DnaSP, DNA polymorphism analyses by the coalescent and other methods

A phylogeographic approach of three species of Clinostomum Leidy, 1856, (Trematoda: Clinostomidae) from the Neotropical region of Mexico, with the description of a new species from Ardea herodias (Ardeidae)

Clinostomum Leidy, 1856 is a globally distributed group of endoparasites that reside attached to the mucosa of the mouth cavity and oesophagus of fish-eating birds (mainly herons) in the adult stage, whereas larvae known as metacercariae ("yellow grubs") damage freshwater fish and amphibians that serve as secondary intermediate hosts. In the Nearctic and Neotropical regions of Mexico, species of the genus Clinostomum have been intensively studied, revealing seven species that share a common ancestor. In the present study, sequences of the ITS from nuclear ribosomal DNA and cox 1 from mitochondrial DNA were generated for C. tataxumui, C. cichlidorum, and an unidentified species identified as lineage 3 sensu Pérez-Ponce de León et al. 2026, which is distributed sympatrically in Mexico and Middle America. The objectives of the present study were to 1) describe a new species of Clinostomum, named herein as Clinostomum chaacci n. sp., which combines morphological and molecular characters; 2) analyse the population genetic structure of two previously described species in addition to C. chaacci n. sp.; and 3) infer phylogeographic patterns using cox 1 sequences. The inferred phylogeographic results indicated that the populations of C. tataxumui, and C. cichlidorum lack a geographic structure with high haplotype diversity, low nucleotide diversity, and low Fst values among the populations with negative values on the neutrality test, suggesting that the populations are expanding. In contrast, the populations of C. chaacci n. sp., are less connected and subdivided into smaller populations, leading to slight genetic differentiation, suggesting that the populations have undergone significant demographic changes, such as recent expansion or selection effects.

Deciphering the First Mitochondrial Genome of the Liolophura Pilsbry, 1893 Genus: An Extensive Phylogenetic Study Within the Chitonidae Family

Background: The Polyplacophora class, which includes all chitons, is distinguished by its unique eight-piece interlocking armor, showcasing a vast diversity in marine environments. However, the detailed evolutionary relationships within the Chitonidae family remain largely unknown. The mitochondrial genome is essential for understanding these relationships, but there has been a significant lack of such genomic information, especially for the Liolophura genus. Methods: We generated the first mitogenome of Liolophura japonica by assembling Illumina reads with GetOrganelle, polishing with Pilon, annotating genes with MitoZ and MITOS2, and inferring phylogeny from 13 concatenated protein-coding genes (PCGs) using MAFFT and IQ-TREE. Results: The mitogenome is 15,209 base pairs long and includes 13 protein-coding genes, 22 transfer RNAs, and 2 ribosomal RNAs. The mitogenome exhibited a slight AT bias common in Chitonidae and showcased structural uniqueness with no control region found. Notably, all protein-coding genes demonstrated evidence of purifying selection, with Ka/Ks ratios below 1, highlighting evolutionary conservation. Phylogenetic analysis reveals a close relationship between L. japonica, Acanthopleura loochooana Broderip & Sowerby 1829, and Acanthopleura vaillantii Rochebrune, 1882, potentially warranting future taxonomic re-evaluation. This research emphasizes the crucial role of mitochondrial genomes in mollusk phylogeny and sets the stage for advanced genetic studies within this group. Conclusions: The significance of this study lies in its contribution to understanding the mitochondrial genome of L. japonica, a key species within the Polyplacophora class. By analyzing its mitogenome, we aim to enhance our understanding of evolutionary processes in chitons and other mollusks.

Allelic variation in a cluster of epsilon glutathione S-transferase genes contributes to DDT and pyrethroid resistance in the major African malaria vector Anopheles funestus

BACKGROUND

Insecticide resistance in malaria vectors is a serious challenge to malaria control and elimination. Elucidation of the role of detoxification genes in resistance is necessary to develop targeted strategies to reduce malaria burden. Glutathione S-transferase epsilon clusters (GSTe genes) are upregulated in DDT- and pyrethroid-resistant Anopheles funestus mosquitoes across Africa. However, except for GSTe2, the molecular mechanisms behind this upregulation remain unclear. Here, we established that overexpression and allelic variation of GSTe genes contribute to insecticide resistance in African malaria vector An. funestus s.s.

METHODS

Transcriptomic and genomic analyses of GSTe genes were conducted, followed by in silico structural analysis, and functional characterization of GSTe3, GSTe4 and GSTe6 using metabolic assay and transgenic expression in Drosophila flies.

RESULTS

Transcriptomic and genomic analyses reveal changes in gene expression and genetic diversity of GSTes cluster in An. funestus across Africa. Cloning of cDNAs of GSTes from different regions of Africa detected allelic variants under selection, including A17D26T158-GSTe3, L135H191A189-GSTe4 in West/Central Africa, and T169S201 E210-GSTe6 present only in West/Southern Africa. Furthermore, in silico analysis of BN-GSTe3, MWI-GSTe3, BN-GSTe4, MWI-GSTe4, CMR-GSTe6 and, BN-GSTe6 alleles revealed that allelic variations increase the binding cavity in the active site of these GSTes with stronger affinities observed towards DDT and permethrin. All recombinant GSTes significantly metabolize DDT (41-63%) and permethrin (13-25%). Additionally, BN-GSTe4 (L135H191A189-GSTe4) variant significantly metabolizes deltamethrin (28.75%), compared to the wild-type allele (15.99%; p < 0.05). Transgenic expression of the GSTes in Drosophila melanogaster flies revealed reduced DDT mortalities in flies expressing the selected alleles (39-55%; p˂0.001), compared to control group (98%). Similar resistance patterns were observed toward permethrin and deltamethrin.

CONCLUSION

These findings established the role of GSTes in conferring cross-resistance to pyrethroids and DDT, highlighting the role of these genes in metabolic resistance in An. funestus, which complicates malaria control using the above key insecticides.

Introgression and Genetic Diversity Between Two Cactophilic Drosophila (Drosophila repleta group) Species: A Case Study of an Isolated Population from the Sandstone Hills in the Southeast of Brazil

Introgressive hybridization involves the integration of genetic material from one population into another genetically distinct population. Despite its widespread occurrence in nature, the mechanisms and consequences of introgression remain poorly understood. In this study, we examine the hypothesis that the mitochondrial gene COI from Drosophila antonietae has been introgressed into the gene pool of a specific population of D. gouveai. Additionally, we extended our analysis to include other genes associated with the COX complex, such as mitochondrial (COII) and nuclear genes (CoVa, CG9603, and levy), across various populations of both species from different locations. We estimated indices of genetic diversity, constructed haplotype networks in both mitochondrial and nuclear genes, and performed selection tests to assess the evolutionary dynamics of mitochondrial genes. Our results confirm the hypothesis of a historical secondary contact between D. gouveai and D. antonietae in the region of Analândia, SP, showing asymmetric unidirectional introgression, with signs of positive selection in the mitochondrial genes.

The Evolutionary History of the Extinct Baltic Sea Harp Seal Population

The now-extinct harp seal population that inhabited the Baltic Sea from the Mesolithic to the Iron Age is an enigma. It occurred outside the species' contemporary Arctic range, likely deviated from typical harp seal migratory behaviour, and experienced body size reductions and dramatic population fluctuations leading up to its extinction. Here we use ancient DNA analyses to shed more light on the evolutionary history of the Baltic Sea harp seal population, including its origin, timing of colonisation, diversity and factors contributing to its demise. We generated 49 ancient Baltic and eight ancient Arctic harp seal mitogenomes, which we analysed together with 53 contemporary Arctic harp seal mitogenomes. We detected limited phylogeographic resolution among ancient and contemporary populations, which we interpret as a late Pleistocene range expansion from a common refugial population with subsequent gene flow. Ancient Baltic harp seals were significantly genetically differentiated from contemporary harp seal populations and retained their own genetic composition throughout time. The genetic diversity of Baltic harp seals decreased over time, yet was comparable to that of contemporary populations. This suggests that Baltic harp seals formed a distinct breeding population, which may occasionally have received immigrants from the Arctic but was itself confined in the Baltic Sea until the end. We hypothesise that loss of genetic diversity and the ultimate extinction of the Baltic harp seal population was a consequence of population fluctuations caused by climatic change, reduced salinity and biological productivity, and periodic intense human harvest.

Developing a crop- wild-reservoir pathogen system to understand pathogen evolution and emergence

Crop pathogens reduce yield and contribute to global malnourishment. Surveillance not only detects presence/absence but also reveals genetic diversity, which can inform our understanding of rapid adaptation and control measures. An often neglected aspect is that pathogens may also use crop wild relatives as alternative hosts. This study develops the beet (Beta vulgaris) rust (Uromyces beticola) system to explore how crop pathogens evolve to evade resistance using a wild reservoir. We test predictions that crop selection will drive virulence gene differentiation and affect rates of sex between crop- and wild-host rust populations. We sequenced, assembled, and annotated the 588 Mb beet rust genome, developed a novel leaf peel pathogen DNA extraction protocol, and analysed genetic diversity in 42 wild and crop isolates. We found evidence for two populations: one containing exclusively wild-host isolates; the other containing all crop-host isolates, plus five wild isolates. Effectors showed greater diversity in the exclusively wild population and greater differentiation between populations. Preliminary evidence suggests the rates of sexual reproduction may differ between populations. This study highlights how differences in pathogen populations might be used to identify genes important for survival on crops and how reproduction might impact adaptation. These findings are relevant to all crop-reservoir systems and will remain unnoticed without comparison to wild reservoirs.

Molecular Characterization and Analysis of Human Trichostrongylus Species in an Endemic Region of Iran Based on COX 1 Gene; A Cross-Sectional Study

Background and Aims

Trichostrongylus species are the causative agents of zoonotic disease, which has been frequently reported from animals in Iran. The aim of this study was to identify, molecular characterization and analysis of Trichostrongylus species isolated from humans, in an endemic region, based on cytochrome c oxidase (COX) 1.

Methods

A total of 206 fresh stool samples were collected from residents of endemic villages of sampling area. All samples had been examined using conventional parasitological methods, along with the PCR technique. After amplification and sequencing of a discriminative region of COX1 gene, the phylogeny relationship, haplotype network, and molecular diversity between Trichostrongylus spp., were scrutinized using PopART networking, DnaSP v.6, and MEGA10 software.

Results

In total, from 206 fecal samples, 71 people (34.4%) were infected with Trichostrongylus spp. The ~700-bp fragment of the COX1 was amplified in all 71 morphological positive samples, however, 33 samples were successfully sequenced, belonging to Trichostrongylus spp. In this study, T. colubriformis was the predominant species and one sequence was characterized as T. vitrinus. Our sequences were grouped together with sequences, which were obtained from animals in the same region (97.17% similarity). In total, 26 haplotypes were identified and haplotype diversity ranged from 0.988 ± 0.012.

Conclusions

In view of the importance of Trichostrongylosis to public health as zoonotic infection, information about its prevalence in animal and human populations can provide valuable information on how different types of this parasite are transmitted between people and animal's host.

Identification of Hybrid Sturgeon (Acipenser baerii × Acipenser schrenckii) from Their Parents Using Germplasm

The hybrid sturgeon Acipenser baerii × A. schrenckii is the most widely cultured commercial sturgeon in China. However, its morphological similarity to the parental species frequently leads to misuse of germplasm in the breeding process, resulting in a decline in the quality of the sturgeon production. In this study, we have developed a protocol by using mitochondrial DNA barcoding and microsatellite locus analysis for the accurate identification of sturgeon species. Genetic distance and phylogenetic analysis based on the mitochondrial COI segment showed that A. baerii exhibited the closest genetic relationship with orthogonal individuals A. baerii (♀) × A. schrenckii (♂). Conversely, A. schrenckii displayed the highest genetic similarity with reciprocal individuals A. schrenckii (♀) × A. baerii (♂). Additionally, genetic structure analysis and factor correlation analysis (FCA) were conducted using six microsatellite loci among 100 samples, including eight species and two hybrid sturgeon. The results showed that all samples, encompassing both hybrid sturgeon (A. baerii × A. schrenckii) and their parental species, were accurately grouped into ten clusters, thereby validating the precision of this species assignment method.

Population Genetic Diversity and Viability of the North China Leopard (Panthera pardus japonensis) in the Eastern Loess Plateau, China

The North China leopard population in the eastern Loess Plateau, China, is highly fragmented and faces an increased risk of extinction due to habitat loss and environmental change. Therefore, timely research on leopard conservation in the Loess Plateau region can provide scientific guidance for its management and population recovery. To investigate the impacts of habitat fragmentation on genetic diversity, we analyzed 129 fecal samples from the eastern foot of the Loess Plateau, China. Using eight pairs of microsatellite loci and mitochondrial ND-5 gene sequences, we genetically identified 41 individual leopards. Analysis of microsatellite data showed an intermediate level of genetic diversity (PIC = 0.60). Based on the ND-5 gene sequence, five haplotypes were identified, with a moderate level of genetic diversity (Hd = 0.23, Pi = 0.00048). Inbreeding analyses documented significant population inbreeding pressure. Using VORTEX, we also explored the future development of the population by analyzing the population viability. The results indicated no extinction risk for the leopard population in the next 100 years under current genetic conditions. However, a loss of 22% genetic diversity is expected. These results emphasize the need to strengthen leopard monitoring, mitigate inbreeding, and restore habitat connectivity to preserve genetic diversity.

Unraveling the Evolutionary Tales of Yunnanopilia longistaminea (Opiliaceae): Insights from Genetic Diversity, Climate Adaptation, and Conservation Strategies

The evolutionary history of Yunnanopilia longistaminea, a vulnerable plant endemic to the Yuanjiang-Honghe River Valley in southwestern China, was investigated using cpDNA and nrDNA sequences along with ecological niche modeling. Understanding the genetic diversity and population structure of Y. longistaminea is crucial for developing effective conservation strategies and managing its genetic resources. This study comprehensively sampled 295 individuals from 16 populations, which represent the species' entire global distribution range, ensuring a thorough and representative analysis of its genetic diversity and population structure. The results revealed high genetic diversity and population structure, with significant genetic differentiation among populations. Specifically, the total nucleotide diversity was 2.40 × 10-3 for cpDNA and 1.51 × 10-3 for nrDNA, while the total haplotype diversity was 0.605 for cpDNA and 0.526 for nrDNA. The divergence time of ancestral haplotypes of Y. longistaminea was estimated to be around 2.19 million years ago based on nrDNA and 2.72 million years ago based on cpDNA. These divergence times are comparable to those of other ancient plant species, suggesting a long evolutionary history. The population size of Y. longistaminea was found to have significantly declined around 30,000 years ago. The current distribution model suggests that Y. longistaminea primarily inhabits the warm temperate zone of China, and the LGM distribution model predicts a concentration of the species in Yuanjiang-Honghe River Valley in southwestern China. This study concludes that the southwestern region of China may have served as a glacial refuge for Y. longistaminea. These findings suggest that establishing protected areas in these regions and creating gene banks for ex situ conservation could be effective strategies to preserve the genetic diversity of Y. longistaminea. Further research on its population dynamics and genetic adaptation to climate change is valuable for understanding the species' evolutionary history and conservation.

Comprehensive Chloroplast Genomic Insights into Amaranthus: Resolving the Phylogenetic and Taxonomic Status of A. powellii and A. bouchonii

Amaranthus, a genus in Amaranthaceae, is divided into three subgenera-Amaranthus, Acnida, and Albersia-and contains approximately 70 to 80 species. Understanding its phylogenetic relationships is essential for species classification, genetic diversity assessment, and evolutionary studies. This knowledge is vital for improving Amaranthus utilization in crop improvement and managing the ecological impacts of invasive weeds. In this study, we analyzed the chloroplast genomes of 27 Amaranthus species across all three subgenera to characterize their genomic features and construct a comprehensive phylogenetic tree. Our aim was to elucidate the phylogenetic relationships within the genus and evaluate interspecific affinities among the subgenera. We also addressed the taxonomic ambiguity surrounding A. bouchonii and A. powellii to determine their distinct species within the genus. Chloroplast genome sizes ranged from 149,949 to 150,818 bp, with GC content varying between 36.52% and 36.63%. Comparative structural analyses confirmed highly conserved quadripartite structures, gene content, and organization, comprising 87 protein-coding genes, 37 tRNAs, and 8 rRNAs. Repeat and codon usage analyses revealed conserved repeat patterns and a preference for codons ending in A or U. Selection pressure analysis indicated a predominantly purifying selection, with matK showing signs of positive selection, particularly in A. spinosus. Phylogenetic analysis of 80 protein-coding genes confirmed the monophyly of subgenus Amaranthus but found Alberisa and Acnida to be paraphyletic. Despite their morphological similarity, A. bouchonii and A. powellii were placed in separate clades within subgenus Amaranthus, with A. bouchonii clustering with A. retroflexus, and A. powellii aligning with the A. hybridus complex. Additionally, we identified 16 variable regions as potential molecular markers for species identification. Our study provides the most comprehensive Amaranthus chloroplast genome dataset to date, offering new insights into its evolutionary relationships and valuable genomic resources for taxonomy, germplasm management, and invasive risk assessment.

The population chloroplast genomes of Populus reveal the phylogenetic relationship between three new taxa of sect. Leucoides and their parents

BACKGROUND

Poplars are important woody plants, which are widely distributed in the forests from the subtropics to the north of the Northern Hemisphere. Poplars have high ecological and economic value. However, there are frequent interspecific and intraspecific hybrids in Populus, resulting in a large number of intermediate taxa, which makes the morphological identification of Populus very challenging. Plastid genome is an important tool to study the evolutionary relationship of plants. Therefore, comparison and phylogenetic analysis were carried out based on the population chloroplast genomes of 34 individuals from 7 taxa.

RESULTS

In this study, seven newly assembled and annotated chloroplast genomes of Populus were reported. They all had typical quadripartite structures with the same GC content (37.6%), but there were differences within the population, and the genome size ranged from 155,736 bp to 156,812 bp. In all Populus species, 134 genes were identified, including 88 protein coding genes (PCGs), 37 tRNA and 8 rRNA genes. The gene sequences alignment of different taxa showed that the gene sequences and content were relatively conservative, there was no gene rearrangement, and only 3 highly variable regions (psbZ-trnG, ndhC-trnV and trnN-trnR) were identified, which can be used as molecular markers. Most PCGs had high codon usage bias and 3 positive selection genes (rps7, rps12 and rpl16) have been identified. The analysis of population genetic structure and phylogeny showed that the chloroplast genomes supported that Populus was a monophyletic taxon, which could be divided into four sections (Abaso, Turanga, Populus and ATL (Aigeiros, Tacamahaca and Leucoides)). Among them, P. dafengensis, P. butuoensis and P. szechuanica had the closest genetic relationship, P. gonggaensis and P. cathayana had the closest genetic relationship, it was speculated that the taxa of Sect. Tacamahaca may be the main female parent of the three new taxa from Sect. Leucoides.

CONCLUSION

In general, this study provides valuable insights for new species identification, phylogenetic relationships, breeding and resource development, and genetic diversity of Populus.

Virulence and Genetic Diversity of Puccinia spp., Causal Agents of Rust on Switchgrass (Panicum virgatum L.) in the USA

Switchgrass (Panicum virgatum L.) is an important cellulosic biofuel grass native to North America. Rust, caused by Puccinia spp. is the most predominant disease of switchgrass and has the potential to impact biomass conversion. In this study, virulence patterns were determined on a set of 38 switchgrass genotypes for 14 single-spore rust isolates from 14 field samples collected in seven states. Single nucleotide polymorphism (SNP) variation was also assessed in 720 sequenced cloned amplicons representing 654 base pairs of the elongation factor 1-α gene from the field samples. Five major haplotypes were identified differing by 11 out of the 39 SNP positions identified. STRUCTURE, Principal Coordinate Analysis, and phylogenetic analyses divided the rust population into two genetic clusters. Virginia and Georgia had the highest and lowest rust genetic diversity, respectively. Only nine accessions showed a differential disease response between the 14 isolates, allowing the identification of eight races, differing by 1-3 virulence factors. Overall, the results suggested clonal reproduction of the pathogen and a North-South differentiation via local adaptation. However, similar haplotypes and races were also recovered from several states, suggesting migration events, and highlighting the need to further investigate the switchgrass rust population structure and evolution in the USA.

Prevalence of Heritable Symbionts in Parisian Bedbugs (Hemiptera: Cimicidae)

Like many insects, the biology of bedbugs is impacted by a range of partner heritable microbes. Three maternally inherited symbionts are recognised: Wolbachia (an obligate partner), Symbiopectobacterium purcellii strain SyClec, and Candidatus Tisiphia sp. (facultative symbionts typically present in some but not all individuals). Past work had examined the presence of these heritable microbes from established laboratory lines, but not from broader field samples. We therefore deployed targeted endpoint PCR assays to determine the symbiont infection status for 50 bedbugs collected from 10 districts of Paris during the 2023 outbreak. All three symbionts were found to be broadly present across Cimex lectularius samples, with the Symbiopectobacterium-Candidatus Tisiphia-Wolbachia triple infection most commonly observed. A minority of individuals lacked either one or both facultative symbionts. Five mtDNA haplotypes were observed across the COI barcode region, and triple infections were found in all mtDNA haplotypes, indicating that symbiont infection is not a recent invasion event. We conclude that the Parisian bedbug outbreak was one in which the host's secondary symbionts were present at high-frequency coinfections, and facultative symbionts are an important but uncharacterised component of bedbug populations.

Pleistocene Refugia Inferred from Molecular Evidence in a Forest-Dwelling Harvestman (Arachnida, Opiliones, Gonyleptidae) Support a Biogeographic Split in Subtropical Argentina

This paper addresses the population genetic structure of the forest-dwelling gonyleptid Geraeocormobius sylvarum (Arachnida, Opiliones). Phylogeographic analyses using cytochrome oxidase subunit I (COI) were conducted on 186 individuals from 43 localities in Argentina and Paraguay, arranged into nine operational sectors and defined upon geographic and vegetation features. Given the current environmental uniformity, it was aimed to assess whether molecular fingerprints of G. sylvarum correlate with Pleistocene fragmentation events, inferred through forest contraction/expansion cycles. The network of 87 haplotypes displayed an unstructured pattern; 75 were found in unique localities (54 on single individuals), with most haplotypes restricted to a single operational sector. The calibrated phylogenetic tree revealed significant admixture, with each clade mainly related to one operational sector. Results suggest multiple fragmentation events; most COI diversity arose in the Late Pleistocene/Early Holocene; recent and relict lineages coexist at a few sites. Banks of major rivers (Paraná and Uruguay) in Misiones Province may have served as main refuge areas, with dispersal within each basin being frequent but sporadic across the watershed divide, keeping basins separated for long periods. The split of the Misiones opiliogeographical area into two sectors corresponding to the major basins is proposed.

A single mutation G454A in the P450 CYP9K1 drives pyrethroid resistance in the major malaria vector Anopheles funestus reducing bed net efficacy

Metabolic mechanisms conferring pyrethroid resistance in malaria vectors are jeopardizing the effectiveness of insecticide-based interventions, and identification of their markers is a key requirement for robust resistance management. Here, using a field-lab-field approach, we demonstrated that a single mutation G454A in the P450 CYP9K1 is driving pyrethroid resistance in the major malaria vector Anopheles funestus in East and Central Africa. Drastic reduction in CYP9K1 diversity was observed in Ugandan samples collected in 2014, with the selection of a predominant haplotype (G454A mutation at 90%), which was completely absent in the other African regions. However, 6 years later (2020) the Ugandan 454A-CYP9K1 haplotype was found predominant in Cameroon (84.6%), but absent in Malawi (Southern Africa) and Ghana (West Africa). Comparative in vitro heterologous expression and metabolism assays revealed that the mutant 454A-CYP9K1 (R) allele significantly metabolizes more type II pyrethroid (deltamethrin) compared with the wild G454-CYP9K1 (S) allele. Transgenic Drosophila melanogaster flies expressing 454A-CYP9K1 (R) allele exhibited significantly higher type I and II pyrethroids resistance compared to flies expressing the wild G454-CYP9K1 (S) allele. Furthermore, laboratory testing and field experimental hut trials in Cameroon demonstrated that mosquitoes harboring the resistant 454A-CYP9K1 allele significantly survived pyrethroids exposure (odds ratio = 567, P < 0.0001). This study highlights the rapid spread of pyrethroid-resistant CYP9K1 allele, under directional selection in East and Central Africa, contributing to reduced bed net efficacy. The newly designed DNA-based assay here will add to the toolbox of resistance monitoring and improving its management strategies.

Differences between mates at the TLR1Lb locus are associated with lower reproductive success in a long-lived seabird

Genetic diversity can influence fitness components such as survival and reproductive success. Yet the association between genetic diversity and fitness based on neutral loci is sometime very weak and inconsistent, with relationships varying among taxa due to confounding effects of population demography and life history. Fitness-diversity relationships are likely to be stronger and more consistent for genes known to influence phenotypic traits, such as immunity-related genes, and may also depend on the genetic differences between breeding partners. We recorded breeding success of individuals and breeding pairs over 20 years to evaluate the relationships between reproductive success and both neutral genetic variation (using 7,830 single nucleotide polymorphisms) and functional variation (four toll-like receptor [TLRs] loci) with reproductive success in thick-billed murres (Uria lomvia). Individual genetic diversity (both neutral and functional) was unrelated to reproductive success, but surprisingly, successful multi-year reproductive success decreased with the genetic difference between breeding partners at TLR1Lb. This result may be due to an advantage of specific alleles at TLR1Lb. This study is one of few addressing both individual genetic variation and genetic similarity between mates at both neutral and functional variation in a long-lived bird.

Exploring the phylogenetic framework and trait evolution of Impatiens through chloroplast genome analysis

BACKGROUND

The genus Impatiens, which includes both annual and perennial herbs, holds considerable ornamental, economic, and medicinal value. However, it posed significant challenges for taxonomic and systematic reconstruction. This was largely attributed to its high intraspecific diversity and low interspecific variation in morphological characteristics. In this study, we sequenced samples from 12 Impatiens species native to China and assessed their phylogenetic resolution using the complete chloroplast genome, in conjunction with published samples of Impatiens. In addition, a comparative analysis of chloroplast genomes were conducted to explore the evolution of the chloroplast genome in Impatiens.

RESULTS

The chloroplast genomes of 12 Impatiens species exhibited high similarity to previously published samples in terms of genome size, gene content, and sequence. The chloroplast genome of Impatiens exhibited a typical four-part structure, with lengths ranging from 146,987 bp(I. morsei)- 152,872 bp(I. jinpingensis). Our results identified 10 mutant hotspot regions (rps16, rps16-trnG, trnS-trnR, and rpoB-trnC) that could serve as effective molecular markers for phylogenetic analyses and species identification within the Impatiens. Phylogenetic analyses supported the classification of Impatiens as a monophyletic taxon. The identified affinities supported the taxonomic classification of the subgenus Clavicarpa within the Impatiens, with subgenus Clavicarpa being the first taxon to diverge. In phylogenetic tree,the Impatiens was divided into eight distinct clades. The results of ancestral trait reconstruction suggested that the ancestral traits of Impatiens included a perennial life cycle, four sepals and three pollen grooves. However, the ancestral morphology regarding fruit shape, flower colour, and spacing length remained ambiguous.

CONCLUDE

Our study largely supported the family-level taxonomic treatment of Impatiens species in China and demonstrated the utility of whole chloroplast genome sequences for phylogenetic resolution. Comparative analysis of the chloroplast genomes of Impatiens facilitated the development of molecular markers.The results of ancestral trait reconstruction showed that the ancestor type of habit was perennial, the number of sepals was 4, and morphology and number of aperture was 3 colpus. The traits of capsule shape, flower colour, and spur length underwent a complex evolutionary process. Our results provided data support for further studies and some important new insights into the evolution of the Impatiens.

Genetic diversity and phylogeography of the endemic species Prunus mira in the Qinghai-Tibetan Plateau

Studying the evolutionary history of plants in the Qinghai-Tibetan Plateau region provides a theoretical basis for the conservation and use of plant genetic resources. In this study, we analyzed five chloroplast gene fragments to examine the genetic diversity and phylogeography of Prunus mira in 577 individuals from 32 populations. The results indicated that P. mira populations exhibit high genetic diversity and significant phylogeographic structure (NST > GST). High genetic differentiation (FST = 0.979) and limited gene flow were detected among populations, likely due to geographic isolation. Neutrality tests and mismatch analysis indicated that the P. mira population has not experienced significant expansion during the historical period and remains relatively stable. Additionally, based on haplotype distribution and genetic diversity levels, we propose that P. mira had three refugia during the glacial period. Considering the genetic diversity of P. mira populations, we propose dividing all populations into two conservation units and prioritizing in situ conservation of populations with high genetic diversity within each unit. Furthermore, ex situ conservation of specific populations could prevent the loss of unique genes, such as those in populations with low genetic diversity but distinct haplotypes.

Diversity of Colletotrichum Species Causing Anthracnose in Chayote in Brazil, with a Description of Two New Species in the C. magnum Complex

Anthracnose caused by Colletotrichum species is the most important disease of chayote (Sicyos edulis) in Brazil. The etiology of chayote anthracnose has been assigned to the species C. orbiculare, an important plant pathogenic fungus also reported as the causal agent of anthracnose in other cucurbits worldwide. However, there is no recent survey of the Colletotrichum species causing anthracnose in chayote in Brazil. In this study, Colletotrichum isolates associated with anthracnose on the fruit and leaves of chayote, from various producing regions in Brazil, were collected and identified. Haplotype analysis based on sequences of the β-tubulin genomic region (TUB2) of 44 Colletotrichum isolates was carried out as a first measure of genetic diversity. A subset of 22 isolates were sequenced using the partial sequences of actin (ACT), glyceraldehyde-3-phosphate dehydrogenase (GAPDH), and the rDNA ITS (ITS) region. Maximum likelihood analysis was performed using the concatenated sequences. The multilocus sequence analysis revealed four previously described species, Colletotrichum chrysophilum, C. menezesiae, C. plurivorum, and C. karsti, and two novel species, named C. cucurbitacearum and C. sicyi. All species were able to induce typical symptoms of anthracnose in chayote fruits but varied in their aggressiveness. The species C. menezesiae and C. sicyi were the most aggressive, while C. plurivorum was the least aggressive. The species C. orbiculare was not found to cause chayote anthracnose in Brazil.

Intragenomic variations of the harmful algal bloom species Phaeocystis globosa through single-strain metabarcoding analysis

Recent studies demonstrated that the existence of high-levels intragenomic variations (IGVs) may lead to overinterpretation of species diversity and genetic diversity in metabarcoding analysis. In this study, IGVs of the V4 region of 18S rRNA gene (18S rDNA V4) in Phaeocystis globosa were ascertained through metabarcoding analysis results of 54 P. globosa strains. Each P. globosa strain harbored over 200 ASVs, in which one ASV was dominant with higher relative abundance than others. According to different dominant ASVs, 54 strains could be divided into two groups, suggesting the high genetic diversity of P. globosa. ASVs were shared in different strains, suggesting that IGVs were genuine existed, rather than sequencing errors. Metabarcoding analysis of field samples identified large numbers of IGVs. High levels of IGVs may be due to incomplete homogenization or existence of nonfunctional pseudogenes. An accurate understanding of IGVs is necessary for the correct interpretation of metabarcoding analysis results.

DNA barcoding, micromorphology and metabolic traits of selected Ficus L. (Moraceae) species from Egypt

The genus Ficus of the family Moraceae, is one of the largest genera of angiosperms, with diverse pharmaceutical applications and biological activities. The traditional approaches based on the morphological traits have been frequently implemented for taxonomical identification of the different taxa of Ficus, however, encompassing these features are quite laborious, due to the dependence of these phenotypic traits on the environmental conditions. So, authenticating the taxonomical identity of the Ficus taxa with molecular barcoding and metabolic profiling, as relatively stable traits, could be a relevant approach for confirming the traditional phenotypic traits of this genus. Nine species of the genus Ficus namely F. amplissima Sm., F. benjamina L. F. binnendijkii, F. drupacea var. pubescens, F. elastica Roxb., F. microcarpa L., F. religiosa L., F. tinctoria subsp. gibbosa and F. virens var. sublancelata in Egypt, were selected for this study. From the anatomical features, three species of subsection Urostigma, F. religiosa, F. virens var. sublanceolata have cystoliths on the abaxial layer, whereas in F. amplissima it was on the adaxial layer. The UPGMA dendrogram of the studied Ficus taxa has been generated from the 21 anatomical characters, categorized the studied taxa into two clusters (I and II) of average distance ~ 3.5, each cluster has been further divided into subclusters I and II. The sub-cluster I includes F. religiosa, F. virens var. sublanceolata and F. tinctoria subsp. gibbosa were grouped together to subsection Urostigma, while the sub-cluster II of the cluster I includes F. benjamina and F. amplissima. From the DNA barcoding analysis, three clusters I, II and III were emerged, the cluster I includes F. benjamina, F. binnendjikee, and F. amplissima. The cluster II, F. virens var. sublanceolata and F. religiosa that belong to subsection Urostigma, while, the cluster III includes F. elastica and F. drupacea var. pubescens, F. microcarpa that belongs to subsection Conosycea. From the metabolic profiling of Ficus species, the major compounds; H-cycloprop-azulen-7-ol, 3,7,11,15-Tetramethyl-2-hexadecen-1-ol, 2-(9-octadecenyloxy), pentadecanoic acid, phytol, sitosterol and 9,12-octadecadienoic acid were the common among the taxa, with an obvious fluctuation, that could be a chemotaxonomic markers for these species of Ficus. Based on the metabolic profiling, two distinct clusters I and II were evolved, the cluster I involve F. elastica, F. benjamina, F. drupacea var. pubescens, F. amplissima, while, the cluster II had F. tinctoria subsp. gibbosa and F. religiosa. The fluctuation on the metabolites of the tested Ficus species could be a metabolic fingerprint for each species. So, the delamination of the tested plants based on their anatomical traits was typically matched to the separation based on the ITS sequence analysis.

Chloroplast genome characteristic, comparative and phylogenetic analyses in Capsicum (Solanaceae)

BACKGROUND

Capsicum (Solanaceae) is a globally important vegetable crop and is also used therapeutically in traditional medicine systems. However, little is known of the genetic variation within the commonly grown cultivars, the evolutionary relationships and differences in the chloroplast (cp.) genomes between Capsicum species remain unclear.

RESULTS

The cp. genomes of 32 Capsicum varieties in three species from 6 countries were investigated. The cp. genome of Capsicum was found to be ~ 156 kb in length and to contain 113 unique genes, of which 79 encoded proteins, 30 encoded transfer tRNAs, and 4 were for ribosomal RNAs. The 32 varieties that we chose for study represented 13 genotypes, containing a total of 608 indels, 83 SNPs, 47 SSRs and 281-306 repeat sequences. We then included several previously sequenced Capsicum cp. genomes, and found that the nine investigated species showed a number of differences in the characteristics of the four IR boundaries, and it was the non-coding regions that contained the most variable regions. We conducted a phylogenetic reconstruction using the cp. genomes of 43 representative species of Solanaceae, and the resulting phylogeny generally reflected the currently accepted classification, with the species of the pungent group having close relationship with one another.

CONCLUSIONS

This study provides a comprehensive analysis of Capsicum chloroplast genomes, revealing significant variations in IR boundaries and other genomic features. These findings enhance our understanding of Capsicum evolution and genetic diversity.

Ethnoprimatology reveals new extended distribution of critically endangered banded langur Presbytis femoralis (Martin, 1838) in Pahang, Malaysia: Insights from indigenous traditional knowledge and molecular analysis

The banded langur (Presbytis femoralis) is a critically endangered primate, which within Malaysia has not been known to extend significantly outside the state of Johor. Traditionally, distribution studies on this highly threatened primate have relied on conventional methods such as DNA identification, live counting, and camera trapping. However, ethnoprimatology offers an alternative approach to data collection, involving the active participation of indigenous and local communities possessing valuable knowledge and experience with local primate species. This study employed an integrated approach incorporating ethnoprimatology by utilizing pooled local expert opinion, local surveys, interviews, and fecal DNA analysis, resulting in a novel distribution range for the banded langur. The combination of expert opinions revealed this species' most optimistic distribution scenario across Johor and Pahang, inhabiting various ecosystems, including lowland forests, peat swamps, and human-modified landscapes. Further interviews and surveys conducted within the Orang Asli community in Tasik Chini and Tasek Bera have provided additional support for the revised distribution, documenting occurrences of banded langur utilization in indigenous practices, such as food consumption, cultural beliefs, medicinal applications, and craftsmanship. Phylogenetic analysis demonstrated genetic differentiation between populations in Johor and Pahang, with the populations in the southern part of Peninsular Malaysia likely serving as ancestral sources for other populations. Consequently, this study not only elucidated the updated distribution of banded langur through DNA records and direct observations but also established the efficacy of ethnoprimatology as a precursory tool for uncovering the present distribution patterns of other primate species in Malaysia.

Three Mitochondrial Genomes of Chrysochroinae (Coleoptera, Buprestidae) and Phylogenetic Analyses

Three mitochondrial genomes of Chrysochroinae (Buprestidae) were sequenced and analyzed. The mitogenomes of the genera Catoxantha and Nipponobuprestis are first reportedand Chrysochroa opulenta is a first record for China. The complete mitogenomes of Catoxantha luodiana, Nipponobuprestis guangxiensis and Chrysochroa opulenta exhibit striking similarities in their lengths and composition. Specifically, their lengths are 15,594 bp, 15,775 bp and 15,587 bp, respectively. Each of these genomes encodes 37 typical mitochondrial genes. The overwhelming majority of protein-coding genes (PCGs) have the typical ATN (ATT, ATA, ATG or ATC) as the start codon and terminate with TAR (TAA or TAG) as the stop codon or an incomplete stop codon T-. Among the three mitogenomes, Leu2, Ser2 and Phe were the most frequently encoded amino acids. In the PCGs, the Ka/Ks ratio of cox1 is the lowest, whereas atp6 has the highest value. This suggests that cox1 can be used as a molecular barcode for species delimitation and phylogeny in Chrysochroinae. The phylogenetic results showed that C. luodiana and two Chrysochroa species formed a clade. Based on the topology of the phylogenetic tree, the genus Catoxantha should be reassigned as a subgenus of Chrysochroa.

Exploring Distribution and Evolution of Pi-ta Haplotypes in Rice Landraces across Different Rice Cultivation Regions in Yunnan

Background: Rice blast, caused by Magnaporthe oryzae, seriously damages the yield and quality of rice worldwide. Pi-ta is a durable resistance gene that combats M. oryzae carrying AVR-Pita1. However, the distribution of the Pi-ta gene in rice germplasms in Yunnan Province has been inadequately studied. Methods: We analyzed the potential molecular evolution pattern of Pi-ta alleles by examining the diversity in the coding sequence (CDS) among rice varieties. Results: The results revealed that 95% of 405 rice landraces collected from different ecological regions in Yunnan Province carry Pi-ta alleles. We identified 17 nucleotide variation sites in the CDS regions of the Pi-ta gene across 385 rice landraces. These variations led to the identification of 28 Pi-ta haplotypes, encoding 12 novel variants. Among these, 5 Pi-ta haplotypes (62 rice landraces) carried R alleles. The evolutionary cluster and network of the Pi-ta haplotypes suggested that the Pi-ta S alleles were the ancestral alleles, which could potentially evolve into R variants through base substitution. Conclusions: This study suggests that Pi-ta alleles are diverse in the rice landraces in Yunnan, and the Pi-ta sites resistant to blast evolved from the susceptible plants of the rice landraces. These results provide the basis for breeding resistant varieties.

Mitogenome selection shaped the terrestrial adaptation of Grapsidae (Decapoda: Brachyura)

The colonization of aquatic to terrestrial habitats by brachyuran crabs requires genetic innovations as well as morphological adaptations to adapt to terrestrial environments. The genetic basis of such adaptive evolution, however, is largely unknown. This study focuses on terrestrialization in Geograpsus (Grapsidae) the only highly terrestrial genus in this family, which represents a notable example of terrestrial adaptive radiation. Here, we sequenced the mitogenomes of two Geograpsus species and used the mitogenomes of 215 representative crabs to construct phylogenetic and time frameworks that we used to infer terrestrial origins and evolution. Using mitochondrial genomic data, we demonstrated that marine crab ancestors began to settle on land during the early Eocene. Ocean acidification, the Paleocene-Eocene Thermal Maximum (PETM), and mangrove expansion at that time may have driven the diversification and ecological expansion of these terrestrial crabs. Evolutionary analyses reveal strong positive selection signals on monophyletic lineages of Grapsidae, especially the terrestrial species of Geograpsus. Positively selected sites in functionally important regions of ND5 and ND4 may imply enhanced energy metabolism in Grapsidae compared to other crabs, and may have played an important role in their terrestrial adaptation. Overall, our work provides valuable resources and opportunities to reveal the adaptation of crabs to complex terrestrial environments.

Genetic Characterization of Myf5 and POU1F1 Genes in Different Egyptian Local Rabbit Breeds and Their Association with Growth Traits

Genetic characterization and its association with quantitative traits in local breeds are important tools for the genetic improvement and sustainable management of animal genetic resources. Myogenic regulatory factor 5 (MYf5) and POU class 1 homeobox 1 (POU1F1) are candidate genes which play important roles in growth and development of mammals. The present study aims to detect the genetic diversity of the MYf5 and POU1F1 genes in four local Egyptian rabbit breeds and their association with growth traits, using PCR-restriction enzyme (PCR-RFLP), PCR-single-strand conformational polymorphism (PCR-SSCP), and direct sequencing techniques. The results showed that MYF5 exon 1 was observed with two genotypes in Baladi Black (BB), Gabali (GB) and New Zealand White (NZW) breeds while APRI-line (APRI) presented one genotype. The genetic diversity of Myf5 exon 2 between breeds showed two genotypes in APRI compared to three in NZW and four genotypes in BB and GB breeds. The genetic diversity of the POU1F1 gene (intron 5 and partial cds) in different rabbit breeds was two genotypes in NZW and three genotypes in BB, GB, and APRI breeds with different frequencies for each genotype. Based on the statistically significant difference between genes genotypes and growth weight, the results suggested that the genotypes of Myf5 exon 2 (1 and 2) of the BB breed, Myf5 exon 2 genotype 2 of the APRI breed, and genotype 1 of Myf5 exon 1 and genotype 1 of POU1F1 of the NZW breed compared to genotypes for each gene can be considered candidate molecular markers associated with the improvement of growth traits in these breeds.

Molecular and morphological identification of larvae of Carangidae (Teleostei, Carangiformes) species from southern Gulf of California

The description of diagnostic morphological characters and DNA barcoding of fish larvae from nine species of the carangid family are provided from specimens collected during a weekly zooplankton time-series (2016-2017) at Cabo Pulmo National Park, Gulf of California, Mexico. Five nominal species (Caranxsexfasciatus, C.caballus, Naucratesductor, Selarcrumenophthalmus, and Seleneperuviana) and three morphotypes of Decapterus spp. and one of Caranx spp. were identified and separated based on morphological, meristic, and pigmentary diagnostic characters. All larvae were genetically sequenced for a fragment of the cytochrome c oxidase subunit I mitochondrial gene. Sequences of larval Caranx and Decapterus showed high genetic similarity (> 99%), low intraspecific divergence (< 1%), and an interspecific divergence between 6% and 11%, allowing the discrimination of diagnostic pigmentation patterns of fish larvae among three sibling species from each genus: Caranx (C.caballus, C.caninus, and C.sexfasciatus) and Decapterus (D.macarellus, D.macrosoma, and D.muroadsi). DNA barcoding supported the presence of Caranxcaballus, C.caninus, C.sexfasciatus, Decapterusmacarellus, D.muroadsi, Selarcrumenophthalmus, and Seleneperuviana, and for the first time Naucratesductor and D.macrosoma at the CPNP. Abundance of these nine species (confirmed molecularly) was estimated throughout the 2016-2017 weekly time series. Decapterusmacarellus and Caranxcaninus were the most abundant species. The morphological and molecular taxonomic methods allowed us to infer the species number and abundance of these commercial species at the CPNP to improve conservation in protected areas and fishery management.

The assembly and comparative analysis of the first complete mitogenome of Lindera aggregata

Lindera aggregata, a member belongs to the genus Lindera of Lauraceae family. Its roots and leaves have been used as traditional Chinese medicine or functional food for thousands of years. However, its mitochondrial genome has not been explored. Our aim is to sequence and assemble the mitogenome of L. aggregata to elucidate the genetic mechanism and evolutionary pathway. The results had shown that the mitogenome was extremely complex and had a unique multi-branched conformation with total size of 912,473 bp. Comprehensive analysis of protein coding genes of 7 related species showed that there were 40 common genes in their mitogenome. Interestingly, positive selection had become an important factor in the evolution of ccmB, ccmFC, rps10, rps11 and rps7 genes. Furthermore, our data highlighted the repeated trend of homologous fragment migrations between chloroplast and mitochondrial organelles, and 38 homologous fragments were identified. Phylogenetic analysis identified a tree that was basically consistent with the phylogeny of Laurales species described in the APG IV system. To sum up, this study will be helpful to the study of population genetics and evolution of Lindera species.

Phylogenomics analysis of Scutellaria (Lamiaceae) of the world

BACKGROUND

Scutellaria, a sub-cosmopolitan genus, stands as one of the Lamiaceae family's largest genera, encompassing approximately 500 species found in both temperate and tropical montane regions. Recognized for its significant medicinal properties, this genus has garnered attention as a research focus, showcasing anti-cancer, anti-inflammatory, antioxidant, and hepatoprotective qualities. Additionally, it finds application in agriculture and horticulture. Comprehending Scutellaria's taxonomy is pivotal for its effective utilization and conservation. However, the current taxonomic frameworks, primarily based on morphological characteristics, are inadequate. Despite several phylogenetic studies, the species relationships and delimitations remain ambiguous, leaving the genus without a stable and reliable classification system.

RESULTS

This study analyzed 234 complete chloroplast genomes, comprising 220 new and 14 previously published sequences across 206 species, subspecies, and varieties worldwide. Phylogenetic analysis was conducted using six data matrices through Maximum Likelihood and Bayesian Inference, resulting in a robustly supported phylogenetic framework for Scutellaria. We propose three subgenera, recommending the elevation of Section Anaspis to subgeneric rank and the merging of Sections Lupulinaria and Apeltanthus. The circumscription of Subgenus Apeltanthus and Section Perilomia needs to be reconsidered. Comparative analysis of chloroplast genomes highlighted the IR/SC boundary feature as a significant taxonomic indicator. We identified a total of 758 SSRs, 558 longer repetitive sequences, and ten highly variable regions, including trnK-rps16, trnC-petN, petN-psbM, accD-psaI, petA-psbJ, rpl32-trnL, ccsA-ndhD, rps15-ycf1, ndhF, and ycf1. These findings serve as valuable references for future research on species identification, phylogeny, and population genetics.

CONCLUSIONS

The phylogeny of Scutellaria, based on the most comprehensive sample collection to date and complete chloroplast genome analysis, has significantly enhanced our understanding of its infrageneric relationships. The extensive examination of chloroplast genome characteristics establishes a solid foundation for the future development and utilization of Scutellaria, an important medicinal plant globally.

Genetic diversity of Flaviviridae and Rhabdoviridae EVEs in Aedes aegypti and Aedes albopictus on Hainan Island and the Leizhou Peninsula, China

BACKGROUND

Hainan Island and the Leizhou Peninsula, the southernmost part of mainland China, are areas where Aedes aegypti and Ae. albopictus are sympatric and are also high-incidence areas of dengue outbreaks in China. Many studies have suggested that Aedes endogenous viral components (EVEs) are enriched in piRNA clusters which can silence incoming viral genomes. Investigation the EVEs present in the piRNA clusters associated with viral infection of Aedes mosquitoes in these regions may provide a theoretical basis for novel transmission-blocking vector control strategies.

METHODS

In this study, specific primers for endogenous Flaviviridae elements (EFVEs) and endogenous Rhabdoviridae elements (ERVEs) were used to detect the distribution of Zika virus infection associated EVEs in the genomes of individuals of the two Aedes mosquitoes. Genetic diversity of EVEs with a high detection rate was also analyzed.

RESULTS

The results showed that many EVEs associated with Zika virus infection were detected in both Aedes species, with the detection rates were 47.68% to 100% in Ae. aegypti and 36.15% to 92.31% in sympatric Ae. albopictus populations. EVEs detection rates in another 17 Ae. albopictus populations ranged from 29.39% to 89.85%. Genetic diversity analyses of the four EVEs (AaFlavi53, AaRha61, AaRha91 and AaRha100) of Ae. aegypti showed that each had high haplotype diversity and low nucleotide diversity. The number of haplotypes in AaFlavi53 was 8, with the dominant haplotype being Hap_1 and the other 7 haplotypes being further mutated from Hap_1 in a lineage direction. In contrast, the haplotype diversity of the other three ERVEs (AaRha61, AaRha91 and AaRha100) was more diverse and richer, with the haplotype numbers were 9, 15 and 19 respectively. In addition, these EVEs all showed inconsistent patterns of both population differentiation and dispersal compared to neutral evolutionary genes such as the Mitochondrial COI gene.

CONCLUSION

The EFVEs and ERVEs tested were present at high frequencies in the field Aedes mosquito populations. The haplotype diversity of the EFVE AaFlavi53 was relatively lower and the three ERVEs (AaRha61, AaRha91, AaRha100) were higher. None of the four EVEs could be indicative of the genetic diversity of the Ae. aegypti population. This study provided theoretical support for the use of EVEs to block arbovirus transmission, but further research is needed into the mechanisms by which these EVEs are antiviral to Aedes mosquitoes.

The Low Genetic Diversity of Dientamoeba fragilis Isolates in Southwest Turkey and Analysis of Clinical Findings

PURPOSE

Dientamoeba fragilis (D. fragilis) is a common intestinal protozoan with a global distribution. In the present study, we aimed to determine genetic diversity of D. fragilis isolates with multilocus sequence typing (MLST) in the southwest of Turkey and analyse the clinical findings.

MATERIALS AND METHODS

The study included faecal samples from 200 individuals in Aydin, Turkey. The positivity of D. fragilis was determined with 18 S rRNA gene-based PCR assay. Six nested-PCR reactions were set to amplify partial D. fragilis housekeeping genes in the positive samples. The sequences were aligned with the references from GenBank to detect nucleotide polymorphisms and haplotypes. Additionally, the clinical findings and demographic characteristics of patients were statistically analysed between D. fragilis-infected and non-infected cases.

RESULTS

The positivity of D. fragilis was 16% (32 out of 200 cases) with 18 S rRNA based-PCR, and all were classified as "genotype 1". The analysis of six MLST loci revealed different haplotypes only at one locus; the remaining five loci exhibited no polymorphisms. The haplotypes in the present study were identical to at least one previously reported reference, except the locus "large subunit of RNA polymerase II" locus. There were no significant differences in any of the clinical findings or demographic characteristics between the infected and non-infected groups.

CONCLUSIONS

Our study revealed a low genetic diversity of D. fragilis isolates from Turkey, like other countries including Italy, Denmark, the UK, Australia, and Brazil. The high degree of sequence similarity in housekeeping genes indicated the clonal distribution of D. fragilis.

Comparative assessment of the intragenomic variations of dinoflagellate Tripos species through single-cell sequencing

Tripos is a large dinoflagellate genus widely distributed in the world's oceans. Morphology-based species identification is inconclusive due to high morphological intraspecific variability. Metabarcoding analysis has been demonstrated to be effective for species identification and tracking their spatiotemporal dynamics. However, accumulating evidence suggests high levels of intragenomic variations (IGVs) are common in many algae, leading to concerns about overinterpretation of molecular diversity in metabarcoding studies. In this project, we evaluated and compared IGVs in Tripos species by conducting the first high-throughput sequencing (HTS) of 18S rDNA V4 of Tripos single cells. High numbers of haplotypes (19-172) were identified in each of the 30 Tripos cells. Each cell contained one dominant haplotype with high relative abundance and many haplotypes with lower abundances. Thus, the presence of multiple minor haplotypes substantially overestimate the molecular diversity identified in metabarcoding analysis, which encompass not only interspecific and intraspecific diversities, but high levels of IGVs.

Decoding the Chloroplast Genome of Tetrastigma (Vitaceae): Variations and Phylogenetic Selection Insights

Tetrastigma (Vitaceae) is known for its ornamental, medicinal, and ecological significance. However, the structural and variational characteristics of the Tetrastigma chloroplast genome and their impact on phylogenetic relationships remain underexplored. This study utilized bioinformatics methods to assemble and annotate the chloroplast genomes of 10 Tetrastigma species and compare them with five previously sequenced species. This study analyzed gene composition, simple sequence repeats, and codon usage patterns, revealing a high A/T content, uniquely identified pentanucleotide repeats in five species and several preferred codons. In addition, comparative analyses were conducted of the chloroplast genomes of 15 Tetrastigma species, examining their structural differences and identifying polymorphic hotspots (rps16, rps16-trnQ, trnS, trnD, psbC-trnS-psbZ, accD-psaI, psbE-petL-petG, etc.) suitable for DNA marker development. Furthermore, phylogenetic and selective pressure analyses were performed based on the chloroplast genomes of these 15 Tetrastigma species, validating and elucidating intra-genus relationships within Tetrastigma. Futhermore, several genes under positive selection, such as atpF and accD, were identified, shedding light on the adaptive evolution of Tetrastigma. Utilizing 40 Vitaceae species, the divergence time of Tetrastigma was estimated, clarifying the evolutionary relationships within Tetrastigma relative to other genera. The analysis revealed diverse divergences of Tetrastigma in the Miocene and Pliocene, with possible ancient divergence events before the Eocene. Furthermore, family-level selective pressure analysis identified key features distinguishing Tetrastigma from other genera, showing a higher degree of purifying selection. This research enriches the chloroplast genome data for Tetrastigma and offers new insights into species identification, phylogenetic analysis, and adaptive evolution, enhancing our understanding of the genetic diversity and evolutionary history of these species.

Plastome structure, phylogeny and evolution of plastid genes in Reevesia (Helicteroideae, Malvaceae)

Reevesia is an eastern Asian-eastern North American disjunction genus in the family Malvaceae s.l. and comprises approximately 25 species. The relationships within the genus are not well understood. Here, 15 plastomes representing 12 Reevesia species were compared, with the aim of better understanding the species circumscription and phylogenetic relationships within the genus and among genera in the family Malvaceae s.l. The 11 newly sequenced plastomes range between 161,532 and 161, 945 bp in length. The genomes contain 114 unique genes, 18 of which are duplicated in the inverted repeats (IRs). Gene content of these plastomes is nearly identical. All the protein-coding genes are under purifying selection in the Reevesia plastomes compared. The top ten hypervariable regions, SSRs, and the long repeats identified are potential molecular markers for future population genetic and phylogenetic studies. Phylogenetic analysis based on the whole plastomes confirmed the monophyly of Reevesia and a close relationship with Durio (traditional Bombacaceae) in subfamily Helicteroideae, but not with the morphologically similar genera Pterospermum and Sterculia (both of traditional Sterculiaceae). Phylogenetic relationships within Reevesia suggested that two species, R. pubescens and R. thyrsoidea, as newly defined, are not monophyletic. Six taxa, R. membranacea, R. xuefengensis, R. botingensis, R. lofouensis, R. longipetiolata and R. pycnantha, are suggested to be recognized.

Structure, Evolution, and Mitochondrial Genome Analysis of Mussel Species (Bivalvia, Mytilidae)

Based on the nucleotide sequences of the mitochondrial genome (mitogenome) of specimens taken from two mussel species (Arcuatula senhousia and Mytilus coruscus), an investigation was performed by means of the complex approaches of the genomics, molecular phylogenetics, and evolutionary genetics. The mitogenome structure of studied mussels, like in many other invertebrates, appears to be much more variable than in vertebrates and includes changing gene order, duplications, and deletions, which were most frequent for tRNA genes; the mussel species' mitogenomes also have variable sizes. The results demonstrate some of the very important properties of protein polypeptides, such as hydrophobicity and its determination by the purine and pyrimidine nucleotide ratio. This fact might indirectly indicate the necessity of purifying natural selection for the support of polypeptide functionality. However, in accordance with the widely accepted and logical concept of natural cutoff selection for organisms living in nature, which explains its action against deleterious nucleotide substitutions in the nonsynonymous codons (mutations) and its holding of the active (effective) macromolecules of the polypeptides in a population, we were unable to get unambiguous evidence in favor of this concept in the current paper. Here, the phylogeny and systematics of mussel species from one of the largest taxons of bivalve mollusks are studied, the family known as Mytilidae. The phylogeny for Mytilidae (order Mytilida), which currently has no consensus in terms of systematics, is reconstructed using a data matrix of 26-27 mitogenomes. Initially, a set of 100 sequences from GenBank were downloaded and checked for their gender: whether they were female (F) or male (M) in origin. Our analysis of the new data confirms the known drastic differences between the F/M mitogenome lines in mussels. Phylogenetic reconstructions of the F-lines were performed using the combined set of genetic markers, reconstructing only protein-coding genes (PCGs), only rRNA + tRNA genes, and all genes. Additionally, the analysis includes the usage of nucleotide sequences composed of other data matrices, such as 20-68 mitogenome sequences. The time of divergence from MRCA, estimated via BEAST2, for Mytilidae is close to 293 Mya, suggesting that they originate in the Silurian Period. From all these data, a consensus for the phylogeny of the subfamily of Mytilinae and its systematics is suggested. In particular, the long-debated argument on mussel systematics was resolved as to whether Mytilidae, and the subfamily of Mytilinae, are monophyletic. The topology signal, which was strongly resolved in this paper and in the literature, has refuted the theory regarding the monophyly of Mytilinae.

Uniparental silencing of 5S rRNA genes in plant allopolyploids - insights from Cardamine (Brassicaceae)

While the phenomenon of uniparental silencing of 35S rDNA in interspecific hybrids and allopolyploids is well documented, there is a notable absence of information regarding whether such silencing extends to the 5S RNA component of ribosomes. To address this gap in knowledge, we analyzed the 5S and 35S rDNA expression in Cardamine (Brassicaceae) allopolyploids, namely C. × insueta (2n = 3x = 24, genome composition RRA), C. flexuosa (2n = 4x = 32, AAHH), and C. scutata (2n = 4x = 32, PPAA) which share a common diploid ancestor (AA). We employed high-throughput sequencing of transcriptomes and genomes and phylogenetic analyses of 5S rRNA variants. The genomic organization of rDNA was further scrutinized through clustering and fluorescence in situ hybridization. In the C. × insueta allotriploid, we observed uniparental dominant expression of 5S and 35S rDNA loci. In the C. flexuosa and C. scutata allotetraploids, the expression pattern differed, with the 35S rDNA being expressed from the A subgenome, whereas the 5S rDNA was expressed from the partner subgenome. Both C. flexuosa and C. scutata but not C. × insueta showed copy and locus number changes. We conclude that in stabilized allopolyploids, transcription of ribosomal RNA components occurs from different subgenomes. This phenomenon appears to result in the formation of chimeric ribosomes comprising rRNA molecules derived from distinct parental origins. We speculate that the interplay of epigenetic silencing and rDNA rearrangements introduces an additional layer of variation in multimolecule ribosomal complexes, potentially contributing to the evolutionary success of allopolyploids.

Genetic Variation among the Partial Gene Sequences of the Ribosomal Protein Large-Two, the Internal Transcribed Spacer, and the Small Ribosomal Subunit of Blastocystis sp. from Human Fecal Samples

In the present study, we compared the genetic variability of fragments from the internal transcribed spacer region (ITS) and the small subunit ribosomal DNA (SSUrDNA) as nuclear markers, in contrast with the ribosomal protein large two (rpl2) loci, placed in the mitochondrion-related organelles (MROs) within and among human fecal samples with Blastocystis. Samples were analyzed using polymerase chain reaction (PCR)-sequencing, phylogenies, and genetics of population structure analyses were performed. In total, 96 sequences were analyzed, i.e., 33 of SSUrDNA, 35 of rpl2, and 28 of ITS. Only three subtypes (STs) were identified, i.e., ST1 (11.4%), ST2 (28.6%), and ST3 (60%); in all cases, kappa indexes were 1, meaning a perfect agreement among ST assignations. The topologies of phylogenetic inferences were similar among them, clustering to each ST in its specific cluster; discrepancies between phylogeny and assignment of STs were not observed. The STRUCTURE v2.3.4 software assigned three subpopulations corresponding to the STs 1-3, respectively. The population indices were consistent with those previously reported by other groups. Our results suggest the potential use of the ITS and rpl2 genes as molecular markers for Blastocystis subtyping as an alternative approach for the study of the genetic diversity observed within and between human isolates of this microorganism.

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.

Diversity, Prevalence and Virulence of Colletotrichum Species Causing Anthracnose on Cassava Leaves in the Northern Region of Brazil

Cassava (Manihot esculenta Crantz) is a staple crop widely cultivated by small farmers in tropical countries. However, despite the low level of technology required for its management, it can be affected by several diseases, with anthracnose as the main threat. There is little information about the main species of Colletotrichum that infect cassava in Brazil. Thus, the objective of this work was to study the diversity, prevalence and virulence of Colletotrichum species that cause anthracnose in cassava leaves in northern Brazil. Twenty municipalities of the Pará and Tocantins states were selected, and leaves with symptoms were collected in those locations. Pure cultures were isolated in the laboratory. Species were identified using phylogenetic analyses of multiple loci, and their pathogenicity, aggressivity and virulence levels were assessed. Our results showed the greatest diversity of Colletotrichum associated with anthracnose in cassava plants of the "Formosa" cultivar in the Tocantins and Pará states. We determined the presence of Colletotrichum chrysophilum, C. truncatum, C. siamense, C. fructicola, C. plurivorum, C. musicola and C. karsti, with C. chrysophilum as the most aggressive and virulent. Our findings provide accurate identifications of species of Colletotrichum causing anthracnose in cassava crops, which are of great relevance for cassava breeding programs (e.g., the search for genotypes with polygenic resistance since the pathogen is so diverse) and for developing anthracnose management strategies that can work efficiently against species complexes of Colletotrichum.

HOMEOBOX2, the paralog of SIX-ROWED SPIKE1/HOMEOBOX1, is dispensable for barley spikelet development

The HD-ZIP class I transcription factor Homeobox 1 (HvHOX1), also known as Vulgare Row-type Spike 1 (VRS1) or Six-rowed Spike 1, regulates lateral spikelet fertility in barley (Hordeum vulgare L.). It was shown that HvHOX1 has a high expression only in lateral spikelets, while its paralog HvHOX2 was found to be expressed in different plant organs. Yet, the mechanistic functions of HvHOX1 and HvHOX2 during spikelet development are still fragmentary. Here, we show that compared with HvHOX1, HvHOX2 is more highly conserved across different barley genotypes and Hordeum species, hinting at a possibly vital but still unclarified biological role. Using bimolecular fluorescence complementation, DNA-binding, and transactivation assays, we validate that HvHOX1 and HvHOX2 are bona fide transcriptional activators that may potentially heterodimerize. Accordingly, both genes exhibit similar spatiotemporal expression patterns during spike development and growth, albeit their mRNA levels differ quantitatively. We show that HvHOX1 delays the lateral spikelet meristem differentiation and affects fertility by aborting the reproductive organs. Interestingly, the ancestral relationship of the two genes inferred from their co-expressed gene networks suggested that HvHOX1 and HvHOX2 might play a similar role during barley spikelet development. However, CRISPR-derived mutants of HvHOX1 and HvHOX2 demonstrated the suppressive role of HvHOX1 on lateral spikelets, while the loss of HvHOX2 does not influence spikelet development. Collectively, our study shows that through the suppression of reproductive organs, lateral spikelet fertility is regulated by HvHOX1, whereas HvHOX2 is dispensable for spikelet development in barley.

The Phylogeography of Deciduous Tree Ulmus macrocarpa (Ulmaceae) in Northern China

Disentangling how climate oscillations and geographical events significantly influence plants' genetic architecture and demographic history is a central topic in phytogeography. The deciduous ancient tree species Ulmus macrocarpa is primarily distributed throughout Northern China and has timber and horticultural value. In the current study, we studied the phylogenic architecture and demographical history of U. macrocarpa using chloroplast DNA with ecological niche modeling. The results indicated that the populations' genetic differentiation coefficient (NST) value was significantly greater than the haplotype frequency (GST) (p < 0.05), suggesting that U. macrocarpa had a clear phylogeographical structure. Phylogenetic inference showed that the putative chloroplast haplotypes could be divided into three groups, in which the group Ⅰ was considered to be ancestral. Despite significant genetic differentiation among these groups, gene flow was detected. The common ancestor of all haplotypes was inferred to originate in the middle-late Miocene, followed by the haplotype overwhelming diversification that occurred in the Quaternary. Combined with demography pattern and ecological niche modeling, we speculated that the surrounding areas of Shanxi and Inner Mongolia were potential refugia for U. macrocarpa during the glacial period in Northern China. Our results illuminated the demography pattern of U. macrocarpa and provided clues and references for further population genetics investigations of precious tree species distributed in Northern China.

Molecular phylogeny confirms the subspecies delineation of the Malayan Siamang (Symphalangussyndactyluscontinentis) and the Sumatran Siamang (Symphalangussyndactylussyndactylus) based on the hypervariable region of mitochondrial DNA

Siamangs (Symphalangussyndactylus) are native to Peninsular Malaysia, Sumatra and southern Thailand and their taxonomical classification at subspecies level remains unclear. Morphologically, two subspecies were proposed as early as 1908 by Thomas namely Symphalangus s.syndactylus and Symphalanguss.continentis. Thus, this study aims to clarify the Siamang subspecies status, based on mtDNA D-loop sequences. Faecal samples were collected from wild Siamang populations at different localities in Peninsular Malaysia. A 600-bp sequence of the mitochondrial D-loop region was amplified from faecal DNA extracts and analysed along with GenBank sequences representing Symphalangus sp., Nomascus sp., Hylobates sp., Hoolock sp. and outgroups (Pongopygmaeus, Macacafascicularis and Papiopapio). The molecular phylogenetic analysis in this study revealed two distinct clades formed by S.s.syndactylus and S.s.continentis which supports the previous morphological delineation of the existence of two subspecies. Biogeographical analysis indicated that the Sumatran population lineage was split from the Peninsular Malaysian population lineage and a diversification occurrred in the Pliocene era (~ 3.12 MYA) through southward expansion. This postulation was supported by the molecular clock, which illustrated that the Peninsular Malaysian population (~ 1.92 MYA) diverged earlier than the Sumatran population (~ 1.85 MYA). This is the first study to use a molecular approach to validate the subspecies statuses of S.s.syndactylus and S.s.continentis. This finding will be useful for conservation management, for example, during Siamang translocation and investigations into illegal pet trade and forensics involving Malayan and Sumatran Siamangs.

Sequence characteristics, genetic diversity and phylogenetic analysis of the Cucurbita ficifolia (Cucurbitaceae) chloroplasts genome

BACKGROUND

Curcubita ficifolia Bouché (Cucurbitaceae) has high value as a food crop and medicinal plant, and also has horticultural value as rootstock for other melon species. China is home to many different cultivars, but the genetic diversity of these resources and the evolutionary relationships among them, as well as the differences between C. ficifolia and other Cucurbita species, remain unclear.

RESULTS

We investigated the chloroplast (cp) genomes of 160 C. ficifolia individuals from 31 populations in Yunnan, a major C. ficifolia production area in China. We found that the cp genome of C. ficifolia is ~151 kb and contains 128 genes, of which 86 are protein coding genes, 34 encode tRNA, and eight encode rRNAs. We also identified 64 SSRs, mainly AT repeats. The cp genome was found to contain a total of 204 SNP and 57 indels, and a total of 21 haplotypes were found in the 160 study individuals. The reverse repeat (IR) region of C. ficifolia contained a few differences compared with this region in the six other Cucurbita species. Sequence difference analysis demonstrated that most of the variable regions were concentrated in the single copy (SC) region. Moreover, the sequences of the coding regions were found to be more similar among species than those of the non-coding regions. The phylogenies reconstructed from the cp genomes of 61 representative species of Cucurbitaceae reflected the currently accepted classification, in which C. ficifolia is sister to the other Cucurbita species, however, different interspecific relationships were found between Cucurbita species.

CONCLUSIONS

These results will be valuable in the classification of C. ficifolia genetic resources and will contribute to our understanding of evolutionary relationships within the genus Cucurbita.

Impact of persistent barrier to gene flow and catastrophic events on red algae evolutionary history along the Chilean coast

Historical vicariance events, linked to the existence of stable physical barriers to gene flow, generate concordant genetic breaks in co-distributed species while stochastic processes (e.g., costal uplift) could cause species-specific genetic breaks as a result of local strong demographic bottlenecks or extinction. In Chile, previous studies show that the area of the 30°S-33°S could correspond to a stable barrier to gene flow that have affected the genetic structure of various algae and marine invertebrates. Here we sequenced two organellar genes (COI and rbcL) in four taxonomically accepted co-distributed red seaweeds species characterized by a low dispersal potential: Mazzaella laminarioides, M. membranacea, Asterfilopsis disciplinalis, and Ahnfeltiopsis vermicularis. Our results revealed the existence of ten strongly differentiated linages in the taxa studied. Strong genetic breaks, concordant in both space and time (divergence estimated to have occurred some 2.9-12.4 million years ago), were observed between taxa distributed across the 33°S. Conversely, in the Central/South part of the Chilean coast, the localization of the genetic breaks/sub-structure observed varied widely (36°S, 38°S, 39°S, and 40°S). These results suggest that a major historical vicariance event has modeled the genetic structure of several Chilean marine organisms in the north of the Chilean coast during the mid-Miocene, while more recent stochastic events and genetic drift could be the driving forces of genetic divergence/structuration in the central-southern part of the coast.

Application of Nested-qPCR-High Resolution Melting (HRM) Technology on Strongyloides stercoralis Isolates from Iran

PURPOSE

Strongyloides stercoralis is a parasite with special characteristics presenting it as a unique nematode. Iran is an endemic area for S. stercoralis. In this study, nested-qPCR-high resolution melting (HRM) technology was applied on some human isolates of S. stercoralis from this country by focusing on evolutionary genetics analysis.

METHODS

Twelve human isolates of S. stercoralis were collected from four endemic provinces of Iran. Genomic DNA was extracted from a single filariform larva for every isolate. Using specific primers targeting partial regions in cox1 gene, nested-qPCR-HRM was performed and melting-curve profiles were analyzed alongside the evaluation of genetic proximity and phylogenetic analysis using MEGA7 and DnaSP5 software.

RESULTS

The melting temperature (Tm) values of the isolates were 77.9 °C-78.3 °C. All isolates from Guilan, Mazandaran, and Khouzestan Provinces shared Tm values of 78.2 °C to 78.3 °C, while the isolates from Hormozgan Province showed Tm values of 77.9 °C, 78.0 °C, and 78.1 °C. The phylogenetic tree illustrated that the sequences of the current study included nine haplotypes. Tajima's D index analyses showed that cox1 gene in S. stercoralis isolates was negative (Tajima's D = - 0.27).

CONCLUSION

The isolates were divided into five temperature groups. Although HRM assay compared to PCR sequencing identified more limited genetic changes, it revealed that the mean of Tm of the isolates from Hormozgan Province was lower than those of other provinces and represented specific haplotypes for this geographical region on the phylogenetic tree.

Topographic barriers drive the pronounced genetic subdivision of a range-limited fossorial rodent

Due to their limited dispersal ability, fossorial species with predominantly belowground activity usually show increased levels of population subdivision across relatively small spatial scales. This may be exacerbated in harsh mountain ecosystems, where landscape geomorphology limits species' dispersal ability and leads to small effective population sizes, making species relatively vulnerable to environmental change. To better understand the environmental drivers of species' population subdivision in remote mountain ecosystems, particularly in understudied high-elevation systems in Africa, we studied the giant root-rat (Tachyoryctes macrocephalus), a fossorial rodent confined to the afro-alpine ecosystem of the Bale Mountains in Ethiopia. Using mitochondrial and low-coverage nuclear genomes, we investigated 77 giant root-rat individuals sampled from nine localities across its entire ~1000 km2 range. Our data revealed a distinct division into a northern and southern group, with no signs of gene flow, and higher nuclear genetic diversity in the south. Landscape genetic analyses of the mitochondrial and nuclear genomes indicated that population subdivision was driven by slope and elevation differences of up to 500 m across escarpments separating the north and south, potentially reinforced by glaciation of the south during the Late Pleistocene (~42,000-16,000 years ago). Despite this landscape-scale subdivision between the north and south, weak geographic structuring of sampling localities within regions indicated gene flow across distances of at least 16 km at the local scale, suggesting high, aboveground mobility for relatively long distances. Our study highlights that despite the potential for local-scale gene flow in fossorial species, topographic barriers can result in pronounced genetic subdivision. These factors can reduce genetic variability, which should be considered when developing conservation strategies.

First molecular description of Neorhadinorhynchus nudus (Acanthocephala: Cavisomidae) from fish in the pacific coast of Vietnam, with notes on biogeography

Neorhadinorhynchus nudus (Harada, 1938) Yamaguti, 1939 (Cavisomidae) was morphologically described from the frigate tuna Auxis thazard (Lacépède) (Scombridae) in Nha Trang, Pacific south Vietnam. Females of N. nudus were fully described for the first time in the Pacific. Its original inadequate description as Rhadinorhynchus nudus (Harada, 1938) was corrected in material from Fiji Island, the Red Sea and Pacific Vietnam and errors in the text and line drawings of Harada were repeated in subsequent major publications where it underwent considerable nomenclature changes. New descriptive and biogeographical notes are included. We also provided here the molecular characterization of the nuclear gene (18S) and the mitochondrial cytochrome c oxidase subunit 1 (cox1) sequence data of N. nudus. Furthermore, to elucidate the phylogenetic relationship of N. nudus within the family Cavisomidae and with other isolates were performed incorporating nuclear (18S) and mitochondrial (cox1) sequence data using maximum likelihood (ML) and Bayesian inference (BI). The phylogenetic results showed that N. nudus has a relationship with other isolates of the same species and the median-joining network showed the pattern of haplotypes that reflected the structure of the populations.

Characterization of the chloroplast genome of Gleditsia species and comparative analysis

The genus Gleditsia has significant medicinal and economic value, but information about the chloroplast genomic characteristics of Gleditsia species has been limited. Using the Illumina sequencing, we assembled and annotated the whole chloroplast genomes of seven Gleditsia species (Gleditsia sinensis, Gleditsia japonica var. delavayi (G. delavayi), G. fera, G. japonica, G. microphylla, Fructus Gleditsiae Abnormalis (Zhū Yá Zào), G. microphylla mutant). The assembled genomes revealed that Gleditsia species have a typical circular tetrad structure, with genome sizes ranging from 162,746 to 170,907 bp. Comparative genomic analysis showed that most (65.8-75.8%) of the abundant simple sequence repeats in Gleditsia and Gymnocladus species were located in the large single copy region. The Gleditsia chloroplast genome prefer T/A-ending codons and avoid C/G-ending codons, positive selection was acting on the rpoA, rpl20, atpB, ndhA and ycf4 genes, most of the chloroplast genes of Gleditsia species underwent purifying selection. Expansion and contraction of the inverted repeat (IR)/single copy (SC) region showed similar patterns within the Gleditsia genus. Polymorphism analysis revealed that coding regions were more conserved than non-coding regions, and the IR region was more conserved than the SC region. Mutational hotspots were mostly found in intergenic regions such as "rps16-trnQ", "trnT-trnL", "ndhG-ndhI", and "rpl32-trnL" in Gleditsia. Phylogenetic analysis showed that G. fera is most closely related to G. sinensis,G. japonica and G. delavayi are relatively closely related. Zhū Yá Zào can be considered a bud mutation of the G. sinensis. The albino phenotype of G. microphylla mutant is not caused by variations in the chloroplast genome, and that the occurrence of the albino phenotype may be due to mutations in chloroplast-related genes involved in splicing or localization functions. This study will help us enhance our exploration of the genetic evolution and geographical origins of the Gleditsia genus.