Mapping and functional characterization of structural variation in 1060 pig genomes.

BACKGROUND: Structural variations (SVs) have significant impacts on complex phenotypes by rearranging large amounts of DNA sequence. RESULTS: We present a comprehensive SV catalog based on the whole-genome sequence of 1060 pigs (Sus scrofa) representing 101 breeds, covering 9.6% of the pig genome. This catalog includes 42,487 deletions, 37,913 mobile element insertions, 3308 duplications, 1664 inversions, and 45,184 break ends. Estimates of breed ancestry and hybridization using genotyped SVs align well with those from single nucleotide polymorphisms. Geographically stratified deletions are observed, along with known duplications of the KIT gene, responsible for white coat color in European pigs. Additionally, we identify a recent SINE element insertion in MYO5A transcripts of European pigs, potentially influencing alternative splicing patterns and coat color alterations. Furthermore, a Yorkshire-specific copy number gain within ABCG2 is found, impacting chromatin interactions and gene expression across multiple tissues over a stretch of genomic region of ~200 kb. Preliminary investigations into SV's impact on gene expression and traits using the Pig Genotype-Tissue Expression (PigGTEx) data reveal SV associations with regulatory variants and gene-trait pairs. For instance, a 51-bp deletion is linked to the lead eQTL of the lipid metabolism regulating gene FADS3, whose expression in embryo may affect loin muscle area, as revealed by our transcriptome-wide association studies. CONCLUSIONS: This SV catalog serves as a valuable resource for studying diversity, evolutionary history, and functional shaping of the pig genome by processes like domestication, trait-based breeding, and adaptive evolution.

[Investigation of the population diversity of intermediate host snails and crabs of Paragonimus along Jiulong River, Zhangjiang River and Dongxi River basins in southern Fujian Province].

OBJECTIVE: To investigate the population distribution of intermediate host snails and crabs of Paragonimus along the Jiulongjiang River, Zhangjiang River, and Dongxi River basins in Bopingling Mountain, southern Fujian Province, so as to provide baseline data for researches on parasitic disease prevention and control and enlargement of samples in the parasitic resource bank. METHODS: A total of 23 villages in 8 counties (districts) along the Jiulong River, Zhangjiang River, and Dongxi River basins in Zhangzhou City, Fujian Province were selected as survey sites during the period from November 2020 through March 2023, and snail and freshwater crabs were sampled from 1 to 3 streams and ditches neighboring residential areas in each village. Morphological identification of snails was performed according to the external morphological characteristics of collected snail shells, and the unidentified snail species sampled from the natural foci of paragonimiasis in Yunxiao County were subjected to se-quence analysis of the mitochondrial cytochrome oxidase 1 (CO1) gene. The crab species was identified by observing the morphological characteristics of the terminal segment of the first pleopod of male crabs, and Paragonimus cercariae and metacercariae were detected in collected snails. RESULTS: The shells of the unidentified snails sampled from the natural foci of paragonimiasis in Yunxiao County were approximately 50 mm in height and 18 mm in width, thick and solid, long tower cone-shaped, and had 8 to 10 whorls. CO1 gene sequence analysis identified the snail species as Sulcospira hainanensis. A total of 6 freshwater snail species belonging to 5 genera within 3 families, identified 23 survey sites, including Semisulcospira libertina, Paludomus zhangchouensis and S. hainanensis that belonged to the Family Pleurceridae, Tricula fujianensis and T. huaanensis that belonged to the subfamily Triculinae, Family Pomatiopsidae, and Melanoides tuberculata (Family Thiaridae), and 11 species of freshwater crabs belonging to 5 genera within 2 families were identified, including Sinopotamon genus of S. jianglense, S. pinheense, and S. zhangzhouense, Huananpotamon genus of H. planopodum and H. zhangzhouense, Nanhaipotamon genus of N. huaanense and N. longhaiense, and Minpotamon genus of M. nasicum and M. auritum that belonged to the Family Potamidae, and Somanniathelphusa genus of S. huaanensis and S. zhangpuensis (Family Parathelphusidae). In addition, the prevalence of P. westermani cercariae infections was 0.08% (2/2 317) in P. zhangchouensis from Danyan Village in Changtai District and 0.09% (1/1 039) in S. hainanensis from Jinkeng Village in Yunxiao County, and the prevalence of P. westermani metacercariae infections was 25.81% (8/31) in S. jianglense from Danyan Village in Changtai District, and 26.31% (5/19) in S. zhangzhouense from Jinkeng Village in Yunxiao County, respectively. CONCLUSIONS: There is a population diversity in the intermediate host snails and crabs along the Jiulongjiang River, Zhangjiang River, and Dongxi River basins in Bopingling Mountain, southern Fujian Province, and P. zhangzhouensis and S. hainanensis are, for the first time, confirmed as the first intermediate hosts of P. westermani.

Development of novel SSR markers and validation by assessing the genetic diversity of endangered Deccan mahseer, Tor khudree.

BACKGROUND: The Deccan mahseer, Tor khudree (Sykes, 1839) is a potential game and food fish species belonging to the family cyprinidae and is categorized as endangered. Its distribution is restricted to southern part of India, specifically to Peninsular Rivers. This study is first to assess the genetic diversity and differentiation in Tor khudree by developing novel simple sequence repeat (SSR) markers. METHODS AND RESULTS: Low depth next generation sequencing followed by sequence analysis in MISA software identified 187,649 SSRs. The novel fourteen validated SSR loci were used for population genetic analysis. All of the SSR loci were highly informative with mean PIC > 0.5. High mean allelic richness (9.29) observed heterozygosity (0.98) and expected heterozygosity (0.79) were observed across the loci. However, genetic differentiation was low but significant (0.052). Negative FIS values were observed in both locus-wise and populations indicating the presence of high heterozygosity. Intrapopulation variation was found to be high (96.29%). The population structure revealed two genetic stocks. CONCLUSIONS: The results from the present study including the highly polymorphic markers developed would be a useful resource for further research on population genetics and conservation genetics of the species.

NUDT15 and TPMT polymorphisms in three distinct native populations of the Brazilian Amazon.

This is the first report of the distribution of TPMT and NUDT15 single nucleotide polymorphisms and metabolic phenotypes associated with cytotoxicity of thiopurine drugs, in indigenous groups of Brazilian Amazon: Munduruku, Paiter-Suruí and Yanomami. The minor allele frequency (MAF) of NUDT15 rs116855232 did not differ significantly across the groups; TPMT rs1800462 was absent, while rs1800460 and rs1142345 were in strong linkage disequilibrium, and 10- and 30-fold more common in Paiter-Suruí. Indeed, the MAFs in Paiter-Surui (0.193 and 0.188) are the largest report globally. The distribution of combined NUDT15/TPMT metabolic phenotypes differed significantly (p < 0.0001) and largely (Cramér´s V = 0.37) across cohorts. This has important pharmacogenetic implications: the Clinical Pharmacogenetics Implementation Consortium recommendations to reduce or consider reduction of thiopurine dose applies to 4.4% Yanomami, 5.6% Munduruku, versus 41% Paiter-Suruí. The proportion of Paiter-Suruí at risk of thiopurine intolerance is 3- to 4-fold higher than any other population worldwide.

Diversity and Clonality in Populations of Phytophthora citrophthora and P. syringae Causing Brown Rot of Citrus in California.

Phytophthora citrophthora and P. syringae are currently the primary causal organisms of brown rot of citrus fruits in California. To possibly find an explanation for the prevalence of the previously minor species P. syringae, we determined the population structures of both pathogens in California using next-generation sequencing and population genomics analyses. Whole-genome sequencing and aligning with newly assembled reference genomes identified 972,266 variants in 132 isolates of P. citrophthora and 422,208 variants in 154 isolates (including 24 from noncitrus tree crops) of P. syringae originating from three major growing regions. The resulting data sets were visualized using principal component analysis, discriminant analysis of principal components, unweighted pair-group method with arithmetic mean dendrograms, fastStructure, and minimum spanning networks, and we obtained the index of association, diversity summary statistics, and genetic distance statistics values GST, G''ST, and Jost's D. Subpopulations of both species were mostly defined by their geographic origin indicating restricted dispersal of inoculum. Except for five isolates, the population structure of P. citrophthora (that is heterothallic and unlikely to reproduce sexually) was clonal to semi-clonal, with very little genetic diversity within and among subgroups. In contrast, the population structure of P. syringae was also clonal to semi-clonal, but isolates were placed into four main clusters of much higher diversity. Clonality in both species can be explained by a high level of asexual reproduction. The higher diversity in the homothallic P. syringae is likely due to commonly occurring sexual reproduction. One distinct cluster of P. syringae consisted solely of isolates from noncitrus hosts; therefore, the origin of P. syringae in citrus could not be resolved.

Microgeographic variation in demography and thermal regimes stabilize regional abundance of a widespread freshwater fish.

Predicting the persistence of species under climate change is an increasingly important objective in ecological research and management. However, biotic and abiotic heterogeneity can drive asynchrony in population responses at small spatial scales, complicating species-level assessments. For widely distributed species consisting of many fragmented populations, such as brook trout (Salvelinus fontinalis), understanding the drivers of asynchrony in population dynamics can improve the predictions of range-wide climate impacts. We analyzed the demographic time series from mark-recapture surveys of 11 natural brook trout populations in eastern Canada over 13 years to examine the extent, drivers, and consequences of fine-scale population variation. The focal populations were genetically differentiated, occupied a small area (~25 km2 ) with few human impacts, and experienced similar climate conditions. Recruitment was highly asynchronous, weakly related to climate variables and showed population-specific relationships with other demographic processes, generating diverse population dynamics. In contrast, individual growth was mostly synchronized among populations and driven by a shared positive relationship with stream temperature. Outputs from population-specific models were unrelated to four of the five hypothesized drivers (recruitment, growth, reproductive success, phylogenetic distance), but variation in groundwater inputs strongly influenced stream temperature regimes and stock-recruitment relationships. Finally, population asynchrony generated a portfolio effect that stabilized regional species abundance. Our results demonstrated that population demographics and habitat diversity at microgeographic scales can play a significant role in moderating species responses to climate change. Moreover, we suggest that the absence of human activities within study streams preserved natural habitat variation and contributed to asynchrony in brook trout abundance, while the small study area eased monitoring and increased the likelihood of detecting asynchrony. Therefore, anthropogenic habitat degradation, landscape context, and spatial scale must be considered when developing management strategies to monitor and maintain populations that are diverse, stable, and resilient to climate change.

The Impact of Recent Demography on Functional Genetic Variation in North African Human Groups.

The strategic location of North Africa has made the region the core of a wide range of human demographic events, including migrations, bottlenecks, and admixture processes. This has led to a complex and heterogeneous genetic and cultural landscape, which remains poorly studied compared to other world regions. Whole-exome sequencing is particularly relevant to determine the effects of these demographic events on current-day North Africans' genomes, since it allows to focus on those parts of the genome that are more likely to have direct biomedical consequences. Whole-exome sequencing can also be used to assess the effect of recent demography in functional genetic variation and the efficacy of natural selection, a long-lasting debate. In the present work, we use newly generated whole-exome sequencing and genome-wide array genotypes to investigate the effect of demography in functional variation in 7 North African populations, considering both cultural and demographic differences and with a special focus on Amazigh (plur. Imazighen) groups. We detect genetic differences among populations related to their degree of isolation and the presence of bottlenecks in their recent history. We find differences in the functional part of the genome that suggest a relaxation of purifying selection in the more isolated groups, allowing for an increase of putatively damaging variation. Our results also show a shift in mutational load coinciding with major demographic events in the region and reveal differences within and between cultural and geographic groups.

Investigation of the population diversity of intermediate host snails and crabs of Paragonimus along Jiulong River, Zhangjiang River and Dongxi River basins in southern Fujian Province / 中国血吸虫病防治杂志

Objective To investigate the population distribution of intermediate host snails and crabs of Paragonimus along the Jiulongjiang River, Zhangjiang River, and Dongxi River basins in Bopingling Mountain, southern Fujian Province, so as to provide baseline data for researches on parasitic disease prevention and control and enlargement of samples in the parasitic resource bank. Methods A total of 23 villages in 8 counties (districts) along the Jiulong River, Zhangjiang River, and Dongxi River basins in Zhangzhou City, Fujian Province were selected as survey sites during the period from November 2020 through March 2023, and snail and freshwater crabs were sampled from 1 to 3 streams and ditches neighboring residential areas in each village. Morphological identification of snails was performed according to the external morphological characteristics of collected snail shells, and the unidentified snail species sampled from the natural foci of paragonimiasis in Yunxiao County were subjected to se-quence analysis of the mitochondrial cytochrome oxidase 1 (CO1) gene. The crab species was identified by observing the morphological characteristics of the terminal segment of the first pleopod of male crabs, and Paragonimus cercariae and metacercariae were detected in collected snails. Results The shells of the unidentified snails sampled from the natural foci of paragonimiasis in Yunxiao County were approximately 50 mm in height and 18 mm in width, thick and solid, long tower cone-shaped, and had 8 to 10 whorls. CO1 gene sequence analysis identified the snail species as Sulcospira hainanensis. A total of 6 freshwater snail species belonging to 5 genera within 3 families, identified 23 survey sites, including Semisulcospira libertina, Paludomus zhangchouensis and S. hainanensis that belonged to the Family Pleurceridae, Tricula fujianensis and T. huaanensis that belonged to the subfamily Triculinae, Family Pomatiopsidae, and Melanoides tuberculata (Family Thiaridae), and 11 species of freshwater crabs belonging to 5 genera within 2 families were identified, including Sinopotamon genus of S. jianglense, S. pinheense, and S. zhangzhouense, Huananpotamon genus of H. planopodum and H. zhangzhouense, Nanhaipotamon genus of N. huaanense and N. longhaiense, and Minpotamon genus of M. nasicum and M. auritum that belonged to the Family Potamidae, and Somanniathelphusa genus of S. huaanensis and S. zhangpuensis (Family Parathelphusidae). In addition, the prevalence of P. westermani cercariae infections was 0.08% (2/2 317) in P. zhangchouensis from Danyan Village in Changtai District and 0.09% (1/1 039) in S. hainanensis from Jinkeng Village in Yunxiao County, and the prevalence of P. westermani metacercariae infections was 25.81% (8/31) in S. jianglense from Danyan Village in Changtai District, and 26.31% (5/19) in S. zhangzhouense from Jinkeng Village in Yunxiao County, respectively. Conclusions There is a population diversity in the intermediate host snails and crabs along the Jiulongjiang River, Zhangjiang River, and Dongxi River basins in Bopingling Mountain, southern Fujian Province, and P. zhangzhouensis and S. hainanensis are, for the first time, confirmed as the first intermediate hosts of P. westermani.

Global Terrapin Character-Based DNA Barcodes: Assessment of the Mitochondrial COI Gene and Conservation Status Revealed a Putative Cryptic Species.

Technological and analytical advances to study evolutionary biology, ecology, and conservation of the Southern River Terrapin (Batagur affinis ssp.) are realised through molecular approaches, including DNA barcoding. We evaluated the use of COI DNA barcodes in Malaysia's Southern River Terrapin population to better understand the species' genetic divergence and other genetic characteristics. We evaluated 26 sequences, including four from field specimens of Southern River Terrapins obtained in Bota Kanan, Perak, Malaysia, and Kuala Berang, Terengganu, Malaysia, as well as 22 sequences from global terrapins previously included in the Barcode of Life Database (BOLD) Systems and GenBank. The species are divided into three families: eight Geoemydidae species (18%), three Emydidae species (6%), and one Pelomedusidae species (2%). The IUCN Red List assigned the 12 species of terrapins sampled for this study to the classifications of critically endangered (CR) for 25% of the samples and endangered (EN) for 8% of the samples. With new haplotypes from the world's terrapins, 16 haplotypes were found. The intraspecific distance values between the COI gene sequences were calculated using the K2P model, which indicated a potential cryptic species between the Northern River Terrapin (Batagur baska) and Southern River Terrapin (Batagur affinis affinis). The Bayesian analysis of the phylogenetic tree also showed both species in the same lineage. The BLASTn search resulted in 100% of the same species of B. affinis as B. baska. The Jalview alignment visualised almost identical sequences between both species. The Southern River Terrapin (B. affinis affinis) from the west coast of Peninsular Malaysia was found to share the same haplotype (Hap_1) as the Northern River Terrapin from India. However, B. affinis edwardmolli from the east coast of Peninsular Malaysia formed Hap_16. The COI analysis found new haplotypes and showed that DNA barcodes are an excellent way to measure the diversity of a population.

Circulating epigenomic biomarkers correspond with kidney disease susceptibility in high-risk populations with type 2 diabetes mellitus.

AIMS: To investigate epigenomic indices of diabetic kidney disease (DKD) susceptibility among high-risk populations with type 2 diabetes mellitus. METHODS: KDIGO (Kidney Disease: Improving Global Outcomes) clinical guidelines were used to classify people living with or without DKD. Differential gene methylation of DKD was then assessed in a discovery Aboriginal Diabetes Study cohort (PROPHECY, 89 people) and an external independent study from Thailand (THEPTARIN, 128 people). Corresponding mRNA levels were also measured and linked to levels of albuminuria and eGFR. RESULTS: Increased DKD risk was associated with reduced methylation and elevated gene expression in the PROPHECY discovery cohort of Aboriginal Australians and these findings were externally validated in the THEPTARIN diabetes registry of Thai people living with type 2 diabetes mellitus. CONCLUSIONS: Novel epigenomic scores can improve diagnostic performance over clinical modelling using albuminuria and GFR alone and can distinguish DKD susceptibility.

Differential evolution for population diversity mechanism based on covariance matrix.

Differential evolution (DE) is a heuristic global search algorithm based on population. It has exhibited great adaptability in solving continuous-domain problems, but sometimes suffered from insufficient local search ability and being trapped in local optimum when dealing with complicated optimization problems. To solve these problems, an improved differential evolution algorithm with population diversity mechanism based on covariance matrix (CM-DE) is proposed. First, a new parameter adaptation strategy is used to adapt the control parameters, in which the scale factor F is updated according to the improved wavelet basis function in the early stage and Cauchy distribution in the later stage and the crossover rate CR is generated according to normal distribution. The diversity of population and convergence speed are improved by employing the method above. Second, the perturbation strategy is incorporated into crossover operator to enhance the search ability of DE. Finally, the covariance matrix of the population is constructed, where the variance in the covariance matrix is used as indicator to measure the similarity between individuals in the population in order to prevent the algorithm from falling into local optimum resulted by low population diversity. The CM-DE is compared with the state-of-art DE variants including LSHADE (Tanabe and Fukunaga, 2014), jSO [1], LPalmDE [2], PaDE [3] and LSHADE-cnEpSin [4] under 88 test functions from CEC2013 [5], CEC2014 [6] and CEC2017 (Wu et al., 2017) test suites. From the experiment results, it is obvious that among 30 benchmark functions from CEC2017 on 50D optimization, the CM-DE algorithm has 22, 20, 24, 23, 28 better performances comparing with LSHADE, jSO, LPalmDE, PaDE, and LSHADE-cnEpsin. For CEC2017 on 30D optimization, the proposed algorithm secures better performance on 19 out of 30 benchmark functions in terms of convergence speed. In addition, a real-world application is also used to verify the feasibility of the proposed algorithm. The experiment results validate the highly competitive performance in terms of solution accuracy and convergence speed.

Analysis of leaf forage value and screening of different populations of Pteroceltis tatarinowii, a rare and endemic species in China.

To fully exploit the economic value of the Chinese endemic species Pteroceltis tatarinowii and provide new resources for forage production, the forage nutritional value of P. tatarinowii leaves from different populations was analyzed and evaluated. The results were as follows: 1) There were significant differences in the forage nutrient indices of leaves from different populations. The crude protein content was 10.77%-18.65%, with an average of 14.58%, and the SDJN population had the highest crude protein content. The average crude fat, crude fiber content was 7.62%; the average neutral detergent fiber content was 25.33%; and the average acid detergent fiber contents were 6.79%, 7.62%, 25.33%, and 17.52%, respectively. The average phosphorus and calcium content in the leaves was 0.785 g·kg-1 and 58.01 g·kg-1, respectively. The tannin content was much lower than the antifeedant standard, at an average of 4.97 g·kg-1. The average total amounts of hydrolyzed and free amino acids in the leaves were 108.20 mg·g-1 and 47.87 mg·g-1, respectively. Thus, P. tatarinowii leaves have high crude protein, crude fat, and calcium contents, and low fiber, tannin contents, and are protein-rich. These results provide evidence that this species can be developed into an excellent woody forage tree. 2) There were significant differences in the forage quality evaluation indices among the populations. The forage indices of NDP, ADP, DMI, DDM, and RFV of 21 populations all met the super standard of the American Grass and Grassland Association (AFGC) for hay, two crude protein indices met the grade 1 standard, and 12 crude protein indices met the grade 2 standard. Four high-protein and high-RFV forage populations (SDJN, SDZZ, SXLQ, and AHXX) were selected. 3) The results of the correlation analysis showed that there was no significant correlation between the forage characteristics of P. tatarinowii leaves and latitude and longitude, indicating no significant geographical variation. However, the forage characteristics were strongly correlated with elevation, average annual temperature, and annual precipitation. Thus, high elevation, low temperatures, and rainy weather can improve the forage value of the leaves. P. tatarinowii can be planted to provide leaf forage in cold and wet areas at a specific elevation. Moreover, the forage value of P. tatarinowii leaves can be further improved by increasing nitrogen fertilizer and reducing K and Ca fertilizers during cultivation. 4) Cluster analysis revealed obvious regionalism. Taking the Yangtze River Basin as the limit, cluster analysis divided the species into four population groups: the Yangtze River Basin and northern, southwestern, and eastern coastal populations.

Genetic footprint of population diversity and genetic structure of Venturia inaequalis infecting apple (Malus × domestica Borkh.).

Apple scab instigated by Venturia inaequalis impels remarkable losses to apple fruit production. In an effort to comprehend the key mechanisms of evolutionary potential defining V. inaequalis population, 132 isolates of V. inaequalis from five commercial apple orchards were collected and assayed using 14 microsatellite markers. The average diversity was observed within the individuals of populations based on the Shannon-Wieners index (I) and observed heterozygosity (Ho) was average but considerably lower than expected heterozygosity (He). The genetic differentiation based on FST values was revealed as an average measure of divergence between populations and had varying proportions of gene flow and migration among themselves. Analysis of Molecular Variance (AMOVA) revealed that variance (94%) was dispersed across individuals with a significant (6%) variation between populations from different regions. To examine host specialization within the V. inaequalis population, the assignment approach based on K-means of clustering (an unsupervised machine learning approach), revealed that the clustering method supported three clusters at (K = 3) and three major clusters were also observed in Principle Component Analysis (PCA). Additionally, Nei's genetic distance values, pairwise estimates of genetic differentiation, dendrogram using the neighbor-joining and PCoA revealed the random distribution of V. Inaequalis isolates that depicted a high proportion of genotypic diversity within populations and population genetic structure. Supplementary Information: The online version contains supplementary material available at 10.1007/s13205-023-03672-2.

Improved Environmental Stimulus and Biological Competition Tactics Interactive Artificial Ecological Optimization Algorithm for Clustering.

An interactive artificial ecological optimization algorithm (SIAEO) based on environmental stimulus and a competition mechanism was devised to find the solution to a complex calculation, which can often become bogged down in local optimum because of the sequential execution of consumption and decomposition stages in the artificial ecological optimization algorithm. Firstly, the environmental stimulus defined by population diversity makes the population interactively execute the consumption operator and decomposition operator to abate the inhomogeneity of the algorithm. Secondly, the three different types of predation modes in the consumption stage were regarded as three different tasks, and the task execution mode was determined by the maximum cumulative success rate of each individual task execution. Furthermore, the biological competition operator is recommended to modify the regeneration strategy so that the SIAEO algorithm can provide consideration to the exploitation in the exploration stage, break the equal probability execution mode of the AEO, and promote the competition among operators. Finally, the stochastic mean suppression alternation exploitation problem is introduced in the later exploitation process of the algorithm, which can tremendously heighten the SIAEO algorithm to run away the local optimum. A comparison between SIAEO and other improved algorithms is performed on the CEC2017 and CEC2019 test set.

Latitudinal variation and plasticity in response to temperature in Geukensia demissa.

As global temperatures warm, species must adapt to a changing climate or transition to a different location suitable for their survival. Understanding the extent to which species are able to do so, particularly keystone species, is imperative to ensuring the survival of key ecosystems. The ribbed mussel Geukensia demissa is an integral part of salt marshes along the Atlantic coast of North America. Spatial patterns of genomic and phenotypic divergence have been previously documented, although their link with coastal environmental variation is unknown. Here, we study how populations of G. demissa in the northern (Massachusetts) and southern (Georgia) portions of the species range respond to changes in temperature. We combine assays of variation in oxygen consumption and RNA transcriptomic data with genomic divergence analyses to identify how separate populations of G. demissa may vary in distinct thermal environments. Our results show differences in constitutive oxygen consumption between mussels from Georgia and Massachusetts, as well as shared and disparate patterns of gene expression across temperature profiles. We also find that metabolic genes seem to be a strong component of divergence between these two populations. Our analysis highlights the importance of studying integrative patterns of genomic and phenotypic variation in species that are key for particular ecosystems, and how they might respond to further changes in climate.

Archaic humans have contributed to large-scale variation in modern human T cell receptor genes.

Human T cell receptors (TCRs) are critical for mediating immune responses to pathogens and tumors and regulating self-antigen recognition. Yet, variations in the genes encoding TCRs remain insufficiently defined. Detailed analysis of expressed TCR alpha, beta, gamma, and delta genes in 45 donors from four human populations-African, East Asian, South Asian, and European-revealed 175 additional TCR variable and junctional alleles. Most of these contained coding changes and were present at widely differing frequencies in the populations, a finding confirmed using DNA samples from the 1000 Genomes Project. Importantly, we identified three Neanderthal-derived, introgressed TCR regions including a highly divergent TRGV4 variant, which mediated altered butyrophilin-like molecule 3 (BTNL3) ligand reactivity and was frequent in all modern Eurasian population groups. Our results demonstrate remarkable variation in TCR genes in both individuals and populations, providing a strong incentive for including allelic variation in studies of TCR function in human biology.

Insular holobionts: persistence and seasonal plasticity of the Balearic wall lizard (Podarcis lilfordi) gut microbiota.

Background: Integrative studies of animals and associated microbial assemblages (i.e., the holobiont) are rapidly changing our perspectives on organismal ecology and evolution. Insular vertebrates provide ideal natural systems to understand patterns of host-gut microbiota coevolution, the resilience and plasticity these microbial communities over temporal and spatial scales, and ultimately their role in the host ecological adaptation. Methods: Here we used the endemic Balearic wall lizard Podarcis lilfordi to dissect the drivers of the microbial diversity within and across host allopatric populations/islets. By focusing on three extensively studied populations/islets of Mallorca (Spain) and fecal sampling from individually identified lizards along two years (both in spring and autumn), we sorted out the effect of islet, sex, life stage, year and season on the microbiota composition. We further related microbiota diversity to host genetics, trophic ecology and expected annual metabolic changes. Results: All the three populations showed a remarkable conservation of the major microbial taxonomic profile, while carrying their unique microbial signature at finer level of taxonomic resolution (Amplicon Sequence Variants (ASVs)). Microbiota distances across populations were compatible with both host genetics (based on microsatellites) and trophic niche distances (based on stable isotopes and fecal content). Within populations, a large proportion of ASVs (30-50%) were recurrently found along the four sampling dates. The microbial diversity was strongly marked by seasonality, with no sex effect and a marginal life stage and annual effect. The microbiota showed seasonal fluctuations along the two sampled years, primarily due to changes in the relative abundances of fermentative bacteria (mostly families Lachnospiraceae and Ruminococcaceae), without any major compositional turnover. Conclusions: These results support a large resilience of the major compositional aspects of the P. lilfordi gut microbiota over the short-term evolutionary divergence of their host allopatric populations (<10,000 years), but also indicate an undergoing process of parallel diversification of the both host and associated gut microbes. Predictable seasonal dynamics in microbiota diversity suggests a role of microbiota plasticity in the lizards' metabolic adaptation to their resource-constrained insular environments. Overall, our study supports the need for longitudinal and integrative studies of host and associated microbes in natural systems.

Disentangling a Neotropical pest species complex: genetic diversity and population structure of the native rice stink bug Oebalus poecilus and the invasive O. ypsilongriseus.

BACKGROUND: A first step in any pest management initiative is recognizing the existing problem - identifying the pest species and its abundance and dispersal capacities. This is not simple and even more challenging when insidious (invasive) species are involved constituting a pest complex. Understanding a species' population diversity and structure can provide a better understanding of its adaptation and relative pest potential. Such is the need for the native rice stink bug Oebalus poecilus and the invasive O. ypsilongriseus in low and high flatlands of South America. RESULTS: The genetic structure differed between both rice stink bug species (FST  = 0.157, P = 0.001), where 84% of the overall genetic variability takes place within species and three genetic groups were recognized through Bayesian approach (K = 3). Oebalus poecilus exhibited slightly higher genetic diversity (HE  = 0.253) and structuring (FST  = 0.050, P = 0.001) than the invasive O. ypsilongriseus (HE  = 0.211; FST  = 0.038, P = 0.013). Nonetheless, only the former exhibited significant correlation between genetic and geographic distances (r = 0.48, P = 0.013). CONCLUSION: Despite the pointed peculiarities, the obtained results indicate overlap in both species' occurrence and similar genetic structure allowing for a compound problem to be dealt with as the complex requires managing without, as yet, a prevailing species or a niche specialization. © 2022 Society of Chemical Industry.

Novel Multilocus Sequence Typing and Global Sequence Clustering Schemes for Characterizing the Population Diversity of Streptococcus mitis.

Streptococcus mitis is a common oral commensal and an opportunistic pathogen that causes bacteremia and infective endocarditis; however, the species has received little attention compared to other pathogenic streptococcal species. Effective and easy-to-use molecular typing tools are essential for understanding bacterial population diversity and biology, but schemes specific for S. mitis are not currently available. We therefore developed a multilocus sequence typing (MLST) scheme and defined sequence clusters or lineages of S. mitis using a comprehensive global data set of 322 genomes (148 publicly available and 174 newly sequenced). We used internal 450-bp sequence fragments of seven housekeeping genes (accA, gki, hom, oppC, patB, rlmN, and tsf) to define the MLST scheme and derived the global S. mitis sequence clusters using the PopPUNK clustering algorithm. We identified an initial set of 259 sequence types (STs) and 258 global sequence clusters. The schemes showed high concordance (100%), capturing extensive S. mitis diversity with strains assigned to multiple unique STs and global sequence clusters. The tools also identified extensive within- and between-host S. mitis genetic diversity among isolates sampled from a cohort of healthy individuals, together with potential transmission events, supported by both phylogeny and pairwise single nucleotide polymorphism (SNP) distances. Our novel molecular typing and strain clustering schemes for S. mitis allow for the integration of new strain data, are electronically portable at the PubMLST database (https://pubmlst.org/smitis), and offer a standardized approach to understanding the population structure of S. mitis. These robust tools will enable new insights into the epidemiology of S. mitis colonization, disease and transmission.

A paradigm shift in pharmacogenomics: From candidate polymorphisms to comprehensive sequencing.

Genetic factors have long been recognized as important determinants of interindividual variability in drug efficacy and toxicity. However, despite the increasing number of established gene-drug associations, candidate polymorphisms can only explain a fraction of the genetically encoded functional variability in drug disposition. Advancements in genetic profiling methods now allow to analyse the landscape of human pharmacogenetic variations comprehensively, which opens new opportunities to identify novel factors that could explain the "missing heritability." Here, we provide an updated overview of the landscape of pharmacogenomic variability based on recent analyses of population-scale sequencing projects. We then summarize the current state-of-the-art how the functional consequences of variants with unknown effects can be quantitatively estimated while discussing challenges and peculiarities that are specific to pharmacogenes. In the last sections, we discuss the importance of considering ethnogeographic diversity to provide equitable benefits of pharmacogenomics and summarize current roadblocks for the implementation of sequencing-based guidance of clinical decision-making. Based on the current state of the field, we conclude that testing is likely to gradually shift from the interrogation of selected candidate polymorphisms to comprehensive sequencing, which allows to consider the full spectrum of pharmacogenomic variations for a true personalization of genomic prescribing.