Complex Population Structure Research Articles

Large-scale genomic analysis of Elizabethkingia anophelis

The recent emergence of Elizabethkingia anophelis as a human pathogen is a major concern for global public health. This organism has the potential to cause severe infections and has inherent antimicrobial resistance. The potential for widespread outbreaks and rapid global spread highlights the critical importance of understanding the biology and transmission dynamics of this infectious agent. We performed a large-scale analysis of available 540 E. anophelis, including one novel strain isolated from raw milk and sequenced in this study. Pan-genome analysis revealed an open and diverse pan-genome in this species, characterized by the presence of many accessory genes. This suggests that the species has a high level of adaptability and can thrive in a variety of environments. Phylogenetic analysis has also revealed a complex population structure, with limited source-lineage correlation. We identified diverse antimicrobial resistance factors, including core-genome and accessory ones often associated with mobile genetic elements within specific lineages. Mobilome analysis revealed a dynamic landscape primarily composed of genetic islands, integrative and conjugative elements, prophage elements, and small portion of plasmids emphasizing a complex mechanism of horizontal gene transfer. Our study underscores the adaptability of E. anophelis, characterized by a diverse range of antimicrobial resistance genes, putative virulence factors, and genes enhancing fitness. This adaptability is also supported by the organism’s ability to acquire genetic material through horizontal gene transfer, primarily facilitated by mobile genetic elements such as integrative and conjugative elements (ICEs). The potential for rapid evolution of this emerging pathogen poses a significant challenge to public health efforts.

Estimation of Direct and Indirect Polygenic Effects and Gene-Environment Interactions using Polygenic Scores in Case-Parent Trio Studies.

Family-based studies provide a unique opportunity to characterize genetic risks of diseases in the presence of population structure, assortative mating, and indirect genetic effects. We propose a novel framework, PGS-TRI, for the analysis of polygenic scores (PGS) in case-parent trio studies for estimation of the risk of an index condition associated with direct effects of inherited PGS, indirect effects of parental PGS, and gene-environment interactions. Extensive simulation studies demonstrate the robustness of PGS-TRI in the presence of complex population structure and assortative mating compared to alternative methods. We apply PGS-TRI to multi-ancestry trio studies of autism spectrum disorders (N trio = 1,517) and orofacial clefts (N trio = 1,904) to establish the first transmission-based estimates of risk associated with pre-defined PGS for these conditions and other related traits. For both conditions, we further explored offspring risk associated with polygenic gene-environment interactions, and direct and indirect effects of genetically predicted levels of gene expression and metabolite traits.

Patterns of persistence: Genetic and behavioral population complexity of winter flounder amid population declines.

Winter flounder Pseudopleuronectes americanus (Walbaum 1792) are a coastal flatfish species of economic and cultural importance that have dwindled to <15, % of their historic abundance in the southern New England/Mid-Atlantic region of the United States, with evidence indicating near-extirpation of certain local populations. This species exhibits intricate behaviors in spawning and migration that contribute to population complexity and resilience. These behaviors encompass full or partial philopatry to natal estuaries, the generation of multiple pulses of larval delivery, and partial migration. The patterns of genetic diversity within and among estuaries and cohorts presented here carry important implications in understanding the susceptibility to demographic shocks, even if the full extent of genetic diversity within and among winter flounder stocks on the US East Coast remains unresolved. Our findings reveal connectivity between estuaries in Long Island, New York, suggesting the potential for genetic rescue of depleted subpopulations. Family reconstruction and relatedness analysis indicate that split cohorts and migration contingents are not the result of genetically distinct lineages. We found no evidence for genetic structure separating these groups, and in some instances, we were able to detect closely related individuals that belonged to different migratory contingents or cohorts. Characterizing the spatial and behavioral organization of this species at the population level is crucial for comprehending its potential for recovery, not only in terms of biomass but also in reinstating the complex population structure that supports resilience. The search for generality in winter flounder spawning and migration behavior remains elusive, but perhaps the lack of generalities within this species is what has allowed it to persist in the face of decades of environmental and anthropogenic stressors.

A Study on the Measurement of Relative Poverty in Developing Countries with Large Populations

Under the goal of global poverty eradication, it has become a forward-looking research aim to establish relative poverty criteria and identify people experiencing relative poverty in countries with different demographic characteristics. This paper introduces a new method to measure the relative poverty standard, which is to use the fuzzy decision tree algorithm to objectively estimate the relative poverty standard. The advantage of this algorithm lies in (1) it not only maintaining the regression idea of measuring absolute poverty, but also emphasizing the nonlinearity when the demand is increasing, which can reflect the change in human needs. (2) It overcomes the division of the traditional method which clearly distinguishes between those experiencing poverty and those who are not by means of a subjective threshold, and it also avoids the subjectivity of the selection of multidimensional indicators. (3) It overcomes the problems of data skewness and extreme value issues that traditional methods have, and can exhibit multi-dimensional characteristics. (4) Most importantly, this method can overcome the gap problem caused by the complex population structure in developing countries with huge populations, and is more adaptable under big data conditions than traditional methods. Taking China as an example, using data from the China Household Finance Survey for validation, the validation results show that the relative poverty standard in China in 2019 can be approximately delineated as 5288.5 RMB; this result is higher than the absolute poverty standard line delineated in China in that year, lower than the relative poverty standard line measured using the proportion method, and it can satisfy the average per capita food, tobacco, and alcohol consumption expenditure of Chinese residents in that year. Thus, compared with other methods, the fuzzy decision tree algorithm can better match the identification of relative poverty in developing countries with large populations.

Neutral markers reveal complex population structure across the range of a widespread songbird.

Understanding how both contemporary and historical physical barriers influence gene flow is key to reconstructing evolutionary histories and can allow us to predict species' resilience to changing environmental conditions. During the last glacial maximum (LGM), many high latitude North American bird species were forced into glacial refugia, including mountain bluebirds (Silia currucoides). Within their current breeding range, mountain bluebirds still experience a wide variety of environmental conditions and barriers that may disrupt gene flow and isolate populations. Using single nucleotide polymorphisms (SNPs) obtained through restriction site-associated DNA sequencing, we detected at least four genetically distinct mountain bluebird populations. Based on this structure, we determined that isolation-by-distance, the northern Rocky Mountains, and discontinuous habitat are responsible for the low connectivity and the overall history of each population going back to the last glacial maximum. Finally, we identified five candidate genes under balancing selection and three loci under diversifying selection. This study provides the first look at connectivity and gene flow across the range of these high-altitude and high latitude songbirds.

Evaluation method investigation of public decontamination time in off-site nuclear emergency under the influence of human factors

Decontamination is an important means to reduce the personnel radioactive contamination under sever nuclear accidents. Public decontamination time estimation with the process simulation is helpful for emergency organizations to improve efficiency. To date, most studies focus on improving personal decontamination technology and decontamination strategies, while research on the overall decontamination process and time estimating is limited. Due to the complex population structure, the unknown contaminated proportion and the complicated psychological emotions, it is hard to quantify the decontamination process and calculate the decontamination time with numerous procedures and diverse facility configurations. Combined with public contaminated proportion, crowd structure and waiting psychology, a public decontamination model based on queuing theory and system dynamics method is established for offsite nuclear emergency to simulate the decontamination process and give an estimate of decontamination time. A hypothetical nuclear leakage accident of Changjiang Nuclear Power Plant in Hainan, China is conducted to simulate the established model. The results show the working status of different facilities at different stages and the changes in waiting queues at different times, which can effectively calculate the duration time of each link and the overall public decontamination progress. A plan for adding devices is provided to meet the decontamination time requirements and control the number of waiting queues within the specified threshold efficiently. The method proposed in this paper could help nuclear emergency decision-makers estimate the public decontamination time, optimize site configuration plans, give guidance on public decontamination procedures and prepare for the subsequent nuclear emergency evacuation.

Parallel patterns of genetic diversity and structure in circumboreal species of the Sphagnum capillifolium complex.

Shared geographical patterns of population genetic variation among related species is a powerful means to identify the historical events that drive diversification. The Sphagnum capillifolium complex is a group of closely related peat mosses within the Sphagnum subgenus Acutifolia and contains several circumboreal species whose ranges encompass both glaciated and unglaciated regions across the northern hemisphere. In this paper, we (1) inferred the phylogeny of subg. Acutifolia and (2) investigated patterns of population structure and genetic diversity among five circumboreal species within the S. capillifolium complex. We generated RAD sequencing data from most species of the subg. Acutifolia and samples from across the distribution ranges of circumboreal species within the S. capillifolium complex. We resolved at least 14 phylogenetic clusters within the S. capillifolium complex. Five circumboreal species show some common patterns: One population system comprises plants in eastern North America and Europe, and another comprises plants in the Pacific Northwest or around the Beringian and Arctic regions. Alaska appears to be a hotspot for genetic admixture, genetic diversity, and sometimes endemic subclades. Our results support the hypothesis that populations of five circumboreal species within the S. capillifolium complex survived in multiple refugia during the last glacial maximum. Long-distance dispersal out of refugia, population bottlenecks, and possible adaptations to conditions unique to each refugium could have contributed to current geographic patterns. These results indicate the important role of historical events in shaping the complex population structure of plants with broad distribution ranges.

Spatial structuring of Mediterranean fisheries landings in relation to their seasonal and long-term fluctuations

The Western Mediterranean fisheries significantly contribute to the regional blue economy, despite evidence of ongoing, widespread overexploitation of stocks. Understanding the spatial distribution and population dynamics of species is crucial for comprehending fisheries dynamics combining local and regional scales, although the underlying processes are often neglected. In this study, we aimed to (i) evaluate the seasonal and long-term spatio-temporal fluctuations of crustacean, cephalopod, and fish populations in the Western Mediterranean, (ii) determine whether these fluctuations are driven by the spatial structure of the fisheries or synchronic species fluctuations, and (iii) compare groupings according to the individual species and life history-based groups. We used dynamic factor analysis to detect underlying patterns in a Landing Per Unit Effort (LPUE) time series (2009–2020) for 23 commercially important species and 33 ports in the Western Mediterranean. To verify the spatial structure of ports and species groupings we investigated the seasonal and long-term spatio-temporal fluctuations and common LPUE trends that exhibit non-homogeneous and species-specific trends, highlighting the importance of life history, environmental and demographic preferences. Long-term trends revealed spatial segregation with a north-south gradient, demonstrating complex population structures of Western Mediterranean resources. Seasonal patterns exhibited a varying spatial aggregation based on species-port combinations. These findings can inform the Common Fishery Policy on gaps challenging their regionalisation objectives in the Mediterranean Sea. We highlight the need for a nuanced and flexible approach and a better understanding of sub-regional processes for effective management and conservation – a current challenge for global fisheries. Our LPUE approach provides insight into population dynamics and changes in regional fisheries, relevant beyond the Mediterranean Sea.

High performance Legionella pneumophila source attribution using genomics-based machine learning classification.

Fundamental to effective Legionnaires' disease outbreak control is the ability to rapidly identify the environmental source(s) of the causative agent, Legionella pneumophila. Genomics has revolutionized pathogen surveillance, but L. pneumophila has a complex ecology and population structure that can limit source inference based on standard core genome phylogenetics. Here, we present a powerful machine learning approach that assigns the geographical source of Legionnaires' disease outbreaks more accurately than current core genome comparisons. Models were developed upon 534 L. pneumophila genome sequences, including 149 genomes linked to 20 previously reported Legionnaires' disease outbreaks through detailed case investigations. Our classification models were developed in a cross-validation framework using only environmental L. pneumophila genomes. Assignments of clinical isolate geographic origins demonstrated high predictive sensitivity and specificity of the models, with no false positives or false negatives for 13 out of 20 outbreak groups, despite the presence of within-outbreak polyclonal population structure. Analysis of the same 534-genome panel with a conventional phylogenomic tree and a core genome multi-locus sequence type allelic distance-based classification approach revealed that our machine learning method had the highest overall classification performance-agreement with epidemiological information. Our multivariate statistical learning approach maximizes the use of genomic variation data and is thus well-suited for supporting Legionnaires' disease outbreak investigations.IMPORTANCEIdentifying the sources of Legionnaires' disease outbreaks is crucial for effective control. Current genomic methods, while useful, often fall short due to the complex ecology and population structure of Legionella pneumophila, the causative agent. Our study introduces a high-performing machine learning approach for more accurate geographical source attribution of Legionnaires' disease outbreaks. Developed using cross-validation on environmental L. pneumophila genomes, our models demonstrate excellent predictive sensitivity and specificity. Importantly, this new approach outperforms traditional methods like phylogenomic trees and core genome multi-locus sequence typing, proving more efficient at leveraging genomic variation data to infer outbreak sources. Our machine learning algorithms, harnessing both core and accessory genomic variation, offer significant promise in public health settings. By enabling rapid and precise source identification in Legionnaires' disease outbreaks, such approaches have the potential to expedite intervention efforts and curtail disease transmission.

Genomic Data Reveal Diverse Biological Characteristics of Scleractinian Corals and Promote Effective Coral Reef Conservation.

Reef-building corals (Scleractinia, Anthozoa, Cnidaria) are the keystone organisms of coral reefs, which constitute the most diverse marine ecosystems. Since the first decoded coral genome reported in 2011, about 40 reference genomes are registered as of 2023. Comparative genomic analyses of coral genomes have revealed genomic characters that may underlie unique biological characteristics and coral diversification. These include existence of genes for biosynthesis of mycosporine-like amino acids, loss of an enzyme necessary for cysteine biosynthesis in family Acroporidae, and lineage-specific gene expansions of DMSP lyase-like genes in the genus Acropora. While symbiosis with endosymbiotic photosynthetic dinoflagellates is a common biological feature among reef-building corals, genes associated with the intricate symbiotic relationship encompass not only those shared by many coral species, but also genes that were uniquely duplicated in each coral lineage, suggesting diversified molecular mechanisms of coral-algal symbiosis. Coral genomic data have also enabled detection of hidden, complex population structures of corals, indicating the need for species-specific, local-scale, carefully considered conservation policies for effective maintenance of corals. Consequently, accumulating coral genomic data from a wide range of taxa and from individuals of a species not only promotes deeper understanding of coral reef biodiversity, but also promotes appropriate and effective coral reef conservation. Considering the diverse biological traits of different coral species and accurately understanding population structure and genetic diversity revealed by coral genomic analyses during coral reef restoration planning could enable us to "archive" coral reef environments that are nearly identical to natural coral reefs.

Ontogenetic growth responses to the environmental changes of the swordtip squid (Uroteuthis edulis) spring stock in the East China Sea

AbstractSwordtip squid (Uroteuthis edulis) is characterized by a complex population structure and rapid generation renewal and sensitive to habitat changes. Its population growth response to environmental variations implies its flexible life history traits. In this study, with the samples collected in the north‐central waters of the East China Sea from 2017 to 2021, the daily growth of the spring stock was analyzed based on the age and increment width of statolith. The gradient forest method (GFM) and generalized additive mixed models (GAMMs) were used to explore the changes in the weights of environmental variables and the relationships between daily growth and environmental variables in various growth stages. The age of the samples collected from 2017 to 2021 mainly ranged from 180 to 240 days, and the spring stock was the dominant stock. According to the distance from daily increment to core in the statolith, the life history of the spring stock was divided into four growth stages (S1 embryo–larval stage, S2 juvenile stage, S3 subadult stage, and S4 adult stage). For the spring stock, the cumulative weight of temperature and salinity in the population growth was the largest in S1 stage; the cumulative weight of temperature and velocity was the largest in S2 stage; the cumulative weight of temperature was the largest in S3 stage; and the cumulative weight of mixed layer depth (MLD), temperature, and salinity was the largest in S4 stage. The relationship between temperature at the depth of 25 m (T25) and daily growth of the spring stock was first positively correlated (S1–S2), then negatively correlated (S3), and finally positively correlated (S4). The relationship between environment variable and growth of the spring stock gradually decreased with the increase in MLD (30 to 50 m) and SSS (S3–S4, 32.2‰ to 33.2‰) and gradually increased with the increase in the velocity of currents (S1, .1 to .2 m/s). The differences in the responses of the spring stock to environmental variations in different growth stages may lead to the changes in the growth traits for the spring stock. This study provides a scientific basis for a comprehensive understanding of the life history traits of U. edulis.

Leveraging Angler Effort to Inform Fisheries Management: Using Harvest and Harvest Rate to Estimate Abundance of White Sturgeon

Abstract Traditional methods for estimating abundance of fish populations are not feasible in some systems due to complex population structure and constraints on sampling effort. Lincoln’s estimator provides a technique that uses harvest and harvest rate to estimate abundance. Using angler catch data allows assumptions of the estimator to be addressed without relying on methods that could be prohibitively field-intensive or costly. Historic estimates of White Sturgeon Acipenser transmontanus abundance in the Sacramento–San Joaquin River basin have been obtained using mark–recapture methods; however, White Sturgeon population characteristics often cause violations of model assumptions, such as population closure and independent capture probabilities. We developed a version of Lincoln’s estimator using a joint likelihood, estimated abundance of White Sturgeon in the Sacramento–San Joaquin River basin in 2015 using this method and empirical data and assessed accuracy and precision of estimates in a simulation study. Estimating abundance using harvest and harvest rate, as represented by our model framework, has the potential to be precise and accurate. The joint likelihood–based approach fitted using Bayesian methods is advantageous because it includes all sources of variation in a single model. Precision of abundance estimates was low with application of the model to White Sturgeon in the Sacramento–San Joaquin River basin and to similar conditions in a simulated dataset. Using simulation, precision and accuracy increased with increases in the number of high-reward and standard tags released, tag reporting rate, tag retention rate, and harvest rate. Results demonstrate potential sources of error when using this approach and suggest that increasing the number of tagged fish and tag reporting rate are potential actions to improve precision and accuracy of abundance estimates of the model.

Genomic signals of local adaptation in Picea crassifolia

BackgroundGlobal climate change poses a grave threat to biodiversity and underscores the importance of identifying the genes and corresponding environmental factors involved in the adaptation of tree species for the purposes of conservation and forestry. This holds particularly true for spruce species, given their pivotal role as key constituents of the montane, boreal, and sub-alpine forests in the Northern Hemisphere.ResultsHere, we used transcriptomes, species occurrence records, and environmental data to investigate the spatial genetic distribution of and the climate-associated genetic variation in Picea crassifolia. Our comprehensive analysis employing ADMIXTURE, principal component analysis (PCA) and phylogenetic methodologies showed that the species has a complex population structure with obvious differentiation among populations in different regions. Concurrently, our investigations into isolation by distance (IBD), isolation by environment (IBE), and niche differentiation among populations collectively suggests that local adaptations are driven by environmental heterogeneity. By integrating population genomics and environmental data using redundancy analysis (RDA), we identified a set of climate-associated single-nucleotide polymorphisms (SNPs) and showed that environmental isolation had a more significant impact than geographic isolation in promoting genetic differentiation. We also found that the candidate genes associated with altitude, temperature seasonality (Bio4) and precipitation in the wettest month (Bio13) may be useful for forest tree breeding.ConclusionsOur findings deepen our understanding of how species respond to climate change and highlight the importance of integrating genomic and environmental data in untangling local adaptations.

Parasites as indicators of habitat preferences by hybrids between estuarine and freshwater congeneric silversides (Atherinopsidae)

Silversides of the genus Odontesthes are characterized by their conserved morphology and vast phenotypic plasticity. They have developed complex population structures, promoting hybridization and speciation phenomena and often leading to intricate taxonomies. Within this genus, O. argentinensis, an originally marine species and O. bonariensis, a freshwater species, coexist in Mar Chiquita Coastal Lagoon (central Argentina). This lagoon has an inlet to the sea, creating a saline gradient that promotes highly variable conditions throughout the system. While O. argentinensis has established a resident population inside the lagoon, O. bonariensis is only sporadically found, inhabiting mainly tributary streams. Notably, hybrids between the two have been found in the lagoon. Parasites can significantly influence hybridization in host species, either promoting or hindering the process. From an evolutionary standpoint, parasites can impact hybridization by altering host immune responses, affecting host ecology and fitness. As a result, parasites can be valuable indicators of hybrid host ecology and their evolutionary trajectories. The present study analyzes the parasite communities of these sympatric Odontesthes and their hybrids, and determines their habitat preferences. While O. argentinensis showed evidence of marine parasites, O. bonariensis had a dominance of freshwater species as expected. And, although parasites of hybrids displayed similarities with both parental species, they indicated a preference of these hosts by freshwater habitats or longer periods of permanence in the oligohaline areas of Mar Chiquita. The presence of pure parental species, the differences in habitat use found between them and hybrids, and the conditioning effect of environmental heterogeneity over the hybridization event support a mosaic model for this hybrid zone. Finally, studies of parasitism in hybrid zones may contribute to understand the evolutionary history and stability of boundaries or possible biological barriers between host species, and they also provide insight on how natural selection and evolution drive speciation, colonization and habitat use in transitional environments.

Developmental validation of a high-resolution panel genotyping 639 Y-chromosome SNP and InDel markers and its evolutionary features in Chinese populations

Uniparental-inherited haploid genetic marker of Y­chromosome single nucleotide polymorphisms (Y-SNP) have the power to provide a deep understanding of the human evolutionary past, forensic pedigree, and bio-geographical ancestry information. Several international cross-continental or regional Y-panels instead of Y-whole sequencing have recently been developed to promote Y-tools in forensic practice. However, panels based on next-generation sequencing (NGS) explicitly developed for Chinese populations are insufficient to represent the Chinese Y-chromosome genetic diversity and complex population structures, especially for Chinese-predominant haplogroup O. We developed and validated a 639-plex panel including 633 Y-SNPs and 6 Y-Insertion/deletions, which covered 573 Y haplogroups on the Y-DNA haplogroup tree. In this panel, subgroups from haplogroup O accounted for 64.4% of total inferable haplogroups. We reported the sequencing metrics of 354 libraries sequenced with this panel, with the average sequencing depth among 226 individuals being 3,741×. We illuminated the high level of concordance, accuracy, reproducibility, and specificity of the 639-plex panel and found that 610 loci were genotyped with as little as 0.03 ng of genomic DNA in the sensitivity test. 94.05% of the 639 loci were detectable in male-female mixed DNA samples with a mix ratio of 1:500. Nearly all of the loci were genotyped correctly when no more than 25 ng/μL tannic acid, 20 ng/μL humic acid, or 37.5 μM hematin was added to the amplification mixture. More than 80% of genotypes were obtained from degraded DNA samples with a degradation index of 11.76. Individuals from the same pedigree shared identical genotypes in 11 male pedigrees. Finally, we presented the complex evolutionary history of 183 northern Chinese Hans and six other Chinese populations, and found multiple founding lineages that contributed to the northern Han Chinese gene pool. The 639-plex panel proved an efficient tool for Chinese paternal studies and forensic applications.

Patterns of genetic differentiation imply distinct phylogeographic history of the mosquito species Anopheles messeae and Anopheles daciae in Eurasia.

Detailed knowledge of phylogeography is important for control of mosquito species involved in the transmission of human infectious diseases. Anopheles messeae is a geographically widespread and genetically diverse dominant vector of malaria in Eurasia. A closely related species, An. daciae, was originally distinguished from An. messeae based on five nucleotide substitutions in its ribosomal DNA (rDNA). However, the patterns of phylogeographic history of these species in Eurasia remain poorly understood. Here, using internal transcribed spacer 2 (ITS2) of rDNA and karyotyping for the species identification we determined the composition of five Anopheles species in 28 locations in Eurasia. Based on the frequencies of 11 polymorphic chromosomal inversions used as genetic markers, a large-scale population genetics analysis was performed of 1932 mosquitoes identified as An. messeae, An. daciae and their hybrids. The largest genetic differences between the species were detected in the X sex chromosome suggesting a potential involvement of this chromosome in speciation. The frequencies of autosomal inversions in the same locations differed by 13%-45% between the species demonstrating a restricted gene flow between the species. Overall, An. messeae was identified as a diverse species with a more complex population structure than An. daciae. The clinal gradients in frequencies of chromosomal inversions were determined in both species implicating their possible involvement in climate adaptations. The frequencies of hybrids were low ~1% in northern Europe but high up to 50% in south-eastern populations. Thus, our study revealed critical differences in patterns of phylogeographic history between An. messeae and An. daciae in Eurasia. This knowledge will help to predict the potential of the malaria transmission in the northern territories of the continent.

Accurate, automated taxonomic assignment of genebank accessions: a new method demonstrated using high-throughput marker data from 10,000 Capsicum spp. accessions

Key messageWe demonstrate how an algorithm that uses cheap genetic marker data can ensure the taxonomic assignments of genebank samples are complete, intuitive, and consistent—which enhances their value.To maximise the benefit of genebank resources, accurate and complete taxonomic assignments are imperative. The rise of genebank genomics allows genetic methods to be used to ensure this, but these need to be largely automated since the number of samples dealt with is too great for efficient manual recategorisation, however no clearly optimal method has yet arisen. A recent landmark genebank genomic study sequenced over 10,000 genebank accessions of peppers (Capsicum spp.), a species of great commercial, cultural, and scientific importance, which suffers from much taxonomic ambiguity. Similar datasets will, in coming decades, be produced for hundreds of plant taxa, affording a perfect opportunity to develop automated taxonomic correction methods in advance of the incipient genebank genomics explosion, alongside providing insights into pepper taxonomy in general. We present a marker-based taxonomic assignment approach that combines ideas from several standard classification algorithms, resulting in a highly flexible and customisable classifier suitable to impose intuitive assignments, even in highly reticulated species groups with complex population structures and evolutionary histories. Our classifier performs favourably compared with key alternative methods. Possible sensible alterations to pepper taxonomy based on the results are proposed for discussion by the relevant communities.

Development of a 20 K SNP array for the leopard coral grouper, Plectropomus leopardus

Single nucleotide polymorphism (SNP) genotyping array is a powerful tool for providing information on polymorphic variations of species of interest. These genomic variations can be used to investigate the genetic architecture of complex traits, population structures, and genomic selection of breeding programs. The aquaculture of the leopard coral grouper (Plectropomus leopardus), is rapidly developing in South China and Southeast Asia. However, the lack of a high-efficient genotyping platform has hampered the progress of both genetic studies and selective breeding practices of this fish. Here we developed and evaluated a 20 K SNP array namely “DongXin-I” for P. leopardus. Using the genome re-sequencing data of 730 leopard coral groupers, we identified over 3.67 million SNPs, from which 20,737 loci, with even distribution across the genome, were finally involved in the SNP array. Evaluation of the array performance with 232 fish showed a high overall SNP call rates (> 99%) and an average minor allele frequency (MAF) of 0.312. Comparison of genotyping results of 87 fish from both the “DongXin-I” array and genome resequencing demonstrated a high genotyping repeatability and accurate performance of the genotyping array. Furthermore, using the gentyping results generated by the “DongXin-I” array, we revealed the genetic structure of breeding populaitons currently used the in Hainan Province. To summarize, the “DongXin-I” array should be a useful tool for the genetic studies and genomic selection breeding in the aquaculture industry of the coral leopard grouper.

Migration Route of Sthenoteuthis oualaniensis in the South China Sea Based on Statolith Trace Element Information.

Sthenoteuthis oualaniensis (Lesson, 1830) is a pelagic species with a complex population structure and wide migration range. The trace elements in statoliths are effective indicators for reconstructing the life history of an individual. In this study, the trace elements in statoliths were determined via laser ablation inductively coupled plasma mass spectrometry, and a multiple regression tree (MRT) model was used to trace the migration of S. oualaniensis and identify its potential habitats in the South China Sea. Na, Mg, Fe, Sr, and Ba were the effective trace elements, with significant differences found among stocks (p < 0.05). The MRT was divided into five clusters representing five life history stages. The Mg:Ca and Sr:Ca ratios decreased initially and increased thereafter, and the Mg:Ca, Sr:Ca, and Ba:Ca ratios differed significantly among the stages of the life history in each stock (p < 0.05). The hatching water temperatures for the winter and summer-autumn spawning populations were 28.05-28.88 °C (temperature at 25 m) and 27.15-27.92 °C (temperature at 25 m). The winter stock hatched in the southern South China Sea, and the larvae then migrated northwest during the summer monsoon. The summer-autumn stocks hatched in the northern South China Sea, and the larvae migrated southward under the mesoscale closed anticyclonic circulation in the northern South China Sea. These results provide insight into the migration of S. oualaniensis in the South China Sea.

Genomic analysis reveals complex population structure within the smooth newt, Lissotriton vulgaris, in Central Europe.

Species with wide-range distributions usually display high genetic variation. This variation can be partly explained by historical lineages that were temporally isolated from each other and are back into secondary reproductive contact, and partly by local adaptations. The smooth newt (Lissotriton vulgaris) is one of the most widely distributed amphibians species across Eurasia and forms a species complex with a partially overlapping distribution and morphology. In the present study, we explored the population genomic structure of smooth newt lineages in the Carpathian Basin (CB) relying on single-nucleotide polymorphisms. Our dataset included new and previously published data to study the secondary contact zone between lineages in the CB and also tested for the barrier effect of rivers to gene flow between these lineages. We confirmed the presence of the South L. v. vulgaris Lineage distributed in Transdanubia and we provided new distribution records of L. v. ampelensis inhabiting the eastern territories of the CB. High genetic diversity of smooth newts was observed, especially in the North Hungarian Mountains and at the interfluves of the main rivers in the South with four distinct lineages of L. v. vulgaris and one lineage of L. v. ampelensis showing a low level of admixture with the spatially closest L. v. vulgaris lineage. Moreover, admixture detected at the interfluve of the main rivers (i.e. Danube and Tisza) suggested a secondary contact zone in the area. Finally, we found that the river Danube has a very weak effect on population divergence, while the river Tisza is a geographical barrier limiting gene flow between smooth newt lineages. As the range boundaries of L. v. vulgaris and L. v. ampelensis in the CB coincide with the river Tisza, our study underpins the influence of rivers in lineage diversification.