Similar Genetic Composition Research Articles

Assessing the Impacts of Adaptation to Native-Range Habitats and Contemporary Founder Effects on Genetic Diversity in an Invasive Fish.

Species invading non-native habitats can cause irreversible environmental damage and economic harm. Yet, how introduced species become widespread invaders remains poorly understood. Adaptation within native-range habitats and rapid adaptation to new environments may both influence invasion success. Here, we examine these hypotheses using 7058 SNPs from 36 native, 40 introduced and 19 farmed populations of tench, a fish native to Eurasia. We examined genetic structure among these populations and accounted for long-term evolutionary history within the native range to assess whether introduced populations exhibited lower genetic diversity than native populations. Subsequent to infer genotype-environment correlations within native-range habitats, we assessed whether adaptation to native environments may have shaped the success of some introduced populations. At the broad scale, two glacial refugia contributed to the ancestry and genomic diversity of tench. However, native, introduced and farmed populations of admixed origin exhibited up to 10-fold more genetic diversity (i.e., observed heterozygosity, expected heterozygosity and allelic richness) compared to populations with predominantly single-source ancestry. The effects of introduction to a new location were also apparent as introduced populations exhibited fewer private alleles (mean = 9.9 and 18.9 private alleles in introduced and native populations, respectively) and higher population-specific Fst compared to native populations, highlighting their distinctiveness relative to the pool of allelic frequencies across tench populations. Finally, introduced populations with varying levels of genetic variation and similar genetic compositions have become established and persisted under strikingly different climatic and ecological conditions. Our results suggest that lack of prior adaptation and low genetic variation may not consistently hinder the success of introduced populations for species with a demonstrated ability to expand their native range.

Geomorphic impacts within Red River Fault and island shifting as witnessed by the phylogeography of the largest water strider

Palaeogeological events and climate oscillations profoundly impact the demographics and distributions of small-range species, increasing the extinction risk. The largest water strider worldwide, Gigantometra gigas (Hemiptera: Gerridae), exhibits restricted distributions in Vietnam and southern China. Herein, we generated three genomic datasets (mitogenomes, 146 nuclear protein-coding genes and single nucleotide polymorphisms) with ecological niche modelling (ENM) to explicitly test whether the present-day distribution of G. gigas actually resulted from geographical and climatic effects. We found that the origin of this largest water strider reached the divergence time of the genus within Gerridae, providing a greater opportunity to explore its response to geographic movements. The right-lateral motion of the Red River Fault facilitated the divergence of two phylogeographic lineages, resulting in the “north–south component” genetic pattern in G. gigas. The Hainan and southeast Vietnam populations of the southern linage were completely separated by the Beibu Gulf but exhibited similar genetic compositions, confirming that Hainan had a continental origin and that Hainan Island joined with the Indo-China Peninsula to promote gene exchange among populations. Additionally, we noticed the low genetic diversity but long demographic history of the northern lineage, which displayed population dynamics opposite to those of other organisms. Integrating the demographic changes and ENM findings revealed that suitable habitat contraction and rapid demographic decline during the Last Glacial Maximum (LGM) triggered the low genetic diversity of the northern lineage. Overall, the demographic history of the largest water strider was mainly shaped by geographical features, and first provided evidence from the phylogeographic perspective of aquatic insects to support the hypothesis of Hainan Island shifting.

Connectivity between sea turtles off Jeju Island on the Korean Peninsula, and other populations in the western Pacific

The northwestern Pacific region is an important habitat for sea turtles, hosting five species out of seven. There is still limited information available about the sea turtle aggregations around the Korean Peninsula, which is the northern boundary for many sea turtle species in the western Pacific area. The present study aims to investigate the migratory route of sea turtles visiting Jeju Island. Five species of sea turtles were identified from by-catch and stranding data between 2013 and 2022 on Jeju Island in Korea: green (Chelonia mydas; 24 individuals), loggerhead (Caretta caretta; 9), hawksbill (Eretmochelys imbricata; 2), olive ridley (Lepidochelys olivacea; 2), and leatherback (Dermochelys coriacea; 1). Mixed stock analysis using mitochondrial DNA haplotypes revealed that Jeju green turtles primarily originate from the rookeries of the Japanese Archipelago. This connectivity between two regions was also supported by the similar genetic composition of loggerhead turtles. Similarly, satellite tracking data showed that several green turtles originating from Jeju Island migrated to waters near the Ryukyu Archipelago in Japan. Nevertheless, about 60% of the tracked green turtles stayed near Jeju Island, with most overwintering there, indicating the long residency in Jeju Island. This study also provides the genetic sequences of other three species including new orphan haplotypes of hawksbill and olive ridley turtles. Our findings suggest that Jeju Island serves as a stable foraging habitat and provide insight into understanding the habitat range of sea turtles in the western Pacific.

Mitogenomics, phylogeny and morphology reveal two new entomopathogenic species of Ophiocordyceps (Ophiocordycipitaceae, Hypocreales) from south-western China.

Ophiocordyceps encompasses over 300 species, demonstrating a wide range of morphological features, hosts and habitats within its species diversity. In this study, two novel species in Ophiocordyceps were revealed parasitising Hepialidae larva buried in soil. Ophiocordycepsalbastroma was morphologically characterised by white stromata, solitary and cylindrical conidiogenous cells and smooth ovoid or ellipsoidal conidia. Ophiocordycepsnigristroma was characterised by woody and dark brown stromata, monophialidic, swollen base and lageniform conidiogenous cells and smooth fusiform or oval conidia. The two new species formed a separate clade, respectively, based on the phylogenetic analyses of a combined dataset including nrSSU, nrLSU, rpb1, rpb2, and tef-1α, as well as a dataset of mitochondrial 14 protein coding genes (PCGs). They were all closely grouped with O.sinensis. The mitochondrial genomes of them were first reported. Their mitogenomes were all typical of circular molecules, with positive AT and GC skew, similar GC content, similar genetic composition, similar codon usage and conservative gene positions. However, the length of the mitogenomes varied. Changes in the length of the genes were the leading cause of changes in the length of mitochondrial genome of Ophiocordyceps. The discovery and identification of new Ophiocordyceps species and analysis their mitochondrial genomes may serve as foundations for phylogeny and diversity research within the genus Ophiocordyceps.

Variations in body condition of green turtles (Chelonia mydas) in two nearby foraging grounds indicate their sensitivity to foraging habitats

Abstract Coastal seagrass habitats are critical foraging grounds for endangered green turtles (Chelonia mydas). However, these habitats are vulnerable to anthropogenic effects, potentially leading to their degradation with consequent impacts on the health status of foraging green turtles. Two foraging habitats of green turtles in Tun Mustapha Park, Sabah, Malaysia were surveyed: Kudat Mainland and Balambangan Island, by capturing green turtles and evaluating their physical body condition as well as assessing seagrass cover. Despite having similar genetic compositions, the Kudat Mainland aggregation had significantly higher body size (curved carapace length: 61.7 ± 14.5 cm, body weight: 30.0 ± 22.2 kg), Fulton's body condition index (BCI: 1.49 ± 0.13), barnacle (Chelonibia testudinaria) occurrence (78.8%) and barnacle abundance (5.46 ± 9.90 barnacles/turtle) than the Balambangan Island aggregation (curved carapace length: 51.6 ± 8.1 cm, body weight: 17.3 ± 7.7 kg, BCI: 1.40 ± 0.09, barnacle occurrence: 31.0%, barnacle abundance: 0.50 ± 0.92 barnacles/turtle). The differences in BCI between the nearby aggregations could not be attributed to size and barnacle occurrence differences, suggesting the foraging habitat is the primary factor affecting the body condition of green turtles. Seagrass cover at Kudat Mainland was only slightly higher than at Balambangan Island. These findings suggest that the body condition of green turtles is potentially sensitive to the quality of foraging habitats such as nutrients and water quality. It is crucial to monitor the health of foraging habitats and their impact on the body condition of turtles. It is recommended that habitat‐turtle dynamics are given conservation priority, in parallel to water quality monitoring – with action taken to reduce pollution if necessary. A holistic approach to turtle conservation is therefore required.

Systematically exploring the performance of a self-developed Multi-InDel system in forensic identification, ancestry inference and genetic structure analysis of Chinese Manchu and Mongolian groups

The insertion/deletion (InDel) polymorphism has promising applications in forensic DNA analysis. However, the insufficient forensic efficiencies of the present InDel-based systems restrict their applications in parentage testing, due to the lower genetic polymorphism of the biallelic InDel locus and the limited number of InDel loci in a multiplex amplification system. Here, we introduced an in-house developed system which contained 41 polymorphic Multi-InDel markers (equivalent to 82 InDels in total), to serve as an efficient and reliable tool for different forensic applications in the Manchu and Mongolian groups. We demonstrated that the new system exhibited potential efficiencies for personal identification, parentage testing, two-person DNA mixture interpretation and ancestry inference of intercontinental populations. Meanwhile, we explored the genetic backgrounds of the Manchu and Mongolian groups by conducting a series of population genetic analyses. We showed that the Manchu and Mongolian groups shared closer genetic relationships with East Asian populations, especially Han Chinese populations in northern China. Moreover, more similar genetic compositions were detected between the Manchu group and the northern Han populations in this study, suggesting that the Manchu group had higher genetic affinities with northern Han populations than the Mongolian group. Overall. this study provided the necessary evidence that these Multi-InDel genetic markers could play an important role in forensic applications.

Screening of Mango Landraces for Polyembryony and Confirmation of Seedling Origin using Microsatellite Markers

Background: The introduction of polyembryonic rootstocks in the area of propagation is of great importance since they produce one zygotic and several nucellar plantlets. Proper identification of sexual embryo from each hybrid seed is necessary in order to preserve only the nucellar seedlings, which would help to maintain the rootstock’s genetic characteristics as well as to overcome the major constraints in the area of fruit breeding especially in hybridization programme by eliminating the nucellar ones to advanced generations. Contrasting reports exists regarding the vigour of zygotic seedlings of polyembryonic mango genotypes. It is necessary to identify/ distinguish the zygotic seedling from the nucellar population at an early stage, for which, microsatellite analysis could be a reliable tool. Methods: The experiment was laid out in completely randomized design (CRD) with 20 treatments replicated thrice. The twenty local mango landraces from Thiruvananthapuram (Kerala) were screened for polyembryony and were geo-referenced. Germination studies were conducted. Microsatellite analysis of all the plantlets from two varieties which exhibited the highest polyembryony were done using SSR primers and their banding patterns were compared with those of their respective mother plants. Result: Out of twenty mango varieties screened, seventeen were polyembryonic. Kappa Manga recorded the highest germination, germination index and seedling vigour index-I. Kotookonam Varikka recorded the highest polyembryony and followed by Kochu Kilichundan. Microsatellite analysis revealed that all the seedlings obtained from the respective stones of Kotookonam Varikka and Kochu Kilichundan had identical SSR profile to the mother plant, which indicated nucellar origin of seedlings having similar genetic composition to the mother plant.

Genetic diversity and population structure of Leptosphaeria maculans isolates in Western Canada

Leptosphaeria maculans is a serious concern for canola production worldwide. For effective disease management, knowledge of the pathogen's genetic variability and population structure is a prerequisite. In this study, whole-genome sequencing was performed for 162 of 1590 L. maculans isolates collected in the years 2007–2008 and 2012–2014 in Western Canada. DNA variants in genome-wide and specific regions including avirulence (Avr) genes were characterized. A total of 31,870 high-quality polymorphic DNA variants were used to study L. maculans genetic diversity and population structure. Cluster analysis showed that 150 isolates were clustered into 2 main groups and 4 subgroups by DNA variants located in either Avr or small secreted protein-encoding genes and into 2 main groups and 6 subgroups by genome-wide variants. The analysis of nucleotide diversity and differentiation also confirmed genetic variation within a population and among populations. Principal component analysis with genome-wide variants showed that the isolates collected in 2012–2014 were more genetically diverse than those collected in 2007–2008. Population structure analysis discovered three distinct sub-populations. Although isolates from Saskatchewan and Alberta were of similar genetic composition, Manitoba isolates were highly diverse. Genome-wide association study detected DNA variants in genes AvrLm4-7, Lema_T86300, and Lema_T86310 associated with the years of collection.

Microglial Implications in SARS-CoV-2 Infection and COVID-19: Lessons From Viral RNA Neurotropism and Possible Relevance to Parkinson's Disease.

Since December 2019, humankind has been experiencing a ravaging severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) outbreak, the second coronavirus pandemic in a decade after the Middle East respiratory syndrome coronavirus (MERS-CoV) disease in 2012. Infection with SARS-CoV-2 results in Coronavirus disease 2019 (COVID-19), which is responsible for over 3.1 million deaths worldwide. With the emergence of a second and a third wave of infection across the globe, and the rising record of multiple reinfections and relapses, SARS-CoV-2 infection shows no sign of abating. In addition, it is now evident that SARS-CoV-2 infection presents with neurological symptoms that include early hyposmia, ischemic stroke, meningitis, delirium and falls, even after viral clearance. This may suggest chronic or permanent changes to the neurons, glial cells, and/or brain vasculature in response to SARS-CoV-2 infection or COVID-19. Within the central nervous system (CNS), microglia act as the central housekeepers against altered homeostatic states, including during viral neurotropic infections. In this review, we highlight microglial responses to viral neuroinfections, especially those with a similar genetic composition and route of entry as SARS-CoV-2. As the primary sensor of viral infection in the CNS, we describe the pathogenic and neuroinvasive mechanisms of RNA viruses and SARS-CoV-2 vis-à-vis the microglial means of viral recognition. Responses of microglia which may culminate in viral clearance or immunopathology are also covered. Lastly, we further discuss the implication of SARS-CoV-2 CNS invasion on microglial plasticity and associated long-term neurodegeneration. As such, this review provides insight into some of the mechanisms by which microglia could contribute to the pathophysiology of post-COVID-19 neurological sequelae and disorders, including Parkinson’s disease, which could be pervasive in the coming years given the growing numbers of infected and re-infected individuals globally.

Incursion of Novel Highly Pathogenic Avian Influenza A(H5N8) Virus, the Netherlands, October 2020.

Highly pathogenic avian influenza A(H5N8) virus was detected in mute swans in the Netherlands during October 2020. The virus shares a common ancestor with clade 2.3.4.4b viruses detected in Egypt during 2018–2019 and has similar genetic composition. The virus is not directly related to H5N8 viruses from Europe detected in the first half of 2020.

Currently favored sampling practices for tumor sequencing can produce optimal results in the clinical setting

Tumor heterogeneity is a consequence of clonal evolution, resulting in a fractal-like architecture with spatially separated main clones, sub-clones and single-cells. As sequencing an entire tumor is not feasible, we ask the question whether there is an optimal clinical sampling strategy that can handle heterogeneity and hypermutations? Here, we tested the effect of sample size, pooling strategy as well as sequencing depth using whole-exome sequencing of ovarian tumor specimens paired with normal blood samples. Our study has an emphasis on clinical application—hence we compared single biopsy, combined local biopsies and combined multi-regional biopsies. Our results show that sequencing from spatially neighboring regions show similar genetic compositions, with few private mutations. Pooling samples from multiple distinct regions of the primary tumor did not increase the overall number of identified mutations but may increase the robustness of detecting clonal mutations. Hypermutating tumors are a special case, since increasing sample size can easily dilute sub-clonal private mutations below detection thresholds. In summary, we compared the effects of sampling strategies (single biopsy, multiple local samples, pooled global sample) on mutation detection by next generation sequencing. In view of the limitations of present tools and technologies, only one sequencing run per sample combined with high coverage (100–300 ×) sequencing is affordable and practical, regardless of the number of samples taken from the same patient.

Latency and interval therapy affect the evolution in metastatic colorectal cancer

While comparison of primary tumor and metastases has highlighted genomic heterogeneity in colorectal cancer (CRC), previous studies have focused on a single metastatic site or limited genomic testing. Combining data from whole exome and ultra-deep targeted sequencing, we explored possible evolutionary trajectories beyond the status of these mutations, particularly among patient-matched metastatic tumors. Our findings confirm the persistence of known clinically-relevant mutations (e.g., those of RAS family of oncogenes) in CRC primary and metastases, yet reveal that latency and interval systemic therapy affect the course of evolutionary events within metastatic lesions. Specifically, our analysis of patient-matched primary and multiple metastatic lesions, developed over time, showed a similar genetic composition for liver metastatic tumors, which were 21-months apart. This genetic makeup was different from those identified in lung metastases developed before manifestation of the second liver metastasis. These results underscore the role of latency in the evolutionary path of metastatic CRC and may have implications for future treatment options.

Distinct Gut Microbiota Induced by Different Fat-to-Sugar-Ratio High-Energy Diets Share Similar Pro-obesity Genetic and Metabolite Profiles in Prediabetic Mice.

Gut microbiota play important roles in host metabolism, especially in diabetes. However, why different diets lead to similar diabetic states despite being associated with different microbiota is not clear. Mice were fed two high-energy diets (HED) with the same energy density but different fat-to-sugar ratios to determine the associations between the microbiota and early-stage metabolic syndrome. The two diets resulted in different microbiota but similar diabetic states. Interestingly, the microbial gene profiles were not significantly different, and many common metabolites were identified, including l-aspartic acid, cholestan-3-ol (5β, 3α), and campesterol, which have been associated with lipogenesis and inflammation. Our study suggests that different metabolic-syndrome-inducing diets may result in different microbiota but similar microbiomes and metabolomes. This suggests that the metagenome and metabolome are crucial for the prognosis and pathogenesis of obesity and metabolic syndrome.IMPORTANCE Various types of diet can lead to type 2 diabetes. The gut microbiota in type 2 diabetic patients are also different. So, two questions arise: whether there are any commonalities between gut microbiota induced by different pro-obese diets and whether these commonalities lead to disease. Here we found that high-energy diets with two different fat-to-sugar ratios can both cause obesity and prediabetes but enrich different gut microbiota. Still, these different gut microbiota have similar genetic and metabolite compositions. The microbial metabolites in common between the diets modulate lipid accumulation and macrophage inflammation in vivo and in vitro This work suggests that studies that only use 16S rRNA amplicon sequencing to determine how the microbes respond to diet and associate with diabetic state are missing vital information.

Intra-species variation and geographic differentiation among the populations of the quarantine agricultural pest leucinoides orbonalis (lepidoptera: Crambidae) in the global assemblage – a prospective of DNA barcoding

Leucinodes orbonalis Guenée is serious quarantine pest occurring globally, studies are needed to enlighten the genetic complexities associated with the species. India is considered to be the origin of the L. orbonalis, therefore availability of species records from this region enable to analyse the genetic differences and dispersal of the lineages. The results of the study reported 47 haplotypes in four clusters pertaining to their ancestral lineage. The transition/transversion bias (R) was observed to be higher with 1.238 and 1.312 in the first and third codon positions respectively. The overall intraspecies divergence was found to be 0.302. AMOVA revealed that the total variations were then as reported 67.15 among the south-east countries but our studies reported the total variation to be 77.25% (Germany, India, South east and Australia). FST and Mantel’s test indicated that there was no correlation between the genetic variation and geographical distance. The overall haplotype diversity was 0.852, where the nucleotide diversity of H31 (0.00593) was highest and H1 (0.00087) was lowest. The genetic diversity indices Tajima D and Fu's Fs static for H1, H13 and H31 had negative values which possibly inferred for the bottle neck effect. The ML tree was constituted the branch length of 5.0157 with one out-group. The tree was formed with ten distinctive clades with the haplotypes congregated together based on similar genetic composition.

Whole genome sequencing and function prediction of 133 gut anaerobes isolated from chicken caecum in pure cultures

BackgroundIn order to start to understand the function of individual members of gut microbiota, we cultured, sequenced and analysed bacterial anaerobes from chicken caecum.ResultsAltogether 204 isolates from chicken caecum were obtained in pure cultures using Wilkins-Chalgren anaerobe agar and anaerobic growth conditions. Genomes of all the isolates were determined using the NextSeq platform and subjected to bioinformatic analysis. Among 204 sequenced isolates we identified 133 different strains belonging to seven different phyla - Firmicutes, Bacteroidetes, Actinobacteria, Proteobacteria, Verrucomicrobia, Elusimicrobia and Synergistetes. Genome sizes ranged from 1.51 Mb in Elusimicrobium minutum to 6.70 Mb in Bacteroides ovatus. Clustering based on the presence of protein coding genes showed that isolates from phyla Proteobacteria, Verrucomicrobia, Elusimicrobia and Synergistetes did not cluster with the remaining isolates. Firmicutes split into families Lactobacillaceae, Enterococcaceae, Veillonellaceae and order Clostridiales from which the Clostridium perfringens isolates formed a distinct sub-cluster. All Bacteroidetes isolates formed a separate cluster showing similar genetic composition in all isolates but distinct from the rest of the gut anaerobes. The majority of Actinobacteria clustered closely together except for the representatives of genus Gordonibacter showing that the genome of this genus differs from the rest of Actinobacteria sequenced in this study. Representatives of Bacteroidetes commonly encoded proteins (collagenase, hemagglutinin, hemolysin, hyaluronidase, heparinases, chondroitinase, mucin-desulfating sulfatase or glutamate decarboxylase) that may enable them to interact with their host. Aerotolerance was recorded in Akkermansia and Cloacibacillus and was also common among representatives of Bacteroidetes. On the other hand, Elusimicrobium and the majority of Clostridiales were highly sensitive to air exposure despite their potential for spore formation.ConclusionsMajor gut microbiota members utilise different strategies for gut colonisation. High oxygen sensitivity of Firmicutes may explain their commonly reported decrease after oxidative burst during gut inflammation.

RNA Oncoimmune Phenotyping of HPV-Positive p16-Positive Oropharyngeal Squamous Cell Carcinomas by Nodal Status

Clinical trials that deintensify treatment for patients with suspected human papillomavirus (HPV)-positive oropharyngeal squamous cell carcinoma (OPSCC) use p16 expression to identify HPV-mediated tumors and guide treatment. While p16 staining has a strong correlation with good outcomes, approximately 12% of p16-positive patients have recurrent disease. Biomarkers that reveal tumor-specific characteristics, such as nodal involvement, may change therapy decisions. To assess whether if a tumor-specific genetic signature exists for node-negative vs node-positive HPV 16-positive/p16-positive OPSCCs. This was a retrospective cohort study with randomized case selection for p16 OPSCCs undertaken at a university-based, tertiary care cancer center. Samples were collected from patients with p16-positive OPSCC. A total of 21 HPV 16/p16-positive tumors were used in this study. Gene expression profiles of node-negative vs node-positive tumor samples were evaluated using a differential expression analysis approach and the sensitivity and specificity of a molecular signature was determined. Among the 21 patients in the study (3 women, 18 men; mean [SD] age, 54.6 [9.6] years), 6 had node-negative disease and 15 had node-positive disease. Using differential expression analysis, we found 146 genes that were significantly different in patients with node-negative disease vs those with node-positive disease, of which 15 genes were used to create a genetic signature that could distinguish node-negative-like from node-positive-like disease. The resultant molecular signature has a sensitivity of 88.2% (95% CI, 63.6%-98.5%) and specificity of 85.7% (95% CI, 42.1%-99.6%). The positive likelihood ratio of this signature was 6.1 (95% CI, 1.0-38.2) and the negative likelihood ratio was 0.1 (95% CI, 0.04-0.5). Given this population's prevalence of node-positive disease of 70.8%, the positive- and negative-predicative values for this gene signature were 93.7% (95% CI, 70.8%-98.9%) and 75.0% (95% CI, 44.1%-92.0%), respectively. In addition, we developed a gene signature using agnostic, machine learning software that identified a 40-gene profile that predicts node-negative disease from node-positive disease (area under the curve, 0.93; 95% CI, 0.63-1.00). Many HPV-16 and p16-positive tumors are treated as "lower-risk," but they do not have similar genetic compositions at the biological level. The identification of subgroups with unique expression patterns, such as those with nodal metastases, may guide physicians toward alternative or more aggressive therapies. In our study, unguided clustering suggested that that the larger biological characteristics of a tumor could be a better prognostic biomarker.

Habitat restoration and native grass conservation: a case study of switchgrass (Panicum virgatum)

Switchgrass (Panicum virgatum) has been planted extensively for habitat restoration across the United States, such as with the Conservation Reserve Program (CRP). However, genetic profiles of these populations have never been studied nor compared with those of remnant prairies or cultivars. In this study, we sampled 16 CRP and 17 prairie populations across eastern Kansas. We assessed ploidy levels of all populations and compared genetic diversity and structure of 10 prairies, 10 CRP areas, and 5 standard cultivars, using nine simple sequence repeat (SSR) DNA markers. All CRP and prairie populations were octaploid (8x), except two prairies with both hexaploid (6x) and octaploid (8x) individuals. Based on the results of SSR analyses, there were no significant differences between CRP and prairie populations in genetic diversity, and 94% of total variation was partitioned within populations. Similarities among prairie and CRP populations were also observed in Bayesian clustering algorithms and principal coordinate analysis, suggesting that they had similar genetic compositions. In addition, positive spatial autocorrelations were detected up to 42 and 46 km among prairie and among CRP populations, respectively. To conclude, the CRP and prairie populations shared similar genetic profiles. However, remnant prairies still harbored unique genotypes and a high level of genetic diversity, highlighting the importance of seed sources for restoration efforts, that is using local wild seeds or cultivars from the same geographical region. A popular tetraploid (4x) cultivar known as “Kanlow” was genetically distinct from the prairie populations and therefore is not recommended for habitat restoration in this region.

Taxonomic reassessment of two subspecies of Chinese skink in Taiwan based on morphological and molecular investigations (Squamata, Scincidae).

The Chinese skink, Plestiodon chinensis (Gray, 1838), is widely distributed across continental China, Taiwan, the Korean Peninsula, and offshore islets, and consists of several subspecies. Here morphological and molecular methods have been used to reassess the taxonomic status and distributions of P. c. formosensis (Van Denburgh, 1912) and P. c. leucostictus (Hikida, 1988), which are endemic to Taiwan and Green Island (an islet off the east coast of Taiwan), respectively. It can be confirmed that the eastern Taiwanese populations of P. c. formosensis exhibit similar juvenile color patterning and genetic composition to the islet subspecies P. c. leucostictus, and are distinct from consubspecific populations in western Taiwan. Therefore, the eastern Taiwanese populations are assigned to P. c. leucostictus, and this subspecies is recognized as a distinct species, Plestiodon leucostictus (Hikida, 1988), based on their unique juvenile coloration and highly divergent DNA sequences. Our results also revealed that P. c. formosensis in western Taiwan is close to nominotypical subspecies from the continent, suggesting the necessity of a comprehensive taxonomic analysis in the future.

Genetic and functional diversity of ubiquitous DNA viruses in selected Chinese agricultural soils

Viral community structures in complex agricultural soils are largely unknown. Electron microscopy and viromic analyses were conducted on six typical Chinese agricultural soil samples. Tailed bacteriophages, spherical and filamentous viral particles were identified by the morphological analysis. Based on the metagenomic analysis, single-stranded DNA viruses represented the largest viral component in most of the soil habitats, while the double-stranded DNA viruses belonging to the Caudovirales order were predominanted in Jiangxi-maize soils. The majority of functional genes belonged to the subsystem “phages, prophages, transposable elements, and plasmids”. Non-metric multidimensional analysis of viral community showed that the environment medium type was the most important driving factor for the viral community structure. For the major viral groups detected in all samples (Microviridae and Caudovirales), the two groups gathered viruses from different sites and similar genetic composition, indicating that viral diversity was high on a local point but relatively limited on a global scale. This is a novel report of viral diversity in Chinese agricultural soils, and the abundance, taxonomic, and functional diversity of viruses that were observed in different types of soils will aid future soil virome studies and enhance our understanding of the ecological functions of soil viruses.

The Expansion Route of Ryegrasses (Lolium spp.) into Sandy Coasts in Japan

Although an increasing number of investigations have been made into the evolution of alien species once introduced, few studies have identified the invasion routes of these introduced species. Because multiple introductions are common in invasive species, failing to take into account the introduced lineages can be misleading when studying evolutionary change in alien species after they begin to extend their ranges. In Japan, diverse lineages of ryegrasses (Loliumspp.) were introduced as forage crops and contaminants in trading grain and have expanded to sandy coasts. We studied the expansion route of populations established along the coasts of three geographic regions within Japan by comparing variations in morphology and nuclear microsatellite and chloroplast DNA in the two habitats where ryegrasses were first introduced: croplands and international seaports. Chloroplast DNA haplotypes did not differ significantly among habitats and regions, but the coastal and seaport populations displayed similar microsatellite genetic compositions and morphological characteristics. Our results revealed that coastal populations originated from seaport populations derived from contaminants. Selective forces from the past, including domestication and naturalization, may have assisted the introduced lineages in colonizing new habitats.