with resistance (rpoC (E1092D)) and of uncertain significance: rpoC (I491V), rpoB (H674N), rpoB (V496A), were detected only in combination with “strictly associated” positions in phenotypic-resistant isolates of the genotype Beijing. The canonical single amino acid substitution katG S315T was detected in all isolates selected for sequencing. All 8 strains resistant to H showed mutations in genes associated with resistance to the drug. Mutations in the key Bdq resistance genes - atpE and mmpR - were not detected in any genome. In 1 strain of MBT, a C154R mutation associated with Lzd resistance was detected in the rplC gene. Similarly, in 1 strain of MBT, a mutation in ddn (D30S0) was detected with an as yet undetermined significance of association with resistance to Dlm. Conclusions. The study provided information on the genetic diversity of modern MBT isolates in TB patients. The predominance of the Beijing genotype testified to the stable population structure of the TB pathogen and the preservation of trends of high levels of the spread of TB forms of infection on the territory of the country. The combination of phenotype and molecular genetic data made it possible to give a more complete assessment of DR isolates. A large share of MDR was caused by mutations that did not have a negative effect on the viability and transmissibility of the pathogen, indicating a large epidemic reservoir of MBT strains with MDR/pre-XDR. The highly transmissible strains of Beijing carried mostly single uncombined R and H mutations, which were associated with a high level of resistance. Key words: genetic diagnostics, sequencing, pulmonary tuberculosis.

Ancient vicariance is reinforced by adaptive divergence in the southern beech: Contributions from geogenomics

AbstractAimGeogenomics seeks to understand geological processes linked to lineage divergence. However, the mechanisms that conserve ancient signals in spite of gene flow are still unclear. In the southern beech, the deep lineage divergence produced by vicariant events is associated with ancient marine transgressions. We hereby evaluate the hypothesis that this divergence is maintained by diversifying selection.LocationSouthern Argentina and Chile.Taxon Nothofagus dombeyi. MethodsThe lineage divergence by means of analysis of molecular variance (AMOVA), principal coordinate analysis, assignment tests and multiple matrix regression analyses were assessed using chloroplast DNA and neutral and outlier single nucleotide polymorphisms (SNPs). Several environmental variables were used to characterize potential within‐species niche structuring and genotype–environment associations.ResultsTwo deep‐rooted latitudinally structured lineages resulted from cpDNA, the northern cluster being more genetically diverse than the southern one. Of the total of 2943 SNPs, 33 identified as outliers and produced two genetic clusters. Neutral SNPs yielded no structure by AMOVA, whereas higher (>75%) FST values were obtained for cpDNA and outlier SNPs. Precipitation variables were mostly associated with population clusters and suggested two climatic niches, consisting of cold and dry in the south and more variable precipitation, temperature and soil conditions in the north. Associations of genetic distance with environment and geography suggested isolation‐by‐distance and isolation‐by‐ecology or isolation‐by‐environment effects.Main conclusionsAncient lineage divergence in N. dombeyi, originally driven by vicariance, has been maintained by diversifying selection under distinct environmental conditions that also define distinct within‐species niches. Deeply rooted phylogeographical breaks can be conserved in continuously distributed species in the absence of current geographical barriers. Yet, physical gradients exert differential selective pressures, which are maintained in the face of potential gene flow. As a result, selection can lead to geographically localized and differentially adapted groups of populations that can be detected by a combination of traditional phylogeographical and novel genomic methods.

The genomic scale of fluctuating selection in a natural plant population.

This study characterizes evolution at ≈1.86 million Single Nucleotide Polymorphisms (SNPs) within a natural population of yellow monkeyflower (Mimulus guttatus). Most SNPs exhibit minimal change over a span of 23 generations (less than 1% per year), consistent with neutral evolution in a large population. However, several thousand SNPs display strong fluctuations in frequency. Multiple lines of evidence indicate that these 'Fluctuating SNPs' are driven by temporally varying selection. Unlinked loci exhibit synchronous changes with the same allele increasing consistently in certain time intervals but declining in others. This synchrony is sufficiently pronounced that we can roughly classify intervals into two categories, "green" and "yellow," corresponding to conflicting selection regimes. Alleles increasing in green intervals are associated with early life investment in vegetative tissue and delayed flowering. The alternative alleles that increase in yellow intervals are associated with rapid progression to flowering. Selection on the Fluctuating SNPs produces a strong ripple effect on variation across the genome. Accounting for estimation error, we estimate the distribution of allele frequency change per generation in this population. While change is minimal for most SNPs, diffuse hitchhiking effects generated by selected loci may be driving neutral SNPs to a much greater extent than classic genetic drift.

Demographic, physiological and genetic factors linked to the poleward range expansion of the snail Nerita yoldii along the shoreline of China.

Species range shift is one of the most significant consequences of climate change in the Anthropocene. A comprehensive study, including demographic, physiological and genetic factors linked to poleward range expansion, is crucial for understanding how the expanding population occupies the new habitat. In the present study, we investigated the demographic, physiological and genetic features of the intertidal gastropod Nerita yoldii, which has extended its northern limit by ~200 km over the former biogeographical break of the Yangtze River Estuary in recent decades. Data from neutral single nucleotide polymorphisms (SNPs) showed that the new marginal populations formed a distinct cluster established by a few founders. Demographic modelling analysis revealed that the new marginal populations experienced a strong genetic bottleneck followed by recent demographic expansion. Successful expansion that overcame the founder effect might be attributed to its high capacity for rapid population growth and multiple introductions. According to the non-neutral SNPs under diversifying selection, there were high levels of heterozygosity in the new marginal populations, which might be beneficial for adapting to the novel thermal conditions. The common garden experiment showed that the new marginal populations have evolved divergent transcriptomic and physiological responses to heat stress, allowing them to occupy and survive in the novel environment. Lower transcriptional plasticity was observed in the new marginal populations. These results suggest a new biogeographical pattern of N. yoldii has formed with the occurrence of demographic, physiological and genetic changes, and emphasize the roles of adaptation of marginal populations during range expansion.

Population genomics reveals a single semi-continuous population of a commercially exploited marine gastropod

Buccinum undatum is a commercially important marine gastropod with limited dispersal capabilities. Previous genetic studies utilising microsatellites and Double-digest Restriction-site Associated DNA sequencing (ddRADseq) provided evidence that B. undatum exhibits fine-scale genetic structure. Using ddRADseq, 128 individuals from the southern North Sea, English Channel, and the Irish Sea were genotyped using 7015 filtered single nucleotide polymorphisms (SNPs), 19 of which were identified as being under putative selection. Multiple genetic clustering methods – Discriminant analysis of principal components, Principal component analysis, and Sparse non-negative matrix factorisation,– were used to investigate population structure. Spatially explicit genetic structure was investigated using an Estimated Effective Migration Surface analysis and a Mantel correlogram. A single genetic population was found using neutral SNPs, with weak within-population structuring. Global F ST was low (0.0046, p < 0.001), and pairwise F ST estimates between sampling locations were between 0.0004 and 0.0224. There was a significant trend of isolation-by-distance across all sampling locations (r = 0.743, p < 0.001). Positive spatial autocorrelation indicated whelks located ≤ 50 km of one another were significantly more related than by chance (r = 0.12, p = 0.003), further emphasising the low dispersal capabilities of B. undatum . Finally, two barriers of lower-than-average dispersal were discovered; the Thames estuary and across the English Channel. Management implications are discussed for the sustainability of whelks from inshore fisheries.

A convoluted tale of hybridization between two Petunia species from a transitional zone in South America

Recently diverged species may hybridize in their contact zones if complete reproductive isolation has not yet emerged. Petunia inflata and P. interior are closely related species with a narrow geographic distribution in Argentina and southern Brazil. They share morphological features, genetic markers, pollinators, and occupy a transitional area between the Pampa grasslands and the Brazilian Atlantic Forest. Here, we used genomic data to verify species boundaries, identify putative hybrids, and shed light on their speciation process. We characterized 59 individuals from allopatric and contact zones using genotyping-by-sequencing technology, resulting in a final dataset with 21,759 neutral single nucleotide polymorphisms used to perform structure, demographic, and hybridization analyses. These species belong to distinct evolutionary lineages that hybridized after secondary contact. A combination of geographic distance, elevation, and climate explains the genetic divergence between species. Niche overlap analysis revealed that even though these species have overlapping distributions and similar habitat preferences, they are more distinct than expected by chance, rejecting the niche conservatism hypothesis. Demographic analysis suggested that the Pleistocene climatic changes led species to diverge but they came into secondary contact during the Holocene. The secondary contact led to limited gene flow between species and bidirectional introgression. The distribution expansion of these species’ ancestor to a transitional zone between biomes, associated with elevational ranges and habitat fragmentation promoted speciation and niche differentiation. • Climate, elevation, and geographic distance drove species’ divergence. • Species hybridized after secondary contact during mid-Holocene. • Bidirectional introgression possibly allowed species to adapt to new habitats.

Signatures of polygenic adaptation align with genome-wide methylation patterns in wild strawberry plants.

Epigenetic inheritance can drive adaptive evolution independently of DNA sequence variation. However, to what extent epigenetic variation represents an autonomous evolutionary force remains largely elusive. Through gene ontology and comparative analyses of genomic and epigenomic variation of wild strawberry plants raised in distinct drought settings, we characterised genome-wide covariation between single nucleotide polymorphisms (SNPs) and differentially methylated cytosines (DMCs). Covariation between SNPs and DMCs was independent of genomic proximity, but instead associated with fitness-related processes such as stress responses, genome regulation and reproduction. We expected this functional SNP-DMC covariation to be driven by adaptive evolution canalising SNP and DMC variation, but instead observed significantly lower covariation with DMCs for adaptive rather than for neutral SNPs. Drought-induced DMCs frequently co-varied with tens of SNPs, suggesting high genomic redundancy as a broad potential basis for polygenic adaptation of gene expression. Our findings suggest that stress-responsive DMCs initially co-vary with many SNPs under increased environmental stress, and that natural selection acting upon several of these SNPs subsequently reduces standing covariation with stress-responsive DMCs. Our study supports DNA methylation profiles that represent complex quantitative traits rather than autonomous evolutionary forces. We provide a conceptual framework for polygenic regulation and adaptation shaping genome-wide methylation patterns in plants.

Genetic Diversity and Population Structure of Lethrinus Lentjan (Lethrinidae) in Vietnam Based on SNP Markers

Lethrinus lentjan (Lacepède, 1802) is an important commercial species for marine fisheries in subtropical and tropical regions of the Indian and Indo-Pacific oceans. Although heavily exploited, their genetic diversity and population structuring along the Vietnam coastline are unclear. Here, we used a panel of single nucleotide polymorphisms (SNPs) generated from restriction site-associated DNA sequencing (RADseq). After removing 405 outlier loci, 1,506 putatively neutral SNPs from 62 individuals were used to assess the genetic population structure of L. lentjan. Observed/expected heterozygosity (Ho/He) within sites ranged from 0.170/0.202 (Southeast) to 0.188/0.213 (Central). Pairwise FST values, Structure and Discriminant Analysis of Principal Components (DAPC) analysis indicate the lack of spatial genetic structure, suggesting the presence of a single panmictic population. Larval dispersal by ocean currents may facilitated high gene flow of L. lentjan along the Vietnamese coastline, and Mekong River outflow may not act as the natural barrier.

Neutral and outlier single nucleotide polymorphisms disentangle the evolutionary history of a coastal Solanaceae species.

Speciation begins with the isolation of some individuals or subpopulations due to drivers promoting a diverging genetic distribution. Such isolation may occur, followed by different processes and pressures. Isolation-by-distance (IBD), isolation-by-adaptation (IBA), and isolation-by-colonization (IBC) have been recognized as the main divergence patterns. Still, it is not easy to distinguish which one is the main pattern as each one may act at different points in time or even simultaneously. Using an extensive genome coverage from a Petunia species complex with coastal and inland distribution and multiple analytical approaches on population genomics and phylogeography, we showed a complex interplay between neutral and selective forces acting on the divergence process. We found 18,887 SNPs potentially neutral and 924 potentially under selection (outlier) loci. All analyses pointed that each subspecies displays its own genetic component and evolutionary history. We suggested plausible ecological drivers for such divergence in a southernmost South Atlantic coastal plain in Brazil and Uruguay and identified a connection between adaptation and environment heterogeneity.

The lineage of coronavirus SARS-CoV-2 of Russian origin: Genetic characteristics and correlations with clinical parameters and severity of coronavirus infection

The identification of new SARS-CoV-2 and human protein and gene targets, which may be markers of the severity and outcome of the disease, are extremely important during the COVID-19 pandemic. The goal of this study was to carry out genetic analysis of SARS-CoV-2 RNA samples to elucidate correlations of genetic parameters (SNPs) with clinical data and severity of COVID-19 infection.Material and Methods. The study included viral RNA samples isolated from 56 patients with COVID-19 infection who received treatment at the City Hospital No. 40 of St. Petersburg from 04/18/2020 to 04/18/2021. Patients underwent physical examination with the assessments of hemodynamic and respiratory parameters, clinical risk according to National Early Warning Score (NEWS), computed tomography (CT) of the chest, and laboratory studies including clinical blood analysis, assessment of ferritin, C-reactive protein (CRP), interleukin-6 (IL-6), lactate dehydrogenase (LDH), D-dimer, creatinine, and glucose levels. All patients tested positive for SARS-CoV-2 RNA by polymerase chain reaction (PCR). Single nucleotide polymorphisms (SNPs) in viral RNA were identified through the creation of cDNA libraries by targeted sequencing (MiSeq Illumina). Bioinformatic analysis of viral samples was performed using the viralrecon v2 pipeline with the further annotation via Pangolin and Nextlade. Sampled genomes were visualized using the Integrative Genomics Viewer (IGV) software. Statistical data processing (descriptive statistics and graphical analysis of data relationships from diff erent tables) was performed using a GraphPad device on the Prism 8.01 platform.Results. A comparative analysis of SNP frequencies in the virus genome in samples from deceased and discharged patients was carried out. The SNPs associated with risk of death (OR &gt; 1), neutral SNPs (OR = 1), and protective SNPs (OR &lt; 1) were identifi ed. Patient samples were infected with 14 lines of SARS-CoV-2, fi ve of which (B.1.1.129, B.1.1.407, B.1.1.373, B.1.1.397, and B.1.1.152) were of Russian origin. The SNPs in the samples infected with the strains of non-Russian origin were associated with an increased risk of mortality (OR = 2.267, 95% confi dence interval 0.1594-8.653) compared to the SNPs in the samples obtained from the group of patients infected with the strains of Russian origin. Positive correlations were identifi ed between the average SNP number, nonsynonymous SNPs, and S-protein SNPs with the degree of respiratory failure, total NEWS score, CT-based form of disease, duration of treatment with mechanical ventilation, disease outcome, levels of LDH, glucose, D-dimer, and ferritin, and RNA amount in the PCR test. S-protein SNPs negatively correlated with the leukocyte and neutrophil counts.