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The population-averaged contact maps generated by the chromosome conformation capture technique provide important information about the average frequency of contact between pairs of chromatin loci as a function of the genetic distance between them. However, these datasets do not tell us anything about the joint statistics of simultaneous contacts between genomic loci in individual cells. This kind of statistical information can be extracted using the single-cell Hi-C method, which is capable of detecting a large fraction of simultaneous contacts within a single cell, as well as through modern methods of fluorescent labeling and super-resolution imaging. Motivated by the prospect of the imminent availability of relevant experimental data, in this work, we theoretically model the joint statistics of pairs of contacts located along a line perpendicular to the main diagonal of the single-cell contact map. The analysis is performed within the framework of an ideal polymer model with quenched disorder of random loops, which, as previous studies have shown, allows us to take into account the influence of the loop extrusion process on the conformational properties of interphase chromatin. [ABSTRACT FROM AUTHOR]

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

Background: Bovine respiratory disease (BRD) is common in intensively raised cattle and is often treated with antibiotics. For practitioners, knowledge of the bacteria involved in an outbreak and their antibiotic susceptibility is warranted. To this end, samples from the upper or lower respiratory tract of calves can be submitted for bacteriological culture and susceptibility testing of relevant isolates. However, it is debated whether isolates from the upper respiratory tract are representative of bacteria causing infections in the lower respiratory tract. In this study, we used MALDI-TOF MS, multilocus sequence typing (MLST) and core-genome multilocus sequence typing (cgMLST) to compare culture results of 219 paired samples (sample pairs) of deep nasal swabs (DNS) and tracheobronchial lavage (TBL). The sample pairs came from 171 calves in 30 calf groups across 25 farms with 48 calves sampled twice. Results: The predominant bacterial pathogen was Pasteurella multocida, which was isolated from 37.4% of DNS and 22.4% of TBL. There was no statistically significant difference in isolation frequency of P. multocida between calves considered healthy and those suspected for BRD for DNS (P = 0.778) or TBL (P = 0.410). Among the 49 sample pairs where P. multocida was isolated from TBL, the same species was isolated from DNS in 29 sample pairs (59.2%). Isolates from 28 of these sample pairs were evaluated by MLST, and in 24 pairs (86.0%) P. multocida from DNS and TBL were of the same sequence type (ST). Moreover, cgMLST showed that the genetic distance between isolates within 21 of the 28 sample pairs (75.0%), was less than two alleles, and DNS and TBL isolates were considered identical. In seven sample pairs (25%), the genetic distance was greater, and DNS and TBL isolates were considered nonidentical. Conclusions: Pasteurella multocida was readily isolated from DNS and in calves where this species was isolated also from TBL, DNS and TBL isolates were identical in 75% of the sample pairs. This suggests that during an outbreak of BRD, submission of DNS samples from 4 to 6 calves could be a convenient approach for practitioners seeking guidance on P. multocida present in the lower respiratory tract and their antibiotic susceptibility. [ABSTRACT FROM AUTHOR]

Understanding of non-geniculate coralline algal (NGCA) diversity, prevalence, and distribution in the tropical western North Atlantic is currently limited by reliance on morphological and anatomical features that are inadequate for species identifications. Reef surveys from two study sites, the Florida Keys (Florida, USA) and Roatán (Honduras), provided prevalence data for the main benthic organisms as well as relative abundance for NGCA genera. NGCA collected during these surveys and from additional sites and depths were identified using DNA sequences from two plastid genes, psbA and rbcL, and two nuclear genes, SSU and LSU, and supported by morphological and anatomical descriptions. Bayesian and Maximum Likelihood phylogenetic analyses, along with species delimitation and genetic distance methods, resolved 11 genera within two orders. Within the Corallinales, the genera Dawsoniolithon, Porolithon and Spongites each had one species, Harveylithon and Lithophyllum had two, Titanoderma three, Hydrolithon four, Neogoniolithon eight, and an unknown genus within the subfamily Neogoniolithoideae had 11 putative species. Within the Hapalidiales, the genera Phymatolithon and Roseolithon each had one species. This study reinforces the inability of morphological and anatomical features to distinguish NGCA species in the tropical western North Atlantic, resulting in substantial underestimations of species richness and diversity. [ABSTRACT FROM AUTHOR]

Utilizing the full potential of rice collections mainly depends on an in‐depth exploration and understanding of the vast diversity in its germplasm. The AfricaRice genebank holds the largest collection of rice germplasm originating from the African continent. In the present study, we comprehensively characterized a collection of 9013 accessions, including Oryza barthii A. Chev., Oryza glaberrima Steud., Oryza longistaminata A. Chev. & Roehr., Oryza sativa L. ssp. indica, and Oryza sativa L. ssp. japonica, for genetic diversity and population structure using genotyping‐by‐sequencing through DArTseq analysis. We identified 27,718 high‐quality single nucleotide polymorphism markers after the genotypic data were filtered. Based on the analyses, the collection has extensive genetic diversity, and the average genetic distance of the entire set was 0.267 (range 0.001–0.469), with 45.1% of pairs of accessions being highly distant and 40.1% moderately distant from each other. Neighbor‐joining tree, principal component, and Bayesian population structure analyses clustered the 9013 accessions into six groups, based roughly on their taxonomic and biological status. The first, second, and third groups consisted of accessions belonging to O. glaberrima, O. barthii, and O. longistaminata, respectively. The fourth, fifth, and sixth groups were improved‐indica, japonica, and traditional‐indica accessions, respectively. The highest value of genetic variance proportion (PhiPT) was found in the species group followed by groups based on cluster analysis and on Bayesian population structure at K = 6. These results allow us to better understand the genetic diversity present in 9013 rice accessions maintained in the AfricaRice genebank and offer a valuable tool for pre breeding, breeding, and further genetic applications. [ABSTRACT FROM AUTHOR]

Molecular studies have contributed to the taxonomy of carrageenan-producing Kappaphycus spp. and Eucheuma denticulatum. However, unresolved species complexes and the lack of standardization in the use of genetic markers impede the identification of specimens and the delineation of a robust taxonomic framework. Here, nine molecular markers (cox1, cox2–3 spacer, cox2, cox3, COB, ITS, psbA, UPA and rbcL) were used to generate a multilocus phylogeny for 113 fresh eucheumatoid samples and four herbarium specimens. Analyses of species delineation and genetic distances confirmed the monophyly of currently accepted taxa. These analyses suggest that clades previously reported as K. striatus KS1 and KS2 are conspecific, and that E. denticulatum EDA 'spinosum' and EDB 'endong/cacing' are also conspecific. The results also unveiled possible new taxa from Hawaii and Indonesia. Each molecular marker and combinations thereof were assessed with regard to species identification, ease of amplification and sequencing, and haplotype characterization. All genetic markers recorded at least 94% success in the amplification and sequencing of fresh specimens, with cox1 being the most phylogenetically informative. Automatic partitioning, phylogenetic and tree-based assessments showed cox1, cox2–3 spacer, cox2 and rbcL were able to correctly identify species while cox1+ rbcL, COB+rbcL, cox2+ rbcL or cox1+ COB+rbcL trees best represented the phylogeny with consistently high nodal support. Among individual markers, cox1 identified the greatest number of haplotypes, while UPA, partial rbcL (750 bp), ITS, cox3 and cox2–3 spacer were able to retrieve information from herbarium specimens of 12–16 years of age. These molecular results provide a basis for a database essential for the taxonomic framework, cultivar development and germplasm conservation of eucheumatoids. Highlights: Mitochondria cox1, cox2–3 spacer, cox2 and plastid rbcL can be used for species identification and cox1 for haplotype detection of eucheumatoids. cox1+rbcL, COB+rbcL, cox2+rbcL or cox1+COB+rbcL are the most cost-effective molecular markers for phylogenetic inference. The most comprehensive up to date multilocus phylogeny of Kappaphycus spp. and Eucheuma denticulatum is presented. [ABSTRACT FROM AUTHOR]

STR loci localized on the X chromosome provide information additional to the autosomal markers routinely analyzed in forensic genetics, integrating genetic systems as Y-STRs and mitochondrial DNA in the investigation of complex kinship scenarios and mass disaster cases. In this study we genotyped 12 X-STR loci in 251 male samples from four populations of Namibia in southern Africa using the Investigator Argus X-12 kit (Qiagen, Hilden, Germany). Forensic efficiency parameters indicated high power of discrimination in the considered populations. As part of our investigation, we highlighted partial linkage associations between loci within known linkage groups (LGs) and identified several occurrences of previously unreported out-of-ladder (OL) alleles. Genetic distances between the Namibian populations here investigated and other African (Eritrea, Ethiopia, Somalia, Guinea, Cape Verde) and non-African (Germany, China, Philippines) populations using loci grouped in LGs mirrored their biogeographical distribution differently for each linkage group. Haplotype sharing within each LG revealed a high degree of population-specific types, hinting to the potential of these markers for ancestry applications. These results highlight the importance to produce specific and freely available population databases especially for multi-ethnic countries. This novel dataset is expected to be of interest for population studies that need an accessible reference dataset of African regions not currently well represented, as well as possible relevance for forensic applications focusing on the biogeographic origin of samples. [ABSTRACT FROM AUTHOR]

Metafounders are a useful concept to characterize relationships within and across populations, and to help genetic evaluations because they help modelling the means and variances of unknown base population animals. Current definitions of metafounder relationships are sensitive to the choice of reference alleles and have not been compared to their counterparts in population genetics—namely, heterozygosities, FST coefficients, and genetic distances. We redefine the relationships across populations with an arbitrary base of a maximum heterozygosity population in Hardy–Weinberg equilibrium. Then, the relationship between or within populations is a cross-product of the form Γ b , b ′ = 2 n 2 p b - 1 2 p b ′ - 1 ′ with p being vectors of allele frequencies at n markers in populations b and b ′ . This is simply the genomic relationship of two pseudo-individuals whose genotypes are equal to twice the allele frequencies. We also show that this coding is invariant to the choice of reference alleles. In addition, standard population genetics metrics (inbreeding coefficients of various forms; FST differentiation coefficients; segregation variance; and Nei's genetic distance) can be obtained from elements of matrix Γ . [ABSTRACT FROM AUTHOR]

Epinephelus bilobatus, Epinephelus maculatus and Epinephelus longispinis are three groupers that share common morphological characteristics and coloration patterns and have been morphologically confused and misidentified with each other for a long time. Complete mitochondrial genomes of the three groupers were determined and analyzed in this study. Mitogenomes of E. bilobatus, E. maculatus and E. longispinis were 17, 354 bp, 17, 066 bp and 17, 221 bp in size respectively and consisted of 13 protein-coding genes, two ribosomal RNA genes and one control region. However, different from most teleosts, which contain canonical 22 tRNAs, more numbers of tRNAs were identified in the three groupers with 27 tRNAs in E. bilobatus and E. longispinis and 25 tRNAs in E. maculatus. The increased number of tRNAs was due to the presence of tandemly duplicated tRNA-Asp genes that were located between tRNA-Ser and COII genes (six duplications in E. bilobatus and E. longispinis, four duplications in E. maculatus). Intact gene tandem duplication was an uncommon feature that was found in the typical teleost mitogenomes. The phylogenetic trees of the 32 groupers (genus Epinephelus) that were constructed based on 12 protein-coding genes revealed that Epinephelus species with tandemly duplicated tRNA-Asp genes were clustered into one monophyletic group, distinct from other Epinephelus species without any duplication features, which indicated that tandemly duplicated tRNA-Asp genes may be the particular linage-specific characteristics that evolve from a common ancestor and have the ability to distinguish them from other Epinephelus species. The results of the mitogenomes comparative analyses of the three groupers revealed the genetic distance of mitogenomes between each two species to be 0.062 (E. bilobatus vs E. maculatus), 0.091 (E. bilobatus vs E. longispinis) and 0.087 (E. maculatus vs E. longispinis). All values were far greater than the minimum value of 0.020 for species identification, which shows that they were three independent species at molecular level. Regarding the relationships between the three groupers, E. bilobatus was found to be more closely related to E. maculatus in comparison to E. longispinis. The results provide valuable molecular data for the species identification and phylogenetic analyses on E. bilobatus, E. maculatus and E. longispinis, and also provided a new insight into the tandem gene duplication features of Epinephelus mitogenomes. [ABSTRACT FROM AUTHOR]

Species of Antarctomyces and Thelebolus (Thelebolaceae), primarily found in Antarctic environments, exhibit psychrophilic adaptations, yet their mitochondrial genomes have not been extensively studied. Furthermore, few studies have compared the mitochondrial genomes of psychrophilic, psychrotrophic, and mesophilic fungi. After successful sequencing and assembly, this study annotated the mitochondrial genomes of Antarctomyces psychrotrophicus CPCC 401038 and Thelebolus microsporus CPCC 401041. We also performed a comparative analysis with the previously characterized mitochondrial genomes of psychrotrophic and mesophilic fungi. The analysis revealed that nad4L was the most conserved gene across the mitochondrial genomes, characterized by its synonymous and non-synonymous substitution rates (Ks and Ka), genetic distance, and GC content and skew within the protein-coding genes (PCGs). Additionally, the mitochondrial genomes of psychrophilic and psychrotrophic fungi showed a higher proportion of protein-coding regions and a lower GC content compared to those of mesophilic fungi, underscoring the genetic basis of cold adaptation. Phylogenetic analyses based on these mitochondrial genes also confirmed the phylogenetic relationships of Thelebolaceae in the class Leotiomycetes. These findings advance our understanding of the phylogenetic relationships and evolutionary dynamics within the family Thelebolaceae, highlighting how different environmental temperatures influence fungal mitochondrial genomic structure and adaptation. [ABSTRACT FROM AUTHOR]

In the present study, the DNA barcoding of the nematode parasite infecting Ompok bimaculatus and Nemacheilus anguilla fish species was carried out in Barvi Reservoir, Maharashtra. To ascertain the taxonomic status of these nematode parasites, an 18S gene marker was used. Accurate identification of fish parasites is essential to formulate preventive strategies and to study host–environment relations. The present study did barcoding of the nematode parasites of the fishes caught from the Barvi Reservoir using the nuclear 18S rDNA (SSU) sequence. The nuclear 18S rDNA (SSU) was amplified into two overlapping amplicons and sequenced to identify the species based on the sequence similarity with the NCBI GenBank database. The present study sequences (both fragments) showed 98% similarity with the species of Eustrongylides. The average genetic distance value between the present study sample and species of Eustrongylides was 0.003. In the phylogenetic tree also, the sequence was clustered with the species of Eustrongylides with significant bootstrap values. The present study identified the nematode parasite of the fish caught from the Barvi Reservoir, as species of Eustrongylides. The species‐level identification could not be possible due to the insufficient/lack of reference sequences in the database. It indicates the knowledge gap concerning the species‐specific molecular markers for nematode parasites of the fish. [ABSTRACT FROM AUTHOR]

As defining various taxonomic ranks, especially at and within a specific level, can often be difficult, we used an evolutionarily young group of Central Asian beetles, the genus Anoplistes, to examine the limits between species, subspecies and ecotype. The molecular data (COI genetic distance, haplotype network and species delimitation) and detailed morphology (using SEM) of taxa assigned to the rank of species, subspecies and ecotype were used to verify their taxonomic status and attempt to more precisely establish the boundaries between these concepts. The minimum threshold for the COI genetic distance between species was found to be approximately 3%, while at the threshold of 4%–5% the morphology left no doubt as to the species distinctiveness. The threshold of approximately 2% was accepted as adequate for a subspecies rank, whereas intraspecific variability among individuals of the same subspecies (including its ecotypes) ranged from 0% to 2%. A newly presented colour/elytral pattern form, possibly another ecotype of A. halodendri distributed in western Mongolia, exemplifies adaptation to different environmental conditions via ecological speciation. Our results provide support that ecotypes can form phylogenetically distinct clades. Based on the results of the haplotype network, it can be tentatively concluded that the sand ecotype was the incipient form from which further ecotypes and subspecies developed. [ABSTRACT FROM AUTHOR]

ABSTRACT A major challenge in analysing single‐nucleotide polymorphism (SNP) genotype datasets is detecting and filtering errors that bias analyses and misinterpret ecological and evolutionary processes. Here, we present a comprehensive method to estimate and minimise genotyping error rates (deviations from the ‘true’ genotype) in any SNP datasets using triplicates (three repeats of the same sample) in a four‐step filtration pipeline. The approach involves: (1) SNP filtering by missing data; (2) SNP filtering by error rates; (3) sample filtering by missing data and (4) detection of recaptured individuals by using estimated SNP error rates. The modular pipeline is provided in an R script that allows customised adjustments. We demonstrate the applicability of the method using non‐invasive sampling from the Asiatic wild ass (Equus hemionus) population in Israel. We genotyped 756 samples using 625 SNPs, of which 255 were triplicates of 85 samples. The average SNP error rate, calculated based on the number of mismatching genotypes across triplicates before filtration, was 0.0034 and was reduced to 0.00174 following filtration. Evaluating genetic distance (GD) and relatedness (r) between triplicates before and after filtration (expected to be at the minimum and maximum respectively) showed a significant reduction in the average GD, from 58.1 to 25.3 (p = 0.0002) and a significant increase in relatedness, from r = 0.98 to r = 0.991 (p = 0.00587). We demonstrate how error rate estimation enhances recapture detection and improves genotype quality. [ABSTRACT FROM AUTHOR]

BACKGROUND RESULTS CONCLUSION Yellow mosaic disease (YMD) is the most devastating disease of soybean under north Indian conditions. A recombinant inbred line population derived from SL 958 (R) × AGS 456 (S) was used to map the genes imparting YMD resistance. Genotyping by sequencing (GBS) of 148 individuals and the parents was used to identify polymorphic SNPs in the population. These were used to generate linkage maps and subsequently map the QTL.A QTL, MYMIV 1‐1.1, was mapped onto chromosome 6. The QTL was mapped at a genetic distance of 114.31 cM, with likelihood ratio of 81.34 (LOD 17.68), explaining 33.80% of the variation for the trait, with an additive effect of 1.22. MYMIV 1‐1.1 was flanked by SNPs Gm06_12614920 explaining 33.80% of variation and Gm06_12887789 explaining 31.04% of the variation. The QTL region spanned for a total of 2.798 Mbp.The QTL was mapped in an approximately 4 cM region. Flanking SNPs can be developed into linked markers for effective marker‐assisted selection. Out of the genes in the QTL region, Glyma.06G161700 (Suppressor of Gene Silencing/SGS3) is the strongest contender for the resistance gene. This is the first study documenting GBS‐based mapping of YMD resistance in soybean. © 2024 Society of Chemical Industry. [ABSTRACT FROM AUTHOR]

Modelling population connectivity is central to biodiversity conservation and often relies on resistance surfaces reflecting multi‐generational gene flow. ResistanceGA (RGA) is a common optimization framework for parameterizing these surfaces by maximizing the fit between genetic distances and cost distances using maximum likelihood population effect models. As the reliability of this framework has rarely been studied, we investigated the conditions maximizing its accuracy for both prediction and interpretation of landscape features' permeability. We ran demo‐genetic simulations in contrasted landscapes for species with distinct dispersal capacities and specialization levels, using corresponding reference cost scenarios. We then optimized resistance surfaces from the simulated genetic distances using RGA. First, we evaluated whether RGA identified the drivers of the genetic patterns, that is, distinguished Isolation‐by‐Resistance (IBR) patterns from either Isolation‐by‐Distance or patterns unrelated to ecological distances. We then assessed RGA predictive performance using a cross‐validation method, and its ability to recover the reference cost scenarios shaping genetic structure in simulations. IBR patterns were well detected and genetic distances were predicted with great accuracy. This performance depended on the strength of the genetic structuring, sampling design and landscape structure. Matching the scale of the genetic pattern by focusing on population pairs connected through gene flow and limiting overfitting through cross‐validation further enhanced inference reliability. Yet, the optimized cost values often departed from the reference values, making their interpretation and extrapolation potentially dubious. While demonstrating the value of RGA for predictive modelling, we call for caution and provide additional guidance for its optimal use. [ABSTRACT FROM AUTHOR]

Simple Summary: The Hemiphyllodactylus is a small gecko. Recently, many species belonging to the genus Hemiphyllodactylus have been discovered in the karst region. Therefore, we conducted a large scale of surveys and specimen collections in multiple karst areas of Yunnan Province. Three populations of Hemiphyllodactylus were found to be morphologically and molecularly distinct from known species, prompting us to describe them as three new species. Our study further illustrates the high diversity of Hemiphyllodactylus species within Yunnan Province. The karst landform in Yunnan Province, China, represents one of the most biodiverse regions for Hemiphyllodactylus. Previous research has revealed that the karst forests in this province host a greater diversity of Hemiphyllodactylus than previously acknowledged. However, substantial fundamental data essential for taxonomic and biogeographical studies are lacking. We conducted extensive surveys for Hemiphyllodactylus in the Yunnan Province that led to the discovery of three new species from Menglian Dai, Lahu, and Wa Autonomous County and Jinghong City based on morphological and genetic data. A phylogenetic reconstruction based on the ND2 gene (1038 bp) placed the three new species into clade 3 and clade 4 of Agung et al. The uncorrected genetic pairwise distance of the Menglian specimens were greater than 5.7%, and those of the Jinghong City specimens were greater than 5.2% and 8.5%, respectively. They could be distinguished from their congeners by body size, chin scales, internasal scales, ventral scales, dorsal scales, and the total number of femoral and precloacal pores. Furthermore, we update the distributional knowledge of the known species. [ABSTRACT FROM AUTHOR]

To determine the role of internal transcribed spacer 2 (ITS2) in the identification of Spatholobus suberectus and explore the genetic diversity of S. suberectus. A total of 292 ITS2s from S. suberectus and 17 other plant species were analysed. S. suberectus was clustered separately in the phylogenetic tree. The genetic distance between species was greater than that within S. suberectus. Synonymous substitution rate (Ks) analysis revealed that ITS2 diverged the most recently within S. suberectus (Ks = 0.0022). These findings suggested that ITS2 is suitable for the identification of S. suberectus. The ITS2s were divided into 8 haplotypes and 4 evolutionary branches on the basis of secondary structure, indicating that there was variation within S. suberectus. Evolutionary analysis revealed that the GC content of paired regions (pGC) was greater than that of unpaired regions (upGC), and the pGC showed a decreasing trend, whereas the upGC remained unchanged. Single-base mutation was the main cause of base pair substitution. In both the initial state and the equilibrium state, the substitution rate of GC was higher than that of AU. The increase in the GC content was partly attributed to GC-biased gene conversion (gBGC). High GC content reflected the high recombination and mutation rates of ITS2, which is the basis for species identification and genetic diversity. We characterized the sequence and structural characteristics of S. suberectus ITS2 in detail, providing a reference and basis for the identification of S. suberectus and its products, as well as the protection and utilization of wild resources. [ABSTRACT FROM AUTHOR]

ABSTRACT Artificial breeding of mantis shrimp Oratosquilla oratoria, using the ecological breeding in earthen pond (EBEP) method, has been carrying out from 2019, and the produced larvae have always been used for supportive breeding programs in Bohai Bay. To assess the degree of fidelity of enhancement programs used an EBEP method to native genetic pools, genetic diversity at 10 microsatellite loci was analyzed in three hatchery offspring populations, their wild parent stocks, and their wild contemporaneous offspring. Significant decrease in the almost genetic diversity parameters and highly significant differences in shannon's information index (decreasing by 22.54%–40.97%) and allelic richness (33.80%–46.87%) were observed between in hatchery populations. This further created relatively more genetic differentiation between the hatchery and wild population, as the pairwise Fst values and genetic distances showed. The mean pairwise relatedness coefficients showed higher values within hatchery populations and lower values within wild populations. Hatchery populations contained the fewest full‐sib families and offspring were extremely distributed in 10–11 full‐sib groups in each hatchery population. The relatively small number of actual spawning females and large variance in parental contribution to the next generation possibly causes allele reduction in the hatchery population, which in turn leads to a decrease in allelic diversity and an increase in genetic similarities among individuals. Promoting synchrony of ovarian development in females, providing good conditions for incubation and larvae culture and balancing the contributions of parents will be important in future breeding propagation. [ABSTRACT FROM AUTHOR]

Although new data and methodologies are gaining prominence in the field of taxonomy, the vast majority of terrestrial isopod species are still described solely based on morphology. The genus Benthana was recently revised and currently comprises 30 species found in South America. However, the broad geographic distribution of some species, coupled with the presence of few diagnostic characters, raises doubts about the validity of the described species. This study aimed to test the applicability of DNA Barcoding to assess the congruence between morphological and molecular identification of Benthana species. We analyzed 72 individuals belonging to 13 species from the scientific collection of the UFRGS Crustacean Laboratory. We obtained 24 sequences from ten Benthana species. The molecular phylogenies demonstrated that Benthana forms a paraphyletic group. Even at the species level, paraphyletic taxa were observed. Species delimitation methods revealed the presence of eight molecular entities within Benthana. Regarding genetic distances, we observed low intra-specific distances and significantly high inter-specific distances. Our results show that molecular analysis does not support the current taxonomy of Benthana. Therefore, a reassessment of the genus systematics based on integrative taxonomy is warranted. [ABSTRACT FROM AUTHOR]

Astroblepus species, commonly known as Andean climbing catfish, exhibit a unique challenge in species delimitation, leading to ongoing taxonomic debates. Here we report data on Astroblepus mindoensis, a vulnerable species endemic to Ecuador, obtained by an integrative approach that includes cytogenetic analysis, molecular identification of the specimens, and recording of morphological and morphometric characters useful for species diagnosis. Thus, this study aimed to associate the karyotype data of the specimens analyzed with morphological and molecular characters, improving and expanding the existing taxonomic information, thus contributing to the systematics of the species. Our morphology results, unlike Regan's original description, which is brief and ambiguous, provide a more detailed morphometric and meristic description. Molecular phylogenetic reconstruction and genetic distance based on a fragment of the cytochrome c oxidase subunit I (COI) showed that our samples constitute a well‐supported and monophyletic clade within the A. grixalvii species complex. The cytogenetic analysis identified distinct chromosomal markers, including a single cluster of major ribosomal genes (on chromosome pair 3) and of minor ribosomal genes (on chromosome pair 12) with their localization differing from those reported in other Astroblepus species analyzed. Additionally, the presence of a heteromorphic chromosome pair in males suggests the presence of an XX/XY sex‐determination system that has not been identified in other congeneric species. Further investigation is necessary to determine if these chromosomes are associated with the accumulation of repeated sequences, as typically occurs with sex chromosomes, and to assess their presence in other species of the genus. [ABSTRACT FROM AUTHOR]

Puumala orthohantavirus (PUUV) is a causative agent of haemorrhagic fever with renal syndrome, mainly transmitted through rodent excretions. Classification of PUUV has traditionally been based on the geographic locations of their discovery, but this system faces challenges due to inconsistencies between the names of lineages and their actual distribution. In this study, we propose a quantitative criterion of "10% nucleotide difference" to distinguish PUUV genotypes, resulting in a subdivision of PUUV into twentyone distinct genotypes. The application of this criterion suggested a further division of the CE, RUS, FIN and N-SCA lineages and was consistent with the current taxonomic position of the S-SCA, LAT, DAN and ALAD lineages. In addition, analysis of reassortment and recombination events showed that PUUV undergoes these processes, but they are relatively rare. Our results emphasise the importance of considering genetic distances in the classification of PUUV and provide a robust criterion for subspecies-level taxonomy. [ABSTRACT FROM AUTHOR]

Mesopsammic polyclad members in the family Boniniidae have attracted attention in terms of their evolutionary shifts of microhabitat and their unique morphology such as a pair of pointed tentacles extending from the anterolateral margins and prostatoid organs harbouring stylets. Here, we establish a new species of this family as Boninia panamensis sp. nov. from the Pacific coasts of Panama, based on its morphological characteristics of (i) four cerebral and 61–80 marginal eyespots, (ii) two prostatoid organs located anterior and posterior to the penis papilla, and (iii) two uterine canals departing from the anterior part of the Lang's vesicle. We also report Boninia cf. uru from Hawai'i, USA, based on its morphological identity with B. uru from Okinawa, Japan, along with their genetic distances for the partial cytochrome c oxidase subunit I (COI) sequences, which were beyond the range of intraspecific differences observed in congeners in this study. Boninia oaxaquensis is also reported from Panama as a new locality for the species. Involving the above-mentioned three species sequenced herein, we reconstructed molecular phylogenetic trees of Boninia based on the four gene markers (18S rDNA, 28S rDNA, 16S rDNA and COI). Our phylogenetic trees indicated the synapomorphy within the genus Boninia of the small numbers of stylets (2–4) and the connection route of the uterine canals to the Lang's vesicle. The results also showed a characteristic distribution pattern in which pairs of species in distinct lineages occurred sympatrically with different microhabitats, as observed in Boninia uru and Boninia yambarensis in Okinawa and B. panamensis sp. nov. and B. oaxaquensis in Panama. In addition, we discuss possible speciation pathways in this genus based on the tree topology. ZooBank: Boniniidae is a family of marine polyclad flatworms harbouring nine named species distributed worldwide. We describe a new boniniid species, Boninia panamensis from the Pacific coasts of Panama based on morphological and molecular data. We also report Boninia cf. uru from Hawai'i and Boninia oaxaquensis from Panama along with morphological descriptions. In addition, we discuss synapomorphic traits and possible speciation pathways in this genus based on the reconstructed molecular phylogenetic results using 18S rDNA, 28S rDNA, 16S rDNA and COI. (Photograph by Marco Curini-Galletti.) [ABSTRACT FROM AUTHOR]

A new cyprinid fish, Opsariichthys rubriventris sp. nov., is described from the Xizhijiang River, a tributary of the Pearl River basin in Huizhou City, Guangdong Province, southern China. The species is distinguished from all other congeners by the following combination of characters: predorsal scales 13–14; lower jaw projecting slightly beyond upper jaw; cheek with two mainly longitudinal rows of tubercles; and lower jaw, belly, pectoral fin, and anterior margin of anal fin in adult males being reddish-orange. The principal component analysis result of the morphological data indicated that O. rubriventris sp. nov. could be clearly distinguished fromfour other congeners. The phylogenetic analysis conducted in this study, utilizing both Maximum Likelihood (ML) and Bayesian Inference (BI) methods, supported the monophyly of the novel species O. rubriventris sp. nov. at the species level. Additionally, the genetic distance analysis revealed that O. rubriventris sp. nov. exhibits a genetic distance ranging from 0.14 to 0.16 with its congeneric species, further affirming its taxonomic status. [ABSTRACT FROM AUTHOR]

Simple Summary: Humans are diploid organisms, carrying one set of chromosomes from our mother and one from our father. Plants can exist as diploid or polyploid, carrying multiple chromosome copies. Plant breeders can cross polyploid crops in unique and beneficial ways that are not possible in diploid crops. It will be necessary to produce food in a more sustainable manner, with less virgin land turned over and fewer resources consumed, therefore the study of hybrid polyploid crops is essential for the improvement of our food system. The improvement in quantitative traits (e.g., yield, size) in F1 offspring over parent lines is described as hybrid vigour, or heterosis. There exists a fascinating relationship between parental genetic distance and genome dosage (polyploidy), and heterosis effects. The contribution of nuclear heterozygosity to heterosis is not uniform across diploid and polyploid crops, even within same species, thus demonstrating that polyploid crops should be part of any discussion on the mechanisms of heterosis. This review examines the records of correlating heterosis with parental genetic distance and the influence of adding supplementary genomes in wide crosses. Increasing nuclear heterozygosity through parental genetic distance has been shown to be an imperfect predictor for heterosis in a variety of commercial crops such as maize, rice, and pepper. However, increasing the ploidy level raises the maximum number of alleles that can be harboured at any one locus, and studies on crops such as oilseed rape, potato, alfalfa, maize, and rice have demonstrated that heterosis may be maximised upon increasing multi-locus nuclear heterozygosity. The novel heterotic phenotypes observed above the diploid level will contribute to our understanding on the mechanisms of heterosis and aid plant breeders in achieving the righteous goal of producing more food with fewer inputs. [ABSTRACT FROM AUTHOR]

Simple Summary: Heptageniidae is the third most species-rich family within Ephemeroptera (mayflies). Although multiple studies have been conducted, the monophyly, phylogenetic relationships, and the divergence time of its subfamilies have always been controversial. The current study sequenced 17 new mitogenomes to reconstruct the phylogenetic relationships and calculate the divergence time within Heptageniidae. Therefore, based on comparing the composition of three mitogenomes bias, phylogenetic relationships, and divergence time of Epeorus montanus Brodsky, 1930, we suggest that cryptic species exist in E. montanus. Heptageniidae are known for their flat heads and bodies and are divided into three subfamilies. Despite the extensive diversity within this group and considerable efforts made to understand their evolutionary history, the internal classifications and origin time of Heptageniidae remains controversial. In this study, we newly sequenced 17 complete mitogenomes of Heptageniidae to reconstruct their phylogenetic positions within this family. Because of the ambiguous time of origin, our study also estimated the divergence time within Heptageniidae based on five fossil calibration points. The results of BI and ML trees all highly supported the monophyly of Heptageniidae and three subfamilies. The phylogenetic relationship of Rhithrogeninae + (Ecdyonurinae + Heptageniinae) was also recovered. The divergence time showed that Heptageniidae originated from 164.38 Mya (95% HPD, 150.23–181.53 Mya) in the mid-Jurassic, and Rhithrogeninae originated from 95.54 Mya (95% HPD, 73.86–120.19 Mya) in the mid-Cretaceous. Ecdyonurinae and Heptageniinae began to diverge at 90.08 Mya (95% HPD, 68.81–113.16 Mya) in the middle Cretaceous. After morphological identification, analysis of the mitogenome's composition, genetic distance calculation, phylogenetic analysis, and divergence time calculation, we suggest that two different populations of Epeorus montanus collected from Aksu, Xinjiang Uygur Autonomous Region (40°16′ N, 80°26′ E) and Xinyuan, Xinjiang Uygur Autonomous Region (43°20′ N, 83°43′ E) in China are cryptic species of E. montanus, but further detailed information on their morphological characteristics is needed to fully identify them. [ABSTRACT FROM AUTHOR]

Here we present, through field collections conducted via monitoring with Sherman traps and phylogenetic analyses of the mitochondrial cytochrome b gene obtained through Sanger sequencing, records worth recognizing of rodent species from Las Joyas Scientific Station (LJSS) within the Sierra de Manantlán Biosphere Reserve. We report for the first time the presence of Nyctomys sumichrasti colimensis in this locality. Additionally, we present new records of Reithrodontomys wagneri and specimens belonging to Reithrodontomys sumichrasti clade IV, a clade recognized as an undescribed species within the R. sumichrasti species complex; the latter expands the geographic distribution of this new species. Finally, we include records of Microtus specimens forming a sister clade with M. mexicanus / M. mogollonensis, albeit with genetic distance values exceeding 9%. Our findings underscore the evolutionary significance of the apparent isolation of Sierra de Manantlán, Jalisco, particularly in influencing the speciation process of various rodent species. These findings underscore the importance of continuing biological inventories in less explored areas of Mexico. [ABSTRACT FROM AUTHOR]

Context: Wheat (Triticum aestivum L.) is an important crop that provides food to millions of people all over the world. Currently, wheat production is limited due to various biotic and abiotic stresses resulting from uneven patterns of climate change. Therefore, it is very important to develop climate-resilient wheat cultivars. Crop genetic diversity allows the scientific community to identify genetic variations that can be utilised in the development of improved cultivars. Aims: This study planned to characterise the wheat germplasm with the iPBS-retrotransposons marker system. Methods: A total of 30 iPBS-retrotransposons markers were screened and among these, the 12 most polymorphic markers were selected for further analysis. Key results: Molecular characterisation yielded a total of 170 bands, of which 143 were polymorphic. A substantial level of genetic diversity was observed (mean effective number of alleles: 1.37, Shannon's information index: 0.23, gene diversity: 0.35). Maximum genetic distance was observed in G9 and G60 genotypes. Analysis of molecular variance revealed that most genetic variation (95%) occurred within the populations. The model-based structure algorithm divided the studied germplasm into three populations based on their collection regions. Similarly, the neighbour-joining analysis also divided 70 tested wheat genotypes into three populations, whereas principal coordinate analysis divided the evaluated germplasm into four populations. Conclusions: This study confirms the iPBS-retrotransposons as an ideal marker for the genetic diversity assessment studies for any crop, especially for wheat. Implications: The results presented here will be helpful for the scientific community in the marker-assisted breeding of wheat. Wheat, a vital global food source, faces production limitations due to climate-induced stresses. Developing resilient cultivars is crucial. Genetic diversity aids in identifying variations for improved cultivars. This study utilised iPBS-retrotransposons to characterise wheat germplasm, yielding 170 bands. Genetic distance highlighted G9 and G60 as genetically distinct genotypes. Different methods identified three or four distinct groups of genotypes amongst the studied germplasm. This informs targeted breeding strategies for enhanced wheat varieties. This article belongs to the Collection Plant breeding- and genetics-based tools for food security under changing climate. [ABSTRACT FROM AUTHOR]

Sucking pests in recent years have become a concern for cotton cultivation worldwide. In this sense, the study aimed to identify cotton genotypes resistant to sucking insect attacks. The experiment was conducted in Cassilândia in the 2016/2017 harvest, using thirteen cotton genotypes. During the crop season, weekly samples of cotton aphid, Silverleaf whitefly, and cotton stainer were obtained. The data obtained were subjected to the analysis of variance and the Scott-Knott clustering algorithm at the level of 5% probability. Cotton genotypes G. thuberi, Gba04, PAYM, G. trilobum, Gba01, Gba02, and Gba03 had the lowest populations of adults and nymphs of Silverleaf whitefly in the period. The genotypes PAYM, TX25, TX16, TX19, GBA03, IAC19, CO417, and EMPI were the most preferred for feeding by the cotton aphid. The cotton genotype IAC19 was the least preferred for feeding by cotton stainer; conversely, PAYM, Gba01, and TX25 were the most preferred for feeding by these insects. G. thuberi, Gba04, PAYM, G. trilobum, Gba01, and Gba02 were less harmed by the attack of Silverleaf whitefly adults and nymphs; however, Gba01, Gba02, and Gba04 were the least preferred for feeding by cotton aphids, and IAC19 was the least preferred for feeding by cotton stainer. The cotton aphids and Silverleaf whitefly adults and/or nymphs have a high negative correlation with cotton yield, making the pests more harmful to the harvest. [ABSTRACT FROM AUTHOR]

The degree to which landscape genetics findings can be extrapolated to different areas of a species range is poorly understood. Here, we used a broadly distributed ectothermic lizard (Sceloporus occidentalis, Western Fence lizard) as a model species to evaluate the full role of topography, climate, vegetation, and roads on dispersal and genetic differentiation. We conducted landscape genetics analyses with a total of 119 individuals in five areas within the Sierra Nevada mountain range. Genetic distances calculated from thousands of ddRAD markers were used to optimize landscape resistance surfaces and infer the effects of landscape and topographic features on genetic connectivity. Across study areas, we found a great deal of consistency in the primary environmental gradients impacting genetic connectivity, along with some site‐specific differences, and a range in the proportion of genetic variance explained by environmental factors across study sites. High‐elevation colder areas were consistently found to be barriers to gene flow, as were areas of high ruggedness and slope. High temperature seasonality and high precipitation during the winter wet season also presented a substantial barrier to gene flow in a majority of study areas. The effect of other landscape variables on genetic differentiation was more idiosyncratic and depended on specific attributes at each site. Across study areas, canyon valleys were always implicated as facilitators to dispersal and key features linking populations and maintaining genetic connectivity, though the relative importance varied in different areas. We emphasize that spatial data layers are complex and multidimensional, and careful consideration of spatial data correlation structure and robust analytic frameworks will be critical to our continued understanding of spatial genetics processes. [ABSTRACT FROM AUTHOR]

Genomic‐scale datasets, sophisticated analytical techniques, and conceptual advances have disproportionately failed to resolve species boundaries in some groups relative to others. To understand the processes that underlie taxonomic intractability, we dissect the speciation history of an Australian lizard clade that arguably represents a "worst‐case" scenario for species delimitation within vertebrates: the Ctenotus inornatus species group, a clade beset with decoupled genetic and phenotypic breaks, uncertain geographic ranges, and parallelism in purportedly diagnostic morphological characters. We sampled hundreds of localities to generate a genomic perspective on population divergence, structure, and admixture. Our results revealed rampant paraphyly of nominate taxa in the group, with lineages that are either morphologically cryptic or polytypic. Isolation‐by‐distance patterns reflect spatially continuous differentiation among certain pairs of putative species, yet genetic and geographic distances are decoupled in other pairs. Comparisons of mitochondrial and nuclear gene trees, tests of nuclear introgression, and historical demographic modelling identified gene flow between divergent candidate species. Levels of admixture are decoupled from phylogenetic relatedness; gene flow is often higher between sympatric species than between parapatric populations of the same species. Such idiosyncratic patterns of introgression contribute to species boundaries that are fuzzy while also varying in fuzziness. Our results suggest that "taxonomic disaster zones" like the C. inornatus species group result from spatial variation in the porosity of species boundaries and the resulting patterns of genetic and phenotypic variation. This study raises questions about the origin and persistence of hybridizing species and highlights the unique insights provided by taxa that have long eluded straightforward taxonomic categorization. [ABSTRACT FROM AUTHOR]

Eight porcine parvovirus (PPV) species, designated as PPV1 through PPV8, have been identified in swine. Despite their similarities, knowledge about their distribution and genetic differences remains limited, resulting in a gap in the genetic classification of these viruses. In this study, we conducted a comprehensive analysis using PPV1 to PPV7 genome sequences from Colombia and others available in the GenBank database to propose a classification scheme for all PPVs. Sera from 234 gilts aged 180 to 200 days were collected from 40 herds in Colombia. Individual detection of each PPV (PPV1 through PPV7) was performed using end-point PCR. Complete nucleotide (nt) sequencing was performed on the PPV1 viral protein (VP), and near-complete genome (NCG) sequencing was carried out for novel porcine parvoviruses (nPPVs) (PPV2 through PPV7). Phylogenetic analyses were conducted by comparing PPV1-VP sequences to 94 available sequences and nPPVs with 565 NCG, 846 nPPV-VP, and 667 nPPV–nonstructural protein (NS) sequences. Bayesian phylogenetic analysis was used to estimate substitution rates and the time to the most recent common ancestor for each PPV. The highest prevalence was detected for PPV3 (40.1%), followed by PPV5 (20.5%), PPV6 (17%), PPV1 (14.5%), PPV2 (9.8%), PPV4 (4.2%), and PPV7 (1.3%). Notably, all tested sera were negative for PPV8 genomes. An analysis of the PPV1-VP sequences revealed two main clades (PPV1-I and PPV1-II), with the sequences recovered in this study grouped in the PPV1-II clade. Comparative analysis showed significant genetic distances for PPV2 to PPV7 at the NCG (>6.5%), NS (>6.3%), and VP (>7.5%) regions, particularly when compared to equivalent regions of PPV genomes recovered worldwide. This study highlights the endemic circulation of nPPVs in Colombian pig herds, specifically among gilts. Additionally, it contributes to the phylogenetic classification and evolutionary studies of these viruses. The proposed method aims to categorize and divide subtypes based on current knowledge and the genomes available in databanks. [ABSTRACT FROM AUTHOR]

A new species of nemacheilid loach, Schistura sonarengaensis sp. nov., is described from three cave‐dwelling populations (Barak–Surma–Meghna drainage) in the South Garo Hills district of Meghalaya, India. The new species possesses prominent eyes but is easily distinguished from all the congeners of the genus Schistura from Barak–Surma–Meghna and adjacent rivers drainages of northeast Indian (except S. syngkai) in having 13–26 vertically elongated to circular mid‐lateral black blotches (brownish in life) overlayered on a grayish‐black mid‐lateral stripe on a dull white or pale‐beige (golden brown in life) body. However, it can be easily distinguished from S. syngkai in having a complete (vs. incomplete) lateral line with more 72–89 (vs. 19–42) lateral‐line pored scales, greater pre‐dorsal length (48.5–53.1 vs. 41.9–44.1 %SL), a wider body at dorsal‐fin origin (11.3–16.7 vs. 9.4–10.3 %SL), greater dorsal (18.1–21.1 vs. 15.1–17.0 %SL) and lateral (20.9–24.1 vs. 17.4–18.9 %SL) head length, a wider head (14.5–18.5 vs. 11.6–13.3 %SL), and moderately forked (vs. emarginated) caudal fin. Further, molecular analysis confirms the distinctiveness of S. sonarengaensis sp. nov. from its congeners found in northeast India by significant divergences with uncorrected genetic distance ranging from 3.7% to 17.3% in the mitochondrial cytochrome c oxidase subunit I (COI) gene dataset. The phylogenetic position of the new species with its sister species was evaluated using maximum likelihood and Bayesian analysis. The species delimitation approaches assemble species by automatic partitioning (ASAP) and Poisson tree processes (PTP) utilized for testing species assignments consistently identified our test group as a distinct species from its sister species. Although the new species lacks typical morphological adaptations usually associated with a subterranean life, such as complete absence (or vestigial presence) of eyes and pigmentation, it exhibits a reduction of pigmentation when compared to the epigean congeners. [ABSTRACT FROM AUTHOR]

The fruit known as wax apple, scientifically named Syzygium samarangense (Blume) Merr. & L.M. Perry, is a well- liked agricultural product originating from Demak Regency in the Central Java Province. When it is difficult to distinguish between different forms of an organism, using DNA barcoding to authenticate the identity of species based on their DNA is an important way. The psbA-trnH intergenic spacer is a commonly used molecular approach to analyse the genetic characteristics of plant species. This study investigated the psbA-trnH intergenic spacer profile of wax apple cultivars from Demak regency. The investigation revealed that the psbA-trnH intergenic spacer sequences of the S. samarangense cultivars, namely Madu Thailand and Madu Deli Hijau, had lengths of 535 and 492 base pairs, respectively. Both cultivars demonstrate a greater nucleotide composition of deoxyadenylic acid (A) and deoxythymidylic acid (T) in comparison to deoxycytidilic acid (C) and deoxyguanylic (G). The genetic distance between S. samarangense ‘Madu Thailand’ and ‘Madu Deli Hijau’ indicates a very tight relationship, with a value of 0.000. The psbA-trnH intergenic spacer proved to be insufficient in differentiating the S. samarangense cultivars from Demak regency, mostly because to its low capacity to discern between the wax apple cultivars. [ABSTRACT FROM AUTHOR]

The Halophila species exhibit complex characteristics due to their high degree of variation across different bioregions. This study delves into the intricate characteristics of Halophila species in the Tanjung Adang Laut shoal, Johor, Malaysia, and offers valuable insights through morphological and genetic evidence. Employing internal transcribed sequences (ITS), we investigated the phylogeny of Halophila species, revealing distinct clades for H. ovalis, H. major, H. spinulosa, and the newly recorded H. nipponica. Notably, H. nipponica from the Tanjung Adang Laut shoal formed a conspecific relationship with its counterparts from Japan and Korea (98.3–98.5% similarity; 5–11 bp differences). Morphologically, distinguishing features, including the ratio of the half-lamina width (1:4.76–6.13 mm) and cross-vein count (4–7 pairs), supported the identification of H. nipponica. Genetic distance analyses revealed differences between H. nipponica, H. ovalis, and H. major, indicating haplotype diversity. Geographical variations were evident, as H. nipponica presented unique haplotypes (H24) in its clade. The 47 haplotypes network identified significant mutation sites, providing a comprehensive understanding of genetic and morphological distinctions. In conclusion, this study highlights the intricate characteristics and phylogeny of Halophila species in the Tanjung Adang Laut shoal, Johor, and provides valuable insights into their genetic and morphological diversity. [ABSTRACT FROM AUTHOR]

Recent collecting efforts in the upper Malagarazi basin (2013–2022) allowed for an integrative study based on qualitative (colour), quantitative (meristic and metric), and barcoding gene [mtDNA, cytochrome c oxidase (COI)] data of specimens similar to Enteromius sp. ‘ascutelatus’, being a previously identified, potentially, new species. Based on these data, the present study confirms its identification as a new species for science, which is here formally described as Enteromius nzigidaherai sp. nov. This new species belongs to the group of Enteromius species for which the last unbranched ray of the dorsal fin is flexible and devoid of serrations along its posterior edge. This species has a horizontal series of black spots at the midlateral level of the sides. Three congeneric species, known from the Congo basin sensu lato, with two of them also found in the upper Malagarazi basin, are most similar to it. However, E. nzigidaherai sp. nov. is distinguished from the two sympatric upper Malagarazi species, that is, E. quadrilineatus and E. lineomaculatus, at least by two meristics and two morphometrics. It is also distinguished from E. urostigma, known from the upper Congo basin, by two meristics and one, apparently related, morphometric. In addition, a barcoding (mtDNA, COI) study revealed that the specimens of E. nzigidaherai sp. nov. form a well‐supported, separate lineage, with a K2P genetic distance of more than 10% with specimens identified as E. quadrilineatus and E. lineomaculatus, both originating from the upper Malagarazi basin and for which tissue samples were available. Finally, the new species was found to be endemic to the upper reaches of two left bank affluents of the upper Malagarazi basin: the Muyovozi and the Kinwa. However, both affluents are threatened by human activities, which seem to have resulted in its local disappearance as recent intensive collecting efforts in the latter affluent have remained unsuccessful. The species should thus be considered Critically Endangered (CR) according to IUCN criteria B1ab(ii,iv)c(i,iii). Therefore, it is hoped that the present description draws renewed attention to the importance of aquatic protection in the region by highlighting the need for the effective establishment of the Malagarazi Nature Reserve and concern for its optimal delimitation to efficiently protect the entire ichthyofauna of the upper Malagarazi, without excluding the fish species confined to its affluent rivers. [ABSTRACT FROM AUTHOR]

DNA barcoding is a popular approach that can aid in identifying species and has led to the discovery of many new amphibian species. In this study, we first performed DNA barcoding for two Hylidae family representatives (Hyla orientalis and Hyla savignyi) in the Anatolia region of Türkiye. Five species delineation tests (ABGD, GMYC, PTP, RESL, and statistical parsimony analysis) were applied, and four of them indicated that three mitochondrial lineages of Hylidae are present in Anatolia. Intraspecific genetic distances (K2P) ranged from 0.0014 to 0.0045, while the interspecific genetic distances ranged from 0.0753 to 0.1933. According to the tree topologies obtained from maximum likelihood (ML) within H. savignyi from Anatolia, two lineages can be differentiated, and further investigation is warranted as to whether these lineages represent distinct species. [ABSTRACT FROM AUTHOR]

Human activities often induce maladaptive effects in urban wildlife, such as increased inbreeding and decreased gene flow, consequently leading to a loss of biodiversity. Although maladaptive effects are commonly reported in urban wildlife, some wildlife species are not affected. Understanding the conditions and factors that affect the genetic structure of wildlife is crucial for its conservation in urban environments. Eurasian red squirrels Sciurus vulgaris in Obihiro City, Hokkaido, Japan, have settled in large residential lots with a high risk of vehicle collisions for approximately 30 years, raising the possibility that the urban population would be genetically isolated from nearby rural populations and may experience a rapid decrease in genetic diversity. In this study, we analysed the population structure, genetic distance, and nucleotide diversity of squirrels in the Obihiro area using genome-wide single nucleotide polymorphisms (SNPs). Principal component analysis and ADMIXTURE showed that urban and rural squirrel populations formed distinct clusters with intermediate urban and rural boundary populations. Genetic distances between the urban populations were greater than that of other pairs. Nucleotide diversities were lower in urban populations than in other populations, suggesting limited gene flow between urban and other populations, possibly due to urbanisation. The change in the genetic characteristics of urban squirrel populations during this short period demonstrates the strong impact of urbanisation. Our findings suggest that a genome-wide approach to the genetic structure of wildlife contributes to its conservation in urban environments. [ABSTRACT FROM AUTHOR]

In the context of rapidly increasing population and diversified market demands, the steady improvement of yield and quality in horticultural crops has become an urgent challenge that modern breeding efforts must tackle. Heterosis, a pivotal theoretical foundation for plant breeding, facilitates the creation of superior hybrids through crossbreeding and selection among a variety of parents. However, the vast number of potential hybrids presents a significant challenge for breeders in efficiently predicting and selecting the most promising candidates. The development and refinement of effective hybrid prediction methods have long been central to research in this field. This article systematically reviews the advancements in hybrid prediction for horticultural crops, including the roles of marker-assisted breeding and genomic prediction in phenotypic forecasting. It also underscores the limitations of some predictors, like genetic distance, which do not consistently offer reliable hybrid predictions. Looking ahead, it explores the integration of phenomics with genomic prediction technologies as a means to elevate prediction accuracy within actual breeding programs. [ABSTRACT FROM AUTHOR]

Bakanae disease, caused by Fusarium fujikuroi, is a major threat to rice production globally, especially in Egypt. No rice variety is completely resistant to bakanae disease. Here, we assessed resistance in 11 Egyptian rice genotypes, identified a novel F. fujikuroi strain using molecular techniques, and developed molecular markers for resistance breeding. ISSR and InDel PCR were used to determine the genetic distance between the genotypes and develop molecular markers for bakanae disease resistance. qRT-PCR was used to assess the gene expression of four resistance candidate genes. Sakha 103 and Sakha 104 were the most tolerant genotypes, while Sakha 101 and Sakha 108 were the most susceptible to bakanae disease. ISSR and InDel PCR showed high polymorphism values among genotypes and distinctive bands in the most tolerant varieties. Gene expression analysis revealed up-regulation of LOC_Os01g41770, LOC_Os01g41780, and LOC_Os01g41790, which encode leucine-rich repeat receptor-like proteins, in susceptible varieties. Additionally, LOC_Os01g41800, encoding a putative cytochrome P450 monooxygenase, was up regulated in tolerant genotypes after inoculation. This study provides tools for screening rice genotypes for bakanae disease resistance and improving resistance breeding programs. The identified molecular markers and candidate genes could potentially be used in future breeding programs to develop new, Bakanae-resistant rice varieties, which is essential for sustainable rice production. [ABSTRACT FROM AUTHOR]

Capsicum annum L. is the most widely cultivated species due to its economic importance and health benefits. West Sumatra is one of the largest chili pepper producers in Indonesia, so it has a lot of local chili genetic resources. There is inadequate information on the genetic diversity of local chilies in West Sumatra. The purpose of this research was to analyze the genetic diversity of 23 genotypes of chili pepper from West Sumatra amplified with 10 markers of ISSR. The material used was leaves from 23 genotypes of West Sumatra's local chili which are collections of the Agriculture Faculty, Andalas University, Padang, West Sumatra. The results showed that ISSR markers (ISSR primer 12, ISSR UBC, and ISSR 3M) had produced 84 polymorphic DNA bands with a total polymorphic percentage of 61.45%. The dendrogram based on 10 ISSR markers showed that the 23 chili genotypes were retrieved into three main groups (I, II, III, IV) with genetic similarity coefficient values ranging from 0.67 to 0.97 or a diversity of features of 0.03-0.33 (30%). Group I consisted of 1 genotype, group II consisted of 3 genotypes, and group III consisted of 14 genotypes. Kopay chili (G20) has a large genetic distance compared to the other genotypes, while Lolai and Gero chilies have a very high similarity. This genetic diversity information can be used as a basis for generating crosses between genotypes in a breeding program. The farther the genetic distance will produce a high population diversity, the greater the chance of getting superior hybrids. [ABSTRACT FROM AUTHOR]

The genus Pourthiaea Decne., a deciduous woody group with high ornamental value, belongs to the family Rosaceae. Here, we reported newly sequenced plastid genome sequences of Pourthiaea beauverdiana (C. K. Schneid.) Hatus., Pourthiaea parvifolia E. Pritz., Pourthiaea villosa (Thunb.) Decne., and Photinia glomerata Rehder & E. H. Wilson. The plastomes of these three Pourthiaea species shared the typical quadripartite structures, ranging in size from 159,903 bp (P. parvifolia) to 160,090 bp (P. beauverdiana). The three Pourthiaea plastomes contained a pair of inverted repeat regions (26,394–26,399 bp), separated by a small single-copy region (19,304–19,322 bp) and a large single-copy region (87,811–87,973 bp). A total of 113 unique genes were predicted for the three Pourthiaea plastomes, including four ribosomal RNA genes, 30 transfer RNA genes, and 79 protein-coding genes. Analyses of inverted repeat/single-copy boundary, mVISTA, nucleotide diversity, and genetic distance showed that the plastomes of 13 Pourthiaea species (including 10 published plastomes) are highly conserved. The number of simple sequence repeats and long repeat sequences is similar among 13 Pourthiaea species. The three non-coding regions (trnT-GGU-psbD, trnR-UCU-atpA, and trnH-GUG-psbA) were the most divergent. Only one plastid protein-coding gene, rbcL, was under positive selection. Phylogenetic analyses based on 78 shared plastid protein-coding sequences and 29 nrDNA sequences strongly supported the monophyly of Pourthiaea. As for the relationship with other genera in our phylogenies, Pourthiaea was sister to Malus in plastome phylogenies, while it was sister to the remaining genera in nrDNA phylogenies. Furthermore, significant cytonuclear discordance likely stems from hybridization events within Pourthiaea, reflecting complex evolutionary dynamics within the genus. Our study provides valuable genetic insights for further phylogenetic, taxonomic, and species delimitation studies in Pourthiaea, as well as essential support for horticultural improvement and conservation of the germplasm resources. [ABSTRACT FROM AUTHOR]

Background: Populations of Olea europaea subsp. europaea var. sylvestris, the ancestor of cultivated olives, are scattered across the Mediterranean Basin. However, after millennia of possible hybridization with cultivated varieties, the genetic identity of many of these populations remain questionable. In the southern Levant, the plausible primary domestication center of olives, many of the naturally growing olive (NGOs) are considered feral, having developed from nearby olive groves. Here, we investigated the genetic identity of NGOs population in the Carmel region, hypothesizing that their specific location, which limit anemophily, provided an opportunity for the persistence of genuine var. sylvestris. Results: We mapped more than 1,000 NGOs on the Kurkar ridge along the Carmel coast, within and outside the residential area of Atlit and used simple sequence repeats of 14 loci to assess the spatial genetic structure of 129 NGOs. Genetic diversity parameters and genetic distances between NGO and cultivated olives, as well as phenotypic and morphometric analyses of their oil content and pits, respectively, indicated the presence of a genuine var. sylvestris population. However, NGOs within the residential area of Atlit and old settlements showed an intermediate admix genetic structure, indicating on hybridization with local varieties, a consequence of their proximity to cultivated trees. Conclusions: Integrating the results of genetic and phenotypic analyses we provide crucial evidence of the presence of a genuine var. sylvestris population in the southern Levant, in close geographical proximity to archaeological sites with the earliest evidence of olive exploitation in the ancient world. We supplement the results with recommendations for a conservation program that combines municipal requirements and the urgent need to preserve the largest population of var. sylvestris in the southern Levant. [ABSTRACT FROM AUTHOR]

Influenza viruses continually evolve new antigenic variants, through mutations in epitopes of their major surface proteins, hemagglutinin (HA) and neuraminidase (NA). Antigenic drift potentiates the reinfection of previously infected individuals, but the contribution of this process to variability in annual epidemics is not well understood. Here, we link influenza A(H3N2) virus evolution to regional epidemic dynamics in the United States during 1997--2019. We integrate phenotypic measures of HA antigenic drift and sequence-based measures of HA and NA fitness to infer antigenic and genetic distances between viruses circulating in successive seasons. We estimate the magnitude, severity, timing, transmission rate, age-specific patterns, and subtype dominance of each regional outbreak and find that genetic distance based on broad sets of epitope sites is the strongest evolutionary predictor of A(H3N2) virus epidemiology. Increased HA and NA epitope distance between seasons correlates with larger, more intense epidemics, higher transmission, greater A(H3N2) subtype dominance, and a greater proportion of cases in adults relative to children, consistent with increased population susceptibility. Based on random forest models, A(H1N1) incidence impacts A(H3N2) epidemics to a greater extent than viral evolution, suggesting that subtype interference is a major driver of influenza A virus infection ynamics, presumably via heterosubtypic cross-immunity. [ABSTRACT FROM AUTHOR]

This study establishes the first core collection (CC) for Taiwanese Phalaenopsis orchids to preserve genetic diversity and key traits essential for breeding and research, thereby enhancing breeding efficiency without the need for a large maintained parent population. We examined 207 commercial orchid cultivars from ten nurseries, characterized by two phenotypes and genotypic data from eight simple sequence repeat markers. Multiple imputation was applied to estimate missing phenotypes, minimizing potential uncertainties and ensuring the reliability of population structure analysis. Weighted k-means clustering identified seven distinct clusters, highlighting substantial genetic diversity. We proposed a two-step phenotype and genotype strategy and modified genetic distance algorithms to effectively preserve both phenotypic and genetic diversity while retaining key features. Consequently, 22 core accessions were selected, distributed across seven clusters, and representing the orchid germplasm collection. Our evaluation revealed significant diversity preservation, particularly in distinct characteristics and rare features, outperforming other methodologies. Pedigree background analysis further confirmed the representativeness of the CC in maintaining diverse genetic materials. We emphasized the importance of evaluating the CC by detailing the criteria and statistical analyses used to ensure the quality, representativeness, and effectiveness of the selected accessions. This study contributes to orchid breeding, conservation efforts, and sustainable agricultural practices by providing a valuable and comprehensive resource. In conclusion, our research establishes a groundbreaking CC, offering insights into the genetic landscape of Taiwanese Phalaenopsis orchids and highlighting potential advancements in breeding commercially desirable varieties. [ABSTRACT FROM AUTHOR]

Background: The association of the oral microbiome with SARS-CoV-2 infections and disease progression has been documented in European, Asian, and American populations but not in Africa. Methods: We conducted a study in Ghana to evaluate and compare the naso-oropharyngeal microbiome in SARS-CoV-2-infected and uninfected persons before (pre-vaccine) and after vaccine availability (post-vaccine) in the country. 16S rRNA V3-V4 variable region was sequenced and analysed from DNA extracted from naso-oropharyngeal swabs. Results: Considering only the infection status, infected and uninfected groups had no difference in their within-group diversity and was evident in the study population pre- and post-vaccine availability. The introduction of vaccines reduced the diversity of the naso-oropharyngeal microbiome particularly among SARS-CoV-2 positive persons and, vaccinated individuals (both infected and uninfected) had higher microbial diversity compared to their unvaccinated counterparts. SARS-CoV-2-positive and -negative individuals were largely compositionally similar varying by 4–7% but considering vaccination*infection statuses, the genetic distance increased to 12% (P = 0.003) and was mainly influenced by vaccination. Common among the pre- and post-vaccine samples, Atopobium and Finegoldia were abundant in infected and uninfected individuals, respectively. Bacteria belonging to major butyrate-producing phyla, Bacillota (particularly class Clostridia) and Bacteroidota showed increased abundance more strikingly in infected individuals before vaccines were available. They reduced significantly after vaccines were introduced into the country with Fusobacterium and Lachnoanaerobaculum being the only common bacteria between pre-vaccine infected persons and vaccinated individuals, suggesting that natural infection and vaccination correlate with high abundance of short-chain fatty acids. Conclusion: Our results show, in an African cohort, the abundance of bacteria taxa known for their protective pathophysiological processes, especially during infection, suggesting that this population is protected against severe COVID-19. The immune-related roles of the members of Bacillota and Bacteroidota that were found associated with infection and vaccination require further studies, and how these may be linked to ethnicity, diet and age. We also recommend expansion of microbiome–disease association studies across Africa to identify possible bacterial-mediated therapeutics for emerging infections. [ABSTRACT FROM AUTHOR]

Although the barred sand burrower, Limnichthys fasciatus, is widely distributed throughout the western Pacific, including Japan, Taiwan, and Australia, its morphology and genetics are poorly known. We discovered four cryptic species of Limnichthys from the western Pacific based on mtDNA cytochrome c oxidase subunit I (COI) and 16S ribosomal RNA (rRNA) sequences. Genetic distances showed remarkably large differences (12.7%–24.3% in COI and 7.9%–19.6% in 16S rRNA) between true L. fasciatus (type locality: southeastern Australia) and the others. A relaxed clock model with optimized selected substitution models showed that their deep divergence began in the middle Miocene epoch and subsequently diverged into the current cryptic species in the Plio‐Pleistocene. A eurythermal common ancestor may have evolved independently in each region due to geographical events and paleoclimatic fluctuations, which made it possible for L. fasciatus complex to be an anti‐equatorial species. Despite their deep genetic divergence, they showed marked phenotypic similarity, suggesting that they have experienced similar selective pressures related to their specific behavior. [ABSTRACT FROM AUTHOR]

Background: African mahogany species (Khaya sp.) have been introduced to Brazil gaining increasing economic interest over the last years, as they produce high quality wood for industrial applications. To this date, however, the knowledge available on the genetic basis of African mahogany plantations in Brazil is limited, which has driven this study to examine the extent of genetic diversity and structure of three cultivated species (Khaya grandifoliola, Khaya senegalensis and Khaya ivorensis) and their prospects for forest breeding. Results: In total, 115 individuals were genotyped (48 of K. grandifoliola, 34 of K. senegalensis and 33 of K. ivorensis) for 3,330 filtered neutral loci obtained from genotyping-by-sequencing for the three species. The number of SNPs varied from 2,951 in K. ivorensis to 4,754 in K. senegalensis. Multiloci clustering, principal component analysis, Bayesian structure and network analyses showed a clear genetic separation among the three species. Structure analysis also showed internal structure within each species, highlighting genetic subgroups that could be sampled for selecting distinct genotypes for further breeding, although the genetic distances are moderate to low. Conclusion: In our study, SNP markers efficiently assessed the genomic diversity of African mahogany forest plantations in Brazil. Our genetic data clearly separated the three Khaya species. Moreover, pairwise estimates of genetic distances among individuals within each species showed considerable genetic divergence among individuals. By genotyping 115 pre-selected individuals with desirable growth traits, allowed us not only to recommend superior genotypes but also to identify genetically distinct individuals for use in breeding crosses. [ABSTRACT FROM AUTHOR]