High Nucleotide Diversity Research Articles

Comparative plastomes of Pueraria montana var. lobata (Leguminosae: Phaseoleae) and closely related taxa: insights into phylogenomic implications and evolutionary divergence

BackgroundPueraria montana var. lobata (kudzu) is an important food and medicinal crop in Asia. However, the phylogenetic relationships between Pueraria montana var. lobata and the other two varieties (P. montana var. thomsonii and P. montana var. montana) remain debated. Although there is increasing evidence showing that P. montana var. lobata adapts to various environments and is an invasive species in America, few studies have systematically investigated the role of the phylogenetic relationships and evolutionary patterns of plastomes between P. montana var. lobata and its closely related taxa.Results26 newly sequenced chloroplast genomes of Pueraria accessions resulted in assembled plastomes with sizes ranging from 153,360 bp to 153,551 bp. Each chloroplast genome contained 130 genes, including eight rRNA genes, 37 tRNA genes, and 85 protein-coding genes. For 24 newly sequenced accessions of these three varieties of P. montana, we detected three genes and ten noncoding regions with higher nucleotide diversity (π). After incorporated publically available chloroplast genomes of Pueraria and other legumes, 47 chloroplast genomes were used to construct phylogenetic trees, including seven P. montana var. lobata, 14 P. montana var. thomsonii and six P. montana var. montana. Phylogenetic analysis revealed that P. montana var. lobata and P. montana var. thomsonii formed a clade, while all sampled P. montana var. montana formed another cluster based on cp genomes, LSC, SSC and protein-coding genes. Twenty-six amino acid residues were identified under positive selection with the site model. We also detected six genes (accD, ndhB, ndhC, rpl2, rpoC2, and rps2) that account for among-site variation in selective constraint under the clade model between accessions of the Pueraria montana var. lobata clade and the Pueraria montana var. montana clade.ConclusionOur data provide novel comparative plastid genomic insights into conservative gene content and structure of cp genomes pertaining to P. montana var. lobata and the other two varieties, and reveal an important phylogenetic clue and plastid divergence among related taxa of P. montana come from loci that own moderate variation and underwent modest selection.

Structural Characteristics and Phylogenetic Analysis of the Mitochondrial Genomes of Four Krisna Species (Hemiptera: Cicadellidae: Iassinae).

Krisna species are insects that have piercing-sucking mouthparts and belong to the Krisnini tribe in the Iassinae subfamily of leafhoppers in the Cicadellidae family. In this study, we sequenced and compared the mitochondrial genomes (mitogenomes) of four Krisna species. The results showed that all four mitogenomes were composed of cyclic double-stranded molecules and contained 13 protein-coding genes (PCGs) and 22 and 2 genes coding for tRNAs and rRNAs, respectively. Those mitogenomes exhibited similar base composition, gene size, and codon usage patterns for the protein-coding genes. The analysis of the nonsynonymous substitution rate (Ka)/synonymous substitution rate (Ks) showed that evolution occurred the fastest in ND4 and the slowest in COI. 13 PCGs that underwent purification selection were suitable for studying phylogenetic relationships within Krisna. ND2, ND6, and ATP6 had highly variable nucleotide diversity, whereas COI and ND1 exhibited the lowest diversity. Genes or gene regions with high nucleotide diversity can provide potential marker candidates for population genetics and species delimitation in Krisna. Analyses of parity and neutral plots showed that both natural selection and mutation pressure affected the codon usage bias. In the phylogenetic analysis, all subfamilies were restored to a monophyletic group; the Krisnini tribe is monophyletic, and the Krisna genus is paraphyletic. Our study provides novel insights into the significance of the background nucleotide composition and codon usage patterns in the CDSs of the 13 mitochondrial PCGs of the Krisna genome, which could enable the identification of a different gene organization and may be used for accurate phylogenetic analysis of Krisna species.

Genetic Evidence for Colletotrichum gloeosporioides Transmission Between the Invasive Plant Ageratina adenophora and Co-occurring Neighbor Plants.

To understand the disease-mediated invasion of exotic plants and the potential risk of disease transmission in local ecosystems, it is necessary to characterize population genetic structure and spatio-temporal dynamics of fungal community associated with both invasive and co-occurring plants. In this study, multiple genes were used to characterize the genetic diversity of 165 strains of Colletotrichum gloeosporioides species complex (CGSC) isolated from healthy leaves and symptomatic leaves of invasive plant Ageratina adenophora, as well as symptomatic leaves of its neighbor plants from eleven geographic sites in China. The data showed that these CGSC strains had a high genetic diversity in each geographic site (all Hd > 0.67 and Pi > 0.01). Haplotype diversity and nucleotide diversity varied greatly in individual gene locus: gs had the highest haplotype diversity (Hd = 0.8972), gapdh had the highest nucleotide diversity (Pi = 0.0705), and ITS had the lowest nucleotide diversity (Pi = 0.0074). Haplotypes were not clustered by geographic site, invasive age, or isolation source. AMOVA revealed that the genetic variation was mainly from within-populations, regardless of geographic or isolation origin. Both AMOVA and neutrality tests indicated these CGSC strains occurred gene exchange among geographic populations but did not experience population expansion along with A. adenophora invasion progress. Our data indicated that A. adenophora primarily accumulated these CGSC fungi in the introduced range, suggesting a high frequency of CGSC transmission between A. adenophora and co-occurring neighbor plants. This study is valuable for understanding the disease-mediated plant invasion and the potential risk of disease transmission driven by exotic plants in local ecosystems.

Studying Genetic Diversity and Relationships between Mountainous Meihua Chickens Using Mitochondrial DNA Control Region.

The Mountainous Meihua chicken is a unique regional germplasm resource from Tongjiang County, Bazhong City, China, but its genetic structure and evolutionary relationships with other native chicken breeds in the Sichuan region remain unclear. Here, we analyzed a total of 469 sequences, including 199 Mountainous Meihua chicken sequences generated in this study, together with 30 sequences representing 13 clades and 240 sequences from seven different Sichuan local chicken breeds downloaded from NCBI. These sequences were further used to analyze genetic diversity, patterns of population differentiation, and phylogenetic relationships between groups. We show that Mountainous Meihua chicken mtDNA sequences have high haplotypic and nucleotide diversity (0.876 and 0.012, respectively) and with a T bias that is suggestive of good breeding potential. Phylogenetic analysis showed that Mountainous Meihua chickens belong to clades A, B, E, and G and have a low affinity to other chicken breeds, with a moderate degree of differentiation. A non-significant Tajima's D indicates that no demographic expansions occurred in the past. Finally, the four maternal lineages identified in Mountainous Meihua chicken showed unique genetic characteristics.

Population genetics and pedigree geography of Trionychia japonica in the four mountains of Henan Province and the Taihang Mountains

Abstract Objective Human activities and climate change have changed the living environment of species, accelerated the rate of species extinction, and global biodiversity is facing a huge threat. The objective of this study is to determine the resource protection strategy of freshwater planarian by systematically exploring the population genetics and pedigree geography of the planarian population in the four mountain systems of Henan Province and Taihang Mountains. Methods Taking the Japanese planarian in the four mountain systems of Henan Province and Taihang Mountains as an example, DNA was extracted with the help of mitochondrial cytochrome c oxidase subunit I gene (COI), mitochondrial cytochrome b gene (Cytb), and nuclear gene internal transcribed spacer-1 (ITS-1), amplified by polymerase chain reaction and sequenced, and genetic diversity, genetic structure, and pedigree geographical pattern were analyzed by single-gene analysis and polygene joint analysis. Results The corresponding length of Cytb, COI, and nuclear gene ITS-1 sequences in the four mountains of Henan Province is 308, 805, and 632 bp, respectively, and the nucleotide diversity and haplotype diversity are 0.00212 and 0.975, respectively. The gene length of ITS-1 and Cytb in Taihang Mountains is 668 and 315 bp, respectively, with a total length of 984 bp. There are 10 shared haplotypes and 36 unique haplotypes. The values of all nucleic acid diversity and haplotype diversity were 0.00156 and 0.965, respectively, and the genetic variation coefficients between populations and groups were 20.28% and 16.40%, respectively (P < 0.05). Different haplotypes of the four mountain systems in Henan Province and Taihang Mountains are scattered in different geographic populations, and there is no correlation between them and their geographic locations, which is consistent with the results of phylogeny. Conclusion The genetic diversity of Trionychia japonica population in the four mountain systems of Henan Province and Taihang Mountains shows high haploid diversity and low nucleotide diversity, and phylogenetic analysis has not found obvious pedigree geographical pattern.

Population structure and genetic diversity of tobacco mild green mosaic virus variants in Western Anatolia of Turkey

Tobamoviruses have been pioneers in understanding the population genetic structure, host-vector interactions, and evolutionary processes of viruses. To better understand the population genetic structure and molecular evolutionary relationships of tobacco mild green mosaic virus (TMGMV), a significant species of tobamoviruses, extensive analyses were performed using bioinformatics tools in this study. 300 samples were collected from plants exhibiting viruses and virus-like symptoms from Turkey's largest tobacco cultivation areas during the plant vegetation period between 2019 and 2020. Samples were tested using conventional molecular techniques for tobamoviruses, including ToBRFV, TMV, TMGMV, ToMV, and ToMMV species. Single and double tobamovirus infections were determined in 258 of 300 samples. Single infections were 225 (75%), 10 (3.33%), and 1 (0.33%) for TMGMV, TMV, and ToMV, respectively. Double infections were 21 (7.0%) and 1 (0.33%) for TMGMV + TMV and TMV + ToMV, respectively. TMGMV-infected samples from each region were chosen, and their complete genomes were revealed. Detailed analyses were carried out from Turkey, with global variants available in GenBank. Molecular evolutionary analyses revealed three main lineages (Clades I, II, and III) at the p126, p183, MP, and complete genome levels and two main lineages at the CP gene (Clades I and II). Variants from Turkey were distributed in two different branches in other phylogenetic trees, except for the CP gene. High haplotype diversity and low nucleotide diversity were determined in each gene region, indicating consistent genetic stability. In addition, purifying selection pressures were determined in specific gene regions. With AMOVA (analysis of molecular variance), it was determined that the source of genetic variation came from within the main lineages, including various hosts and geographies. The differences in lineages were confirmed by independent test statistics. While neutrality tests revealed population expansions in the CP and MP genes, other p183 and p126 genes revealed bottlenecks or balancing selection. The fact that TMGMV was more common than TMV in Turkey strongly supported the phenomenon called “mutational melting” or “Müller latch,” which presumably causes TMV to disappear from its niche.

High Nucleotide Diversity Accompanies Differential DNA Methylation in Naturally Diverging Populations.

Epigenetic mechanisms such as DNA methylation (DNAme) are thought to comprise an invaluable adaptive toolkit in the early stages of local adaptation, especially when genetic diversity is constrained. However, the link between genetic diversity and DNAme has been scarcely examined in natural populations, despite its potential to shed light on the evolutionary forces acting on methylation state. Here, we analyzed reduced-representation bisulfite sequencing and whole-genome pool-seq data from marine and freshwater stickleback populations to examine the relationship between DNAme variation (between- and within-population) and nucleotide diversity in the context of freshwater adaptation. We find that sites that are differentially methylated between populations have higher underlying standing genetic variation, with diversity higher among sites that gained methylation in freshwater than those that lost it. Strikingly, although nucleotide diversity is generally lower in the freshwater population as expected from a population bottleneck, this is not the case for sites that lost methylation, which instead have elevated nucleotide diversity in freshwater compared with marine. Subsequently, we show that nucleotide diversity is higher among sites with ancestrally variable methylation and also positively correlates with the sensitivity to environmentally induced methylation change. The results suggest that as selection on the control of methylation state becomes relaxed, so too does selection against mutations at the sites themselves. Increased epigenetic variance in a population is therefore likely to precede genetic diversification.

Genetic characterization of human adenoviruses in patients using metagenomic next-generation sequencing in Hubei, China, from 2018 to 2019.

This study aimed to characterize the genomic epidemiology of human adenoviruses (HAdVs) in Hubei, China, using metagenomic next-generation sequencing (mNGS). In total, 25 HAdV-positive samples collected from 21 pediatric patients were sequenced and subjected to mNGS using the NextSeq 550 and GenoLab M sequencing platforms. The metagenomic data were assembled de novo for molecular typing, phylogenetic and recombination analyzes. We assembled 50 HAdV genomes, 88% (22/25) genomes from GenoLab M, and 84% (21/25) genomes from NextSeq 550 have perfect alignments to reference genomes with greater than 90%. The most fully assembled 25 genomes were categorized into 7 HAdV genotypes, the most abundant of which were HAdV-B3 (9/25) and HAdV-C2 (6/25). Phylogenetic analyzes revealed that the newly isolated HAdV-B3 strains diverged into separate clusters according to their genotypes. Vigilance is needed that HAdV-B3 isolates have begun to form new distinct clusters. High nucleotide identity was observed in the whole genome level within the same HAdV genotypes, while marked differences of three capsid genes across HAdV genotypes were noted. The high nucleotide diversity regions were concordant with the reported hypervariable regions. Further, three recombinant strains were identified: S64 and S71 originated from the parental strains HAdV-B14 and HAdV-B11, and S28 originated from HAdV-C1, HAdV-C5, and HAdV-CBJ113. GenoLab M and NextSeq 550 showed comparable performance with respect to data yield, duplication rate, human ratio, and assembly completeness. The sequencing quality and assembly accuracy showed that mNGS assembled genomes can be used for subsequently HAdV genotyping and genomic characterization. The high nucleotide diversity of capsid genes and high frequency of recombination events has highlighted the necessity for HAdV epidemiological surveillance in China.

Genetic Diversity and Population Structure of Anopheles funestus in Western Kenya Based on Mitochondrial DNA Marker COII.

The mitochondrial marker, COII, was employed to assess the genetic structure and diversity of Anopheles funestus, a very important malaria vector in Africa that adapt and colonize different ecological niches in western Kenya. Mosquitoes were collected using mechanical aspirators in four areas (Bungoma, Port Victoria, Kombewa, and Migori) in western Kenya. Following morphological identification, PCR was used to confirm the species. The COII gene was amplified, sequenced, and analyzed to determine genetic diversity and population structure. A total of 126 (Port Victoria-38, Migori-38, Bungoma-22, and Kombewa-28) sequences of COII were used for population genetic analysis. Anopheles funestus had a high haplotype diversity (Hd = 0.97 to 0.98) but low nucleotide diversity (Π = 0.004 to 0.005). The neutrality test revealed negative Tajima's D and Fs values indicating an excess of low-frequency variation. This could be attributed to either population expansion or negative selection pressure across all the populations. No genetic or structural differentiation (Fst = -0.01) and a high level of gene flow (Gamma St, Nm = 17.99 to 35.22) were observed among the populations. Population expansion suggests the high adaptability of this species to various ecological requirements, hence sustaining its vectorial capacity and malaria transmission.

Evolutionary and phylogenetic analyses of 11 Cerasus species based on the complete chloroplast genome.

The subgenus Cerasus, one of the most important groups in the genus Prunus sensu lato, comprises over 100 species; however, the taxonomic classification and phylogenetic relationships of Cerasus remain controversial. Therefore, it is necessary to reconstruct the phylogenetic tree for known Cerasus species. Here, we report the chloroplast (cp) genome sequences of 11 Cerasus species to provide insight into evolution of the plastome. The cp genomes of the 11 Cerasus species (157,571-158,830 bp) displayed a typical quadripartite circular structure. The plastomes contain 115 unique genes, including 80 protein-coding genes, four ribosomal RNAs, and 31 transfer RNAs. Twenty genes were found to be duplicated in inverted repeats as well as at the boundary. The conserved non-coding sequences showed significant divergence compared with the coding regions. We found 12 genes and 14 intergenic regions with higher nucleotide diversity and more polymorphic sites, including matK, rps16, rbcL, rps16-trnQ, petN-psbM, and trnL-trnF. During cp plastome evolution, the codon profile has been strongly biased toward the use of A/T at the third base, and leucine and isoleucine codons appear the most frequently. We identified strong purifying selection on the rpoA, cemA, atpA, and petB genes; whereas ccsA, rps19, matK, rpoC2, ycf2 and ndhI showed a signature of possible positive selection during the course of Cerasus evolution. In addition, we further analyzed the phylogenetic relationships of these species with 57 other congenic related species.Through reconstructing the Cerasus phylogeny tree, we found that true cherry is similar to the flora of China forming a distinct group, from which P. mahaleb was separated as an independent subclade. Microcerasus was genetically closer to Amygdalus, Armeniaca, and Prunus (sensu stricto) than to members of true cherry, whereas P. japonica and P. tomentosa were most closely related to P. triloba and P. pedunculata. However, P. tianshanica formed a clade with P. cerasus, P. fruticosa, P. cerasus × P. canescens 'Gisela 6', and P. avium as a true cherry group. These results provide new insights into the plastome evolution of Cerasus, along with potential molecular markers and candidate DNA barcodes for further phylogenetic and phylogeographic analyses of Cerasus species.

Population Genetic Structure of the Blue Swimming Crab (Portunus pelagicus) Along the Andaman Sea Coast of Thailand

The blue swimming crab (Portunus pelagicus) is a valuable commercial species. In Thailand, the consumption of the blue swimming crab is increasing. To construct an effective sustainable management plan, genetic information is required. Knowledge of natural stock genetic information can help policymakers design fishing and conservation management policies to maintain genetic diversity. In our study, we examined the genetic structure of the blue swimming crab population on the Andaman Sea coast of Thailand. Partial sequences of the mitochondrial DNA control region (mtDNA CR) with a size of 369-371 base pairs were studied in 150 individuals collected from five sampling sites along Thailand's Andaman Sea coast. Seventy-one haplotypes were characterized by 127 polymorphic sites, indicating high haplotype diversity but low nucleotide diversity across five localities. The multiple tests of population genetic analysis showed a lack of genetic structure. The absence of genetic structure was possibly caused by a high level of gene flow due to the larval blue swimming crab's high dispersal ability. Demographic history findings indicate that the blue swimming crab population has expanded. The findings of our study can be used to guide the management of the blue swimming crab in this region of the Andaman Sea to conserve genetic diversity.

Conservation initiatives of Syngnathiformes species in the southern Philippines: What does the mitochondrial DNA signature tell us?

Abstract Mitochondrial DNA signatures based on the control region and 12S rRNA gene were used to assess the impact of conservation measures on the effective management of vulnerable Syngnathiformes (seahorses, pipefishes, and allies) species. Results from phylogenetic inference, polymorphism, neutrality indices, haplotype networks and microhabitat information may justify the establishment of distinct management units for different species. For smooth seahorses, Hippocampus kuda was identified as a species complex that formed three clusters with 20 haplotypes. Based on molecular data, these are the first records of Hippocampus capensis and Hippocampus casscsio in the Philippines. High haplotype diversity (h = 28; Hd = 0.943), yet low nucleotide diversity (Pi:0.18095) for polymorphism, suggests minor differences among haplotypes. Neutrality indices calculated using Tajima's D (−2.00774), with P < 0.05 and Fu's Fs (−11.645), were significant. However, both tests were negative, a signature of rapid population expansion from a small effective population size, which could be attributed to past heavy harvests and habitat destruction, as supported by local data. For pipefishes and their allies, there was high haplotype diversity (h = 22; Hd = 0.875) and low nucleotide diversity of Pi: 0.16671. However, neutrality indices calculated using Tajima's D (−1.68518) and Fu's Fs (11.549) were not significant, with P > 0.05, indicating a balancing selection for this population. Results reveal that the recent population expansion of seahorses proves that current conservation measures are effectively safeguarding populations, while balancing selection is maintaining genetic polymorphism in pipefishes and their relatives, making them resilient to changing environments. Moreover, as revealed by haplotype networks, intraspecific variation suggests distinct management for different species. In addition, underwater surveys show an essential association between microhabitats and species' survival, thus encouraging future initiatives regarding habitat protection, especially coral reefs, seagrass beds, sponge gardens, mangrove areas and estuaries.

Phylogeography of the Altai weasel (Carnivora: Mustelidae:Mustela altaica) based on an analysis of mitochondrial control-region haplotypes

AbstractThe phylogeography of the Altai weasel (Mustela altaica) based on mitochondrial control-region sequences was investigated using samples from individuals obtained widely across the species range, including Central Asia, Tibet and southern Siberia. Thirty-four haplotypes were identified among 53 individuals from 32 localities. A maximum-likelihood phylogenetic tree for haplotypes showed two major clades, clades I and II. Clade I contained haplotypes from northern Eurasia, including the continental Far East, Altai Mountains and eastern Kazakhstan. Clade II comprised two subclades: group IIa, with haplotypes from around the Pamir Mountains, and the poorly supported group IIb, with haplotypes from the Tibetan Plateau. High haplotype diversity and low nucleotide diversity for clade I suggest that the range of M. altaica expanded over a relatively short period in northern Eurasia. High haplotype and nucleotide diversity for clade II indicate a longer-term, more stable population resulting from geographical isolation of individuals on the Tibetan Plateau by surrounding mountain ranges. Our study suggests that the ancestral population of M. altaica migrated into Tibet from the outside and has diversified in Tibet, seemingly not supporting the ‘out-of-Tibet’ hypothesis; however, we could not completely refute this hypothesis because an individual having a group IIb haplotype was detected in Mongolia.

Genetic diversity and structure of Callosobruchus maculatus populations in the different agro-ecological zones of Senegal

The objective of this study is to determine the diversity and genetic structure of cowpea weevil populations in the different agro-ecological zones of Senegal. Thus, to achieve this objective, individuals of Callosobruchus maculatus from localities in each zone were used, after sampling and massive breeding. The sequenced gene is Cyt-B. The results showed high haplotypic diversity (0.901 ±0.00033) and low nucleotide diversity (0.010 ±0.0000003). These diversities studied by agro-ecological zone show that the Casamance zone has the greatest haplotypic diversity (0.901; P>0.05) while the eastern Senegal zone has the lowest value (0.439; P>0.05). The nucleotide diversity is lower in the Sylvo-pastoral zone (0.00112; P<0.05) and higher in the Casamance zone (0.01052; P<0.05). The genetic structuring shows that the Senegal River Valley-eastern Senegal zone couple is more differentiated [FST(Fixation index)]=0.70687; P<0.05) and the Casamance-Groundnut Basin zone couple is less differentiated (FST=0.21248; P<0.05). The greatest genetic distance was found between the Sylvo-pastoral zone and the River Valley and the smallest between the eastern Senegal zone and the River Valley. However, a significant genetic variation within the populations was noted (64.93%). Overall we have a low level of diversity and weakly structured populations except those of Tamba and Fouta. A slight influence of the zones was also noted.

The mitochondrial genomes of the Geometroidea (Lepidoptera) and their phylogenetic implications.

The Geometroidea is a large superfamily of Lepidoptera in species composition and contains numerous economically important pest species that cause great loss in crop and forest production. However, understanding of mitogenomes remains limited due to relatively fewer mitogenomes previously reported for this megadiverse group. Here, we sequenced and annotated nine mitogenomes for Geometridae and further analyzed the mitogenomic evolution and phylogeny of the whole superfamily. All nine mitogenomes contained 37 mitochondrial genes typical in insects, and gene organization was conserved except for Somatina indicataria. In S.indicataria, the positions of two tRNAs were rearranged. The trnR was located before trnA instead of after trnA typical in Lepidoptera, whereas the trnE was detected rarely on the minority strand (N-strand). This trnR-trnA-trnN-trnS1-trnE-trnF newly recognized in S.indicataria represents the first gene rearrangement reported for Geometroidea and is also unique in Lepidoptera. Besides, nucleotide composition analyses showed little heterogeneity among the four geometrid subfamilies involved herein, and overall, nad6 and atp8 have higher nucleotide diversity and Ka/Ks rate in Geometridae. In addition, the taxonomic assignments of the nine species, historically defined by morphological studies, were confirmed by various phylogenetic analyses based on the hitherto most extensive mitogenomic sampling in Geometroidea.

Polymorphism and Differentiation of the Evoron Vole Three Populations according to the mtDNA Control Region Variability

As a result of the control region mtl DNA analysis for the Evoron vole, a high haplotype (97%) and nucleotide (1.53%) diversity was found. The data obtained indicate a low level of genetic differentiation populations. At the same time, populations geographically located closer are subdivided more strongly than remote ones. In general, there is agreement between the data on the variability of the mitochondrial DNA control region and chromosome races. However, if the data of chromosomal analysis indicate the preservation of the karyotype more ancient variants in the Evoron-Chukchagir lowland (“evoron” chromosomal race), then the data of molecular genetic analysis testify in favor of the preservation of the most ancient mt haplotype (106-19) in the upper Bureya depression population (“argi” chromosomal race).

Genetic Diversity of Jinshaia sinensis (Cypriniformes, Balitoridae) Distributed Upstream of the Yangtze River

The upper reaches of the Yangtze River (upper YR) are a biological zone with extremely rich fish diversity, especially endemic fish. However, long-term human interference, such as environmental pollution and cascade hydropower construction, has significantly changed the habitat of many fish and is threatening the number and genetic diversity of fish populations. Jinshaia sinensis is a typical small and endemic but rare fish that is found in the upper YR, and its genetic diversity and structure still need further study. To understand the current levels of genetic diversity in J. sinensis, we analyzed the genetic diversity, population history, genetic structure, etc., of three J. sinensis populations based on two mitochondrial genes (the cytochrome-c oxidase subunit I, COI, and cytochrome-b gene, Cytb) and two nuclear genes (recombination-activating protein 1, RAG1, and rhodopsin, RH). The genetic diversity analysis indicated that J. sinensis had high genetic diversity, with high haplotype diversity (h) and nucleotide diversity (Pi). Population pairwise FST analysis revealed a significant genetic divergence between the Lijiang and Luzhou populations for all genes and between the Panzhihua and Luzhou populations, except for the COI gene; however, analyses of molecular variance (AMOVA) showed no significant geographic genetic structure among populations, and gene flow analysis also indicated a certain degree of gene exchange among populations. Haplotype network structure analyses revealed low levels of shared haplotypes among populations. Neutrality test and mismatch distribution results indicated that only the Lijiang population had experienced obvious population expansion. Overall, these results indicate that J. sinensis is still a single evolutionarily significant unit, but when considering the threat of habitat disturbance to the population, it is still necessary to carry out long-term genetic monitoring on J. sinensis and on other endemic fishes with similar ecological habits in order to maintain the genetic diversity of fishes in the upper YR.

Morphological characterization and genetic diversity of a new microsporidium, Neoflabelliforma dubium n. sp. from the adipose tissue of Diaphanosoma dubium (Crustacea: Sididae).

We reported a new microsporidium Neoflabelliforma dubium n. sp. from the adipose tissue of Diaphanosoma dubium in China. The infected daphnids generally appeared opaque due to the presence of numerous spore aggregates located in the adipose tissue. All developmental stages were in direct contact with the host cell cytoplasm. Multinucleate sporogonial plasmodia developed into uninucleate sporoblasts by rosette-like fashion. Mature spores were pyriform and monokaryotic, measuring 4.02 ± 0.24 (3.63-4.53) µm long and 2.27 ± 0.15 (2.12-2.57) µm wide (N = 40). The polaroplast was bipartite with a tightly packed anterior lamellae and a loosely aligned posterior lamellae. Isofilar polar filament was coiled 9-11 turns and arranged in 2-3 rows. The phylogenetic analysis based on the obtained SSU rDNA sequence indicated that the N. dubium n. sp. clustered with the freshwater oligochaete-infecting N. aurantiae to form an independent monophyletic group, positioned at the base of Clade 4. In addition, we analyzed the genetic diversity in three N. dubium n. sp. isolates based on the rDNA (SSU rDNA, ITS and LSU rDNA) and Rpb1 gene. The genetic variation among the rDNA sequences was not distinct, however, high nucleotide diversity could be observed in Rpb1 gene, and a wide variety of Rpb1 haplotypes were identified within each isolate. Genetic recombination detected in the Rpb1 sequences presumes cryptic sexual process occurring in N. dubium n. sp. Statistical evolutionary analyses further indicated that the purifying selection eliminated mutations in the Rpb1 gene.

Genomic data reveal contrasting patterns of divergence among island and mainland birds of the Eastern Mediterranean

Islands have been characterized as natural laboratories because of their distinct and often identifiable role in promoting genetic variation and population differentiation, but they have also been considered evolutionary sinks of biodiversity. Here, we extend classical studies of island biogeography based in the Eastern Mediterranean to compare genetic divergences and population structure among birds in insular and continental populations. We focused on populations of six passerine species (Short‐toed Treecreeper, Great Tit, Eurasian Wren, Eurasian Blackbird, Common Chaffinch and Sardinian Warbler) with breeding populations on the islands of Cyprus and Crete and compared those with a continental population from mainland Greece. We sampled 172 individuals from six species and used double‐digest RAD sequencing to examine population‐level genetic divergence and structure. Population structure analyses using single nucleotide polymorphisms revealed structure between the islands and mainland for all six species, and this was most pronounced in Short‐toed Treecreeper, Great Tit and Eurasian Wren. For all species with the exception of the Sardinian Warbler, the populations from the two islands were more differentiated from each other than either was from mainland Greece, reflecting variation in island colonization dynamics. Patterns ranged from pronounced population differentiation among populations, e.g. in Short‐toed Treecreeper, where taxonomic revisions are potentially warranted, to others with weak structure among insular and continental populations, such as in Common Chaffinch and Sardinian Warbler. Although some patterns are consistent with increased rates of genetic drift in smaller populations explaining greater differences among the island populations than either insular population has from continental source populations, in others, including in Eurasian Blackbird and Common Chaffinch, higher nucleotide diversity in Cyprus may reflect a demographic pattern of post‐glacial north‐westward expansion.

Meloidogyne graminicola Population Structure in China Suggests a South-to-North Expansion.

The distribution range of root-knot nematode Meloidogyne graminicola is rapidly expanding, posing a severe threat to rice production. In this study, the sequences of cytochrome oxidase subunit I (COI) genes of rice M. graminicola populations from all reported provinces in China were amplified and sequenced by PCR. The distribution pattern and phylogenetic tree showed that all 54 M. graminicola populations in China have distinct geographical distribution characteristics; specifically, cluster 1 (southern China), cluster 2 (central south and southwest China), and cluster 3 (central and eastern China). The high haplotype diversity (Hd = 0.646) and low nucleotide diversity (π = 0.00682), combined with the negative value of Tajima's D (-1.252) and Fu's Fs (-3.06764), suggested that all nematode populations were expanding. The existence of high genetic differentiation (Fst = 0.5933) and low gene flow (Nm = 0.3333) indicated that there was a block of gene exchange between most populations. Mutation accumulation with population expansion might be directly responsible for the high genetic differentiation; therefore, the tested nematode population showed high within-group genetic variation (96.30%). The haplotype Hap8 was located at the bottom of the network topology, with the widest distribution and the highest frequency (59.26%), indicating that it was the ancestral haplotype. The populations in cluster 3 were newly invasive according to the lowest frequency of occurrence of Hap8, the highest number of endemic haplotypes, and the highest total haplotype frequency (60%). In contrast, cluster 1 having the highest genetic diversity (Hd = 0.772, π = 0.01127) indicated that it was the most primitive. Interestingly, the highest gene flow (Nm > 1), lowest genetic differentiation (Fst ≤ 0.33), and closest genetic distance (0.000) only occurred between the Guangdong/Hainan population and others, which suggested that there might be channels for gene exchange between them and that long-distance dispersal occurred. This suggestion is further confirmed by the weak correlation between genetic distance and geographical distance. Based on these data, a hypothesis can be drawn that M. graminicola populations in China were spreading from south to north, specifically from Guangdong and Hainan Provinces to other regions. Natural selection (including anthropogenic) and genetic drift were the main drivers of their evolution. Coincidentally, this hypothesis was consistent with the gradual warming trend and the chronological order of reporting these populations. The main factors influencing current M. graminicola population expansion and distribution patterns might be geography, climate, long-distance seedling transport, interregional operations of agricultural machinery, and rotation mode. It reminds human beings of the necessity to be vigilant about preventing nematode disease according to local conditions all year round.