DnaSP v5: a software for comprehensive analysis of DNA polymorphism data

Mycotoxigenic Fusarium species and zearalenone concentration in commercial maize kernels in northern Ghana

The fungal genus Fusarium contains many toxigenic pathogens of maize with associated yield losses, reduction of grain quality, and accumulation of mycotoxins in harvested grains. To determine zearalenone (ZEN) concentration and identify the various Fusarium species in commercial maize grains, a survey of 75 maize samples, collected from 11 market centers in the five regions in northern Ghana was identified based on morphological characteristics, sequence analysis of the internal transcribed spacer region, and polymerase chain reaction using species-specific primers. ZEN levels were determined using HPLC. ZEN contamination was recorded in 33.3% of the maize samples, with concentrations ranging from 0.61 to 3.05 µg/kg. Based on VERT1/2 and TEF 1-α sequencing, F. verticillioides was the most prevalent species in the studied samples: 40.35% from the Upper East Region, 28.07% from the North East Region, 19.30% from the Upper West Region, 10.53% from the Savannah Region, and 1.75% for the Northern Region. Other fungal species found were F. equiseti and F. solani. A higher number of the Fusarium isolates were found in white maize (609 isolates from 27 samples) compared to yellow maize (225 isolates from 23 samples).

Unravelling the genomic landscape reveals the presence of six novel odorant-binding proteins in whitefly Bemisia tabaci Asia II-1

Genome wide analysis identified 14 OBPs in B. tabaci Asia II-1, of which six are new to science. Phylogenetic analysis traced their diversity and evolutionary lineage among Hemipteran insects. Comparative analysis reclassified the OBP gene families among B. tabaci cryptic species: Asia I, II-1, MEAM1, and MED. The 14 OBPs were clustered on four chromosomes of B. tabaci. RT-qPCR showed high expression of OBP3 and 8 across all body tissues and OBP10 in the abdomen. Molecular docking showed that OBP 3 and 10 had high affinity bonding with different candidate ligands, with binding energies ranging from -5.0 to -7.7 kcal/mol. Competitive fluorescence binding assays revealed that β-caryophyllene and limonene had high binding affinities for OBP3 and 10, with their IC50 values ranging from 9.16 to 14 μmol·L-1 and KD values around 7 to 9 μmol·L-1. Behavioural assays revealed that β-caryophyllene and carvacrol were attractants, β-ocimene and limonene were repellents, and γ-terpinene and β-ocimene were oviposition deterrents to B. tabaci. Functional validation by RNAi demonstrated that OBP3 and OBP10 modulated host recognition of B. tabaci. This study expands our understanding of the genomic landscape of OBPs in B. tabaci, offering scope for developing novel pest control strategies.

Wild rice GL12 synergistically improves grain length and salt tolerance in cultivated rice

The abounding variations in wild rice provided potential reservoirs of beneficial genes for rice breeding. Maintaining stable and high yields under environmental stresses is a long-standing goal of rice breeding but is challenging due to internal trade-off mechanisms. Here, we report wild rice GL12W improves grain length and salt tolerance in both indica and japonica genetic backgrounds. GL12W alters cell length by regulating grain size related genes including GS2, and positively regulates the salt tolerance related genes, such as NAC5, NCED3, under salt stresses. We find that a G/T variation in GL12 promoter determined its binding to coactivator GIF1 and transcription factor WRKY53. GIF1 promotes GL12W expression in young panicle and WRKY53 represses GL12W expression under salt stresses. The G/T variation also contributes to the divergence of indica and japonica subspecies. Our results provide useful resources for modern rice breeding and shed insights for understanding yield and salt tolerance trade-off mechanism.

Genetic analyses of Anisakis pegreffii (Nematoda: Anisakidae) from the East Asian finless porpoise Neophocaena asiaeorientalis sunameri (Cetacea: Phocoenidae) in Korean waters

The East Asian finless porpoise, Neophocaena asiaeorientalis sunameri, is an endangered species that inhabits the coastal marine environments of East Asia. In the present study, we investigated the overall infection status of anisakid nematodes in East Asian finless porpoises from three sea sectors off the Korean Peninsula. The genetic diversity and population genetic structure of the identified nematode species were evaluated. The prevalence of all stages of anisakid nematodes collected from the stomach was 57.55% (61 among the 106 porpoises examined), and 16 of the hosts were found to have adult worms. The mean number of infected adults was 211 (± 419.54, 5-1455 per host). Only one species of anisakids, Anisakis pegreffii, was identified from randomly selected worms by molecular approaches. Analysis of the mitochondrial (mt) cox2 partial gene in 50 newly generated sequences of A. pegreffii revealed 24 haplotypes, including 14 new haplotypes. We observed below-average levels of nucleotide diversity and haplotype diversity compared to other seas around the world. The mtDNA cox2 haplotypes of the species in the three Korean sea areas showed no genetic structure, suggesting well-connected gene flow within these areas. This study represents the first record of a definitive host of A. pegreffii in Korean waters, providing important information regarding anisakids genetic diversity in the cetacean species inhabiting limited regions.

Comparative analysis of complete chloroplast genomes of 14 Asteraceae species

BACKGROUND

The Asteraceae family, the largest and one of the most diverse families of angiosperms, presents significant challenges in taxonomic classification and systematic research due to its vast species diversity and morphological complexity. A comprehensive understanding of the chloroplast genomes within this family is essential for refining taxonomic classifications and advancing phylogenetic studies.

METHODS AND RESULTS

In this study, we sequenced the complete chloroplast genomes of 14 Asteraceae species and conducted a thorough bioinformatic analysis of their characteristics. The chloroplast genomes, ranging from 150,907 bp to 152,858 bp, exhibit a typical quadripartite structure: a large single-copy (LSC) region (83,044 bp to 84,625 bp), a small single-copy (SSC) region (18,223 bp to 18,673 bp), and a pair of inverted repeats (IRs) (24,806 bp to 25,201 bp). These genomes encode 87 to 89 protein-coding genes (PCGs), 36 to 37 tRNA genes, and 8 rRNA genes, with high conservation in size, structure, gene content, and order. Comparative analysis with other Asteraceae species' chloroplast genomes revealed notable similarities and structural variations, particularly in the IR regions. Nucleotide polymorphism analysis identified four genes-trnY-GUA, trnE-UUC, ycf1, and rrn23-with higher Pi values, suggesting potential hotspots for evolutionary studies. Phylogenetic analysis using maximum likelihood (ML) and Bayesian inference (BI) approaches provided new insights, proposing the reclassification of Himalaiella auriculata and Jacobaea raphanifolia as independent genera, distinct from Saussurea and Senecio.

CONCLUSIONS

This study presents a comprehensive analysis of the chloroplast genome structures and phylogenetic relationships of 14 Asteraceae species, offering critical data for future molecular identification, evolutionary biology, and population genetics research. The findings hold significant implications for the ongoing refinement of Asteraceae taxonomic classifications and enhance our understanding of the evolutionary dynamics within this complex family.

Comparative and phylogenetic analysis of the chloroplast genomes of four commonly used medicinal cultivars of Chrysanthemums morifolium

'Boju' and 'Huaiju' are cultivars of the Chrysanthemum (Chrysanthemum morifolium Ramat.) in the family Asteraceae, valued for their medicinal, tea, and ornamental properties, and valued by individuals. However, the yield and quality of medicinal chrysanthemums are limited by the characteristics of the germplasm resources, including the identification at the varieties and cultivation levels. Currently, research characterizing the chloroplast genomes of medicinal Chrysanthemum flowers is relatively limited. This study conducted chloroplast whole-genome sequencing on two cultivars of Chrysanthemum, 'Boju' and 'Huaiju', and compared them with the previously published chloroplast genomes of 'Hangbaiju' and 'Gongju'. The study analyzed the chloroplast genome structures of these four medicinal Chrysanthemums, identifying mutation hotspots and clarifying their phylogenetic relationships. The chloroplast genome sizes of four medicinal Chrysanthemum cultivation products ranged from 151,057 to 151,109 bp, with GC content ranging from 37.45% to 37.76%. A total of 134 genes were identified, including 89 protein-coding genes, 37 ribosomal RNA genes, and 8 transfer RNA genes. Comparative genomic analysis revealed 159 large repeat sequences, 276 simple sequence repeats, 1 gene, and 8 intergenic regions identified as highly variable regions. Nucleotide diversity (Pi) values were high (≥ 0.004) for the petN-psbM, trnR-UCU-trnT-GGU, trnT-GGU-psbD, ndhC-trnV-UCA, ycf1, ndhI-ndhG, trnL-UGA-rpl32, rpl32-ndhF, and ndhF-ycf1 fragments, aiding in variety identification. Phylogenetic analysis revealed consistent results between maximum likelihood and Bayesian inference trees, showing that the four medicinal Chrysanthemum cultivars, along with their wild counterparts and related species, evolved as a monophyletic group, forming a sister clade to Artemisia and Ajania. Among the six Chrysanthemum species, the wild Chrysanthemum diverged first (Posterior probability = 1, bootstrap = 1,000), followed by Ajania, while C. indicum and C. morifolium clustered together (Bootstrap = 100), indicating their closest genetic relationship. The chloroplast whole-genome data and characteristic information provided in this study can be used for variety identification, genetic conservation, and phylogenetic analysis within the family Asteraceae.

Mitochondrial genome insights into the spatio-temporal distribution and genetic diversity of Dendrobium hancockii Rolfe (Orchidaceae)

Introduction

With its distinctive evolutionary rate and inheritance patterns separate from the nuclear genome, mitochondrial genome analysis has become a prominent focus of current research. Dendrobium hancockii Rolfe, a species of orchid with both medicinal and horticultural value, will benefit from the application of the fully assembled and annotated mitochondrial genome. This will aid in elucidating its phylogenetic relationships, comparative genomics, and population genetic diversity.

Methods

Based on sequencing results from Illumina combined with PacBio and Nanopore, the mitochondrial genome map of D. hancockii was constructed. Comparative analysis was conducted from the perspectives of phylogeny across multiple species, selection pressure on protein-coding genes, and homologous segments. The population diversity of D. hancockii was analyzed using single nucleotide polymorphism (SNP) data from the mitochondrial genome and single-copy nuclear genes.

Results and discussion

This research constructed a circular mitochondrial map for D. hancockii, spanning 523,952 bp, containing 40 unique protein-coding genes, 37 transfer RNA genes, and 4 ribosomal RNA genes. Comparative analysis of mitochondrial genes from 26 land plants revealed a conserved gene cluster, "rpl16-ccmFn-rps3-rps19," particularly within the Dendrobium genus. The mitochondrial genome of D. hancockii exhibits a lower point mutation rate but significant structural variation. Analysis of 103 resequencing samples identified 19,101 SNP sites, dividing D. hancockii into two major groups with limited gene flow between them, as supported by population diversity, genetic structure analysis, principal component analysis, and phylogenetic trees. The geographical distribution and genetic differentiation of D. hancockii into two major groups suggest a clear phytogeographical division, likely driven by ancient geological or climatic events. The close alignment of mitochondrial data with nuclear gene data highlights the potential of the mitochondrial genome for future studies on genetic evolution in this species.

Polymorphic Loci of Adaptively Significant Genes Selection for Determining Nucleotide Polymorphism of Pinus sylvestris L. Populations in the Urals

BACKGROUND

Scots Pine is one of the main forest-forming species in boreal forests; it has great economic and ecological significance. This study aimed to develop and test primers for detecting nucleotide polymorphisms in genes that are promising for detecting adaptive genetic variability in populations of Pinus sylvestris in the Urals and adjacent territories.

OBJECTIVES

The objects of the study were 13 populations of Scots Pine located in the Perm Territory, Chelyabinsk Region, and the Republic of Bashkortostan.

RESULTS

Sixteen pairs of primers to loci of potentially adaptively significant genes were developed, from which three pairs of primers were selected to detect the nucleotide diversity of the studied populations. The indicator of total haplotype diversity determined in the three studied loci varied from 0.620 (Pinus-12 locus) to 0.737 (Pinus-11 locus) and, on average, amounted to 0.662. The nucleotide diversity indicators in P. sylvestris in the study region were, on average, low (π = 0.004, θW = 0.013). Their highest values were found at the Pinus-12 locus (π = 0.005; θW = 0.032), and the lowest were found at the Pinus-15 locus (π = 0.003; θW = 0.002). This indicates that Pinus-15 is the most conserved of the three studied loci. In the three studied P. sylvestris loci associated with adaptation to environmental factors, 97 polymorphic positions were identified. The 13 populations of P. sylvestris are characterized by an average level of genetic diversity (Hd = 0.662; π = 0.004; θ = 0.013).

CONCLUSIONS

The polymorphic loci of adaptively significant genes of P. sylvestris can help identify the adaptive potential of pine forests in conditions of increasing ambient temperatures.

Comparative analysis of the whole mitochondrial genomes of four species in sect. Chrysantha (Camellia L.), endemic taxa in China

BACKGROUND

The sect. Chrysantha Chang of plants with yellow flowers of Camellia species as the "Queen of the Tea Family", most of these species are narrowly distributed endemics of China and are currently listed Grde-II in National Key Protected Wild Plant of China. They are commercially important plants with horticultural medicinal and scientific research value. However, the study of the sect. Chrysantha species genetics are still in its infancy, to date, the mitochondrial genome in sect. Chrysantha has been still unexplored.

RESULTS

In this study, we provide a comprehensive assembly and annotation of the mitochondrial genomes for four species within the sect. Chrysantha. The results showed that the mitochondrial genomes were composed of closed-loop DNA molecules with sizes ranging from 850,836 bp (C. nitidissima) to 1,098,121 bp (C. tianeensis) with GC content of 45.71-45.78% and contained 48-58 genes, including 28-37 protein-coding genes, 17-20 tRNA genes and 2 rRNA genes. We also examined codon usage, sequence repeats, RNA editing and selective pressure in the four species. Then, we performed a comprehensive comparison of their basic structures, GC contents, codon preferences, repetitive sequences, RNA editing sites, Ka/Ks ratios, haplotypes, and RNA editing sites. The results showed that these plants differ little in gene type and number. C. nitidissima has the greatest variety of genes, while C. tianeensis has the greatest loss of genes. The Ka/Ks values of the atp6 gene in all four plants were greater than 1, indicating positive selection. And the codons ending in A and T were highly used. In addition, the RNA editing sites differed greatly in number, type, location, and efficiency. Twelve, six, five, and twelve horizontal gene transfer (HGT) fragments were found in C. tianeensis, Camellia huana, Camellia liberofilamenta, and C. nitidissima, respectively. The phylogenetic tree clusters the four species of sect. Chrysantha plants into one group, and C. huana and C. liberofilamenta have closer affinities.

CONCLUSIONS

In this study, the mitochondrial genomes of four sect. Chrysantha plants were assembled and annotated, and these results contribute to the development of new genetic markers, DNA barcode databases, genetic improvement and breeding, and provide important references for scientific research, population genetics, and kinship identification of sect. Chrysantha plants.

Construction of a full-length infectious cDNA clone of zucchini tigre mosaic virus infecting snake gourd and genetic diversity analysis based on complete genome sequences of ZTMV isolates

Zucchini tigre mosaic virus (ZTMV) is a positive-sense single-stranded RNA virus belonging to the genus Potyvirus. In this study, a full-length infectious cDNA clone of a ZTMV strain infecting snake gourd (Trichosanthes cucumerina var. anguina L.) was constructed and shown to infect snake gourd, chieh-qua, zucchini, ridge gourd, and bitter melon. The complete genome sequence of ZTMV-FS7 (PP291701) showed the highest nucleotide sequence similarity to ZTMV-TW (86.2% identity). Genetic diversity analysis of 12 ZTMV isolates showed that the P1 gene had the highest variability. Selection pressure analysis indicated that all of the ZTMV genes were under negative selection. However, some sites, particularly within the P1 gene, were under positive selection.

High-throughput sequencing discovered diverse monopartite and bipartite begomoviruses infecting cucumbers in Saudi Arabia

Limited research in Saudi Arabia has devolved into the prevalence and genetic diversity of begomoviruses. Utilizing Illumina MiSeq sequencing, we obtained 21 full-length begomovirus sequences (2.7-2.8 kb) from eight cucumber plants grown in fields and greenhouses. We found that two complete begomovirus genomes were variants of the Boushehr strain of tomato yellow leaf curl virus (TYLCV) with nucleotide (nt) sequence identities of 94.7-95.9%. Another full-length genome was a variant of TYLCV-Iran with 94.6% identity. Five full-length sequences closely matched the DNA-A of watermelon chlorotic stunt virus (WmCSV) isolates with 97.9-98.7% nt sequence identities, while five sequences had their highest nt sequence identities (95.8-96.3%) with the DNA-B of WmCSV isolates. Simultaneously, four sequences were 99.1-99.6% identical to the DNA-A of tomato leaf curl Palampur virus (ToLCPalV). Four sequences matched the DNA-B of ToLCPalV reported from Iran and Saudi Arabia with identities ranging from 96.2-100%. Four plants showed a mixed infection of these begomoviruses. Most ORFs showed evidence of negative selection pressure, suggesting that purifying selection plays a crucial role in shaping the diversity of these begomoviruses. Additionally, potential intra- and interspecies recombination events were detected in the TYLCV and WmCSV DNA-B genomic regions. The ToLCPalV isolates identified in this study formed a cluster with the other ToLCPalV isolates reported from Saudi Arabia, Iran and Iraq, representing a unique lineage distinct from ToLCPalV reported from Southeast Asia. High mutation rate and robust selection facilitated the independent evolution of ToLCPalV without recombination. Overall, this study offers valuable insights into the diversity and evolutionary dynamics of begomoviruses infecting cucumber crops in Al-Ahsa, Saudi Arabia.

Assembly and comparative analysis of the first complete mitochondrial genome of zicaitai (Brassica rapa var. Purpuraria): insights into its genetic architecture and evolutionary relationships

Introduction

Zicaitai (Brassica rapa var. purpuraria) is a Brassica variety renowned for its distinctive taste and rich nutritional profile. In recent years, the mitochondrial genomes of several Brassica species have been documented, but the mitogenome of Zicaitai remains unreported.

Methods

In this study, we characterized the Zicaitai mitogenome achieved through the assembly of sequencing reads derived from both the Oxford Nanopore and Illumina platforms. A detailed comparative analysis was carried out with other Brassica species to draw comparisons and contrasts. In-depth analyses of codon usage patterns, instances of RNA editing, and the prevalence of sequence repeats within the mitogenome were also conducted to gain a more nuanced understanding of its genetic architecture. A phylogenetic analysis was performed, utilizing the coding sequences (CDS) from the mitochondrial genome of Zicaitai and that of 20 closely related species/varieties to trace evolutionary connections.

Results

The Zicaitai mitogenome is characterized by a circular structure spanning 219,779 base pairs, and it encompasses a total of 59 genes. This gene set includes 33 protein-coding genes, 23 tRNA genes, and 3 rRNA genes, providing a rich foundation for further genomic study. An analysis of the Ka/Ks ratios for 30 protein-coding genes shared by the mitogenomes of Zicaitai and seven other Brassica species revealed that most of these genes had undergone purifying selection. Additionally, the study explored the migration of genes between the chloroplast and nuclear genomes and the mitogenome, offering insights into the dynamics of genetic exchange within the Brassica genus.

Discussion

The collective results in this study will serve as a foundational resource, aiding future evolutionary studies focused on B. rapa, and contributing to a broader understanding of the complexities of plant evolution.

Genome-wide identification of m6A-related gene family and the involvement of TdFIP37 in salt stress in wild emmer wheat

KEY MESSAGE

The genomic organization, phylogenetic relationship, expression patterns, and genetic variations of m6A-related genes were systematically investigated in wild emmer wheat and the function of TdFIP37 regulating salt tolerance was preliminarily determined. m6A modification is one of the most abundant and crucial RNA modifications in eukaryotics, playing the indispensable role in growth and development as well as stress response in plants. However, its significance in wild emmer wheat remains elusive. Here, a genome-wide search of m6A-related genes was conducted in wild emmer wheat to obtain 64 candidates, including 21 writers, 17 erasers, and 26 readers. Phylogenetic and collinearity analysis demonstrated that segmental duplication and polyploidization contributed mainly to the expansion of m6A-related genes in wild emmer. A number of cis-acting elements involving in stress and hormonal regulation were found in the promoter regions of them, such as MBS, LTR, and ABRE. Genetic variation of them was also investigated using resequencing data and obvious genetic bottleneck was occurred on them during wild emmer wheat domestication process. Furthermore, the salt-responsive candidates were investigated through RNA-seq data and qRT-PCR validation using the salt-tolerant and -sensitive genotypes and the co-expression analysis showed that they played the hub role in regulating salt stress response. Finally, the loss-function mutant of Tdfip37 displayed the significantly higher salt-sensitive compared to WT and then RNA-seq analysis demonstrated that FIP37 mediated the MAPK pathway, hormone signal transduction, as well as transcription factor to regulate salt tolerance. This study provided the potential m6A genes for functional analysis, which will contribute to better understand the regulatory roles of m6A modification and also improve the salt tolerance from the perspective of epigenetic approach in emmer wheat and other crops.

Landscape Heterogeneity Drives Genetic Diversity in the Highly Dispersive Moss Funaria hygrometrica Hedw

Funaria hygrometrica, a cosmopolitan moss species known for its remarkable dispersal capacity, was selected as the focal organism to investigate the relationship between landscape features and genetic diversity. Our study encompassed samples collected from two distinct regions: the Spanish Sierra Nevada Mountains (SN), characterized by a diverse landscape with an altitudinal difference of nearly 3500 m within a short distance, and the Murcia Region (MU) in Southeast Spain, characterized by a uniform landscape akin to the lowlands of Sierra Nevada. Genotyping analysis targeted three genetic regions: the nuclear ribosomal internal transcribed spacer (nrITS), the chloroplast rps3-rpl16 region, and the mitochondrial rpl5-rpl16 spacer. Through this analysis, we aimed to assess genetic variability and population structure across these environmentally contrasting regions. The Sierra Nevada populations exhibited significantly higher haplotype diversity (Hd = 0.78 in the highlands and 0.67 overall) and nucleotide diversity (π% = 0.51 for ITS1) compared to the Murcia populations (Hd = 0.35, π% = 0.14). Further investigation unveiled that samples from the lowlands of Sierra Nevada showed a closer genetic affinity to Murcia than to the highlands of Sierra Nevada. Furthermore, the genetic differentiation between highland and lowland populations was significant (ΦST = 0.55), with partial Mantel tests and ResistanceGA analysis revealing a strong correlation between ITS1-based genetic diversity and landscape features, including altitude and bioclimatic variables. Our study elucidated potential explanations for the observed genetic structuring within F. hygrometrica samples' populations. These included factors such as a high selfing rate within restricted habitats, a limited average dispersal distance of spores, hybrid depression affecting partially incompatible genetic lineages, and recent migration facilitated via human activities into formerly unoccupied areas of the dry zones of Southeast Spain.

Hemoplasmas in wild rodents and marsupials from the Caatinga Biome, Brazil

A total of 231 blood samples from wild mammals belonging to the orders Rodentia (n = 142) and Didelphimorphia (n = 89) were screened by real-time PCR assay (qPCR), being six Rhipidomys sp., 118 Thrichomys laurentius, nine Rattus rattus, four Kerodon rupestris, five Necromys lasiurus, 42 Didelphis albiventris and 47 Monodelphis domestica. Results using qPCR showed that 32 of the total 231 (13.85 %) samples were positive for hemoplasma sequences of the 16S rRNA gene. Sequences from two D. albiventris showed 99.77-99.89 % identity with 'Candidatus Mycoplasma haemoalbiventris' and 99.09 % with 'Candidatus Mycoplasma haemodidelphidis', respectively. Furthermore, one M. domestica and five T. laurentius showed 99.72-99.77 % identity with Mycoplasma sp., and one K. rupestris showed 98.13 % identity with 'Candidatus Mycoplasma haematohydrochaerus'; and from two Rattus rattus showed 99.65-99.89 % identity with Mycoplasma sp. and 'Candidatus Mycoplasma haemomuris'. The 23S rRNA gene sequences obtained from the two D. albiventris showed 100 % identity with 'Ca. M. haemoalbiventris' whereas the sequences from the R. rattus showed only 85.31 % identity with 'Candidatus Mycoplasma haematohydrochaerus'. Two T. laurentius and one K. rupestris showed 84.66-92.97 % identity with 'Candidatus Mycoplasma haemosphiggurus'. Based on phylogenetic and Neighbor-Net network analyses of the 16S and 23S rRNA genes, potential novel species are described. In addition, 'Ca. M. haemoalbiventris' was detected in Didelphis albiventris, and Mycoplasma sp. was detected in Rattus sp. rodents from the Caatinga biome, Brazil.

Genetic Structure of Monochamus alternatus (Hope) in Qinling-Daba Mountains and Expansion Trend: Implications for Pest Prevention and Management

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

Conservation genomics of the critically endangered Chinese pangolin

The Chinese pangolin (Manis pentadactyla, MP) has been extensively exploited and is now on the brink of extinction, but its population structure, evolutionary history, and adaptive potential are unclear. Here, we analyzed 94 genomes from three subspecies of the Chinese pangolin and identified three distinct genetic clusters (MPA, MPB, and MPC), with MPB further divided into MPB1 and MPB2 subpopulations. The divergence of these populations was driven by past climate change. For MPB2 and MPC, recent human activities have caused dramatic population decline and small population size as well as increased inbreeding, but not decrease in genomic variation and increase in genetic load probably due to strong gene flow; therefore, it is crucial to strengthen in situ habitat management for these two populations. By contrast, although human activities have a milder impact on MPA, it is at high risk of extinction due to long-term contraction and isolation, and genetic rescue is urgently needed. MPB1 exhibited a relatively healthy population status and can potentially serve as a source population. Overall, our findings provide novel insights into the conservation of the Chinese pangolin and biogeography of the mammals of eastern Asia.

Mitogenomics clarifies the position of the Nearctic magpies (Pica hudsonia and Pica nuttalli) within the Holarctic magpie radiation

Partial separation of a peripheral population may lead to its divergence and, potentially, speciation due to genetic drift followed by selection and geographic isolation. This process may cause taxonomic uncertainty because reproductive isolation in allopatry cannot be verified directly. The two Nearctic allopatric species of magpies (Aves, Corvidae: Pica) serve as a good example of these problems. The Black-billed magpie Pica hudsonia is widely distributed in North America, whereas the Yellow-billed Magpie Pica nuttalli is endemic to a restricted range in California. Their relationships with Palearctic species have been little studied. We obtained complete mitochondrial genomes of both Nearctic magpie species, along with the Eurasian Magpie (Pica pica) and the Oriental Magpie (Pica serica), 20 mitogenomes in total. Phylogenetic analysis reveals a basal position of P. serica, and P. pica as a sister clade to the two Nearctic species. P. hudsonia and P. nuttalli form reciprocal monophyletic subclades, showing recent divergence between and within them. Our data show that the Nearctic magpie lineage diverged from the common ancestor with P. pica, with a single migration wave via the Beringia. Within the Nearctic, we hypothesize a peripatric mode of speciation among Pica taxa due to the divergence and separation of the small marginal population in California below the Sierra-Nevada mountains. Diversifying amino acid substitutions in ND4-ND5-ND6 genes along the branch leading to the New World clade may indicate selection for heat-tolerance. Considering the clear phenotypic differences between P. hudsonia and P. nuttalli, our data, showing their reciprocal monophylies and genetic distinctness, is consistent with the two-species taxonomy.

Seascape Genetics and Distinct Intraspecific Diversification of the Decapod Nephrops norvegicus in the Adriatic Sea

Norway lobster Nephrops norvegicus, a prized decapod crustacean species, is found at different depths across the East Atlantic Ocean and Mediterranean Sea. Despite management efforts, the stocks are globally characterised as overexploited. In the present study, the impact of biogeographical boundaries on the phylogeographical and demographic population status was investigated within the Adriatic Sea, addressing important genetic indices for decapod functional conservation management. Central Mediterranean, Adriatic Sea A total of 482 individuals of Nephrops divided into the 12 samples were collected across biogeographical range of the Adriatic Sea. Using the mtDNA D-loop and microsatellite markers, methods of phylogeography and seascape genetics were applied to infer offshore versus coastal population divergence, demography and structure. Significant findings include genetic differentiation between offshore and coastal samples, with higher diversity indices in open waters. The limited gene flow observed between these two areas emphasises the self-sustained nature of coastal populations. Recent demographic changes in coastal populations reflect geographical constraints, fishing pressures and fluctuations in self-recruitment success. Additionally, the study reveals historical biogeographic events shaping the Adriatic populations, with evidence suggesting lineage divergence during the upper Pleistocene and postglacial recolonisation from southern Adriatic refugia. The role of biogeographical conditions in shaping genetic structure and limited gene flow between inshore and offshore areas underscore the need for improved management strategies, emphasising the importance of marine protected areas in conserving coastal populations and maintaining overall genetic diversity of the Norway lobster in the Adriatic Sea. Genomic monitoring within current management practices is recommended.

Comparative study on chloroplast genome of Tamarix species

Tamaricaceae comprises about 120 species and has a long evolutionary history, Tamarix Linn accounts for approximately 75% of the total species in this family. It is the most widely distributed and diverse genus in the family. They have important ecological significance for transforming deserts and improving climate conditions. However, Tamarix is the most poorly classified genera among flowering plants owing to its large variability and high susceptibility to interspecific hybridization. In this study, the complete chloroplast genomes of three Tamarix species and one draft chloroplast genome were obtained in this study. Combined with eight chloroplast genomes deposited in GenBank, complete chloroplast sequences of 12 Tamarix species were used for further analysis. There are 176 non-SSR-related indels and 681 non-indel-related SSRs in the 12 Tamarix chloroplast genomes. The mononucleotide SSRs are the most prevalent among all types of SSRs. The mVISTA results indicate high sequence similarities across the chloroplast genome, suggesting that the chloroplast genomes are highly conserved, except for sample Tamarix androssowii (ENC850343). The IR regions and the coding regions are more conserved than the single-copy and noncoding regions. The trnF-ndhJ, ndhC-trnM-CAU, ycf1, and trnL-UAG-ndhF regions are the most variable and have higher variability than those of the universal DNA markers. Finally, the first phylogenetic tree of Tamaricaceae was constructed which confirmed the monophyly of Tamarix in Tamaricaceae. The first phylogenetic tree of Tamarix was based on the complete chloroplast genome to date, the changes in branch length and support rate can potentially help us clarify the phylogenetic relationships of Tamarix. All the obtained genetic resources will facilitate future studies in population genetics, species identification, and conservation biology of Tamarix.

Apennine-Pyrenees disjunct distribution: an unusual biogeographic pattern revealed in flea beetles of the Longitarsus candidulus species-group (Coleoptera, Chrysomelidae)

European mountain systems have played a crucial role in shaping the distribution of species and of their genetic diversity during the Quaternary climatic changes, with the establishment of allopatric patterns across main mountain ranges. Here we investigated the evolutionary history of flea beetles of the Longitarsus candidulus species-group showing an uncommon disjunct biogeographic pattern across the Apennine and the Pyrenees. We applied a multilocus molecular approach and multispecies coalescent models to establish a phylogenetic and systematic framework for this morphologically homogeneous species-group and to estimate the time of main cladogenetic events underlying the origin of the Apennine-Pyrenees pattern. We found strong support for the monophyly of the candidulus group with a sister relationship between Longitarsus laureolae and L. leonardii endemic to the Apennine and the Pyrenees mountains respectively. The timing of speciation events in the candidulus species-group coincides with 2 major climatic transitions during the Early and Middle Pleistocene which resulted in significant environmental changes in Europe and suggest a scenario of allopatric isolation and divergence on distinct mountain ranges. The split between the thermophilic species L. candidulus and the ancestor of the temperate species L. laureolae and L. leonardii is estimated at ~3 Ma during the transition from Pliocene to Pleistocene and was probably triggered by their segregation in xerophilous and temperate habitats. The speciation between L. laureolae and L. leonardii, estimated at ~1 Ma during the Mid-Pleistocene Transition, can be explained by the establishment of unfavorable conditions in West Alps and Central Massif underlying the onset of the Apennine-Pyrenees disjunct pattern. Finally, the strict association between members of the candidulus group and distinct Thymelaeaceae plants suggests further studies to address the hypothesis that speciation in these flea beetles might have been also associated with Pleistocene range changes of their host plants.

DWARF AND LESS TILLERS ON CHROMOSOME 3 promotes tillering in rice by sustaining FLORAL ORGAN NUMBER 1 expression

Three key factors determine yield in rice (Oryza sativa): panicle number, grain number, and grain weight. Panicle number is strongly associated with tiller number. Although many genes regulating tillering have been identified, whether Dof proteins are involved in controlling plant architecture remains unknown. The dwarf and less tillers on chromosome 3 (dlt3) rice mutant produces fewer tillers than the wild type. We cloned DLT3, which encodes a Dof protein that interacts with MONOCULM 3 (MOC3) in vivo and in vitro and recruits MOC1, forming a DLT3-MOC3-MOC1 complex. DLT3 binds to the promoter of FLORAL ORGAN NUMBER 1 (FON1) to activate its transcription and positively regulate tiller number. The overexpression of MOC1, MOC3, or FON1 in the dlt3 mutant increased tiller number. Collectively, these results suggest a model in which DLT3 regulates tiller number by maintaining the expression of MOC1, MOC3, and FON1. We discovered that DLT3 underwent directional selection in the Xian/indica and Geng/japonica populations during rice domestication. To provide genetic resources for breeding varieties with optimal panicle numbers, we performed large-scale diversity sequencing of the 1,080-bp DLT3 coding region of 531 accessions from different countries and regions. Haplotype analysis showed that the superior haplotype, DLT3H1, produced the most tillers, while haplotype DLT3H6 produced the fewest tillers. Our study provides important germplasm resources for breeding super high-yielding rice varieties with combinations of superior haplotypes in different target genes, which will help overcome the challenge of food and nutritional security in the future.

Characterization of the Complete Mitochondrial Genome of Pleurogenoides japonicus (Digenea, Pleurogenidae): Comparison With the Members of Microphalloidea and Phylogenetic Implications

Pleurogenoides japonicus (Trematoda: Microphalloidea) is an important parasite in wood frogs with high infection rates and significant ecological, economic, and societal importance. The scarcity of molecular data for these parasites severely limits population genetics and phylogenetic studies. In the present study, for the first time, we determined and described the entire mitochondrial (mt) genome of P. japonicus as the first representative of the family Pleurogenidae. The entire mt genome of P. japonicus was circular, with 15,043 bp (GenBank accession number OR900118), containing 36 genes, comprising 12 protein-coding genes (cox1-3, nad1-6, nad4L, cytb, and atp6), two ribosomal RNA genes, 22 transfer RNA genes, and two non-coding regions. There were 23 intergenic spacers, ranging from 2 to 162 bp, and only one 40 bp overlap between nad4L and nad4 genes in the P. japonicus mt genome. The nucleotide composition of P. japonicus mt genome exhibited a strong AT bias with a 63.75% A + T content, while the AT- and GC-skews were - 0.435 and 0.407, respectively. Comparative analysis demonstrated that the P. japonicus mt genome shared the most common characteristics with Microphalloidea trematodes, and the cox1 gene was the longest and most conserved gene in Microphalloidea trematodes. The gene arrangements of Xiphidiata trematodes were of the same order based on protein-coding genes and rRNA genes, except for tRNA. More than two gene arrangement types exist in Echinostomata and Xiphidiata, and the gene rearrangement events mainly occurred in "trnE-trnG" and "trnG-trnE". Phylogenetic analysis suggested that trematodes of the family Pleurogenidae clustered more with Prosthogonimidae than Eucotylidae. The mt genome data of P. japonicus provide an accurate genetic marker for further studies of Xiphidiata trematodes.

Comparative analyses of plastomes in Allaeanthus and Malaisia: structure, evolution, and phylogeny

The small genera Allaeanthus and Malaisia within the Moraceae have important edible, medicinal, and economic value. However, complete plastome blueprints and a well-resolved evolutionary history of these two genera are still lack, thereby limiting their conservation and application. The recent discovery of a new distribution of Allaeanthus kurzii in Hainan, China, marked by the collection of two unique samples, alongside three samples of Malaisia scandens, has opened new avenues for research. This study aimed to compare the Allaeanthus and Malaisia plastomes of Hainan Province samples with those of samples from other regions, focusing on plastome structure, codon usage bias, natural selection, and the evolutionary history of A. kurzii and M. scandens. The results showed that both species had a quadripartite plastome structure, with sizes ranging from 162,134 to 162,170 bp for A. kurzii and 161,235 to 162,134 bp for M. scandens. Both species displayed loss of the infA gene and reduction of the rpl22 gene. Two highly variable regions (petD-trnD-GUC and rpl20-clpP) and three highly variable genes (rpl20, petB, and rpl16) were identified in A. kurzii, while two highly variable regions (ycf2-ndhB and ccsA-ndhE) and three highly variable genes (psbT, rpl36, and ycf2) were found in M. scandens. The protein-coding sequences (CDSs) of the Allaeanthus and Malaisia plastomes exhibited similar patterns of adaptive indices and codon usage frequencies. The genes associated with photosynthesis underwent strong purifying selection. Phylogenetic analysis revealed that Allaeanthus, Broussonetia, and Malaisia constituted a monophyletic group, with Malaisia being more closely related to Broussonetia. Broussonetia diversified approximately 19.78 million years ago, Malaisia approximately 4.74 million years ago, and Allaeanthus approximately 16.18 million years ago. These new plastome-based discoveries will guide conservation planners and medicinal plant breeders and genetic resource development for these species in the region.

Genetic Attributes and Conservation of an Endangered Giant Water Bug Species, Diplonychus esakii Miyamoto and Lee, 1966 (Hemiptera: Belostomatidae)

Diplonychus esakii, a water bug from the family Belostomatidae, plays an important role in freshwater ecosystems as one of the top predators. In this study, we investigated the genetic diversity and population structure of D. esakii by analyzing 318 specimens across 27 sites in South Korea. We found that the populations of D. esakii possess 11 haplotypes with a haplotype diversity of 0.623. This represents a relatively low level of genetic diversity compared to other known belostomatids and endangered species. AMOVA and FST analyses revealed significant genetic differentiation among populations, with most populations harboring only 1-2 haplotypes, suggesting restricted gene flow between populations and a low level of genetic diversity. This low genetic diversity and limited gene flow suggest a potential vulnerability to environmental changes and an increased risk of extinction, indicating that D. esakii should be designated as a protected species in South Korea as part of future conservation efforts. Based on the results of this study, Upo Wetland, which maintains relatively high levels of genetic diversity and Jeju Island, which, despite its lower genetic diversity compared to the mainland, does not share haplotypes with other regions, should be considered key conservation units for this species. This study highlights the importance of incorporating genetic information into conservation status assessments under the Red List Categories and Criteria and also emphasizes the need to evaluate this species on the Korean Red List. The data provided here will serve as essential baseline information and valuable resources for the development of effective conservation strategies.

Random epigenetic inactivation of the X-chromosomal HaMSter gene causes sex ratio distortion in persimmon

In contrast to the recent progress in the genome sequencing of plant sex chromosomes, the functional contribution of the genes in sex chromosomes remains little known1. They were classically thought to be related to sexual dimorphism, which is beneficial to male or female functions, including segregation ratios. Here we focused on the functional evolution of the sex ratio distortion-related locus Half Male Sterile/Inviable (HaMSter), which is located in the short sex-linked region in diploid persimmon (Diospyros lotus). The expression of HaMSter, encoding a plant1589-like undefined protein, is necessary for production of viable seeds. Notably, only X-allelic HaMSter is substantially expressed and half of the maternal X alleles of HaMSter is randomly inactivated, which results in sex ratio distortion in seeds. Genome-wide DNA methylome analyses revealed endosperm-specific DNA hypermethylation, especially in the X-linked region. The maintenance/release of this hypermethylation is linked to inactivation/activation of HaMSter expression, respectively, which determines the sex ratio distortion pattern.

Hot Spots of Site-Specific Integration into the Sinorhizobium meliloti Chromosome

The diversity of phage-related sequences (PRSs) and their site-specific integration into the genomes of nonpathogenic, agriculturally valuable, nitrogen-fixing root nodule bacteria, such as Sinorhizobium meliloti, were evaluated in this study. A total of 314 PRSs, ranging in size from 3.24 kb to 88.98 kb, were identified in the genomes of 27 S. meliloti strains. The amount of genetic information foreign to S. meliloti accumulated in all identified PRSs was 6.30 Mb. However, more than 53% of this information was contained in prophages (Phs) and genomic islands (GIs) integrated into genes encoding tRNAs (tRNA genes) located on the chromosomes of the rhizobial strains studied. It was found that phiLM21-like Phs were predominantly abundant in the genomes of S. meliloti strains of distant geographical origin, whereas RR1-A- and 16-3-like Phs were much less common. In addition, GIs predominantly contained fragments of phages infecting bacteria of distant taxa, while rhizobiophage-like sequences were unique. A site-specific integration analysis revealed that not all tRNA genes in S. meliloti are integration sites, but among those in which integration occurred, there were "hot spots" of integration into which either Phs or GIs were predominantly inserted. For the first time, it is shown that at these integration "hot spots", not only is the homology of attP and attB strictly preserved, but integrases in PRSs similar to those of phages infecting the Proteobacteria genera Azospirillum or Pseudomonas are also present. The data presented greatly expand the understanding of the fate of phage-related sequences in host bacterial genomes and also raise new questions about the role of phages in bacterial-phage coevolution.

Next Generation Sequencing and Genetic Analyses Reveal Factors Driving Evolution of Sweetpotato Viruses in Uganda

Sweetpotato (Ipomoea batatas L.) is an essential food crop globally, especially for farmers facing resource limitations. Like other crops, sweetpotato cultivation faces significant production challenges due to viral infections. This study aimed to identify and characterize viruses affecting sweetpotato crops in Uganda, mostly those associated with sweetpotato virus disease (SPVD). Infected leaf samples were collected from farmers' fields in multiple districts spanning three regions in Uganda. MiSeq, a next-generation sequencing platform, was used to generate reads from the viral nucleic acid. The results revealed nine viruses infecting sweetpotato crops in Uganda, with most plants infected by multiple viral species. Sweet potato pakakuy and sweet potato symptomless virus_1 are reported in Uganda for the first time. Phylogenetic analyses demonstrated that some viruses have evolved to form new phylogroups, likely due to high mutations and recombination, particularly in the coat protein, P1 protein, cylindrical inclusion, and helper component proteinase regions of the potyvirus. The sweet potato virus C carried more codons under positive diversifying selection than the closely related sweet potato feathery mottle virus, particularly in the P1 gene. This study provides valuable insights into the viral species infecting sweetpotato crops, infection severity, and the evolution of sweet potato viruses in Uganda.

The Complete Mitochondrial Genomes of Penthe kochi (Coleoptera: Tetratomidae) with Its Phylogenetic Implications

To explore the mitogenome characteristics of Tetratomidae and the phylogenetic position of this family in Tenebrionoidea, the mitogenome of Penthe kochi Mařan, 1940 was sequenced, annotated, and analyzed. The P. kochi mitogenome is consistent with Tenebrionoidea species in gene length, genomic organization, codon usage, and secondary structures of transfer genes (tRNAs). Most protein-coding genes (PCGs) originate with a typical ATN start codon, except nad1 and nad3, which start with TTG. In total, 10 PCGs are terminated with complete stop codon TAA and TAG, while cox1, cox2, and nad 4 contain an incomplete stop codon T-. Among the 13 PCGs, nad2 (Pi = 0.282) has the most diverse nucleotide composition, and cox2 is the most conserved gene with the lowest value (Pi = 0.154). The Ka/Ks ratio of cox1 (0.076) and cox2 (0.124) has a lower value. All the tRNAs can be folded in a typical clover-leaf secondary structure, except trnS1, which lacked a dihydrouridine arm. And phylogenetic analyses were performed based on 13 PCGs using the Bayesian inference (BI) method. The results showed that the clade of Tenebrionoidea was well separated from the outgroups, and Tetratomidae and Mycetophagidae were not well resolved. Phylogenetic analyses with more mitogenome samplings are needed to resolve the phylogeny of Tenebrionoidea.

Geographic genetic variation in the Coral Hawkfish, Cirrhitichthys oxycephalus (Cirrhitidae), in relation to biogeographic barriers across the Tropical Indo-Pacific

The Tropical Indo-Pacific (TIP) includes about two thirds of the world's tropical oceans and harbors an enormous number of marine species. The distributions of those species within the region is affected by habitat discontinuities and oceanographic features. As well as many smaller ones, the TIP contains seven large recognized biogeographic barriers that separate the Red Sea and Indian Ocean, the Indian from the Pacific Ocean, the central and eastern Pacific, the Hawaiian archipelago, the Marquesas and Easter Islands. We examined the genetic structuring of populations of Cirrhitichthys oxycephalus, a small cryptic species of reef fish, across its geographic range, which spans the longitudinal limits of the TIP. We assessed geographic variation in the mitochondrial cytb gene and the nuclear RAG1 gene, using 166 samples collected in 46 localities from the western to eastern edges of the TIP. Sequences from cytb show three well-structured groups that are separated by large genetic distances (1.58-2.96%): two in the Tropical Eastern Pacific (TEP), one at Clipperton Atoll another occupying the rest of that region and the third that ranges across the remainder of the TIP, from the central Pacific to the Red Sea and South Africa. These results indicate that the ~4,000 km wide Eastern Pacific Barrier between the central and eastern Pacific is an efficient barrier separating the two main groups. Further, the ~950 km of open ocean that isolates Clipperton Atoll from the rest of the TEP is also an effective barrier. Contrary to many other cases, various major and minor barriers from the Central Indo-Pacific to the Red Sea are not effective against dispersal by C. oxycephalus, although this species has not colonized the Hawiian islands and Easter Island. The nuclear gene partially supports the genetic structure evident in cytb, although all haplotypes are geographically mixed.

Relationships between crayfish population genetic diversity, species richness, and abundance within impounded and unimpounded streams in Alabama, USA

Understanding the relationship between multi-scale processes driving community- and population-level diversity can guide conservation efforts. While the importance of population-level genetic diversity is widely recognized, it is not always assessed for conservation planning, and positive correlations with community-level diversity are sometimes assumed, such that only the latter is measured. We surveyed species richness and cumulative multispecies abundance of crayfishes in impounded and unimpounded streams in the southern Appalachian Mountains (Alabama, USA). We simultaneously assessed levels of population genetic diversity within two focal crayfishes (Faxonius validus and F. erichsonianus) using nuclear (nDNA; inter-simple sequence repeat (ISSR)) and mitochondrial DNA (mtDNA; mitochondrial DNA cytochrome oxidase subunit I (mtCOI)) markers. We then tested for species-genetic diversity correlations (SGDCs), species diversity-abundance correlations (i.e., more individuals hypothesis, MIH), and abundance-genetic diversity correlations (AGDCs) across sites. We also examined the relationship between each of the three different types of correlation (i.e., species richness, cumulative multispecies abundance, and population genetic diversity) and stream habitat characteristics and fragmentation. Surprisingly, based on F. validus mtDNA data, sites with the greatest multispecies abundance had the lowest genetic diversity, indicating a negative AGDC. However, no AGDC was evident from nDNA. There was no evidence of SGDCs for F. validus based on either of the two genetic data types. For F. erichsonianus, there was no evidence for SGDC or AGDC. When considering the community-level data only, there was no support for the MIH. Stream width was positively correlated with F. validus genetic diversity, but negatively correlated with multispecies abundance. Similarly, species richness was positively correlated with stream width in unimpounded streams but negatively correlated with width in impounded streams. These findings indicate that community-level diversity cannot be indiscriminately used as a proxy for population-level diversity without empirically testing this correlation on the focal group. As such, community- and population-level assessments for multiple crayfish species are needed to better understand drivers of diversity and eco-evolutionary processes which will aid in the conservation of this vulnerable taxonomic group.

Comparison of organelle genomes between endangered mangrove plant Dolichandrone spathacea to terrestrial relative provides insights into its origin and adaptative evolution

Dolichandrone spathacea is a mangrove associate with high medicinal and ecological values. However, due to the dual-pressure of climate change and human activities, D. spathacea has become endangered in China. Moreover, misidentification between D. spathacea and its terrestrial relative D. cauda-felina poses further challenges to field protection and proper medicinal usage of D. spathacea. Thus, to address these problems, we sequenced and assembled mitochondrial (mt) and chloroplast (cp) genomes for both D. spathacea and D. cauda-felina. Comparative analysis revealed apparently different size and scaffold number between the two mt genomes, but a high similarity between the cp genomes. Eight regions with high sequence divergence were identified between the two cp genomes, which might be used for developing candidate DNA markers for distinguishing the two species. The splitting between D. spathacea and D. cauda-felina was inferred to occur at ~6.8 - 7.7 million years ago (Mya), which may be driven by the environment fluctuations in late Miocene. In the cp genome, 12 genes related to the expression of photosynthesis-associated proteins were detected with signatures of positive selection, which may contribute to the origin and evolutionary adaptation of Dolichandrone mangrove species. These new findings do not only enrich organelle genomic resources of Dolichandrone species, but also provide important genetic clues for improving the conservation and proper usage of endangered mangrove associate D. spathacea.

Glacial history of Saxifragawahlenbergii (Saxifragaceae) in the context of refugial areas in the Western Carpathians

Despite the wealth of data available for mountain phylogeography, local-scale studies focused on narrow endemic species remain rare. Yet, knowledge of the genetic structure of such species biogeographically linked to a restricted area is of particular importance to understand the history of the local flora and its diversity patterns. Here, we aim to contribute to the phylogeographical overview of the Western Carpathians with a genetic study of Saxifragawahlenbergii, one of the most characteristic endemic species of this region. We sampled populations from all discrete parts of the species' distribution range to apply sequencing of selected non-coding cpDNA and nuclear ribosomal DNA (ITS) regions, as well as Amplified Fragment Length Polymorphism (AFLP) fingerprinting. First, while ITS sequences showed weak diversification, the genetic structure based on cpDNA sequences revealed two well-differentiated groups of haplotypes. One of them is restricted to the main center of the distribution range in the Tatra Mountains (Mts), while the second group included a series of closely related haplotypes, which in most cases were unique for particular isolated groups of populations in peripheral mountain ranges and in the south-eastern part of the Tatra Mts. AFLP fingerprinting also revealed a pattern of divergence among populations, while only partly corroborating the division observed in cpDNA. Taking into account all the data, the pattern of genetic structure, supported by the high levels of unique genetic markers in populations, may reflect the historical isolation of populations in several local refugia during the last glacial period. Not only the center of the range in the Tatra Mts, but also other, neighboring massifs (Malá Fatra, Nízke Tatry, Chočské vrchy, Muránska planina), where populations are characterized by separate plastid DNA haplotypes, could have acted as separate refugia.

Age-dependent variation of aedeagal morphology in Agabusuliginosus and the status of A.lotti (Coleoptera, Dytiscidae)

A doubt has arisen about the taxonomic status of Agabuslotti within the Agabusuliginosus species group due to morphological similarities and lack of molecular data. In this study, a comprehensive morphological and molecular analysis of specimens from Central Europe was conducted, focusing on the Hungarian population. Morphological comparisons of genital structures revealed age-dependent variations, suggesting a gradual transition from A.lotti to A.uliginosus. Molecular analysis of COI sequences further supported this hypothesis, showing minimal genetic differences among most specimens, with only one individual exhibiting distinctiveness. Therefore, A.lotti syn. nov. must be regarded as a junior synonym of A.uliginosus. Our findings also highlight the need for additional multi-marker studies covering a broader geographic range and including both molecular and morphological approaches to elucidate the taxonomic and phylogenetic relationships within this species group. The inclusion of Hungarian samples notably enriched the diversity of haplotypes, emphasizing the importance of expanding sampling efforts in future research.

Complete mitochondrial genome and phylogenetic analysis of Dollfustrema vaneyi (Trematoda: Bucephalidae)

BACKGROUND

The Bucephalidae is a large family of digenean trematodes but most previous analyses of its phylogenetic position have relied on a single mitochondrial gene or morphological features. Mitochondrial genomes (mitogenomes) remain unavailable for the entire family. To address this, we sequenced the complete mitogenome of Dollfustrema vaneyi and analyzed the phylogenetic relationships with other trematodes.

RESULTS

The circular genome of Dollfustrema vaneyi spanned 14,959 bp and contained 12 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes, and a major non-coding region. We used concatenated amino acid and nucleotide sequences of all 36 genes for phylogenetic analyses, conducted using MrBayes, IQ-TREE and PhyloBayes. We identified pronounced topological instability across different analyses. The addition of recently sequenced two mitogenomes for the Aspidogastrea subclass along with the use of a site-heterogeneous model stabilized the topology, particularly the positions of Azygiidae and Bucephalidae. The stabilized results indicated that Azygiidae was the closest lineage to Bucephalidae in the available dataset, and together, they clustered at the base of the Plagiorchiida.

CONCLUSIONS

Our study provides the first comprehensive description and annotation of the mitochondrial genome for the Bucephalidae family. The results indicate a close phylogenetic relationship between Azygiidae and Bucephalidae, and reveal their basal placement within the order Plagiorchiida. Furthermore, the inclusion of Aspidogastrea mitogenomes and the site-heterogeneous model significantly improved the topological stability. These data will provide key molecular resources for future taxonomic and phylogenetic studies of the family Bucephalidae.

Phlebotomine sand flies (Diptera: Psychodidae) of Bosnia and Herzegovina: distribution, ecology and environmental preferences

Sand flies (Diptera: Phlebotominae) are the principal vectors for the protozoan parasites Leishmania spp. and for phleboviruses. The sand fly fauna on the Balkan Peninsula, including Bosnia and Herzegovina (BIH), is diverse and the circulation of Leishmania infantum as well as phleboviruses has been proven. However, recent data on the sand fly fauna in BIH are scarce. In this study, we surveyed understudied regions in central and northeastern BIH to update the sand fly distribution and gain insights into the ecological and environmental factors shaping their appearance. CDC light trapping was conducted in 2022 and 2023 and a combination of morphological and molecular methods (cytochrome oxidase I barcoding) was performed for species identifications. We mapped the currently known distribution, modelled climatic suitability patterns and performed environmental analyses by applying machine learning methods. In addition, we analyzed blood meals by host gene sequencing and MALDI-TOF peptide mass mapping and screened for Leishmania spp. DNA and Phlebovirus RNA. Altogether, 591 sand flies of four species were trapped, predominantly Phlebotomus neglectus (97 %), but also Ph. balcanicus, Ph. mascittii, and Ph. papatasi. Records of seven sand fly species known to be endemic were plotted onto distribution maps based on 101 datapoints, identifying Ph. neglectus as the overall predominant species. The environmental analyses of sand fly species indicated variation in altitudinal, thermal, and precipitation conditions across the sand fly-positive sites. Phlebotomus simici, Phlebotomus tobbi, and Sergentomyia minuta are typically found exclusively in Mediterranean and subtropical climate zones, whereas other species typically inhabit continental regions. The Inverse Distance Weighted (IDW) interpolation of sand fly species numbers and Shannon entropy values suggested the southeastern coastal region of BIH as a primary focus for sand fly occurrence. This finding was corroborated by modeled average climatic suitability patterns for sand flies, depicting four distinct meso-regions for sand fly occurrence. The results of the ensemble method highlight the importance of annual precipitation to distinguish between positive and negative sand fly trapping sites in BIH. In total, 55 blood meals of two sand fly species, Ph. neglectus and Ph. balcanicus, were analyzed and five host species identified. Our comprehensive assessment of ecological and environmental preferences of sand flies in BIH may support further entomological surveys and help to better understand and evaluate potential hot spots of disease transmission in the country.

Assessment of the Genetic Diversity of the Monogenean Gill Parasite Lamellodiscus echeneis (Monogenea) Infecting Wild and Cage-Reared Populations of Sparus aurata (Teleostei) from the Mediterranean Sea

The diplectanid monogenean Lamellodiscus echeneis (Wagener, 1857) is a specific and common gill parasite of the gilthead seabream Sparus aurata Linnaeus, 1758, in the Mediterranean Sea. Few isolated molecular studies of this monogenean have been conducted, and its population structure and genetic diversity are poorly understood. This study represents the first analysis of the population genetics of L. echeneis, isolated from wild and cage-reared gilthead seabream from fifteen localities in both the Southern (Tunisia) and Northern (Italy and Spain) regions of the Mediterranean Sea, using nuclear ITS rDNA markers and a partial fragment of the mitochondrial gene cytochrome oxidase subunit I (COI). The phylogenetic trees based on the newly obtained dataset and the previously published sequences of L. echeneis corroborated the spread of only a single species throughout the Mediterranean Sea. The star-like haplotypes network, inferred by COI sequences, suggested a recent population expansion of L. echeneis. This is supported by the observed high haplotype diversity (Hd = 0.918) and low nucleotide diversity (Pi = 0.01595). Population structure-based AMOVA for two groups (the Adriatic Sea and the rest of the Mediterranean Sea) attributed 35.39% of the total variation to differences within populations, 16.63% to differences among populations within groups, and 47.99% to differences among groups. Fixation indices were significant, with a high FST value (0.64612), likely related to the divergence of the parasite populations from the Adriatic Sea and other Mediterranean regions. Phylogenetic analyses grouped all samples into the main clade corresponding to L. echeneis from several localities. This study provides insight into the genetic variation between L. echeneis populations, and did not show a clear genetic structure between populations of L. echeneis throughout Tunisian, Italian, and Spanish localities, which can be attributed to the considerable gene flow between the populations favoured by the potential for host dispersion within the Mediterranean Sea. Finally, haplotypes shared between wild and cage-reared hosts provided evidence for the potential for cross-infection between wild and farmed hosts in the Mediterranean Sea.

Genetic diversity and epidemiological insights into cutaneous leishmaniasis in Pakistan: a comprehensive study on clinical manifestations and molecular characterization of Leishmania species

Cutaneous leishmaniasis (CL) stands out as a significant vector-borne endemic in Pakistan. Despite the rising incidence of CL, the genetic diversity of Leishmania species in the country's endemic regions remains insufficiently explored. This study aims to uncover the genetic diversity and molecular characteristics of Leishmania species in CL-endemic areas of Baluchistan, Khyber Pakhtunkhwa (KPK), and Punjab in Pakistan. Clinical samples from 300 CL patients were put to microscopic examination, real-time ITS-1 PCR, and sequencing. Predominantly affecting males between 16 to 30 years of age, with lesions primarily on hands and faces, the majority presented with nodular and plaque types. Microscopic analysis revealed a positivity rate of 67.8%, while real-time PCR identified 60.98% positive cases, mainly L. tropica, followed by L. infantum and L. major. Leishmania major (p = 0.009) showed substantially greater variation in nucleotide sequences than L. tropica (p = 0.07) and L. infantum (p = 0.03). Nucleotide diversity analysis indicated higher diversity in L. major and L. infantum compared to L. tropica. This study enhances our understanding of CL epidemiology in Pakistan, stressing the crucial role of molecular techniques in accurate species identification. The foundational data provided here emphasizes the necessity for future research to investigate deeper into genetic diversity and its implications for CL control at both individual and community levels.

Cryptic species complex shows population-dependent, rather than lineage-dependent tolerance to a neonicotinoid

Cryptic species are rarely considered in ecotoxicology, resulting in misleading outcomes when using a single morphospecies that encompasses multiple cryptic species. This oversight contributes to the lack of reproducibility in ecotoxicological experiments and promotes unreliable extrapolations. The important question of ecological differentiation and the sensitivity of cryptic species is rarely tackled, leaving a substantial knowledge gap regarding the vulnerability of individual cryptic species within species complexes. In times of agricultural intensification and the frequent use of pesticides, there is an urgent need for a better understanding of the vulnerability of species complexes and possible differences in adaptive processes. We used the cryptic species complex of the aquatic amphipod Gammarus roeselii, which comprises at least 13 genetic mtDNA lineages and spans from small-scale endemic lineages in Greece to a large-scale widely distributed lineage in central Europe. We exposed eleven populations belonging to four lineages to the neonicotinoid thiacloprid in an acute toxicity assay. We recorded various environmental variables in each habitat to assess the potential pre-exposure of the populations to contaminants. Our results showed that the populations differed up to 4-fold in their tolerances. The lineage identity had a rather minor influence, suggesting that the cryptic species complex G. roeselii does not differ significantly in tolerance to the neonicotinoid thiacloprid. However, the observed population differentiation implies that recent pre-exposure to thiacloprid (or similar substances) or general habitat contamination has triggered adaptive processes. Though, the extent to which these mechanisms are equally triggered in all lineages needs to be addressed in the future. Our study provides two key findings: Firstly, it shows that observed phylogenetic differences within the G. roeselii species complex did not reveal differences in thiacloprid tolerance. Second, it confirms that differentiation occurs at the population level, highlighting that susceptibility to toxicants is population-dependent. The population-specific differences were within the range of accepted intraspecific variability from a regulatory standpoint. From an evolutionary-ecological perspective, it remains intriguing to observe how persistent stresses will continue to influence tolerance and whether different populations are on distinct pathways of adaptation. Given that the potential selection process has only lasted a relatively short number of generations, it is crucial to monitor these populations in the future, as even brief exposure periods significantly impact evolutionary responses.

New status of Bichromomyia subspecies (Diptera: Psychodidae: Phlebotominae) based on molecular taxonomy

The sand fly of the genus Bichromomyia (Galati, 1995) includes 3 subspecies considered vectors of Leishmania, which share high morphological similarity. Through information from the Cytochrome Oxidase Subunit I (COI) gene, we provide complementary evidence to support that Bichromomyia olmeca olmeca, and Bichromomyia olmeca bicolor, should be raised to nominal species status. We recovered specimens of Bi. o. olmeca from Quintana Roo, Tabasco, and Oaxaca, Mexico, supply 17 new COI sequences, and also incorporate GenBank sequences for other Bichromomyia species. After a Maximum Likelihood (ML) analysis, all Bichromomyia species clustered with a bootstrap of 100%, although sequences of Bichromomyia flaviscutellata were divided into 2 clusters with an interspecific range distance of 11.16% between them, which confirm cryptic species in Brazil. The genetic distance of Bi. o. olmeca compared to related subspecies ranged between 12.59% and 14.64%. A total of 29 haplotypes (Hd = 0.987; π = 0.08783; S = 136) were recovered from the Bichromomyia sequences. Results of the TC network were consistent with the ML analysis, supporting that subspecies of Bichromomyia are genetically distinct and deserve being raised to valid species category: Bichromomyia olmeca (Vargas & Díaz-Nájera) and Bichromomyia bicolor (Fairchild & Theodor).

Phylogeography and Population Variation in Prunus discoidea (Prunus subg. Cerasus) in China

Prunus discoidea is a unique cherry blossom germplasm resource native to China. It is widely distributed across the provinces of Anhui, Zhejiang, Jiangxi, Jiangsu, and Henan, with significant variation. We employed phylogeographic analysis to reveal the evolutionary history of P. discoidea to better understand its genetic diversity and structure. This study provides more accurate molecular insights for the effective conservation and utilization of this germplasm resource. We conducted a phylogeographic analysis of 348 individual plants from 13 natural populations using three fragments (rpoB, rps16, and trnD-E) of chloroplast DNA (cpDNA) and one fragment (ITS) of ribosomal DNA. The results revealed that P. discoidea demonstrates a significant level of genetic diversity (Hd = 0.782; Rd = 0.478). Gene flow among populations was limited, and the variation within populations was the main source of genetic diversity in P. discoidea (among populations: 34.26%, within populations: 65.74%). Regarding genetic differences among populations, Nst (0.401) showed greater differences than Gst (0.308; p < 0.05), demonstrating that there was a significant geographical structure of lineage. One lineage was the central region of Anhui and the western region of Hubei. The other lineage was the Jiangsu region and the Zhejiang region. P. discoidea diverged from Prunus campanulata approximately 1.5 million years ago, during the Pleistocene epoch. This study provides a scientific theoretical basis for the conservation and utilization of germplasm resources of P. discoidea.

Unveiling genetic variants: Tetra-primer ARMS-PCR diagnosis and structural insights into BLAD, BC, and DUMPS in Pakistani cattle herds

BACKGROUND

Bovine leukocyte adhesion deficiency (BLAD), bovine citrullinemia (BC), and deficiency of Uridine monophosphate synthetase (DUMPS) are the common autosomal recessive disorders affecting the global dairy industry. BLAD leads to poor wound healing and recurrent infections. In BC, ammonia builds up leading to neurological disorders and death. DUMPS results in developmental abnormalities.

METHODOLOGY

In this study, tetra-primer amplification refractory mutation system polymerase chain reaction (ARMS PCR) based diagnostic tests were optimized for BLAD, BC, and DUMPS. A total of 250 animals (58 indigenous and 192 Holstein Friesian (HF)) were screened from all across Pakistan. In addition to validation of ARMS-PCR results through Sanger sequencing, the protein modeling provided structural insights of the disease-associated reported SNPs. Pathway analysis illustrated gene functions under normal and mutated conditions. Furthermore, haplotype and phylogenetic analysis of ASS1 (Argininosuccinate synthetase) gene were performed on study samples and NCBI retrieved sequences.

RESULTS

The study's focus was to screen the herds for prevalence of carriers of genetic disorders, as they are the main source of disease dissemination. One animal was found carrier for BC, whereas no carriers were found for BLAD and DUMPS. The protein models corroborated the reported amino acid change in BLAD, and protein truncation in both BC and DUMPS proteins. SNPs found in NCBI retrieved sequences were either silent or missense and had no effect on protein structure. DNA network presented graphical illustration of haplotype interactions and phylogenetic analysis conferred evolutionary landscape of ASS1 gene. The combination of these approaches produced an in-depth genetic picture of BC in Pakistani cattle.

CONCLUSION

The development of diagnostic tests and identification of the heterozygous BC sample underscores the significance of constant monitoring to avoid the unwanted dissemination of mutant alleles among Pakistani cattle, thereby promoting the general well-being and sustainability of the dairy sector.

The redescription and complete mitogenomes of two Oxycarenus species (Hemiptera, Oxycarenidae) and phylogenetic implications

In this study, the two Oxycarenidae species, O.gossypii Horváth, 1926 and Oxycarenusbicolorheraldus Distant, 1904, are redescribed, and their complete mitogenomes are sequenced and analyzed. The phylogeny of Lygaeoidea is examined using 45 complete mitogenomes of lygaeoid species and four outgroup species. The gene orientation and arrangement of the two mitogenomes are found to be consistent with typical Lygaeoidea mitochondrial features, comprising 37 genes, including 13 PCGs, 22 tRNAs, 2 rRNAs, and a control region. Nucleotide composition of the species was biased towards A and T, with the gene order identical to the putative ancestral arrangement of insects. Start codons, stop codons, RNAs, relative synonymous codon usage (RSCU), and nucleotide diversity (Pi) of Oxycarenidae exhibited characteristics similar to other families in Lygaeoidea. Bayesian-inference (BI) and maximum-likelihood (ML) methods were employed to investigate phylogenetic relationships using PCG datasets from selected species. Phylogenetic analyses reveal slightly different topologies between BI and ML methods, with variation primarily concentrated in Colobathristidae and Rhyparochromidae. Our study confirms that the two sequenced Oxycarenidae species formed a single clade, and the position of Oxycarenidae remains stable in both ML and BI phylogenetic trees. These findings expand the mitochondrial genome databases of Lygaeoidea and provide valuable insights into the phylogenetic relationships within Lygaeoidea or Pentatomomorpha.

A Sister Species for the Blue Crab, Callinectes sapidus? A Tale Revealed by Mitochondrial DNA

The Atlantic blue crab, Callinectes sapidus, is acknowledged as one of the worst invasive alien species in the Mediterranean, impacting biodiversity and human activities. Native to the western Atlantic, it has expanded to European coastal waters since the early 1900s. Despite its ecological and commercial importance, genetic research on this species is limited. Here we show a comprehensive investigation of the genetic variation and evolutionary history in Callinectes sapidus using 667 mitochondrial COI gene sequences. Our dataset encompasses 36 newly generated sequences from previously understudied Mediterranean sites and 631 from worldwide locations obtained from the GenBank public database. Our findings reveal two distinct, but closely related, genetic groups within the species' distribution range, suggesting the occurrence of a potential species complex. Furthermore, in the Mediterranean, low levels of genetic variability were observed except for substantial haplotypic differentiation in Turkish samples. This study depicts the global genetic diversity and evolutionary patterns of Callinectes sapidus, offering new insights into the taxonomic status of the species.

Identification and functional characterization of the npc-2-like domain containing rust effector protein that suppresses cell death in plants

The MD-2-related lipid-recognition (ML/Md-2) domain is a lipid/sterol-binding domain that are involved in sterol transfer and innate immunity in eukaryotes. Here we report a genome-wide survey of this family, identifying 84 genes in 30 fungi including plant pathogens. All the studied species were found to have varied ML numbers, and expansion of the family was observed in Rhizophagus irregularis (RI) with 33 genes. The molecular docking studies of these proteins with cholesterol derivatives indicate lipid-binding functional conservation across the animal and fungi kingdom. The phylogenetic studies among eukaryotic ML proteins showed that Puccinia ML members are more closely associated with animal (insect) npc2 proteins than other fungal ML members. One of the candidates from leaf rust fungus Puccinia triticina, Pt5643 was PCR amplified and further characterized using various studies such as qRT-PCR, subcellular localization studies, yeast functional complementation, signal peptide validation, and expression studies. The Pt5643 exhibits the highest expression on the 5th day post-infection (dpi). The confocal microscopy of Pt5643 in onion epidermal cells and N. benthamiana shows its location in the cytoplasm and nucleus. The functional complementation studies of Pt5643 in npc2 mutant yeast showed its functional similarity to the eukaryotic/yeast npc2 gene. Furthermore, the overexpression of Pt5643 also suppressed the BAX, NEP1, and H₂O₂-induced program cell death in Nicotiana species and yeast. Altogether the present study reports the novel function of ML domain proteins in plant fungal pathogens and their possible role as effector molecules in host defense manipulation.

Horizontal gene transfer from chloroplast to mitochondria of seagrasses in the yellow-Bohai seas

Seagrasses are ideal for studying plant adaptation to marine environments. In this study, the mitochondrial (mt) and chloroplast (cp) genomes of Ruppia sinensis were sequenced. The results showed an extensive gene loss in seagrasses, including a complete loss of cp-rpl19 genes in Zosteraceae, most cp-ndh genes in Hydrocharitaceae, and mt-rpl and mt-rps genes in all seagrasses, except for the mt-rpl16 gene in Phyllospadix iwatensis. Notably, most ribosomal protein genes were lost in the mt and cp genomes. The deleted cp genes were not transferred to the mt genomes through horizontal gene transfer. Additionally, a significant DNA transfer between seagrass organelles was found, with the mt genomes of Zostera containing numerous sequences from the cp genome. Rearrangement analyses revealed an unreported inversion of the cp genome in R. sinensis. Moreover, four positively selected genes (atp8, nad5, atp4, and ccmFn) and five variable regions (matR, atp4, atp8, rps7, and ccmFn) were identified.

Rampant intraspecific variation of plastid genomes in Gentiana section Chondrophyllae

Exploring the level of intraspecific diversity in taxa experienced radiation is helpful to understanding speciation and biodiversity assembly. Gentiana section Chondrophyllae sensu lato encompasses more than 180 species and occupies more a half of species in the genus. In this study, we collected samples across the range of three species (Gentiana aristata, G. crassuloides and G. haynaldii) in section Chondrophyllae s.l., and recovered the intra-species variation by comparing with closely related taxon. Using 25 newly sequenced plastid genomes together with previously published data, we compared structural differences, quantified the variations in plastome size, and measured nucleotide diversity in various regions. Our results showed that the plastome size variation in the three Chondrophyllae species ranged from 285 to 628 bp, and the size variation in LSC, IR and SSC ranged from 236 to 898 bp, 52 to 393 bp and 135 to 356 bp, respectively. Nucleotide diversity of plastome or any of the four regions was much higher than the control species. The average nucleotide diversity in plastomes of the three species ranged from 0.0010 to 0.0023 in protein coding genes, and from 0.0023 to 0.0061 in intergenic regions. More repeat sequence variations were detected within the three Chondrophyllae species than the control species. Various plastid sequence matrixes resulted in different backbone topology in two target species, showed uncertainty in phylogenetic relationship based inference. In conclusion, our results recovered that species of G. section Chondrophyllae s.l. has high intraspecific plastome variation, and provided insights into the radiation in this speciose lineage.

Mitochondrial genomes of Macropsini (Hemiptera: Cicadellidae: Eurymelinae): Structural features, codon usage patterns, and phylogenetic implications

Macropsini is a tribe of Eurymelinae in the family Cicadellidae that is widely distributed worldwide. Still, its taxonomic status has been unstable, and the classification of certain clades at the genus level has been controversial. The aim of this study is to address the patterns and processes that explain the structure and the evolution of the mitogenomes of Macropsini, while contributing to the resolution of systematic issues involving five of their genera. To this task, the mitogenomes of 26 species of the tribe were sequenced and characterized, and their phylogenetic relationships were reconstructed. The results revealed that the nucleotide composition of mitochondrial genes in these 26 species was significantly skewed toward A and T. Codons ending with T or A in relative synonymous codon usage were significantly more prevalent than those ending with C or G. The parity plot, neutrality plot, and correspondence analysis revealed that mutation and selective pressure affect codon usage patterns. In the phylogenetic relationships of the Macropsini, the monophyly of Pedionis and Macropsis was well-supported. Meanwhile, Oncopsis revealed paraphyletic regarding Pediopsoides. In conclusion, this research not only contributes the valuable data to the understanding of the mitogenome of the Macropsini but also provides a reference for future investigations on codon usage patterns, potential adaptive evolution, and the phylogeny of the mitogenome within the subfamily Eurymelinae.

Population genetics and evolutionary history of the intertidal brittle star Ophiothrix (Ophiothrix) exigua in the northern China Sea

Ophiothrix (Ophiothrix) exigua is a common brittle star in the northwestern Pacific. As a dominant species, O. exigua inhabiting the intertidal rocky ecosystem are affected by multiple environmental stressors, but molecular insights into their genetic population structure remain poorly studied. In this study, we investigated the population genetics and evolutionary history of six O. exigua populations from the northern China Sea using mitochondrial (COI, NAD4) and nuclear (ITS2, 18S) gene markers. High haplotype diversity, low nucleotide diversity, and low rates of gene differentiation among the populations of O. exigua were detected. Pairwise genetic differentiation (ΦST) statistics between different localities were negative or low and insignificant, suggesting strong gene flow of this species over the study areas. The phylogenetic analyses showed that the populations exhibited high homogeneity between localities in our study area. Demographic analyses indicated that the populations experienced sustained expansion around 0.2 million years ago. This expansion was likely related to transgressions events in the Yellow Sea during the Pleistocene period. Additional samples of O. exigua from disparate geographical locations, especially the Japan Sea and the Korean Peninsula, will be needed to unravel the population genetic patterns and evolutionary history of this species.

Combining phylogeography and ecological niche modeling to infer the evolutionary history of the Cordoba vesper mouse (Calomys venustus)

The evolutionary dynamics of the ecoregions of southern South America and the species that inhabit them have been poorly studied, and few biogeographic hypotheses have been proposed and tested. Quaternary climatic oscillations are among the most important processes that have led to the current distribution of genetic variation in different regions of the world. In this work, we studied the evolutionary history and distribution of the Córdoba vesper mouse (Calomys venustus), a characteristic rodent of the region of which little is known about its natural history. Since the population dynamics of this species are influenced by climatic factors, this rodent is a suitable model to study the effects of Quaternary climatic oscillations in central Argentina. The mitochondrial cytochrome b gene was sequenced to analyze the phylogeography of C. venustus, and ecological niche modeling tools were used to map its potential distributions. The results of these approaches were combined to provide additional spatially explicit information about this species' past. Our results suggest that the Espinal was the area of origin of this species, which expanded demographically and spatially during the last glacial period. A close relationship was found between the Espinal and the Mountain Chaco. These results are consistent with previous studies and emphasize the role of the Espinal in the biogeographic history of southern South America as an area of origin of several species.