Association analysis of leaf aromatic substances in cultivated and weedy types of Perilla crop using SSR markers.

In East Asia, particularly South Korea, the two cultivated varieties of Perilla are commonly grown. They are clearly distinguished by their aromatic substances and have different uses as leafy vegetables or oil crop. This study was performed for the development of simple sequence repeat (SSR) markers linked to volatile compounds in Perilla leaves that show differences between cultivated var. frutescens (CF), weedy var. frutescens (WF), and weedy var. crispa (WC) of Perilla. Fifty Perilla SSR primer sets were used to analyze genetic diversity for the 80 Perilla accessions of the three types. A total of 276 alleles were detected, with an average of 5.5 alleles per locus. The average genetic diversity values for CF, WF, and WC accessions were 0.402, 0.583, and 0.437, respectively. WF accessions exhibited the highest genetic diversity among the three types of the Perilla crop. Phylogenetic tree analysis classified 80 Perilla accessions of the three types into four groups, showing 37.2 % genetic similarity. Three types of the Perilla crop were clearly distinguished except for outstanding accessions. Through the application of an association analysis involving 50 Perilla SSR primer sets and five volatile compounds (perilla aldehyde, perilla ketone, myristicin, dill apiol, (Z,E)-α-farnesene) in the three types of the Perilla accessions, we detected 11 significant marker-trait associations duplicated in both Q GLM and Q + K MLM methods. These findings serve as valuable insights for identifying the aromatic substances in Perilla plants originating from various regions of South Korea.

Across a phylogeographic break in the Qinling Mountains-Huaihe River Line: Quaternary evolutionary history of a medicinal and edible homologous plant (Allium macrostemon) in China.

Biogeographic barriers to gene flow are central to studies of plant phylogeography. There are many physical and geographic barriers in China, but few studies have used molecular ecological evidence to investigate the natural geographic isolation barrier of the Qinling Mountains-Huaihe River Line (QHL). Allium macrostemon is a precious Chinese perennial herb belonging to the Amaryllidaceae family. It is used as a food and medicine, with a variety of health and healing properties. Five SSR markers, three chloroplast DNA (cpDNA) markers (psbA-trnH, rps16 and trnL-F), one nuclear ribosomal DNA (nrDNA) marker (ITS), and simplified genome GBS sequencing were used to analyse the genetic diversity and structure of A. macrostemon. Combining SSR, cpDNA, nrDNA ITS data and GBS analysis results, we divided A. macrostemon populations into northern and southern groups, with the southern group further divided into southwestern and central-southeastern groups. Niche simulation results reveal that the distribution area of A. macrostemon will reach its maximum in the future. These data indicate that the regional separation of A. macrostemon has been maintained by the combined influence of a geographical barrier and Quaternary climate, and that the back-and-forth fluctuations of QHL and Quaternary climate have played an important role in this process. QHL acts as a north-south dividing line in phylogeography and population genetic structure, promoting physical geographic isolation. This study provides a theoretical basis for the conservation, development, and utilization of A. macrostemon resources. It further provides a reference for understanding the systematic geographical pattern of the large-scale spatial distribution of plants in China and enriches our understanding of Quaternary plant evolution in areas with complex terrain.

Geographical and temporal dynamics of genetic diversity of Plasmodium falciparum merozoite surface proteins 1/2 in India.

The high genetic diversity of Plasmodium falciparum (Pf) is a big obstacle to successful vaccine development programs. Here, the geographical and temporal dynamics of the genetic diversity of Indian Pf isolates from patients living in Ranchi, Raipur, Mewat, and Rourkela were analyzed. Typing and frequency of merozoite surface protein 1 and 2 genes (pfmsp1/2), their genotypes, clonality, heterozygosity, multiplicity of infection, and neutral evolution metrics were computed. A phylogenetic analysis was also performed for these two genes. The dominant allelic types were K1 (55%) and MAD20 (55%) for msp1, and FC27 (64.7%) for msp2. Infections were mainly monoclonal in Ranchi and Mewat while polyclonal in Raipur and Rourkela. Polyclonal infections dropped from 57.1 to 71.3% in 2013 to 33.3-33.4% in 2016 in Raipur. K1 and MAD20 sequences were highly diverse due to the organization of the amino acid units SGG, SVA, SVT, and SGN. The IC/3D7-related G,S,A-rich region showed a large variation of four to eight amino acid repeats, including mostly GAVASA (81.8%), GSGA (54.5%), and GASGSA (45.5%). The 32-amino acid sequence of the FC27 type was present in all isolates with several mutations. The msp1/2 sequences were not under neutral evolution, except the K1 family, which is under balancing selection. The msp1/2 sequences are phylogenetically closer to previous Indian sequences than those from Africa, Asia, the Americas, and Oceania. This study outlines a high genetic diversity of Pf infections with complex structure, and evolutionary signature changed with time. Supplementary Information: The online version contains supplementary material available at 10.1007/s12639-024-01698-8.

Does a coexisting congener of a mixed mating species affect the genetic structure and selfing rate via reproductive interference?

Reproductive interference is defined as an interspecific interaction that reduces fitness via mating processes. Although its ecological and evolutionary consequences have attracted much attention, how reproductive interference affects the population genetic structures of interacting species is still unclear. In flowering plants, recent studies found that self-pollination can mitigate the negative effects of reproductive interference. Selfing-biased seed production is expected to increase population-level inbreeding and the selfing rate, and limits gene flow via pollinator outcrossing among populations. We examined the population genetics of the mixed-mating annual herb Commelina communis f. ciliata, focusing on reproductive interference by the sympatric competing congener C. communis using microsatellite markers. First, we found that almost all C. c. f. ciliata populations had relatively high inbreeding coefficients. Then, comparing sympatric and allopatric populations, we found evidence that reproductive interference from a competing congener increased the inbreeding coefficient and selfing rate. Allopatric populations exhibit varied selfing rates while almost all sympatric populations exhibit extremely high selfing rates, suggesting that population selfing rates were also influenced by unexamined factors, such as pollinator limitation. Besides, our findings revealed that reproductive interference from a competing congener did not limit gene flow among populations. We present the first report on how reproductive interference affects the genetic aspects of populations. Our results suggested that the high selfing rate of C. c. f. ciliata promotes its sympatric distribution with C. communis, even in the presence of reproductive interference, although it is not clear whether reproductive interference directly causes the high selfing rate.

The tissue virome of black-spotted frogs reveals a diversity of uncharacterized viruses.

Amphibians are an essential class in the maintenance of global ecosystem equilibrium, but they face serious extinction risks driven by climate change and infectious diseases. Unfortunately, the virus diversity harbored by these creatures has been rarely investigated. By profiling the virus flora residing in different tissues of 100 farmed black-spotted frogs (Rana nigromaculata) using a combination of DNA and RNA viromic methods, we captured 28 high-quality viral sequences covering at least 11 viral families. Most of these sequences were remarkably divergent, adding at least 10 new species and 4 new genera within the families Orthomyxoviridae, Adenoviridae, Nodaviridae, Phenuiviridae, and Picornaviridae. We recovered five orthomyxovirus segments, with three distantly neighboring two Chinese fish-related viruses. The recombination event of frog virus 3 occurred among the frog and turtle strains. The relative abundance and molecular detection revealed different tissue tropisms of these viruses, with the orthomyxovirus and adenoviruses being enteric and probably also neurotropic, but the new astrovirus and picornavirus being hepatophilic. These results expand the spectrum of viruses harbored by anurans, highlighting the necessity to continuously monitor these viruses and to investigate the virus diversity in a broader area with more diverse amphibian species.

Deciphering the Genetic Landscape: Insights Into the Genomic Signatures of Changle Goose.

The Changle goose (CLG), a Chinese indigenous breed, is celebrated for its adaptability, rapid growth, and premium meat quality. Despite its agricultural value, the exploration of its genomic attributes has been scant. Our study entailed whole-genome resequencing of 303 geese across CLG and five other Chinese breeds, revealing distinct genetic diversity metrics. We discovered significant migration events from Xingguo gray goose to CLG and minor gene flow between them. We identified genomic regions through selective sweep analysis, correlating with CLG's unique traits. An elevated inbreeding coefficient in CLG, alongside reduced heterozygosity and rare single nucleotide polymorphisms (RSNPs), suggests a narrowed genetic diversity. Genomic regions related to reproduction, meat quality, and growth were identified, with the GATA3 gene showing strong selection signals for meat quality. A non-synonymous mutation in the Sloc2a1 gene, which is associated with reproductive traits in the CLG, exhibited significant differences in allelic frequency. The roles of CD82, CDH8, and PRKAB1 in growth and development, alongside FABP4, FAF1, ESR1, and AKAP12 in reproduction, were highlighted. Additionally, Cdkal1 and Mfsd14a may influence meat quality. This comprehensive genetic analysis underpins the unique genetic makeup of CLG, providing a basis for its conservation and informed breeding strategies.

Dispersal patterns of Reeves's pheasant based on genetic and behavioral evidence.

Dispersal is an important life history trait that plays a crucial role in avoiding inbreeding. Uncovering the dispersal pattern of a threatened species facilitates conservation efforts. Most species of Galliformes are forest-dwelling terrestrial birds with a weak dispersal ability and high conservation priorities. However, little is known about the dispersal behavior and dispersal pattern of Galliformes species such as Reeves's pheasant Syrmaticus reevesii, a globally vulnerable species endemic to China. Here, we integrated behavioral and genetic analyses to investigate the dispersal pattern of Reeves's pheasant. Our results revealed that both females and males would disperse, although the overall dispersal pattern was more likely to be male-biased. Reeves's pheasant population had a low level of genetic diversity and a mild level of inbreeding. Speculation low genetic diversity was resulted from fragmented habitat, and male-biased dispersal may reduce the opportunity of inbreeding. Our research indicated that sex-biased dispersal patterns may be a behavioral mechanism adopted by wildlife to avoid inbreeding in a fragmented habitat.

Association mapping of important agronomic traits in Mucuna pruriens (L.) DC.

BACKGROUND: The tropical legume Mucuna pruriens (L.) DC. can meet three agricultural needs: low-cost protein, high-value medicines, and green manure or cover crops. But like other underutilized crops, it needs more modern breeding resources. Identifying marker-trait associations (MTAs) can facilitate marker-assisted breeding and crop improvement. Recent studies have demonstrated the feasibility of identifying MTAs using a small number of accessions (< 100). We have characterized a panel of 70 M. pruriens accessions across two consecutive years and performed association analysis for 16 phenotypic traits related to seed (seed length, seed width, seed thickness, seed yield per plant, hundred seed weight); pod (pod length, pod width, number of pods per cluster, number of pods per plant); inflorescence (inflorescence length, flower buds per inflorescence, flower length, pedicel length), and biochemical attributes (L-DOPA, total protein, total carbohydrate), using 66 genic-microsatellite markers following mixed linear model. RESULTS: The results showed significant phenotypic (P < 0.05) and genetic diversity (Shannon's information index, I = 0.62) in our germplasm collection. Many tested traits were highly heritable (broad-sense heritability ranging from 42.86 to 99.93%). A total of 15 MTAs was detected at an adjusted significance level of P < 5.55 × 10- 3 for nine traits (seed length, seed thickness, seed width, hundred seed weight, seed yield per plant, inflorescence length, flower buds per inflorescence, flower length, and petiole length), contributed by 10 SSR markers (MPU_19, MPU_42, MPU_54, MPU_57, MPU_58, MPU_83, MPU_89, MPU_108, MPU_111, and MPU_122.) with phenotypic variance explained (PVE) ranging from 14.7 to 31.1%. Out of the ten trait-associated markers, the BLAST analysis revealed putative functions of seven markers, except MPU_57, MPU_58, and MPU_83. CONCLUSION: Fifteen MTAs identified for important traits with phenotypic variance explained > 10% from mixed linear model offer a solid resource base for improving this crop. This is the first report on association mapping in M. pruriens and our results are expected to assist with marker-assisted breeding and identifying candidate genes in this promising legume.

Prevalence and genetic diversity of rodent-associated Bartonella in Hulunbuir border regions, China.

Bartonella spp. are globally distributed gram-negative facultative intracellular bacteria that infect a wide range of hosts. Rodents are natural reservoirs of many Bartonella species, some of which are also pathogenic to humans. The rapid development of transportation and tourism has highlighted the risk of Bartonella transmission to humans. Thus, it is essential to maintain surveillance of Bartonella spp. infections in rodents. In China, Bartonella spp. infections have been monitored in various areas; however, these have not included the Hulunbuir border regions. In the present study, we monitored the prevalence and genetics of rodent-associated Bartonella spp. in the Hulunbuir border regions. Eleven rodent species were captured at five ports. Eight species were confirmed as Bartonella-positive using quantitative PCR assay, with an overall positivity rate of 20.05 %. Lasiopodomys brandtii was the predominant rodent species captured for Bartonella detection. Sequencing and phylogenetic analysis (using the maximum likelihood method) revealed the presence of three Bartonella species in these rodents, including two pathogenic to humans, namely, Bartonella alsatica and Bartonella grahamii. B. grahamii was the predominant Bartonella species identified in the rodents. Taken together, these results highlight the prevalence and genetic diversity of Bartonella spp. in rodents in the Hulunbuir border regions, indicating the need for risk assessment of human spillover.

The relationship between neutral genetic diversity and performance in wild arthropod populations.

Larger effective populations (Ne) are characterised by higher genetic diversity, which is expected to predict population performance (average individual performance that influences fitness). Empirical studies of the relationship between neutral diversity and performance mostly represent species with small Ne, while there is limited data from the species-rich and ecologically important arthropods that are assumed to have large Ne but are threatened by massive declines. We performed a systematic literature search and used meta-analytical models to test the prediction of a positive association between neutral genetic diversity and performance in wild arthropods. From 14 relevant studies of 286 populations, we detected a weak (r = 0.15) but non-significant positive association both in the full data set (121 effect sizes) and a reduced data set accounting for dependency (14 effect sizes). Theory predicts that traits closely associated with fitness show relatively stronger correlation with neutral diversity, this relationship was upheld for longevity and marginally for reproduction. Our analyses point to major knowledge gaps in our understanding of relationships between neutral diversity and performance. Future studies using genome-wide data sets across populations could guide more powerful designs to evaluate relationships between adaptive, deleterious and neutral diversity and performance.

Phenotypic diversity and population structure of Pecan (Carya illinoinensis) collections reveals geographic patterns.

Pecan (Carya illinoinensis) is an economically important nut crop known for its genetic diversity and adaptability to various climates. Understanding the growth variability, phenological traits, and population structure of pecan populations is crucial for breeding programs and conservation. In this study, plant growth and phenological traits were evaluated over three consecutive seasons (2015-2017) for 550 genotypes from 26 provenances. Significant variations in plant height, stem diameter, and budbreak were observed among provenances, with Southern provenances exhibiting faster growth and earlier budbreak compared to Northern provenances. Population structure analysis using SNP markers revealed eight distinct subpopulations, reflecting genetic differentiation among provenances. Notably, Southern Mexico collections formed two separate clusters, while Western collections, such as 'Allen 3', 'Allen 4', and 'Riverside', were distinguished from others. 'Burkett' and 'Apache' were grouped together due to their shared maternal parentage. Principal component analysis and phylogenetic tree analysis further supported subpopulation differentiation. Genetic differentiation among the 26 populations was evident, with six clusters highly in agreement with the subpopulations identified by STRUCTURE and fastSTRUCTURE. Principal components analysis (PCA) revealed distinct groups, corresponding to subpopulations identified by genetic analysis. Discriminant analysis of PCA (DAPC) based on provenance origin further supported the genetic structure, with clear separation of provenances into distinct clusters. These findings provide valuable insights into the genetic diversity and growth patterns of pecan populations. Understanding the genetic basis of phenological traits and population structure is essential for selecting superior cultivars adapted to diverse environments. The identified subpopulations can guide breeding efforts to develop resilient rootstocks and contribute to the sustainable management of pecan genetic resources. Overall, this study enhances our understanding of pecan genetic diversity and informs conservation and breeding strategies for the long-term viability of pecan cultivation.

Inter-strain variability in responses to a single administration of the cannabidiol-rich cannabis extract in mice.

Cannabidiol (CBD) has gained widespread popularity; however, its pharmacological and toxicological profiles in the context of human genetic diversity remain largely unexplored. Here, we investigated the variability in metabolism and toxicity of CBD-rich cannabis extract (CRCE) in genetically diverse mouse models: C57BL/6J, B6C3F1/J, and NZO/HlLtJ strains. Mice received a single dose of CRCE containing 57.9% CBD at dosages of 0, 246, 738, and 2460 mg/kg of CBD. At 24 h after treatment, no appreciable histomorphological changes were detected in the liver. Plasma bilirubin levels increased markedly in all strains at the highest CBD dose. Mice in all treatment groups displayed significant but distinct increases in ALT and AST levels. While B6C3F1/J and NZO/HlLtJ mice had negligible plasma CBD levels at 738 mg/kg, C57BL/6J mice exhibited levels exceeding 7000 ng/mL. At 2460 mg/kg, high CBD concentrations were found in B6C3F1/J and C57BL/6J mice, but markedly lower levels were seen in NZO/HlLtJ mice. Gene expression profiling showed significant increases in Cyp2b10 across all strains but varying responses in Cyp1a1 expression, indicating strain-specific CYP dysregulation. Genetically diverse mice exhibited differential pharmacological and toxicological responses to CRCE, suggesting a high potential for inter-individual variability in the pharmacology and toxicology of CBD in humans.

Uncovering novel genes for drought stress in rice at germination stage using genome wide association study.

Introduction: Breeding rice with drought tolerance for harsh environments is crucial for agricultural sustainability. Understanding the genetic underpinnings of drought tolerance is vital for developing resilient rice varieties. Genome-wide association studies (GWAS) have emerged as pivotal tools in unravelling the complex genetic architecture of traits like drought tolerance, capitalizing on the natural genetic diversity within rice germplasm collections. Methods: In this study, a comprehensive panel of 210 rice varieties was phenotyped over ten days in controlled conditions, subjected to simulated drought stress using 20% PEG 6000 in petri dishes. Throughout the stress period, crucial traits such as germination percentage (GP), germination rate index (GRI), mean germination time (MGT), and seedling percentage (SP) were meticulously monitored. Results: The GWAS analysis uncovered a total of 38 QTLs associated with drought tolerance traits, including novel loci like qMGT-5.2, qSP-3, qSP7.2, and qGP-5.2. Additionally, RNA-seq analysis identified ten genes with significant expression differences under drought stress conditions. Notably, haplotype analysis pinpointed elite haplotypes in specific genes linked to heightened drought tolerance. Discussion: Overall, this study underscores the importance of GWAS in validating known genes while unearthing novel loci to enrich the genetic resources for enhancing drought tolerance in rice breeding programs.

New species and species diversity of Desmodesmus (Chlorophyceae, Chlorophyta) in Saga City, Japan.

Desmodesmus spp. are one of the most dominant components of phytoplankton, which are present in most water bodies. However, identification of the species based only on morphological data is challenging. The aim of the present study was to provide a comprehensive understanding of the actual distribution of the Desmodesmus species in Saga City, Saga Prefecture, Japan. In the present study, 38 water bodies were surveyed between June 2017 and March 2023. A total of 86 culture strains were established from the samples collected from the 21 sites, and identified by molecular phylogenetic analysis, comparison of ITS2 rRNA secondary structures, and observation of surface microstructure. In total, four new species, including D. notatus Demura sp. nov., D. lamellatus Demura sp. nov., D. fragilis Demura sp. nov., and D. reticulatus Demura sp. nov. were proposed and 17 Desmodesmus species were identified as described species. The present study revealed > 20 Desmodesmus species, exhibiting high genetic diversity in a small area.

Extremes of snow and temperature affect patterns of genetic diversity and differentiation in the alpine butterfly Parnassius smintheus.

Weather is an important short-term, local driver of population size and dispersal, which in turn contribute to patterns of genetic diversity and differentiation within species. Climate change is leading to greater weather variability and more frequent extreme weather events. While the effects of long-term and broad-scale mean climate conditions on genetic variation are well studied, our understanding of the effects of weather variability and extreme conditions on genetic variation is less developed. We assessed the influence of temperature and snow depth on genetic diversity and differentiation of populations of the alpine butterfly, Parnassius smintheus. We examined the relationships between a suite of variables, including those representing extreme conditions, and population-level genetic diversity and differentiation across 1453 single nucleotide polymorphisms, using both linear and gravity models. We additionally examined effects of land cover variables known to influence dispersal and gene flow in this species. We found that extreme low temperature events and the lowest recorded mean snow depth were significant predictors of genetic diversity. Extreme low temperature events, mean snow depth and land cover resistance were significant predictors of genetic differentiation. These results are congruent with known effects of early winter weather on population size and habitat connectivity on dispersal in P. smintheus. Our results demonstrate the potential for changes in the frequency or magnitude of extreme weather events to alter patterns of genetic diversity and differentiation.

A comparative study of population structure and genetic diversity of commercial and indigenous chickens from different agro-ecological zones in Ghana using SilicoDArT and SNP markers.

Chicken production, both in the local and commercial sectors, contributes significantly to human livelihood and food security. Precise use of diverse genetic resources is primary in breeding programs. The study analyzed the genetic diversity and population structure of commercial chickens and indigenous chicken ecotypes from three different agro-ecological zones (Semi-Deciduous Rainforest Zone, Guinea Savannah, and Coastal Savannah) using SilicoDArT and SNP markers, utilizing whole-genome sequencing and phenotypic data. Phenotypic data were collected from 72 indigenous chicken ecotypes across the three AEZs, and 32 commercial birds kept at the Kwame Nkrumah University of Science and Technology (KNUST). DNA samples used for sequencing were obtained from 88 chickens (62 indigenous chicken ecotypes and 26 commercial chickens). A total of 54,995 SilicoDArT and 85,396 SNPs markers were generated from DArTseq genotyping. After filtering, 44,784 SilicoDArT and 58,353 SNP were used for genetic diversity and population structure analysis. Both markers showed high reproducibility and call rate. Polymorphic information content (PIC) values ranged from 0.00 to 0.50, while ≥ 50 % showed PIC values more than the median. Furthermore, we obtained FST values, Nei's genetic distance, dendrogram analysis, and principal component analysis (PCA) of commercial and indigenous chickens. The FST and Nei's genetic distance showed that there is high genetic diversity between the commercial chickens and the indigenous chicken ecotypes. However, there was low genetic diversity among the indigenous chicken ecotypes. The PCA analysis indicated a clear separation between the commercial and indigenous chicken ecotypes, while no clear separation was observed between the indigenous chicken ecotypes. The phenotypic data and the dendrogram indicated that naked and frizzle genes do not markedly alter the genetics of indigenous and commercial birds, and their influence on economic traits may be solely determined by the prevailing environmental conditions. The results indicate that there is high genetic differentiation between commercial and indigenous chickens based on SilicoDArT and SNP markers. The indigenous chickens from the agro-ecological zones have low genetic diversity and might have a common origin. Naked neck and frizzle genes do not markedly alter the genetic performance of birds in terms of economic traits. Therefore, the superiority of birds carrying these genes in economic traits may be solely due to environmental variation.

Individual and social heterosis act independently in honey bee (Apis mellifera) colonies.

Heterosis occurs in individuals when genetic diversity, i.e., heterozygosity, increases fitness. Many advanced eusocial insects evolved mating behaviors, including polyandry and polygyny, which increase inter-individual genetic diversity within colonies. The possibility of this structure of diversity to improve group fitness has been termed social heterosis. Neither the independence of individual and social heterosis nor their relative effect sizes have been explicitly measured. Through controlled breeding between pairs of Western honey bee queens (Apis mellifera L.; n=3 pairs) from two distinct populations, we created inbred colonies with low genetic diversity, hybrid colonies with high heterozygosity, and mixed colonies (combining inbred workers from each population) with low heterozygosity and high social diversity. We then quantified two independent traits in colonies: survival against bacterial challenge and maintenance of brood nest temperature. For both traits, we found hybrid and mixed colonies outperformed inbred colonies but did not perform differently from each other. During immune challenge assays, hybrid and mixed colonies experienced hazard ratios of 0.49 (95% CI [0.37, 0.65]) and 0.69 (95% CI [0.50, 0.96]) compared to inbred colonies. For nest temperatures, hybrid and mixed colonies experienced 1.94±0.97°C and 2.82±2.46°C less thermal error and 0.14±0.11°C2 and 0.16±0.06°C2 less thermal variance per hour than inbred lines. This suggests social and individual heterosis operate independently and may have similar effect sizes. These results highlight the importance of both inter- and intra-individual diversity to fitness, which may help explain the emergence of polyandry/polygyny in eusocial insects and inform breeding efforts in these systems.

Draft genome of akame (Lates japonicus) reveals possible genetic mechanisms for long-term persistence and adaptive evolution with low genetic diversity.

It is known that some endangered species have persisted for thousands of years despite their very small effective population sizes and low levels of genetic polymorphisms. To understand the genetic mechanisms of long-term persistence in threatened species, we determined the whole genome sequences of akame (Lates japonicus), which has survived for a long time with extremely low genetic variations. Genome-wide heterozygosity in akame was estimated to be 3.3-3.4 × 10-4/bp, one of the smallest values in teleost fishes. Analysis of demographic history revealed that the effective population size in akame was around 1,000 from 30,000 years ago to the recent past. The relatively high ratio of nonsynonymous to synonymous heterozygosity in akame indicated an increased genetic load. However, a detailed analysis of genetic diversity in the akame genome revealed that multiple genomic regions, including genes involved in immunity, synaptic development, and olfactory sensory systems, have retained relatively high nucleotide polymorphisms. This implies that the akame genome has preserved the functional genetic variations by balancing selection, to avoid a reduction in viability and loss of adaptive potential. Analysis of synonymous and nonsynonymous nucleotide substitution rates has detected signs of positive selection in many akame genes, suggesting adaptive evolution to temperate waters after the speciation of akame and its close relative, barramundi (L. calcarifer). Our results indicate that the functional genetic diversity likely contributed to the long-term persistence of this species by avoiding the harmful effects of the population size reduction.

Combining distribution modelling and phylogeography to understand present, past and future of an endangered spider.

BACKGROUND: Understanding how endangered species respond to climatic changes is fundamental for their conservation. Due to its restricted geographic range, its sensitivity to the ongoing global warming and its continuing decline, the Southwestern-Alpine endemic wolf spider Vesubia jugorum is currently classified as Endangered in the IUCN Red List. Here, we combined species distribution modelling (SDM) and phylogeographic inference to describe the present, the past and the future of this species in light of the mtDNA genetic structure of extant populations. RESULTS: Phylogenetic and network analyses show a high level of genetic differentiation and a strong genetic structure of the populations, likely explicable by a long history of isolation and survival in separate refugia. The SDM projection into past climatic conditions supports these results by showing a smaller distribution range compared to present, mostly restricted to the Maritime and Ligurian Alps, which possibly served as main refugium. Future forecast shows a significant shift in the bioclimatic range towards higher altitudes and latitudes, with a drastic decrease of habitat suitability in the central and south-eastern parts of the range, with consequent general loss of haplotype diversity. CONCLUSION: SDM and phylogeographic inference support the hypothesis that the current distribution and the genetic structure of the extant populations mirror the survival in situ of Vesubia jugorum across repeated glacial and interglacial phases, in line with the 'long-term stability hypothesis'. Future predictions show a significant shift in the bioclimatic range that V. jugorum will be likely unable to track, with profound impact on its long-term survival and its genetic diversity. Our considerations have implication for conservation genetics, highlighting the pivotal role of the transboundary protected areas of the SW-Alps in promoting conservation efforts for this species.

Discordance between taxonomy and population genomic data: An avian example relevant to the United States Endangered Species Act.

Population genomics can reveal cryptic biological diversity that may impact fitness while simultaneously serving to delineate relevant conservation units. Here, we leverage the power of whole-genome resequencing for conservation by studying 433 individual lesser prairie-chicken (Tympanuchus pallidicinctus; LEPC, a federally endangered species of conservation concern in the United States) and greater prairie-chicken (Tympanuchus cupido; GRPC, a legally huntable species throughout much of its range). The genomic diversity of two formally recognized distinct population segments (DPSs) of LEPCs is similar, but they are genetically distinct. Neither DPS is depleted of its genomic diversity, neither is especially inbred, and temporal diversity is relatively stable in both conservation units. Interspecific differentiation between the two species was only slightly higher than that observed between LEPC DPSs, due largely to bidirectional introgression. The high resolution provided by our dataset identified a genomic continuum between the two species such that individuals sampled from the hybrid zone were imperfectly assigned to their presumptive species when considering only their physical characteristics. The admixture between the two species is reflected in the spectrum of individual ancestry coefficients, which has legal implications for the "take" of individuals under the Endangered Species Act. Overall, our data highlight the recurring dissonance between static policies and dynamic species boundaries that are increasingly obvious in the population genomic era.