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Background: Mobile element variants (MEVs) have a significant and complex impact on genomic diversity and phenotypic traits. However, the quantity, distribution, and relationship with gene expression and complex traits of MEVs in the pig genome remain poorly understood. Results: We constructed the most comprehensive porcine MEV library based on high-depth whole genome sequencing (WGS) data from 747 pigs across 59 breeds worldwide. This database identified a total of 147,993 polymorphic MEVs, including 121,099 short interspersed nuclear elements (SINEs), 26,053 long interspersed nuclear elements (LINEs), 802 long terminal repeats (LTRs), and 39 other transposons, among which 54% are newly discovered. We found that MEVs are unevenly distributed across the genome and are strongly influenced by negative selection effects. Importantly, we identified 514, 530, and 584 candidate MEVs associated with population differentiation, domestication, and breed formation, respectively. For example, a significantly differentiated MEV is located in the ATRX intron between Asian and European pigs, whereas ATRX is also differentially expressed between Asian and European pigs in muscle tissue. In addition, we identified 4,169 expressed MEVs (eMEVs) significantly associated with gene expression and 6,914 splicing MEVs (sMEVs) associated with gene splicing based on RNA-seq data from 266 porcine liver tissues. These eMEVs and sMEVs explain 6.24% and 9.47%, respectively, of the observed cis-heritability and highlight the important role of MEVs in the regulation of gene expression. Finally, we provide a high-quality SNP–MEV reference haplotype panel to impute MEV genotypes from genome-wide SNPs. Notably, we identified a candidate MEV significantly associated with total teat number, demonstrating the functionality of this reference panel. Conclusions: The present investigation demonstrated the importance of MEVs in pigs in terms of population diversity, gene expression and phenotypic traits, which may provide useful resources and theoretical support for pig genetics and breeding. [ABSTRACT FROM AUTHOR]

Background selection, by which selection on deleterious alleles reduces diversity at linked neutral sites, influences patterns of total neutral diversity, πT, and genetic differentiation, FST, in structured populations. The theory of background selection may be split into two regimes: the background selection regime, where selection pressures are strong and mutation rates are sufficiently low such that deleterious alleles are at a deterministic mutation-selection balance, and the interference selection regime, where selection pressures are weak and mutation rates are sufficiently high that deleterious alleles accumulate and interfere with another, leading to selective interference. Previous work has quantified the effects of background selection on πT and FST only for deleterious alleles in the background selection regime. Furthermore, there is evidence to suggest that migration reduces the effects of background selection on FST, but this has not been fully explained. Here, we derive novel theory to predict the effects of migration on background selection experienced by a subpopulation and extend previous theory from the interference selection regime to make predictions in an island model. Using simulations, we show that this theory best predicts FST and πT. Moreover, we demonstrate that background selection may generate minimal increases in FST under sufficiently high migration rates, because migration reduces correlated effects on fitness over generations within subpopulations. However, we show that background selection may still cause substantial reductions in πT, particularly for metapopulations with a larger effective population size. Our work further extends the theory of background selection into structured populations, and suggests that background selection will minimally confound locus-to-locus FST scans. Author summary: Most mutations that affect fitness incur deleterious effects and are ultimately removed via natural selection. Consequently, nearby neutral variants may also experience the effects of selection; this is termed background selection. Background selection greatly influences patterns of genetic diversity both between and within populations among virtually all extant species, and is therefore of great interest to geneticists. Previous models of background selection have been primarily restricted to populations with completely random mating. However, it is well known that most natural populations exhibit some form of spatial structure. Here, we explore the effects of background selection in spatially structured populations, and we find that migration between subpopulations may attenuate the effects of background selection acting to increase genetic differentiation among populations. We derive novel theory to account for this effect by considering that individuals with deleterious alleles may migrate out of a local subpopulation prior to being removed by the population via selection. Our work demonstrates that, when migration rates are high, background selection does not substantially influence genetic differentiation among populations. Despite this, we find that background selection may greatly decrease genetic diversity within subpopulations and in the whole metapopulation. [ABSTRACT FROM AUTHOR]

The article in the Journal of Fish Diseases discusses the first documented case of 'soft flesh' induced by Kudoa thyrsites in an Atlantic bonito caught in the Mediterranean Sea. The study highlights the impact of Kudoa spp. on fish quality and the potential economic losses in the seafood sector. While Kudoa thyrsites is not known to cause foodborne diseases in humans, further research is needed to understand the prevalence of these parasites in commercially important fish species and their potential implications. [Extracted from the article]

Alternaria alternata is a significant fungal species that can function as both an endophytic fungus and a pathogen in various plant tissues. Unlike pathogenic fungi, endophytic fungi enhance the growth of host plants through different mechanisms. Studying the genetic diversity of endophytic fungi can provide insights into their co-evolution with plants. In this research, the genetic diversity of A. alternata from different hosts was examined using ten pairs of ISSR primers. Seven of the ten primers generated scorable polymorphic bands (total of 65 bands with an average of 9.2 bands per primer) for molecular analysis. Genetic diversity parameters revealed that isolates from Gundelia tournefortii exhibited the highest genetic diversity (Na, Ne, I, and He values of 1.55, 1.45, 0.35, and 0.24, respectively), while isolates from Tamarix ramosissima showed lower diversity (Na, Ne, I, and He values of 1.18, 1.13, 0.11, and 0.07, respectively). Cluster analysis grouped the isolates into four clusters based on Jaccard similarity matrix and UPGMA method. Principal coordinate analysis (PCOA) supported the cluster analysis findings. Analysis of molecular variance (AMOVA) indicated a high level of genetic differentiation within populations (72 %), with only 28 % of diversity between populations. The genetic structure assessment revealed a relatively strong genetic structure among populations, suggesting the presence of a hidden sexual cycle or mitotic recombination as factors contributing to the high genetic differentiation among A. alternata populations. • A. alternata , as an endophytic fungus, were isolated from different hosts. • A high level of genetic differentiation revealed within the populations. • The population is divided into 3 genetic groups with high genetic admixture. • Hidden sexual cycle or mitotic recombination can significantly increase genetic diversity. [ABSTRACT FROM AUTHOR]

Stephania tetrandra S. Moore (family: Menispermaceae), a dioecious herbaceous vine and the only species in the subgenus Botryodiscia of the genus Stephania of the family Menispermaceae, is mainly distributed in hilly areas south of the Huaihe River in China and found in many provinces of China, showing a high genetic diversity. This paper aimed to study genetic diversity of and genetic relationship among individuals of S. tetrandra within China to provide a basis for evaluation, exploitation, and utilization of S. tetrandra by using simple sequence repeat (SSR) molecular markers. Our results show that effective products were amplified from the 26 screened SSR gene loci, a total of 183 alleles amplified (2–16 alleles amplified by each pair of primers). Among the 26 loci, 16 had a PIC value higher than 0.5, indicating a high level of polymorphism. For most of the loci, the number of effective alleles was lower than that of the observed alleles, and the observed heterozygosity was lower than the expected heterozygosity. The genetic differentiation coefficient (0.021–0.547) was lower than 0.05 (low level of genetic differentiation) for 7 loci and higher than 0.25 (very high level of genetic differentiation) for 2 loci, and had a value representing a medium level of genetic differentiation for the remaining 17 loci. The intra-population inbreeding coefficient had a positive value for 21 loci, suggesting the presence of inbreeding and homozygous excess. The gene flow value was bigger than 1, indicating that genetic drift and natural selection played an unimportant role in population genetic differentiation of S. tetrandra. Based on discriminant analysis of principal components and Bayesian Information Criterion, K-means clustering was performed on 620 samples. These samples were divided into 9 genetic clusters, whose similarity coefficients and genetic distances were 0.755–0.918 and 0.067–0.280, respectively, indicating that these clusters were highly similar and short-distanced. The Bayesian clustering analysis was implemented in the STRUCTURE software to analyze the genetic structure of S. tetrandra and it was found that the 620 samples could be clustered into 5 ancestor groups; the 9 clusters and 40 natural populations inherited genes from the 5 groups to varying degrees, but the proportion of genes inherited from the 5 groups by each cluster and natural population differed. S. tetrandra was characterized by the presence of population structure and pronounced genetic subdivision, which, together with the presence of gene flow, may indicate a relatively stable recent state of these populations. [ABSTRACT FROM AUTHOR]

Lablab is a regionally important multipurpose legume crop used for human consumption, animal feed, and soil conservation. Despite these qualities, the potential value of this crop has not been fully utilized, and very little research attention has been given to it. The main objective of the study was molecular genetic diversity analysis of Lablab collections using 15 SSR markers. The molecular genetic diversity study of 91 Lablab collections revealed a total of 225 alleles with an average of 14.80 alleles per locus. All markers across the entire population were found to be highly polymorphic and informative with PIC values ranging from 0.78 to 0.92 with a mean value of 0.85. The average expected heterozygosity and gene diversity were 0.75 and 0.86 respectively, indicating a high level of diversity. Analysis of molecular variance showed that 94% of the total genetic variation was attributed to within populations, while only 6% was attributed to among populations. The fixation index value (0.061) recorded indicates the presence of moderate population differentiation as a result of high gene flow (Nm = 3.820) among populations. Due to high gene flow, Cluster, PCoA, and structure analysis did not exactly categorize the populations into genetic groups corresponding to their geographic origin. The observed relatively higher genetic diversity in Konso and West Wellega populations among the eight populations indicates that these areas could be considered hot-spots for genetic diversity and possible germplasm evaluation. Generally, genetic diversity obtained from this study provides inputs for Lablab conservation and improvement in Ethiopia. [ABSTRACT FROM AUTHOR]

High-altitude regions like the Himalaya, where various slopes are present on a very small spatial scale, are one of the best natural laboratories for investigating how genetic diversity and population structure are distributed across altitudinal gradients. In this study, we investigate the magnitude of genetic diversity and population structure of Rhododendron anthopogon D.Don along an altitudinal gradient in the Kashmir Himalaya. We used the start codon targeted (SCoT) marker to evaluate the genetic diversity and differentiation between different populations across five sites along an altitudinal gradient ranging from 3200 to 4000 m (amsl). Our results demonstrate that the magnitude of genetic diversity differs among the populations of R. anthopogon along the altitudinal gradient. We observed a decreasing trend in genetic diversity with increasing altitude from site-1 to site-3 (3200 to 3600 m), and an increasing trend from site-4 to site-5 (3601 to 4000 m). Furthermore, we also observed the highest genetic diversity at upper altitude (site-5) and the lowest at mid-altitude (site-3). Our results reveal a high genetic differentiation (Gst = 0.7349) and a low gene flow (Nm = 0.1804) among the populations. Analysis of molecular variance (AMOVA) reveals 71% variation among the populations and 29% variation within the populations. We also reveal positive associations between geographic and genetic distances, indicating isolation by distance effect across all altitudes. STRUCTURE and cluster analysis divided all the populations of R. anthopogon into five clusters according to their geographical location. Overall, the study adds to our understanding that altitude is the major driver of genetic variation and differentiation between populations of R. anthopogon which may help increase its range under ongoing projected climate change. Our study also reveals that populations at higher altitudes are not genetically isolated, suggesting that they might be an essential source for migration in the era of climate change. [ABSTRACT FROM AUTHOR]

Aim: As climate change increasingly threatens the world's coral reefs, enhancing their resilience by improving population connectivity for key reef species is crucial for ensuring their persistence. Here, we evaluate the population genomic structure of two common coral species, Pocillopora acuta and Porites sp., chosen due to their divergent life histories. Thousands of single‐nucleotide polymorphisms (SNPs) were sequenced and analysed to infer regional connectivity patterns in Southeast Asia, a region that harbours a tremendous diversity of marine life. Location: Coasts of the Malay Peninsula and northern Borneo, covering ~1 million km2. Method: NextRAD genotyping‐by‐sequencing of 185 Porites sp. and 221 Pocillopora acuta colonies. Libraries were prepared and sequenced on Illumina NovaSeq 6000. Genotyping involved initial quality controls, allele frequency filtering and checks for contamination. Genetic structure was assessed with Bayesian clustering, and relationships between genetic variation and environmental factors were studied through redundancy analysis. Contemporary gene flow was estimated using BayesAss. Results: We observed panmixia among the broadcasting Porites sp. populations, while for the brooding Pocillopora acuta, the Malay Peninsula acts a strong barrier to dispersal between the Malacca Strait and the southern South China Sea. Moreover, its genomic structure seems to follow current marine ecoregion delineation. By analysing contemporary migrant movement, we can prioritise reef localities for conservation. In particular, localities at the Andaman Coral Coast are contemporarily isolated from the other localities, and Tioman is identified as a major larval source for both species. Main Conclusion: Our analyses highlight contrasting population differentiation patterns between the two species that can be explained by the disparity in their reproductive strategies. These findings are important for biodiversity managers in Southeast Asia; incorporation of regional connectivity considerations into conservation planning can help safeguard ecosystem resilience and persistence. [ABSTRACT FROM AUTHOR]

In mobile animals, selection pressures resulting from spatio-temporally varying ecological factors often drive adaptations in migration behavior and associated physiological phenotypes. These adaptations may manifest in ecologically and genetically distinct ecotypes within populations. We studied a meta-population of northern pike (Esox lucius) in brackish environments and examined intrapopulation divergence along environmental gradients. Behavioral phenotypes in habitat use were characterized via otolith microchemistry in 120 individuals sampled from brackish lagoons and adjacent freshwater tributaries. We genotyped 1514 individual pike at 33 highly informative genetic markers. The relationship between behavioral phenotype and genotype was examined in a subset of 101 pikes for which both phenotypic and genomic data were available. Thermosaline differences between juvenile and adult life stages indicated ontogenetic shifts from warm, low-saline early habitats towards colder, higher-saline adult habitats. Four behavioral phenotypes were found: Freshwater residents, anadromous, brackish residents, and cross-habitat individuals, the latter showing intermediary habitat use between brackish and freshwater areas. Underlying the behavioral phenotypes were four genotypes, putative freshwater, putative anadromous, and two putatively brackish genotypes. Through phenotype-genotype matching, three ecotypes were identified: (i) a brackish resident ecotype, (ii) a freshwater ecotype expressing freshwater residency or anadromy, and (iii) a previously undescribed intermediary cross-habitat ecotype adapted to intermediate salinities, showing limited reliance on freshwater. Life-time growth of all ecotypes was similar, suggesting comparable fitness. By combining genetic data with lifelong habitat use and growth as a fitness surrogate, our study revealed strong differentiation in response to abiotic environmental gradients, primarily salinity, indicating ecotype diversity in coastal northern pike is higher than previously believed. [ABSTRACT FROM AUTHOR]

Specimen-based taxonomic research is essential for understanding diversity and setting management frameworks for threatened mammal faunas, and ancient DNA techniques are increasingly used to extract information from taxonomically relevant historical specimens. The largest survivors of the depleted Caribbean mammal fauna are hutias in the genus Capromys , which is usually interpreted as containing a single species, C. pilorides. Previous studies have demonstrated genetic differentiation of Capromys populations across Cuba, but infrageneric species diversity and nomenclature remain unclear. We conducted ancient DNA analysis of historical Capromys samples using cytochrome b and complete mitogenome data sets, and including the 19th-century holotypes of 2 species now considered synonyms, C. fournieri and C. geayi. Our analyses identify distinct western and central/eastern Capromys clades that diverged 1.75 Mya based upon mitogenome data. These clades are separated by the Havana–Matanzas Channel, which represented a barrier to dispersal throughout the Neogene–Quaternary. Divergence date comparisons with other hutia species provide support for interpreting divergence between Capromys populations as species-level differentiation. Although we were unable to yield amplifiable DNA from the C. fournieri holotype, our analyses confidently assign the C. geayi holotype to the western Capromys clade. We therefore recognize 2 extant Capromys species: C. geayi (western Cuba) and C. pilorides (central/eastern Cuba and Cayman Islands). [ABSTRACT FROM AUTHOR]

1. This study combined genome-wide selection signal analysis with RNA-sequencing to identify candidate genes associated with high altitude adaptation and egg production performance in Nixi chickens (NXC). 2. Based on the whole-genome data from 20 NXC (♂:10; ♀:10), the population selection signal was analysed by sliding window analysis. The selected genes were screened by combination with the population differentiation statistic (FST). The sequence diversity statistic (θπ). RNA-seq was performed on the ovarian tissues of NXC (n = 6) and Lohmann laying hens (n = 6) to analyse the differentially expressed genes (DEGs) between the two groups. The functional enrichment analysis of the selected genes and differentially expressed genes was performed. 3. There were 742 genes under strong positive selection and 509 differentially expressed genes screened in NXC. Integrated analysis of the genome and transcriptome revealing 26 overlapping genes. The candidate genes for adaptation to a high-altitude environment, as well as for egg production, disease resistance, vision and pigmentation in NXC were preliminarily screened. 4. The results provided theoretical guidance for further research on the genetic resource protection and utilisation of NXC. [ABSTRACT FROM AUTHOR]

Ecosourcing seed of 'local genetic stock' for ecological restoration has been practiced in New Zealand for about 50 years. However, we believe that it has become unnecessarily restrictive. Ecosourcing ensures plants used for restoration are adapted to local conditions and maintains current distributional patterns. It also restricts genetic diversity, confines species to their historic range, and reduces the conservation options for threatened species. For example, New Zealand tree species, the life form most frequently used in restoration plantings, have low population genetic differentiation and high net migration of alleles throughout their range. Therefore, very little is gained through restrictive ecosourcing of tree seed. Furthermore, avoidance of the danger of inbreeding depression and widening the scope for closer environmental matching, argues for larger rather smaller source areas. Climate change, extinctions across multiple trophic levels, habitat loss and fragmentation, spread of invasive species, and novel habitats have completely altered the contemporary biotic landscape. Conservation needs to engage with these changes if it is to protect and restore ecosystems. Restrictive ecosourcing is counter-productive as it limits utilising genotypic, phenotypic and ecotypic diversity, and thus the evolutionary potential of indigenous species and ecosystems. It also reduces opportunities to protect biodiversity when populations are small, and limits response to climate change. A new approach is needed. We recommend that phylogeographic patterns and biogeographic boundaries be used to set nine broad ecosourcing regions and, within these regions, phenotypic adaptation to particular environments be used as a guide to seed selection. This more relaxed approach to ecosourcing will improve restoration outcomes through increasing species and genetic diversity, reducing the detrimental effects of inbreeding and promoting the genetic rescue of populations of threatened species. Examples of adopting an eco-evolutionary approach to ecosourcing are provided for the early-successional coloniser Kunzea ericoides and late-successional conifer species. [ABSTRACT FROM AUTHOR]

Vestibular afferent neurons occur as two populations with differences in spike timing regularity that are independent of rate. The more excitable regular afferents have lower current thresholds and sustained spiking responses to injected currents, while irregular afferent neurons have higher thresholds and transient responses. Differences in expression of low-voltage-activated potassium (KLV) channels are emphasized in models of spiking regularity and excitability in these neurons, leaving open the potential contributions of the voltage-gated sodium (NaV) channels responsible for the spike upstroke. We investigated the impact of different NaV current modes (transient, persistent, and resurgent) with whole-cell patch clamp experiments in mouse vestibular ganglion neurons (VGNs), the cultured and dissociated cell bodies of afferents. All VGNs had transient NaV current, many had a small persistent (non-inactivating) NaV current, and a few had resurgent current, which flows after the spike when NaV channels that were blocked are unblocked. A known NaV1.6 channel blocker decreased spike rate and altered spike waveforms in both sustained and transient VGNs and affected all three modes of NaV current. A NaV channel agonist enhanced persistent current and increased spike rate and regularity. We hypothesized that persistent and resurgent currents have different effects on sustained (regular) VGNs vs. transient (irregular) VGNs. Lacking blockers specific for the different current modes, we used modeling to isolate their effects on spiking of simulated transient and sustained VGNs, driven by simulated current steps and noisy trains of simulated EPSCs. In all simulated neurons, increasing transient NaV current increased spike rate and rate-independent regularity. In simulated sustained VGNs, adding persistent current increased both rate and rate-independent regularity, while adding resurgent current had limited impact. In transient VGNs, adding persistent current had little impact, while adding resurgent current increased both rate and rate-independent irregularity by enhancing sensitivity to synaptic noise. These experiments show that the small NaV current modes may enhance the differentiation of afferent populations, with persistent currents selectively making regular afferents more regular and resurgent currents selectively making irregular afferents more irregular. [ABSTRACT FROM AUTHOR]

Integrating molecular data is essential for clarifying the distributions and genetic structures of species that have histories of misidentification and misapplication of names. There has been confusion about the species limits of the Vulnerable Prostanthera cineolifera with respect to morphologically similar specimens in the Hunter Valley, New South Wales, Australia and morphologically dissimilar specimens in the Lower Hawkesbury Valley, New South Wales, and from north-eastern New South Wales. To test the species limits of P. cineolifera, and related taxa, specimens were collected from across the range and augmented with herbarium specimens. We used morphometric analysis of 18 morphological characters across 51 samples. Using the DArTseq reduced representation sequencing platform, 4010 single-nucleotide polymorphisms (SNPs) across 110 individuals were recovered for molecular analysis. Both morphological and molecular analyses produced three concordant clusters (A) P. cineolifera, (B) a group sharing similarities with P. sp. Hawkesbury (B.J.Conn 2591), and (C) a group allied with P. lanceolata and P. ovalifolia. These results indicate that the specimens form north-eastern New South Wales are more likely to be P. lanceolata, not P. cineolifera, and that specimens from the Lower Hawkesbury are of an undescribed species with the phrase name P. sp. Hawkesbury (B.J.Conn 2591). Within P. cineolifera there was pronounced genetic differentiation among populations. Little evidence of inbreeding was observed, but the newly recognised, more isolated populations had the lowest genetic diversity. This study provides new information about the range of the species and its genetic structure that informs the conservation priorities for this species. [ABSTRACT FROM AUTHOR]

Many bird populations are declining globally, with migratory sea- and waterbirds among the most threatened groups. Increased isolation between populations, due to habitat loss leading to limited connectivity and reduced gene flow, may accelerate population declines or even cause local extinctions. To address this threat and inform conservation efforts, assessment of the genetic diversity of endangered populations is required. In Central Europe, gull-billed terns (Gelochelidon nilotica) have experienced a severe population decline in the past century, with only one last population of c. 40 breeding pairs remaining. Here, we aimed to characterise the genetic diversity of this population, and to compare it to that of two separate Mediterranean colonies to assess potential population connectivity. To achieve this, we developed a PCR protocol to amplify and sequence the complete mitochondrial genome (mtDNA). We found high genetic diversity in all three populations, and no population structure based on breeding location, as well as moderate population differentiation between Germany and Italy, and low differentiation between Germany and Spain, and between Italy and Spain. The German population, however, showed signs of population restriction, while both Mediterranean colonies showed evidence for population expansion. These results indicate that the last population of gull-billed terns in Central Europe is not acutely threatened by loss of genetic diversity, but instead shows signs of connectivity with other European colonies, which in turn suggests that conservation efforts should best focus on habitat and predation management. [ABSTRACT FROM AUTHOR]

Assisted gene flow can restore genetic diversity when genetic drift has driven deleterious alleles to high frequencies in small, isolated populations. Previous crosses among 20 populations of Gymnadenia conopsea documented the strongest heterosis and the weakest inbreeding depression in sparse and small populations, consistent with fixation of mildly deleterious alleles by genetic drift. We genotyped the populations used for crosses, and used 1200–1728 SNPs to test the following predictions: (1) heterosis increases with genetic differentiation (FST) to donor populations and decreases with genetic diversity in the recipient population, (2) inbreeding depression increases with genetic diversity, and (3) genetic diversity increases, and mean FST to other populations decreases, with population size and density. Pairwise FST ranged from very low to moderate (0.005–0.20) and genetic diversity varied moderately among populations (proportion of polymorphic loci = 0.52–0.75). However, neither FST between populations, nor genetic diversity in the recipient population, were related to the strength of heterosis. There was also no association between genetic diversity and the strength of inbreeding depression. Genetic diversity increased and mean FST decreased with population size, consistent with reduced diversity and increased differentiation of small populations by genetic drift. The results indicate that the loci conferring heterosis are not mirrored by overall population differentiation, and limited additional information on potential source populations for genetic rescue is gained by the genetic data. Instead, the use of controlled crosses can directly reveal positive effects of introducing new genetic material, and is a simple method with high potential in conservation. [ABSTRACT FROM AUTHOR]

The Peninsular Indian population of the endangered Asian elephant occurs in the Western and Eastern Ghats, and further north-east in the Eastern Central Indian (ECI) range. Using DNA obtained from fresh elephant dung, this study assessed the genetic variation, population structure, and gene flow in the two southern populations, SI1 and SI2, separated by the Palghat Gap in the Western Ghats, and the third population in the ECI range. As these populations have been shown to be genetically associated in previous studies, the hypotheses that their combined genetic diversity would be high and gene flow via migration would be evident, were tested. A total of 379 elephants were genotyped at 10 microsatellite markers, and a 630 bp mitochondrial DNA (mtDNA) fragment from the D-loop region was sequenced from 33 individuals. Four previously documented mtDNA haplotypes were identified: SI1 and ECI each had a single haplotype (BN and BL, respectively), while SI2 had two haplotypes (BA and BF). The mtDNA markers indicated substantial genetic differentiation among the populations, while differentiation using microsatellite data was moderate. The populations were assigned to three genetic groups: SI1, SI2, and the ECI. However, 39% of these individuals showed mixed ancestry, indicating ongoing gene flow despite natural and human-made barriers. Several first-generation male migrants were identified providing further evidence of contemporary gene flow. The sex ratio was female-biased, which is consistent with the existing census data. These three populations should be managed as a single conservation unit to ensure their long term viability. [ABSTRACT FROM AUTHOR]

Aquaculture in sub‐Saharan African accounts for less than 2% of world aquaculture production. The use of unimproved species limits the growth of aquaculture. In order to increase production, there is a need to develop aquaculture species that show vigor and adapt to different culture conditions. A genetic improvement program for Oreochromis shiranus was initiated at the National Aquaculture Center (NAC), in Zomba, Malawi. The program used pedigree records during mate allocation to avoid mating of siblings. After six consecutive generations of selection, a sample of 32 fish was taken for genetic analysis using a panel of 16 microsatellite markers. Genetic diversity and population differentiation indices of the sixth filial generation (F6) were compared with wild fish populations sampled from the corresponding locations from which the initial brood stock was collected. The study results show that the genetic diversity of the F6 generation and wild populations was not significantly different after the Kruskal–Wallis tests. However, the number of private alleles was lower in generation F6 (0.80) than in the overall average for wild populations (1.28). Discriminant analysis of principal components (DAPCs) supported analysis of molecular variance (AMOVA) by showing that there were no significant overlaps of inertia ellipses among F6 generation and wild populations. The experimental population differentiated into a separate group because of the random brood stock contribution from only a few fish from the wild population. The results suggest that the initial genetic diversity of the brood stock was sufficient as shown by the high number of alleles and polymorphic information content (PIC) values which contributed to the success of the selection program. The selection program successfully produced large fish at harvest and ensured genetic diversity of the F6 generation. [ABSTRACT FROM AUTHOR]

Pinfish (Lagodon rhomboides) are highly abundant in coastal ecosystems of the Gulf of Mexico and western Atlantic Ocean and serve as a crucial link in marine food webs. Despite their ecological relevance, little is known about this species' susceptibility to anthropogenic climate change. Here, we characterized patterns of mitochondrial genetic divergence and examined the upper thermal tolerance of pinfish across a large portion of the species' range. We found little evidence of population genetic differentiation among distant localities with divergent temperature regimes (e.g., Mexico and North Carolina), using two mitochondrial markers (cytochrome b [CytB] and cytochrome c oxidase I [COI]). This suggests high genetic connectivity, which implies low potential for local adaptation of populations to different thermal conditions along a latitudinal gradient. To further examine population‐scale differences in thermal tolerance, we assessed the critical thermal maxima (CTmax) of pinfish from four localities: North Carolina, Florida Keys, Alabama, and Texas. We found that CTmax was similar across sites, with all localities showing an average CTmax within a 1°C temperature range (34.5–35.5°C). This suggests that southern populations of pinfish may be more susceptible to the detrimental effects of ocean warming, as individuals in lower latitudes regularly experience temperatures within a few degrees of their CTmax. Finally, we examined the influence of varying salinity on the upper thermal limit of the pinfish and found that pinfish show no variation in CTmax under salinity conditions ranging from hypo‐ to hypersaline (15–35 ppt). These results show that pinfish can tolerate a wide range of environmental parameters but may rely on phenotypic plasticity, rather than local adaptation, to distinct conditions to cope with different environmental regimes. [ABSTRACT FROM AUTHOR]

Background: Phoebe zhennan, commonly known as "golden-thread nanmu," is one of the most valuable and protected tree species in China. An accurate understanding of the population genetic structure and its environmental factors is of significance for the protection and selection of new P. zhennan varieties. Results: Sixteen nSSR and six cpSSR markers were used to determine the genetic diversity and population structure of P. zhennan and the effect of environmental factors on the genetic structure. The nSSR markers identified a total of 451 number of alleles (Na), while cpSSR markers detected 20 Na. A relative high level of genetic diversity was observed in the P. zhennan population evidenced by high Shannon's information index (I) of 0.671 and 2.294 based on cpSSR and nSSR datasets. The low value of fixation index (F) observed from the nSSR dataset indicated low breeding within the population. The genetic differentiation was mainly detected within populations (only 28% and 13% of the variance being between populations according to the nSSR and cpSSR datasets). Among them, the HNSZX (H = 0.469) and SCSZZ (I = 1.943) populations exhibited the highest level of genetic diversity, while the HNXXT (H = 0.041) and SCLJS (I = 0.943) populations exhibited the lowest level of genetic diversity. The average genetic differentiation coefficient (Fst) and gene flow (Nm) were 0.022–0.128 and 1.698–11.373, respectively, which indicated a moderate level of genetic differentiation and a high level of gene flow. STRUCTURE, neighbor-joining clustering, and principal coordinate analysis divided 543 individuals into two or three categories based on the nSSR or cpSSR datasets. Four temperature, three precipitation, five chemical, five physical, and one soil texture variable showed significant effects on the genetic structure and distribution of P. zhennan populations. Compared to nSSR, the genetic differentiation among populations based on cpSSR datasets conformed to the geographic isolation model, suggesting that geographic and genetic distances should be considered for further genetic conservation and breeding utilization. The importance of in situ conservation units, such as populations with a high level of genetic diversity, more private alleles, and haplotypes (e.g., population SCGTS, SCYFS, and YNYJX), should be emphasized. Additionally, breeding, along with artificially assisted population regeneration and restoration, should also be carefully planned, taking into account climate and soil properties at the same time. Conclusions: In conclusion, this study provided genetic background information for the genetic conservation, management, and utilization of P. zhennan. [ABSTRACT FROM AUTHOR]

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Copyright of Mycosystema is the property of Mycosystema Editorial Board and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Simple Summary: Understanding how animals adapt to extreme environments, such as high altitudes, is vital for conservation efforts and animal welfare. Tibetan sheep residing on the Qinghai–Tibet Plateau possess unique adaptive traits, enabling them to survive in the severe conditions of high altitudes and low oxygen. However, the specific genes and molecular mechanisms that contribute to this adaptation in Tibetan sheep remain largely unidentified. So, based on whole-genome resequencing data for Tibetan sheep at different altitudes, this study analyzed the population structure and genomic differences of three Tibetan sheep breeds through FST and θπ ratio methods. In addition, we identified a series of candidate genes that may be related to the high-altitude adaptation of Tibetan sheep. This study provides a theoretical basis for the molecular mechanism of adaptation to extreme environments in Tibetan sheep and lays down a cornerstone for research in related fields. Tibetan sheep have developed unique adaptations for survival in the Qinghai–Tibet Plateau environment. However, the functional genes and molecular mechanisms that regulate hypoxia adaptation have not been fully characterized. In this study, based on the whole-genome resequencing data for Tibetan sheep at different altitudes, the population differentiation index (FST) and nucleotide diversity ratio (θπ ratio) were evaluated in populations of 20 Oula sheep (3501 m altitude, OL), 20 Zashijia sheep (4369 m altitude, ZSJ), and 20 Awang sheep (4643 m altitude, AW) to reveal candidate loci related to high-altitude hypoxia. We screened 728 and 524 candidate genes in the AW vs. OL and ZSJ vs. OL groups, respectively, of which 134 genes were jointly screened. Candidate genes were mainly enriched in the Ras, melanoma, melanogenesis, VEGF, and PPAR signaling pathways. HIF1AN, PDGFA, PDGFD, ANXA2, SOCS2, NOXA1, WNT7B, MMP14, GNG2, ATF6, PGAM2, PPP3R1, GSTCD, and PPARA may play important roles in the high-altitude adaptation of Tibetan sheep. In conclusion, this study provides valuable insights into the genes and molecular mechanisms that underlie high-altitude hypoxia adaptation in Tibetan sheep. [ABSTRACT FROM AUTHOR]

Background: Recent reports from Thailand reveal a substantial surge in Plasmodium knowlesi cases over the past decades, with a more than eightfold increase in incidence by 2023 compared to 2018. This study investigates temporal changes in genetic polymorphism associated with the escalating transmission of P. knowlesi malaria in Thailand over time using the prominent vaccine candidate, pkmsp1 as a marker. Methods: Twenty-five P. knowlesi samples collected in 2018–2023 were sequenced for the 42-kDa region of pkmsp1 and compared with 24 retrieved sequences in 2000–2009, focusing on nucleotide diversity, natural selection, recombination rate, and population differentiation. Results: Seven unique haplotypes were identified in recent samples, compared to 15 in earlier samples. Nucleotide and haplotype diversity were lower in recent samples (π = 0.016, Hd = 0.817) than in earlier samples (π = 0.018, Hd = 0.942). Significantly higher synonymous substitution rates were observed in both sample sets (dS–dN = 2.77 and 2.43, p < 0.05), indicating purifying selection and reduced genetic diversity over time. Additionally, 8 out of 17 mutation points were located on predicted B-cell epitopes, suggesting an adaptive response by the parasites to evade immune recognition. Population differentiation analysis using the fixation index (Fst) revealed high genetic differentiation between parasite populations in central and southern Thailand or Malaysia. Conversely, the relatively lower Fst value between southern Thailand and Malaysia suggests a closer genetic relationship, possibly reflecting historical gene flow. Conclusion: This study highlights a decline in genetic diversity and evidence of purifying selection associated with the recently increased incidence of P. knowlesi malaria in Thailand. The minor genetic differentiation between P. knowlesi populations from southern Thailand and Malaysia suggests a shared recent ancestry of these parasites and underscores the need for coordinated efforts between the two countries for the elimination of P. knowlesi. [ABSTRACT FROM AUTHOR]

The rosefin barb, Enteromius argenteus, as currently described, is a freshwater fish with a distribution that is geographically separated and divided into the northern population in the Kwanza River system in Angola, and the southern population in the Inkomati River system in South Africa and Eswatini. Due to this disjunct distribution pattern, it is likely that the two populations represent distinct species. mtDNA sequence data and detailed examination of morphometric characters revealed considerable genetic (2.8%–3.5%) and morphological differentiation of the two populations, suggesting their recognition as two distinct species. Enteromius crocodilensis is revalidated and redescribed for the southern population that is readily distinguished from E. argenteus by nonoverlapping circumpeduncular scale counts (12–13 vs. 14) and color pattern (presence of a conspicuous dark band along the midline vs. absence of characteristic melanin patterns). Phylogenetic analysis based on mtDNA cytochrome oxidase subunit I (COI) data places both E. argenteus and E. crocodilensis in a well‐supported clade that includes a number of morphologically similar sawfin barb species from southern and central Africa. [ABSTRACT FROM AUTHOR]

This study addresses the challenges posed by rainfall variability, leading to water deficits during critical stages of crop growth, resulting in a drastic reduction of cotton yield. In a comprehensive evaluation, thirty cotton genotypes, including five Gossypium arboreum (wild) and twenty-five Gossypium hirsutum (cultivated), were grown under rainfed and irrigated conditions. Drought tolerance indices (DTI) were evaluated, categorizing genotypes based on their resilience. Further, in-vitro screening at the seedling stage (20 days) under PEG-induced drought identified tolerant genotypes exhibiting elevated levels of free proline (19.07±5.31 mg.g−100fr.wt.), amino acids (34.59±6.51 mg.g−100fr.wt.), soluble proteins (13.73±2.65 mg.g−1fr.wt.), and glycine betaine (10.95±3.62 mg.g−100fr.wt.), in their leaves, positively correlating (p<0.001) with relative water content (87.70±3.45 %). Molecular analysis using drought-specific simple sequence repeats (SSR) markers revealed significant genetic variability in a cotton genotypes, with lower observed and higher expected heterozygosity. F statistics exposed a higher level of gene flow corresponding to low differentiation among populations. Among the genotypes group, wild GAM-67 and cultivated Deviraj emerged as the most potent, exhibiting the higher DTI and diverse gene pools. Study exhibited higher total gene diversity in drought-tolerant wild GAM-67 (0.8501) and greater expected heterozygosity (0.626) and gene flow (0.6731) in cultivated Deviraj, underlining their robust genetic adaptability to drought conditions. The integrated approach of field evaluations, in-vitro screening, and molecular analyses explained substantial genetic diversity, with the identification of promising genotypes displaying higher drought tolerance indices, elevated levels of stress-related biochemical osmolytes, and pronounced genetic adaptability, thereby contributing to the advancement of breeding initiatives for enhanced drought resilience in cotton. [Display omitted] • Thirty cotton genotypes were categorized according to their drought tolerance indices (DTI). • GAM-67 (wild) and Deviraj (cultivated) exhibited higher biochemical osmolytes, DTI and productivity, considering promising genotypes. • SSR markers unveiled significant genetic variability, high gene flow, and diverse gene pools in promising genotypes. • These genotypes performed better for the coefficient of gene differentiation and expected heterozygosity. • Molecular analysis reveals substantial genetic diversity, aiding breeding efforts for enhanced drought resilience in cotton. [ABSTRACT FROM AUTHOR]

The aim of this study is to explore the genetic characteristics of Guizhou Black goats and Meigu goats and their relationship to reproductive performance through population structure analysis, genetic diversity assessment, and selection signal analysis. Blood samples of 19 Guizhou Black goats and 11 Meigu goats were collected for whole-genome high-throughput sequencing. Using PCA and ADMIXTURE analyses, their population structure and genetic relationships were revealed. Further genetic diversity analysis showed that although there is significant population differentiation, the levels of genetic diversity are similar. Subsequently, these goats were categorized into high-yield and low-yield groups based on their litter sizes, with 15 goats in each group. Then, a selection signal analysis was performed using FST and π ratios for 33,563 SNP loci. The results identified six candidate genes, including KCNIP4, GFRA2, and DGKH, which are significantly associated with high litter performance. These findings enhanced our understanding of the genetic characteristics and population structure of Guizhou Black goats and Meigu goats. Moreover, they provide an important theoretical foundation and scientific basis for further breeding improvements. [ABSTRACT FROM AUTHOR]

Intercontinental disjunctions are one of the most attractive and interesting biogeographical patterns. Bryophytes often exhibit such distributions, which is partly explained by their great ability to disperse over long distances. However, such intercontinental ranges are sometimes a distorted reality caused by the existence of unnoticed species. This study investigates whether the disjunction between East Africa and southern India of the moss Lewinskya firma reflects the genuine distribution of a single species or implies pseudo-cryptic species (whose morphological differentiation is subtle and have therefore been masked). An integrative taxonomic approach combining morphological and molecular methods (genotyping by sequencing, GBS) was used, based on a representation of samples specifically collected from all the major mountainous regions where this moss occurs. Two species, L. firma s. str. and L. afroindica sp. nov. are involved, whose ranges completely overlap in East Africa, although genetic distance and morphological differences in leaf apex shape, vaginula hairs shape and papillosity, spore ornamentation and peristome constitution and ornamentation allow distinguishing both. In addition, the range of L. afroindica extends into both southern Africa and southern India. The phylogenetic reconstruction obtained shows a certain degree of differentiation of the Indian populations, although they are yet morphologically indistinguishable from African populations. The results thus highlight both the existence of overlooked species and the complexity of bryophyte biogeography. [ABSTRACT FROM AUTHOR]

For the first time, we describe phylogenomic signatures of an epidemic lineage of vesicular stomatitis Indiana virus (VSIV). We applied multiple evolutionary analyses to a dataset of 87 full-length genome sequences representing the circulation of an epidemic VSIV lineage in the US between 2019 and 2020. Based on phylogenetic analyses, we predicted the ancestral relationship of this lineage with a specific group of isolates circulating in the endemic zone of Chiapas, Mexico. Subsequently, our findings indicate that the lineage diversified into at least four different subpopulations during its circulation in the US. We identified single nucleotide polymorphisms (SNPs) that differentiate viral subpopulations and assessed their potential relevance using comparative phylogenetic methods, highlighting the preponderance of synonymous mutations during the differentiation of these populations. Purifying selection was the main evolutionary force favoring the conservation of this epidemic phenotype, with P and G genes as the main drivers of the evolution of this lineage. Our analyses identified multiple codon sites under positive selection and the association of these sites with specific functional domains at P, M, G, and L proteins. Based on ancestral reconstruction analyses, we showed the potential relevance of some of the sites identified under positive selection to the adaptation of the epidemic lineage at the population level. Finally, using a representative group of viruses from Colorado, we established a positive correlation between genetic and geographical distances, suggesting that positive selection on specific codon positions might have favored the adaptation of different subpopulations to circulation in specific geographical settings. Collectively, our study reveals the complex dynamics that accompany the evolution of an epidemic lineage of VSIV in nature. Our analytical framework provides a model for conducting future evolutionary analyses. The ultimate goal is to support the implementation of an early warning system for vesicular stomatitis virus in the US, enabling early detection of epidemic precursors from Mexico. [ABSTRACT FROM AUTHOR]

Background/Objectives: The swimming crab Charybdis feriata is an important commercial fishery species and a major economic contributor to the southeast coastal fishing communities in China. Under the scenario of resource decline and shortage in the market over recent years, it has become more urgent and necessary to explore the fine-scale population genetic characteristics of C. feriata. Methods: In this study, the genotyping-by-sequencing (GBS) method was used to estimate the genome-wide genetic variation in and population differentiation pattern of C. feriata collected from four geographical locations (Zhoushan, Quanzhou, Yangjiang, and Qinzhou) along the southeast coast of China. Results: A total of 18,815 high-quality single-nucleotide polymorphisms (SNPs) were identified and the results revealed the existence of high genetic diversity and low genetic divergence among the populations of C. feriata. Floating eggs and larvae transported by alongshore currents during the reproductive season might enhance the interpopulation genetic exchange. Principal component analysis (PCA) and a phylogenetic tree showed a high genetic connectivity of C. feriata across the southeast coast of China, but C. feriata distributed in the Zhoushan Archipelago might possess some genetic distinctiveness and diversification. Conclusions: The results supplemented basic genetic information of C. feriata at the genome level and also provided specific knowledge that could lead to the improved spatial management of fishery resources. [ABSTRACT FROM AUTHOR]

Understanding population structure is a priority for evaluating population dynamics of commercially fished cephalopods under fishing pressure and environmental changes. This study employed a multidisciplinary approach to clarify the population structure of Loliolus (Nipponololigo) uyii, a common squid in inshore fisheries. Sampling was conducted multiple times to cover the distribution range across the East China Sea and South China Sea. High haplotype diversity was revealed by three gene markers (COI, 16S and ODH). Two geographical clades with significant genetic differentiation were divided through phylogenetic trees and haplotype networks. The boundary between the two clades is delineated by the Dongshan population in the southern East China Sea. Furthermore, the neutrality tests and mismatch analysis suggested that L. (N.) uyii populations may have undergone population expansion. Correspondingly, statolith differences in lateral dome and posterior indentation, along with high classification success, further supported the genetic division. The overall difference in statolith shape also efficiently identified seasonal groups in the Beibu Gulf lacking genetic differentiation. This result offers new insights into the influence of genetic and environmental factors on statolith shape. The integrated results provide a comprehensive understanding of the population structure of L. (N.) uyii, laying the foundation for resource development and the conservation of the species. [ABSTRACT FROM AUTHOR]

The results of a comparative study of the genetic structure, parameters of intraspecific genetic diversity, and spatial differentiation of 35 populations of Picea abies–P. obovata–P. koraiensis species complex, located within the areas of distribution of "pure" species and in the contact zones of their ranges were presented. P. abies populations from Eastern Europe (Belarus, Poland); spruce populations from the European part of Russia, the Urals, and the West Siberian Plain, located in the zone of P. abies and P. obovata introgressive hybridization; P. obovata populations from various parts of the extensive range of this species in Siberia and Mongolia; and P. koraiensis populations from the Russian Far East and Northeast China were analyzed. The study of genetic variability and differentiation of populations was based on the analysis of variability of three microsatellite loci: Pt63718, Pt71936, and Pt26081, developed on the basis of Pinusthunbergii Parl chloroplast genome. The use of these DNA markers made it possible to obtain data indicating a fairly high degree of P. koraiensis genetic divergence from two other spruce species included in the complex, P. abies and P. obovata. Korean spruce growing in the Far East differs significantly from the populations of these species in the number and composition of haplotypes, the level of genetic diversity, and population structure, which gives us reason to consider it as a separate species. [ABSTRACT FROM AUTHOR]

Background: The domestic cat (Felis catus) is a newly evolved species in the family Felidae that has developed some great features among mammals. It is critical to conserve these species and prevent inbreeding from reducing their genetic diversity by understanding their genetic relationships and applying the information to breeding management. The diverse population was an excellent choice for studying genetic diversity and inbreeding phenomena. Objectives: To conduct this research, 128 individuals from 8 populations, including Azerbaijan, Persian, Ahar, Uermia, Tehran, Karaj, Turkish and Shop cat (both genders), were randomly selected from different geographical regions. We selected eight STR markers with different chromosomal locations based on polymorphism and observed allele numbers in the next step. DNA extraction was performed using tail hair root, PCR and electrophoresis, and gel staining was performed according to routine laboratory protocol. For statistical analysis, CONVERT versions POPGENE, ARLEQUIN GenAlEx and R script analysis. Results: Remarkably, our results showed that 23 alleles were identified in 128 samples. The highest number of alleles belonged to the FCa096 locus (eight alleles) in the Persian population, followed by FCa045 (seven alleles) in the Persian and Ahar populations. Another new finding is that the lowest number of alleles belonged to the 35 and FCa77 locus (two alleles). In addition, pairwise differentiation between and within populations was examined using the genetic distance index. Overall, the results showed that the degree of differentiation within the population is high in the Turkish population compared to other population groups and lower in the Azerbaijan population. In addition, principal component discriminant analysis‐based analysis based on the ADAGENET package shows the distribution of samples by geographical location. The results show that genetic mixing between populations is high. Conclusions: On this basis, we conclude that randomly bred domestic cats have a higher level of diversity than Persian domestic cats. This is an interesting topic for future work. [ABSTRACT FROM AUTHOR]

Neotropical forest ecosystems harbour significant biodiversity. To develop effective insect conservation practices, it is important to understand the factors that influence the diversity and population structure of the species.Dispersal, a key determinant of population structure, is well studied in termites nesting in wood, for which it can be influenced by wood transport, or in termites living in urban environments. However, understanding the dispersal of termites whose mobility remains unaffected by wood transport remains understudied.We investigated the dispersal of Embiratermes neotenicus, a soil‐feeding species with short dispersal distance, in the Neotropical region, where both intact and degraded forests exist. Using mitochondrial and nuclear data, we analysed genetic diversity, structure and factors contributing to population differentiation in Suriname and French Guiana at multiple scales for 70 colonies.The population in French Guiana is the ancestral population in the region that subsequently expanded.Significant genetic differentiation between populations was observed, with distinct patterns identified in Suriname and French Guiana. The Suriname population showed higher genetic diversity and no subpopulation differentiation, whereas the French Guiana population showed substructure into distinct genetic clusters.Analyses at the scale of all colonies suggest the influence of landscape features, such as the Maroni River, on genetic differentiation. At the local scale, genetic differentiation between colonies increases with forest alteration, even when this does not include major changes in forest cover.Our results highlight the sensitivity of soil‐feeding termite populations to habitat change. We argue that multi‐scale studies are needed for a comprehensive understanding of genetic patterns, especially for species with short dispersal distances. [ABSTRACT FROM AUTHOR]

Since European settlement of Australia, substantial areas of subtropical rainforest have been cleared. More recently, effort is being made to restore areas of this ecological community. The financial investment and increasing reliance on ecological restoration in biodiversity conservation justifies a need for better understanding of how to improve success at the genetic level. This research measures genetic diversity (allelic richness [Rs], expected heterozygosity [He], and inbreeding using Wright's coefficient [FIS]) for expected neutral DNA markers in three Australian subtropical rainforest trees—White booyong (Argyrodendron trifoliolatum), Watkin's fig (Ficus watkinsiana), and Native tamarind (Diploglottis australis). Wild and restored populations of these species were compared in two neighboring regions in Northeast New South Wales (the Tweed Caldera and the Big Scrub). There were no statistically significant differences in Rs or He between wild and restored populations for any of the target species. Inbreeding was significantly higher in one of the restored versus wild population comparisons: F. watkinsiana in the Tweed (restored F = 0.20; wild F = −0.02; p = 0.01). The comparable levels of genetic diversity observed in restored and wild populations targeted in this study are likely due to informed practitioner perspectives and practices, staged plantings over several years, and high genetic diversity and low genetic differentiation within source populations. [ABSTRACT FROM AUTHOR]

Pterocarpus santalinus L.f. is an endangered tree species that is cherished worldwide for its valuable deep red-colored heartwood, which has multiple uses. This species exhibits a wide range of medicinal properties and offers immense potential for the discovery of bioactive compounds of pharmacological importance. The overharvesting of this species for heartwood has led to a gradual decline in its natural populations, thereby depleting its genetic resources and contributing to the loss of genetic diversity. Therefore, it is essential to assess genetic diversity, as such information allows for the effective conservation and utilization of genetic resources. In the present study, the genetic diversity and population structure among 40 germplasm accessions originating from 8 populations of P. santalinus were analyzed using six cross-species simple sequence repeats (SSR), 20 each of inter simple sequence repeats (ISSR) and random amplified polymorphic DNA (RAPD) markers. SSR markers revealed higher polymorphism (100 %), followed by ISSRs (82.81 %) and RAPDs (67.50 %), across all the accessions. The mean values of the polymorphic information content (PIC), effective multiplex ratio (EMR), and marker index (MI) were higher for SSRs (0.84, 9.17, and 7.7), followed by ISSRs (0.262, 4.474, and 1.251) and RAPDs (0.204, 3.268 and 0.970, respectively), indicating the superiority of SSRs in detecting polymorphisms in red sanders. Similarly, the estimates of Nei's gene diversity (H) and Shannon's information index (I) varied across the studied accessions, with the highest values for SSRs (H = 0.528, I = 0.923), followed by ISSRs (H = 0.287, I = 0.428) and RAPDs (H = 0.206, I = 0.307). However, the genetic statistic (Gst) or fixation statistic (Fst) and gene flow (Nm) values were higher for RAPDs (0.455 and 0.598) and ISSRs (0.446 and 0.620) than for SSRs (0.383 and 0.489, respectively), indicating significant genetic differentiation of the populations and moderate gene flow among the populations. Analysis of molecular variance (AMOVA) with SSR, ISSR, and RAPD markers revealed that a greater proportion of genetic variation resided within populations (74 %, 69 %, and 66 %, respectively) than among populations (26 %, 31 %, and 34 %, respectively). Hierarchical clustering on the basis of RAPDs grouped most of the accessions according to the population of origin; however, this clustering was different for the ISSR and SSR markers. STRUCTURE analysis divided the accessions into four, two, and three groups with SSR, ISSR, and RAPD markers, respectively, with admixtures detected in all the groups pointing toward shared genetic lineages and diverse genetic ancestry among the accessions of different populations. Overall, the populations of Gumudipoondi of Tamil Nadu and K.V. Bhavi of Andhra Pradesh were genetically more diverse than other populations, as revealed by genetic diversity estimates obtained with SSR and ISSR marker systems; therefore, the accessions of these populations must be prioritized for conservation and utilization in breeding programs for genetic improvement. [Display omitted] • Genetic diversity was assessed among 40 accessions of P. santalinus using 6 cross-species SSR, 20 each of ISSR and RAPD primers. • Cross-species SSRs were more efficient in detecting genetic diversity in the studied populations than ISSRs and RAPDs. • The populations of Gumidipoondi of Tamil Nadu (GTN) and K.V. Bhavi of Andhra Pradesh (KAP) exhibited higher genetic diversity than other populations according to SSR and ISSR marker analysis. • Analysis of molecular variance with SSR, ISSR and RAPD markers showed that genetic variations within populations (74 %, 69 % and 66 %) were greater than among populations (26 %, 31 % and 34 %). • STRUCTURE analysis using SSR, ISSR and RAPD markers divided the populations into four, two and three genetic groups, respectively, with admixtures detected in all genetic groups. [ABSTRACT FROM AUTHOR]

Wisteria vein mosaic virus (WVMV, Potyvirus wisteriae), a virus belonging to the genus Potyvirus, is responsible for Wisteria vein mosaic disease (WMD), a severe disease that affects Wisteria, a genus of garden plants acclaimed worldwide. Although probably originating in the Far East, WVMV infection was first reported in the US, and subsequently in numerous countries. Following the first molecular detection of an Italian isolate, WVMV Bari, its full-length genome was achieved using NGS barcoding technology. A PhyML phylogenetic analysis, supported by clustering algorithm validation, identified a clear separation between two phylogroups. One major clade comprised WVMV strains isolated from Wisteria spp. A second clade grouped three highly divergent strains, at the borderline species threshold, all found in non-wisteria hosts. Relying on a Relative Time Dated Tips (RTDT) molecular clock, the first emergence of WVMV clades has been traced back to around the 17th century. A network inference analysis confirmed the sharp separation between the two host-related phylogroups, also highlighting the presence of potential intermediate variants. Inter-population genetic parameters revealed a very high genetic differentiation in both populations, which was made reliable by statistically significant permutation tests. The migrant number (Nm) and fixation index (FST) evidenced a restricted gene flow and strong population structures. According to the dN/dS ratio and negative neutrality tests, it was derived that purifying selection at the expense of non-silent variants is underway within WVMV populations. Targeting WVMV evolutionary traits, the present effort raised interesting questions about the underestimated potential of this culpably neglected species to spread in economically relevant crops. The main intention of our study is, therefore, to propose an evolution-based analysis approach that serves as a case study to investigate how other potyviruses or newly emerging viruses may spread. [ABSTRACT FROM AUTHOR]

Carboxylesterases (CXE, EC 3.1.1.1), a class of hydrolases with an a/b folding domain, play important roles in plant growth and development and stress response. Here, we identified 32, 63, 41, and 45 CXE genes in Oryza sativa Japonica (Nipponbare), Oryza sativa Indica (93-11), Oryza sativa Indica (Xian-1B1 var.IR64), and Oryza sativa Japonica (Geng-sbtrp var.ChaoMeo), respectively. Then, we analyzed the chromosomal location, physical and chemical properties, subcellular localization, collinearity, and selection pressure of CXE genes in four rice varieties. We also analyzed the functional interaction network, cis-regulatory elements, evolutionary relationship, and protein tertiary structure, and performed gene expression profiling and qPCR verification under abiotic stress, as well as diversity analysis of 3010 gene-CDS-haplotype (gcHap) rice samples, aiming to understand the potential function of the 32 OsCXE genes. Our results indicated that fragment replication is the main reason for amplification of the CXE gene family in rice, and the gene family has undergone strong purification selection. OsCXE3.1, OsCXE3.2, OsCXE3.3, OsCXE5.1, and OsCXE7.3 may be used to improve the tolerance of rice to abiotic stress. OsCXE play important roles in rice population differentiation and improvement, and the major gcHaps at most OsCXE locus are significantly associated with yield traits. Therefore, natural variations of most OsCXE locus have great potential value for improvement of rice productivity. [ABSTRACT FROM AUTHOR]

Introduction: Since its introduction about a decade ago, target enrichment sequencing of ultraconserved elements (UCEs) has proven to be an invaluable tool for studies across evolutionary scales, and thus employed from population genetics, to historical biogeography as well as deep-time phylogenetics. Here, we present the first probe set targeting UCEs in crustaceans, specifically designed for decapods and tested beyond decapods in other malacostracan lineages. Methods: Probes were designed using published genomes of nine decapod and one peracarid species, as well as raw Nanopore long reads of one additional brachyuran species. The final probe set consists of about 20,000 probes, targeting 1,384 unique UCE loci. We compiled a dataset across Malacostraca,as well as datasets of a deep-sea squat lobster genus, and an intertidal mangrove crab species, to test the probe set at different phylogenetic levels (i.e., class, order, genus, within species). Results: Final mean UCE recovery from fresh samples across Malacostraca was 568 loci,with up to 847 and 658 loci recovered from decapod and non-decapod species, respectively. Final mean recovery from fresh samples in the genus- and within species-level datasets was 849 and 787 loci, respectively. Up to several hundreds of UCEs were recovered from historicalmuseum specimens (10 to > 150 years old), that were included in all datasets. UCE-based phylogenies largely reflected the known relationships of the included taxa, and we were able to infer population differentiation based on >600 SNPs extracted from the species-level dataset. Discussion: Our results showcase the versatility of this UCE probe set, yielding informative data from phylogenetic as well as population-genetic datasets. They demonstrate once more that UCEs are a promising technique for leveraging museum specimens for genomic studies, and overall highlight the probe set's potential for crustacean evolutionary studies. [ABSTRACT FROM AUTHOR]

ABSTRACT Across the tree of life, many organisms are able to reproduce clonally, via vegetative spread, budding or parthenogenesis. In population genetic analyses of clonally reproducing organisms, it is common practice to retain only a single representative per multilocus genotype. Though this practice of clone correction is widespread, the theoretical justification behind it has been very little studied. Here, I use individual‐based simulations to study the effect of clone correction on the estimation of the genetic summary statistics HO, HS, FIS, FST, F′′ST and Dest. The simulations follow the standard finite island model, consisting of a set of populations connected by gene flow, but with a variable rate of sexual versus asexual reproduction. The results of the simulations show that by itself, the inclusion of replicated genotypes does not lead to a deviation in the values of the summary statistics, except when the rate of sexual reproduction is less than about one in thousand. However, clone correction can introduce a strong deviation in the values of most of the statistics, when compared to a scenario of full sexual reproduction. For HS and FIS, this deviation can be informative about the process of asexual reproduction, but for FST, F′′ST and Dest, clone correction can lead to incorrect conclusions. I therefore argue that clone correction is not strictly necessary, but can in some cases be insightful. However, when clone correction is applied, it is imperative that results for both the corrected and uncorrected data are presented. [ABSTRACT FROM AUTHOR]

The soybean pod borer, Leguminivora glycinivorella (Matsumura), is an important tortricid pest species widely distributed in most parts of China and its adjacent regions. Here, we analyzed the genetic diversity and population differentiation of L. glycinivorella using diverse genetic information including the standard cox1 barcode sequences, mitochondrial genomes (mitogenomes), and single‐nucleotide polymorphisms (SNPs) from genotyping‐by‐sequencing. Based on a comprehensive sampling (including adults or larvae of L. glycinivorella newly collected at 22 of the total 30 localities examined) that covers most of the known distribution range of this pest, analyses of 543 cox1 barcode sequences and 60 mitogenomes revealed that the traditionally recognized and widely distributed L. glycinivorella contains two sympatric and widely distributed genetic lineages (A and B) that were estimated to have diverged ∼1.14 million years ago during the middle Pleistocene. Moreover, low but statistically significant correlations were recognized between genetic differentiation and geographic or environmental distances, indicating the existence of local adaptation to some extent. Based on SNPs, phylogenetic inference, principal component analysis, fixation index, and admixture analysis all confirm the two divergent sympatric lineages. Compared with the stable demographic history of Lineage B, the expansion of Lineage A had possibly made the secondary contact of the two lineages probable, and this process may be driven by the climate fluctuation during the late Pleistocene as revealed by ecological niche modeling. [ABSTRACT FROM AUTHOR]

Background: Anemone shikokiana (Makino) Makino is a perennial herb of the genus Anemone in the family Ranunculaceae. Endemic to the Shandong Peninsula in China and Shikoku Island in Japan, it is a rare and endangered plant with a narrow, disjunct distribution. It is threatened with extinction and is in urgent need of conservation. Evaluating the genetic diversity of species, revealing the population genetic structure and gene flow, and inferring the population history are of great importance for species conservation, especially for rare and endangered plants. Results: In our study, 73 samples from eight wild populations in China were sequenced by Super-GBS, yielding a total of 40.59 G clean reads and 52,231 SNPs. Based on the obtained SNP data set, we evaluated the population genetic diversity, genetic structure, and gene flow of A. shikokiana. A low level of genetic diversity was found (He = 0.1925, Ho = 0.1422). The neighbor-joining (NJ) tree, principal component analysis and ADMIXTURE analysis suggested that these 73 A. shikokiana could be considered as two groups. Pairwise genetic differentiation coefficients (Fst) indicated that genetic differentiation was lower between adjacent populations and higher between geographically separated populations. The gene flow between Kunyu Mountain and Lao Mountain was very low. However, neither of the two regions showed evidence of Isolation by Distance. Conclusions: Here, we revealed the population genetic structure and gene flow of A. shikokiana from the Shandong Peninsula, China. This research provides valuable genetic resources for A. shikokiana and contributes to the scientific and effective conservation of the species. [ABSTRACT FROM AUTHOR]

Understanding population genetic diversity and evolutionary dynamics of marine fish species can provide theoretical bases for fishery management and germplasm conservation, especially facing a changing environment. The rockfish species in genus Sebastiscus are economically important species for farming and sport fisheries in China, Japan and Korea. In this study, inter-annual and inter-specific comparisons on genetic diversity, population differentiation and historical demography of S. marmoratus and S. tertius collected from coastal waters of Zhangzhou, China were conducted using mitochondrial control region sequences. High levels of genetic diversity were observed in both species, indicating high adaptive potential to environmental changes. Demographic analyses detected recent population expansion in population S. tertius (Ste-2020) and population S. marmoratus collected in 2020 (Sma-2020), yet failed in population collected in 2016 (Sma-2016). Moreover, in population Sma-2020, novel haplotypes were detected and grouped into a separate sub-branch, revealed by neighbour-joining topology. Detected recent population expansion and novel haplotypes might be considered as a response to environmental changes. Besides, results of genetic differentiation analysis suggested high intra-specific genetic variation in both species. These genetic data and information will provide novel implications for strengthening the management of S. marmoratus and S. tertius fisheries in climate change scenarios. [ABSTRACT FROM AUTHOR]

Habitat fragmentation reduces gene flow, causing genetic differentiation and diversity loss in endangered species through genetic drift and inbreeding. However, the impact of habitat fragmentation on ectomycorrhizal (ECM) fungi remains unexplored, despite their critical roles in forest ecosystems. Here, we investigated the population genetic structure and the demographic history of Rhizopogon togasawarius, the ECM fungus specifically colonizing the host tree Pseudotsuga japonica, across its entire distribution range (>200 km). These two species are designated as endangered species on the IUCN Red List since they are found only in small, fragmented forests in Japan. We analysed 236 R. togasawarius individuals from five remaining populations across the Kii Peninsula and the Shikoku Island, separated by a sea channel. Simple sequence repeat analyses using 20 loci revealed strong genetic differentiation among populations (FST = 0.255), even significant in the nearest population pair separated by a distance of only 8 km (FST = 0.075), indicating extremely limited gene flow between populations. DIYABC‐RF analyses implied that population divergence occurred approximately 6000 generations ago between the two regions, and nearly 1500 generations ago between the nearest populations within Shikoku Island, related to past climate events. Because of prolonged genetic isolation, significant inbreeding was confirmed in four of five populations, where effective population sizes became very small (Ne = 9.0–58.0). Although evaluation of extinction risks for microorganisms is challenging, our conservation genetic results indicated that habitat fragmentation increases extinction risk through population genetic mechanisms, and therefore should not be overlooked in biodiversity conservation efforts. [ABSTRACT FROM AUTHOR]

Under allopatric speciation, populations of a species become isolated by a geographic barrier and develop reproductive isolation through genetic differentiation. When populations meet in secondary contact, the strength of evolved reproductive barriers determines the extent of hybridization and whether the populations will continue to diverge or merge together. The yellowhammer (Emberiza citrinella) and pine bunting (E. leucocephalos) are avian sister species that diverged in allopatry on either side of Eurasia during the Pleistocene glaciations. Though they differ greatly in plumage and form distinct genetic clusters in allopatry, these taxa show negligible mitochondrial DNA differentiation and hybridize extensively where they overlap in central Siberia, lending uncertainty to the state of reproductive isolation in the system. To assess the strength of reproductive barriers between taxa, we examined genomic differentiation across the system. We found that extensive admixture has occurred in sympatry, indicating that reproductive barriers between taxa are weak. We also identified a putative Z chromosome inversion region that underlies plumage variation in the system, with the 'pine bunting' haplotype showing dominance over the 'yellowhammer' haplotype. Our results suggest that yellowhammers and pine buntings are currently at a crossroads and that evolutionary forces may push this system towards either continued differentiation or population merging. However, even if these taxa merge, recombination suppression between putative chromosome Z inversion haplotypes may maintain divergent plumage phenotypes within the system. In this way, our findings highlight the important role hybridization plays in increasing the genetic and phenotypic variation as well as the evolvability of a system. [ABSTRACT FROM AUTHOR]

Despite showing the greatest primate diversity on the planet, genomic studies on Amazonian primates show very little representation in the literature. With 48 geolocalized high coverage whole genomes from wild uakari monkeys, we present the first population-level study on platyrrhines using whole genome data. In a very restricted range of the Amazon rainforest, eight uakari species (Cacajao genus) have been described and categorized into the bald and black uakari groups, based on phenotypic and ecological differences. Despite a slight habitat overlap, we show that posterior to their split 0.92 Mya, bald and black uakaris have remained independent, without gene flow. Nowadays, these two groups present distinct genetic diversity and group-specific variation linked to pathogens. We propose differing hydrology patterns and effectiveness of geographic barriers have modulated the intra-group connectivity and structure of bald and black uakari populations. With this work we have explored the effects of the Amazon rainforest's dynamism on wild primates' genetics and increased the representation of platyrrhine genomes, thus opening the door to future research on the complexity and diversity of primate genomics. Population study of whole genomes of wild uakary monkeys (Cacajao genus) exposes how the dynamic and highly heterogeneous Amazon basin may have shaped complex connectivity patterns and driven fast population differentiation on these. [ABSTRACT FROM AUTHOR]

Understanding the genetic diversity of snow leopards (Panthera uncia) is crucial for their conservation and man⁃ agement. In this study, DNA was extracted from tissue samples of 104 snow leopard individuals, and combined with 70 snow leopard genotyping data from the literature, a genetic diversity analysis was conducted using nine microsatellite polymorphic loci. The results revealed that as the sample size increased from 70 to 174, the snow leopard population tended to differentiate into two distinct groups: a northwest group and a central group. A total of 45 alleles were detected in the two groups, with an average number of alleles per locus (Na) of 4. 556 and 4. 667, respectively, for the central and northwest populations; The average expected heterozygosity (He) was 0. 574 and 0. 591, while the average observed heterozygosity (Ho) was 0. 517 and 0. 498, respectively. The average inbreeding coefficient (FIS) for the snow leopard population was 0. 137, the average genetic differentiation coefficient (FST) was 0. 067, and the average polymorphic information content (PIC) was 0. 602. The genetic variation between populations accounted for 15. 24%, and the genetic variation within populations is 84. 76%. The nine microsatellite loci exhibited medium to high levels of polymorphism. Compared to other snow leopard studies, the genetic diversity of the two snow leopard groups was moderate, and the level of genetic differentiation between populations was at a medium level. Most of the genetic variation originated within the populations. These findings are significant for global research on snow leopard population structures and genetic diversity, and provide a reliable genetic background for future scientific conservation efforts. [ABSTRACT FROM AUTHOR]

Small and isolated populations face several intrinsic risks, such as genetic drift, inbreeding depression, and reduced gene flow. Thus, patterns of genetic diversity and differentiation have become an important focus of conservation genetics research. The golden snub-nosed monkey Rhinopithecus roxellana , an endangered species endemic to China, has experienced rapid reduction in population size and severe population fragmentation over the past few decades. We measured the patterns of genetic diversity and population differentiation using both neutral microsatellites and adaptive major histocompatibility complex (MHC) genes in 2 R. roxellana populations (DPY and GNG) distributed on the northern and southern slopes of the Qinling Mountains, respectively. Eight MHC-linked haplotypes formed by 5 DQA1 alleles, 5 DQB1 alleles, 5 DRB1 alleles, and 4 DRB2 alleles were detected in the 2 populations. The larger GNG population showed higher genetic variation for both MHC and microsatellites than the smaller DPY population, suggesting an effect of genetic drift on genetic variation. Genetic differentiation index (F ST) outlier analyses, principal coordinate analysis (PCoA), and inferred population genetic structure showed lower genetic differentiation in the MHC variations than microsatellites, suggesting that pathogen-mediated balancing selection, rather than local adaptation, homogenized the MHC genes of both populations. This study indicates that both balancing selection and genetic drift may shape genetic variation and differentiation in small and fragmented populations. [ABSTRACT FROM AUTHOR]

The common practice of using subspecies as conservation targets raises the question of whether efforts are focused on preserving conspicuous components of the species' phenotypic variability rather than evolutionarily significant units. To address this question, in this study we performed a comprehensive morphological and genetic assessment on all the subspecies of wall lizard described for the Aeolian Archipelago (Italy) to determine whether they represent distinct evolutionary lineages and/or discrete phenotypic partitions. Further, we applied a monophyly test to 70 subspecies belonging to seven wall lizard species occurring in Italy, based on our results and on previous phylogeographic studies. We found that none of the Aeolian subspecies represents a distinct evolutionary lineage, despite some morphological differentiation of island populations across the archipelago, suggesting a very recent origin of island populations and of the observed phenotype variation. Across seven wall lizard species, tests revealed that lizard subspecies rarely (< 9% of cases) match evolutionary units. This study demonstrates that intraspecific taxonomy of wall lizards is a poor predictor of phylogeographic partitions and evolutionary units, and therefore of limited use (if not dangerous) for defining conservation and management units. A better approach would be relying on the integration of genomic and phenotypic data to assess the evolutionary significance and conservation value of phenotypic and genetic units within species. [ABSTRACT FROM AUTHOR]

Pine wilt disease (PWD), caused by Bursaphelenchus xylophilus, severely threatens global pine forests. Monochamus alternatus is the primary vector of B. xylophilus in East Asia. Understanding the population structure and evolutionary forces of vector insects is critical for establishing effective PWD management strategies. The present work explores the genetic structure and phylogenetic relationships of 20 populations of M. alternatus from the Qinling‐Daba Mountains (QDM) in China using the mitochondria DNA dataset, supplemented by ecological niche modeling (ENM). All M. alternatus populations were categorized into three phylogeographic clusters (Clade A, Clade B, and Clade C), with Clade A and Clade B corresponding to the western and eastern QDM, respectively. The results of divergence time estimation concur with environmental changes induced by Quaternary glacial climate oscillations in QDM of China. M. alternatus populations exhibited significant genetic differentiation, with expansion in their population size. Ecological niche modeling (ENM) demonstrated that precipitation and temperature significantly influence the distribution of M. alternatus and the species is anticipated to grow into higher latitude and higher altitude regions in the future. In a nutshell, exploring the genetic structure and evolutionary dynamics of M. alternatus can provide valuable insights into the prevention and occurrence of B. xylophilus. These findings also serve as a reference for research on population differentiation and phylogeography of other species in QDM and adjacent areas. [ABSTRACT FROM AUTHOR]