Search

The accessibility of genomic tools in evolutionary biology has allowed for a thorough exploration of various evolutionary processes associated with adaptation and speciation. However, genomic studies in natural systems present numerous challenges, reflecting the inherent complexities of studying organisms in their native habitats. The utilization of museum specimens for genomics research has received increased attention in recent times, facilitated by advancements in ancient DNA techniques. In this study, we have utilized a museum genomics approach to analyze historic specimens of Woolly-necked storks (Ciconia spp.) and examine their genetic composition and taxonomic status and explore the evolutionary and adaptive trajectories of populations over the years. The Woolly-necked storks are distributed in Asia and Africa with a taxonomic classification that has been a matter of ambiguity. Asian and African Woollynecks were recently recognized as different species based on their morphological differences; however, their genomic validation was lacking. In this study, we have used ∼70-year-old museum samples for whole-genome population-scale sequencing. Our study has revealed that Asian and African Woollynecks are genetically distinct, consistent with the current taxonomic classification based on morphological features. However, we also found a high genetic divergence between the Asian subspecies Ciconia episcopus neglecta and Ciconia episcopus episcopus , suggesting this classification requires a detailed examination to explore processes of ongoing speciation. Because taxonomic classification directly impacts conservation efforts, and there is evidence of declining populations of Asian Woollynecks in Southeast Asia, our results highlight that population-scale studies are urgent to determine the genetic, ecological, and phylogenetic diversity of these birds. [ABSTRACT FROM AUTHOR]

Differences in migratory behavior have been suggested to drive speciation, but the genetics underlying this process remain unknown. Identification and study of migratory divides can help us understand how differential migration can lead to reproductive isolation. Here, we genotyped Willow Warblers Phylloscopus trochilus, from the Åland islands, located in between the ranges of the differentially migrating subspecies P. t. trochilus and P. t. acredula. We found that Willow Warblers on the Åland islands were genetically intermediate to allopatric populations of both parental subspecies, providing evidence that the islands constitute a previously unknown hybrid swarm, likely to be a migratory divide. [ABSTRACT FROM AUTHOR]

The Eurasian subspecies of the Goosander Mergus merganser consists of three subclades (Fennoscandian–British, E European–N Asian, and Alpine). Recently, this species expressed a rapid expansion in the Carpathians. In this study, we used mitochondrial DNA to track the origins of this population. Sequencing revealed that the majority of the Carpathian birds are related to the N Polish and Russian populations, whereas one sample has a haplotype known from the Alps. This mixed ancestry was probably caused by an outbreeding enhancement and/or enlarged habitat requirements that allowed the birds to settle in the mountain rivers of the Carpathians. [ABSTRACT FROM AUTHOR]

Elucidating the evolutionary processes that drive population divergence can enhance our understanding of the early stages of speciation and inform conservation management decisions. The honeybee Apis cerana displays extensive population divergence, providing an informative natural system for exploring these processes. The mainland lineage A. cerana includes several peripheral subspecies with disparate ecological and geographical settings radiated from a central ancestor. Under this evolutionary framework, we can explore the patterns of genome differentiation and the evolutionary models that explain them. We can also elucidate the contribution of non‐genomic spatiotemporal mechanisms (extrinsic features) and genomic mechanisms (intrinsic features) that influence these genomic differentiation landscapes. Based on 293 whole genomes, a small part of the genome is highly differentiated between central–peripheral subspecies pairs, while low and partial parallelism partly reflects idiosyncratic responses to environmental differences. Combined elements of recurrent selection and speciation‐with‐gene‐flow models generate the heterogeneous genome landscapes. These elements weight differently between central‐island and other central–peripheral subspecies pairs, influenced by glacial cycles superimposed on different geomorphologies. Although local recombination rates exert a significant influence on patterns of genomic differentiation, it is unlikely that low‐recombination rates regions were generated by structural variation. In conclusion, complex factors including geographical isolation, divergent ecological selection and non‐uniform genome features have acted concertedly in the evolution of reproductive barriers that could reduce gene flow in part of the genome and facilitate the persistence of distinct populations within mainland lineage of A. cerana. [ABSTRACT FROM AUTHOR]

The herpetofauna of the Iberian Peninsula is relatively well-researched, yet detailed studies, at least in part relying on molecular genetic data, continue to reveal taxa new to science, mostly species and subspecies. Newts of the genus Triturus are one such group with undiscovered yet taxonomically relevant variation, as shown by the recent description of new (sub)species of pygmy newts (T. pygmaeus, T. rudolfi). The marbled newt, Triturus marmoratus, shows an equally deep and geographically coherent spatial-genetic diversification. It is here shown that a northern and a southern group are characterized by different mitochondrial dna profiles and are also differentiated in morphometry and colouration pattern. With no firm evidence for selection against intermediate genotypes, the southern group is described at the subspecies level, as T. marmoratus harmannis ssp. nov. The subspecies' contact zone is situated at ca. 41.5 northern latitude and stretches from the Atlantic coast near Porto, Portugal to the northeast of Madrid, Spain. [ABSTRACT FROM AUTHOR]

Whether or where to draw subspecies' taxonomic boundaries is much more than an esoteric argument. Subspecific taxonomies and associated geographic ranges have important conservation and management implications because the Endangered Species Act (ESA) protects distinct populations segments below the species level. Genomic data can help resolve taxonomic disputes and assist with conservation policy; however, because subspecific lineages often exhibit gene flow, genomic lineages for subspecific taxa are rarely distinct. We used genomic data from the eastern pinesnake (Pituophis melanoleucus) to determine the geographic range of the morphologically variable Florida pinesnake (P. m. mugitus), which is petitioned for listing under the ESA. The overall genomic pattern of the eastern pinesnake is one of admixture, and there are gradual differences over the wide range of the species. But there still are discernable areas of genetic differentiation that correspond to the morphologically defined Florida pinesnake, and other subspecies. This pattern of admixture should be expected for subspecies. We propose that boundaries for the Florida pinesnake should maximize the species redundancy, resilience, and representation based on genomic data. We also propose best practices for managers and policymakers interpreting genomic data of subspecies, given that the genomic cutoffs will rarely be truly distinct. [ABSTRACT FROM AUTHOR]

Saimiri cassiquiarensis cassiquiarensis (Cebidae) is a primate subspecies with a wide distribution in the Amazonian region of Brazil, Colombia, and Venezuela. However, the boundaries of its geographic range remain poorly defined. This study presents new occurrence localities for this subspecies and updates its distribution using a compiled data set of 140 occurrence records based on literature, specimens vouchered in scientific collections, and new field data to produce model‐based range maps. After cleaning our data set, we updated the subspecies' extent of occurrence, which was used in model calibration. We then modeled the subspecies' range using a maximum entropy algorithm (MaxEnt). The final model was adjusted using a fixed threshold, and we revised this polygon based on known geographic barriers and parapatric congeneric ranges. Our findings indicate that this subspecies is strongly associated with lowland areas, with consistently high daily temperatures. We propose modifications to all range boundaries and estimate that 3% of the area of occupancy (AOO, as defined by IUCN) has already been lost due to deforestation, resulting in a current range of 224,469 km2. We also found that 54% of their AOO is currently covered by protected areas (PAs). Based on these results, we consider that this subspecies is currently properly classified as Least Concern, because it occupies an extensive range, which is relatively well covered by PAs, and is currently experiencing low rates of deforestation. Research Highlights: We used a model‐based approach to estimate Saimiri cassiquiarensis cassiquiarensis range. This subspecies is a small Amazonian cebid that ranges over wide areas in Brazil, Colombia, and Venezuela. However, the geographic range of this taxon remains poorly defined.The MaxEnt model indicates that the taxon is strongly linked to lowland regions with consistently high daily temperatures. The suitable habitat for this taxon only accounts for 24% of its extent of occurrence.We proposed changes to all range limits and estimated that 3% of the area has already been deforested. This results in a current range of 224,469 km2, with half of this range being encompassed by protected areas. [ABSTRACT FROM AUTHOR]

A major aim of evolutionary biology is to understand why patterns of genomic diversity vary within taxa and space. Large‐scale genomic studies of widespread species are useful for studying how environment and demography shape patterns of genomic divergence. Here, we describe one of the most geographically comprehensive surveys of genomic variation in a wild vertebrate to date; the great tit (Parus major) HapMap project. We screened ca 500,000 SNP markers across 647 individuals from 29 populations, spanning ~30 degrees of latitude and 40 degrees of longitude – almost the entire geographical range of the European subspecies. Genome‐wide variation was consistent with a recent colonisation across Europe from a South‐East European refugium, with bottlenecks and reduced genetic diversity in island populations. Differentiation across the genome was highly heterogeneous, with clear 'islands of differentiation', even among populations with very low levels of genome‐wide differentiation. Low local recombination rates were a strong predictor of high local genomic differentiation (FST), especially in island and peripheral mainland populations, suggesting that the interplay between genetic drift and recombination causes highly heterogeneous differentiation landscapes. We also detected genomic outlier regions that were confined to one or more peripheral great tit populations, probably as a result of recent directional selection at the species' range edges. Haplotype‐based measures of selection were related to recombination rate, albeit less strongly, and highlighted population‐specific sweeps that likely resulted from positive selection. Our study highlights how comprehensive screens of genomic variation in wild organisms can provide unique insights into spatio‐temporal evolutionary dynamics. [ABSTRACT FROM AUTHOR]

Animals that colonize islands often undergo significant evolutionary changes in comparison with their continental counterparts as a response to specific island conditions. The pace of such changes can be relatively fast, which poses challenges in the evaluation of the taxonomic status of island taxa. The Japanese and Manchurian Bush Warbler species complex (Horornis diphone–canturians), which breeds in East Asia and the Japanese Archipelago, is such an avian example. This species complex exhibits significant morphological differentiation between different taxa, and the taxonomic status and phylogenetic relationships within the complex are debated. Here, we updated the taxonomy of this species complex and shed insight on its evolutionary history using multi‐locus phylogeographic and acoustic analyses. Our results support the conventional treatment of the two continental taxa borealis and canturians as subspecies of H. canturians, contrary to some recent proposals that they are affiliated to H. diphone. We also document a reduction in body size, that is dwarfism, and vocal divergence in the nominate subspecies H. d. diphone, which is endemic to the remote and isolated Ogasawara Islands. These changes may have happened following colonization of these islands, which was estimated to have taken place approximately 0.2 million years ago. Although H. d. diphone is clearly distinctive and deserves recognition as an evolutionarily significant unit, H. d. diphone and other H. diphone samples were not reciprocally monophyletic. Because of this lack of reciprocal monophyly and a relatively recent divergence time, we advocate maintaining its current subspecies status. We also detected reduced genetic diversity, measured as heterozygosity, in H. d. diphone. We suggest that conservation efforts in the Ogasawara Islands should prioritize the protection of this endemic subspecies. Collectively, our findings suggest that the separation between the populations on the East Asian continent and the Japanese Archipelago, followed by colonization of remote oceanic islands through long‐distance dispersal, underlie rapid phenotypic and genetic diversification of the Horornis diphone–canturians species complex. [ABSTRACT FROM AUTHOR]

Aim Location Time Period Major Taxa Studied Methods Results Main Conclusions Synthesize literature on genetic structure within species to understand how geographic features and species traits influence past responses to climate change.North America.We synthesized phylogeographic studies from 1978 to 2023, which describe genetic lineages that diverged during the Pleistocene (≥11,700 years ago).Mammals.We conducted a literature review to map genetic breaks in species distributions, then tested a set of geographic hypotheses (e.g., mountains, rivers) to explain their position by comparing break locations to a grid within each species' sampled range using logistic regression. We then conducted a meta‐analysis using species‐specific model estimates to ask if life‐history traits explained variation in which barriers were most important in species' past response to climate change.Our findings reveal heterogeneity in both where North American mammal phylogeography has been studied and the density of genetic breaks across 229 species. We found relatively high concordance among carnivores, ungulates and lagomorphs, where breaks were associated with mountains, major water bodies and relatively even terrain. In contrast, we found high variability within rodents and shrews, and no evidence that intrinsic factors related to dispersal ability explained the importance of hypothesized barriers across all species.Southern Mexico is a hotspot for genetic breaks that has yet to be integrated into the broader story of North American phylogeography. We show that mountains and major water bodies play particularly important roles as barriers, but substantial variation across species within orders suggests that there is more to the story besides shared climatic or phylogenetic histories. Thus, understanding the phylogeography of individual species will continue to be important given that our results suggest high variability in how species may respond to future global change. [ABSTRACT FROM AUTHOR]

The Scorpion Mud Turtle (Kinosternon scorpioides) has been recognized by most recent authors to be a single species (3 subspecies) ranging from Tamaulipas, Mexico, to northern Argentina. However, recent molecular analyses have demonstrated that it is not monophyletic, but rather paraphyletic relative to other Neotropical Kinosternon. Based on extensive genetic sampling across the range of this species, a recent paper elevated the 3 subspecies (albogulare, cruentatum, and scorpioides) to species status, confirmed the divergence of Pacific and Atlantic versant populations of K. cruentatum, and recommended that both be given species status. However, the type locality of K. cruentatum is imprecise, making the allocation of the name problematic. Our study sought to determine the provenance of the type using morphometric analysis of specimens from across the range. That analysis demonstrates unequivocally that the type of K. cruentatum was collected on the Atlantic versant, likely from an eastern population. Furthermore, the analysis also revealed that the type of K. mexicanum, previously synonymized with K. cruentatum, was collected from along the Pacific versant. Hence, the name K. cruentatum should be restricted to populations in Atlantic drainages, and the name K. mexicanum should be restricted to Pacific drainages. Our analysis also indicated divergence among the 3 allopatric Atlantic versant populations, but future genetic work will be needed to determine whether they merit taxonomic recognition. [ABSTRACT FROM AUTHOR]

Simple Summary: Increasing honey bee resilience against the parasitic mite Varroa destructor, while respecting sustainability, may be achieved by enriching natural mite resistance traits in the breeding population. Some of these traits are linked to specific variants in the honey bee genome, which can be pinpointed and characterized with high-throughput molecular lab tests. Breeding by focusing on these genomic variants is thus more efficient and less time-consuming. However, when evaluating the link between a specific varroa resistance trait outcome and its associated variants in the genome, different contributions of the variants may be observed between honey bee races. It is hypothesized that these observations evolve from different linkages between the trait-causing genes and the genomic variants. Therefore, we evaluated the presence of genomic variants associated with a varroa resistance trait in different honey bee samples across the European continent. We observed significant differences in the presence of the genomic variants in the considered honey bee races, which underpin our hypothesis of linkage dissimilarities. This study shows that determining the honey bee race prior to using the genomic variants associated with varroa resistance for selective breeding is of utmost importance. Implementation of marker-assisted selection (MAS) in modern beekeeping would improve sustainability, especially in breeding programs aiming for resilience against the parasitic mite Varroa destructor. Selecting honey bee colonies for natural resistance traits, such as brood-intrinsic suppression of varroa mite reproduction, reduces the use of chemical acaricides while respecting local adaptation. In 2019, eight genomic variants associated with varroa non-reproduction in drone brood were discovered in a single colony from the Amsterdam Water Dune population in the Netherlands. Recently, a new study tested the applicability of these eight genetic variants for the same phenotype on a population-wide scale in Flanders, Belgium. As the properties of some variants varied between the two studies, one hypothesized that the difference in genetic ancestry of the sampled colonies may underly these contribution shifts. In order to frame this, we determined the allele frequencies of the eight genetic variants in more than 360 Apis mellifera colonies across the European continent and found that variant type allele frequencies of these variants are primarily related to the A. mellifera subspecies or phylogenetic honey bee lineage. Our results confirm that population-specific genetic markers should always be evaluated in a new population prior to using them in MAS programs. [ABSTRACT FROM AUTHOR]

Simple Summary: True bugs (Hemiptera: Heteroptera) of the infraorder Nepomorpha are known as aquatic bugs because most of them spend almost their entire life cycle submerged. Naucoridae are the third most diverse family of aquatic bugs, including eight subfamilies, 43 genera, and over 400 species. They are commonly known as saucer bugs, and occur in standing and flowing freshwater courses globally, except for Antarctica and the Pacific oceanic islands. The family is represented in Brazil by 68 species, most of which are endemic. Although the diversity of the family has been the target of several recent studies, large areas of the country are still unexplored and there are several species unknown to science. Aiming to fill these knowledge gaps, a series of expeditions were carried out in seven states of eastern Brazil between 2018 and 2023. In addition, the examination of specimens previously deposited in a national entomological collection resulted in the discovery of a new species and new geographic distribution records for 11 other species and two subspecies of the family. The aquatic bug family Naucoridae (Hemiptera: Heteroptera: Nepomorpha) is currently represented in Brazil by 68 species. Although the diversity of the family has been the target of several recent studies, large areas of the country are still unexplored and several species that have been deposited in entomological collections are waiting for a formal description. Aiming to fill these knowledge gaps, a series of expeditions were carried out in six states of eastern Brazil between 2018 and 2023: Alagoas, Bahia, Ceará, Espírito Santo, Pernambuco, and Sergipe. The fieldwork targeted protected areas, but surrounding regions were also explored. The material obtained, in addition to specimens previously deposited in a national entomological collection, revealed the existence of Australambrysus margaritifer Jordão, Santos and Moreira, a new species herein described, and new records for other 11 species and two subspecies belonging to the genera Carvalhoiella De Carlo, 1963, Limnocoris Stål, 1876, Maculambrysus Reynoso-Velasco and Sites 2021, and Pelocoris Stål, 1876. [ABSTRACT FROM AUTHOR]

Specimens of the genus Phalangium Linnaeus, 1758 (Phalangiidae Latreille, 1802) are reported from northern Iraq and were identified as Phalangium punctipes (L. Koch, 1878). These represent the first record of both, genus and species, for the Iraqi Opiliones fauna. The characteristic features of the species and illustrations of their habitat are presented. This record increases the number of known Opiliones in Iraq to six species, which is a very low number compared to the Opiliones checklists from two nearby countries, namely Iran with 28 species and Türkiye with 89 species and five subspecies. Nineteen species and two subspecies records from the Türkiye checklist are considered misidentifications and therefore omitted in our revised checklist. [ABSTRACT FROM AUTHOR]

The taxonomic status of Asystasia gangetica var. krishnae has been evaluated and compared with the closely resembling taxon A. intrusa (synonyms: A. gangetica subsp. micrantha and A. micrantha). The trait that differentiates the two taxa, as per reports, is the occurrence of vertical violet‐black bands on the sides of anthers in the former taxon. The authors explain that var. krishnae could be the first report of A. intrusa for the country and suggest the possibility of neglecting the violet black bands in the previous descriptions of A. intrusa. [ABSTRACT FROM AUTHOR]

Mycobacterium abscessus belongs to the largest group of mycobacteria, the rapid-growing saprophytic mycobacteria, and is one of the most difficult-to-treat opportunistic pathogen. Several features pertain to the high adaptability of M. abscessus to the host. These include the capacity to survive and persist within amoebae, to transition from a smooth to a rough morphotype that occurs during the course of the disease and to express of a wide array of virulence factors. The main objective of this narrative review consists to report major assets of M. abscessus that contribute to the virulence of these rapid-growing saprophytic mycobacteria. Strikingly, many of these determinants, whether they are from a mycobacterial origin or acquired by horizontal gene transfer, are known virulence factors found in slow-growing and strict pathogens for humans and animals. In the light of recent published work in the field we attempted to highlight major features characterizing M. abscessus pathogenicity and to explain why this led to the emergence of this mycobacterial species in patients with cystic fibrosis. M. abscessus genome plasticity, the smooth-to-rough transition, and the expression of a panel of enzymes associated with virulence in other bacteria are key players in M. abscessus virulence. In addition, the very large repertoire of lipid transporters, known as mycobacterial membrane protein large and small (MmpL and MmpS respectively), deeply influences the pathogenicity of M. abscessus , as exemplified here for some of them. All these traits largely contribute to make M. abscessus a unique mycobacterium regarding to its pathophysiological processes, ranging from the early colonization steps to the establishment of severe and chronic pulmonary diseases. [ABSTRACT FROM AUTHOR]

A taxonomic and nomenclatural account on taxa of Iridaceae proposed by Ferdinand Schur, a famous investigator of the flora of Transylvania (present‐day Romania), is presented. Types are designated for 12 names, namely lectotypes for Crocus banaticus var. niveus, C. exiguus, Iris fieberi var. monantha, I. × binata, I. × cucullata, I. pseudocyperus, I. transsilvanica, I. sibirica var. salina, and neotypes for C. banaticus var. concolor, C. banaticus var. pictus, C. banaticus var. versicolor and I. pumila var. albiflora. Based on a broad examination of Schur's original and authentic material, the taxonomic application of these names, as well as of his invalidly published and unpublished names (appearing only on herbarium labels), are clarified. It is proposed to treat I. fieberi var. monantha as a taxonomic synonym of I. aphylla, I. pumila var. albiflora and I. transsilvanica as synonyms of I. pumila, and I. sibirica var. salina as a synonym of I. spuria. The names I. × binata and I. × cucullata are accepted for the hybrids I. aphylla × pumila and I. × germanica × pallida, respectively. The treatment of I. pseudocyperus as a distinct subspecies within I. graminea is supported. All names validly published by Schur in Crocus are treated as synonyms of C. heuffelianus s.l. until an adequate taxonomic revision covering the southern Carpathian allotetraploid C. cf. heuffelianus (2n = 18) is implemented. If this polyploid deserves the rank of a distinct species, the name C. exiguus, which seems to be the earliest validly published, should be accepted for this taxon. [ABSTRACT FROM AUTHOR]

Streptococcus gallolyticus subspecies pasteurianus is a subtype of Streptococcus bovis (S. bovis) that has become increasingly recognized as a sepsis-causing pathogen in neonates. It is well documented that S. bovis species have a predilection to both cardiac and gastrointestinal tissue, and in adult populations, isolating these organisms in the bloodstream often triggers further evaluation for co-morbid complications such as colon cancer or endocarditis. However, no such guidance currently exists in neonatal literature. We present a case of a preterm infant with S. gallolyticus subsp. pasteurianus bacteremia presenting as necrotizing enterocolitis (NEC) not previously described in the literature. Furthermore, through a complete diagnostic evaluation, including an echocardiogram, our patient was found to have the rare complication of endocarditis. [ABSTRACT FROM AUTHOR]

Xylella fastidiosa is a plant‐pathogenic bacterium that poses a serious threat to the production of economically important plant species including grapes, almonds, olives and a broad range of amenity plants, causing significant economic losses worldwide. While multiple molecular detection assays have been developed for X. fastidiosa, there is a lack of molecular tools available for detection and differentiation of the closely related pear pathogen, Xylella taiwanensis. In this study, we present a novel conventional PCR assay with primers that can amplify both Xylella species. The amplified product could be sequenced and used for discrimination between the two species and the subspecies within the fastidiosa species. This PCR assay was designed using a genome‐informed approach to target the ComEC/Rec2 gene of both Xylella species, ensuring a higher specificity than other previously developed PCR assays. A test performance study across five national plant diagnostic laboratories in Australia and New Zealand demonstrated this assay's high sensitivity and specificity to all known species and subspecies within the Xylella genus. This PCR assay can be used for Xylella identification at the species and subspecies level and is compatible with Sanger sequencing and nanopore sequencing for rapid turnaround time. The newly developed conventional PCR assay presented here offers rapid detection and accurate identification of both Xylella species from plant, insect vector or bacterial samples, enabling timely implementation of biosecurity measures or disease management responses. [ABSTRACT FROM AUTHOR]

The new Checklist of mosses (Bryophyta) of Slovenia within current political boundaries comprises 669 species, 6 subspecies and 18 varieties. Additional 13 species are denoted by a question mark since reports are considered questionable. An alphabetically arranged tabular presentation of genera, species and lower taxa, also shows their presence in particular phytogeographical units of Slovenia. The records from the periods before and after 1959 are marked with different symbols. Each species has also new Red List status in Slovenia. The checklist includes the data from literature and the Herbarium LJU. Annotations to selected species give a critical evaluation of the literature and herbarium data. A list of taxa that should be excluded from the flora of Slovenia and the synonyms used in the floristic literature for Slovenia are also added. [ABSTRACT FROM AUTHOR]

Three species of pocket mice (Chaetodipus artus , C. goldmani , and C. pernix) characterize the Sinaloan subregion of the Sonoran regional desert. They occur primarily in Sinaloan thornscrub and monsoon (dry deciduous) forest biotic communities, both of which have suffered from agricultural conversion. Sinaloan thornscrub occurs along the coastal plains of southern Sonora and Sinaloa, México, and grades into monsoon forest in the foothills of the Sierra Madre Occidental. We describe the geographical and ecological distributions of the 3 species of Chaetodipus , evaluate evolutionary relationships within each species based on mitochondrial DNA sequence data, and compare these to previously described phenetic, allozymic, and chromosomal variation. We elevate the subspecies of C. pernix to full species, delineate evolutionary units within C. goldmani and C. artus that we formally recognize as subspecies, and evaluate the conservation status of all 3 species of Chaetodipus. [ABSTRACT FROM AUTHOR]

Leafless Bossiaea species are a unique group of plants endemic to Australia that present intriguing challenges in taxonomy and conservation because of their morphological simplicity and often small, disjunct populations. We employed whole genome reduced representation sequencing (DArTseq) to enhance our understanding of the population dynamics, diversity and taxonomy of leafless Bossiaea species. Our dataset comprised 52,539 single-nucleotide polymorphisms across 283 samples from 7 leafless Bossiaea species, including 6 listed threatened species. We examined population structure, phylogenetic relationships, kinship and gene flow within and among populations. On the basis of our population-genomic analyses, we propose recognition of the novel taxon Bossiaea vombata subsp. orientalis and a change in status from species (B. milesiae) to subspecies for B. fragrans subsp. milesiae. Additionally, we show extensive clonal reproduction across species and limited gene flow at distances of >1 km, shedding light on the challenges faced by these species. We advocate a coordinated approach to conservation, focusing on restoring self-sustaining populations and leveraging genetic rescue strategies. By addressing the population dynamics of multiple species simultaneously in taxonomically challenging lineages, we can make informed choices to safeguard biodiversity and evolutionary potential. This study investigates the population dynamics, diversity and taxonomy of leafless Bossiaea species, a distinctive group of Australian plants, by using whole-genome single-nucleotide polymorphism data. The findings suggest recognition of a new subspecies, Bossiaea vombata subsp. orientalis , and a change in status for B. milesiae to B. fragrans subsp. milesiae. We also highlight challenges in reproduction and gene flow among Bossiaea populations, emphasising the need for coordinated conservation efforts. (Image credit: Keith McDougall.) [ABSTRACT FROM AUTHOR]

Animal culture evolves alongside genomes, and the two modes of inheritance—culture and genes—interact in myriad ways. For example, stable geographic variation in culture can act as a reproductive barrier, thereby facilitating genetic divergence between "cultural populations." White-crowned sparrows (Zonotrichia leucophrys) are a well-established model species for bird song learning and cultural evolution, as they have distinct, geographically discrete, and culturally transmitted song types (i.e., song dialects). In this study, we tested the hypothesis that divergence between culturally transmitted songs drives genetic divergence within Nuttall's white-crowned sparrows (Z. l. nuttalli). In accordance with sexual selection theory, we hypothesized that cultural divergence between mating signals both preceded and generated genetic divergence. We characterized the population structure and song variation in the subspecies and found two genetically differentiated populations whose boundary coincides with a major song boundary at Monterey Bay, California. We then conducted a song playback experiment that demonstrated males discriminate between songs based on their degree of divergence from their local dialect. These results support the idea that discrimination against non-local songs is driving genetic divergence between the northern and southern populations. Altogether, this study provides evidence that culturally transmitted bird songs can act as the foundation for speciation by sexual selection. [ABSTRACT FROM AUTHOR]

Background: Schaalia species are primarily found among the oral microbiota of humans and other animals. They have been associated with various infections through their involvement in biofilm formation, modulation of host responses, and interaction with other microorganisms. In this study, two strains previously indicated as Actinomyces spp. were found to be novel members of the genus Schaalia based on their whole genome sequences. Results: Whole-genome sequencing revealed both strains with a genome size of 2.3 Mbp and GC contents of 65.5%. Phylogenetics analysis for taxonomic placement revealed strains NCTC 9931 and C24 as distinct species within the genus Schaalia. Overall genome-relatedness indices including digital DNA-DNA hybridization (dDDH), and average nucleotide/amino acid identity (ANI/AAI) confirmed both strains as distinct species, with values below the species boundary thresholds (dDDH < 70%, and ANI and AAI < 95%) when compared to nearest type strain Schaalia odontolytica NCTC 9935 T. Pangenome and orthologous analyses highlighted their differences in gene properties and biological functions compared to existing type strains. Additionally, the identification of genomic islands (GIs) and virulence-associated factors indicated their genetic diversity and potential adaptive capabilities, as well as potential implications for human health. Notably, CRISPR-Cas systems in strain NCTC 9931 underscore its adaptive immune mechanisms compared to strain C24. Conclusions: Based on these findings, strain NCTC 9931T (= ATCC 17982T = DSM 43331T = CIP 104728T = CCUG 18309T = NCTC 14978T = CGMCC 1.90328T) represents a novel species, for which the name Schaalia dentiphila subsp. dentiphila sp. nov. subsp. nov. is proposed, while strain C24T (= NCTC 14980T = CGMCC 1.90329T) represents a distinct novel subspecies, for which the name Schaalia dentiphila subsp. denticola. subsp. nov. is proposed. This study enriches our understanding of the genomic diversity of Schaalia species and paves the way for further investigations into their roles in oral health. Significance: This research reveals two Schaalia strains, NCTC 9931 T and C24T, as novel entities with distinct genomic features. Expanding the taxonomic framework of the genus Schaalia, this study offers a critical resource for probing the metabolic intricacies and resistance patterns of these bacteria. This work stands as a cornerstone for microbial taxonomy, paving the way for significant advances in clinical diagnostics. [ABSTRACT FROM AUTHOR]

A concise set of 4‐substituted pyrazolo[3,4‐d]pyrimidine carboriboside analogues was synthesized in a divergent fashion via a central intermediate. An oxaziridine reagent allowed the synthesis of a crucial hydrazine glycon intermediate, which was transformed through a base‐build‐up strategy into the desired intermediate using a commercially available pyrimidine building block. Reaction with a variety of nucleophiles allowed late‐stage diversification. All analogues were evaluated for activity against a representative panel of Trypanosomatida. A methoxy‐substituted analogue displayed single‐digit micromolar activity against two subspecies of Trypanosoma brucei in cellular assays. [ABSTRACT FROM AUTHOR]

Mycobacteroides (Mycobacterium) abscessus, which causes a variety of infectious diseases in humans, is becoming detected more frequently in clinical specimens as cases are spreading worldwide. Taxonomically, M. abscessus is composed of three subspecies of M. abscessus subsp. abscessus, M. abscessus subsp. bolletii, and M. abscessus subsp. massiliense, with different susceptibilities to macrolides. In order to identify rapidly these three subspecies, we determined useful biomarker proteins, including ribosomal protein L29, L30, and hemophore-related protein, for distinguishing the subspecies of M. abscessus using the matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) profiles. Thirty-three clinical strains of M. abscessus were correctly identified at the subspecies-level by the three biomarker protein peaks. This study ultimately demonstrates the potential of routine MALDI-MS-based laboratory methods for early identification and treatment for M. abscessus infections. [ABSTRACT FROM AUTHOR]

Traditional methods of phylogenetic reconstruction and species delimitation may be impeded by frequent hybridization among lineages. In this study, we conducted phylogenetic and clustering analyses of ddRAD genomic data on the entire genus Salamandra, which includes six species and over 25 subspecies of terrestrial salamanders. We expanded previous datasets to include missing subspecies and incorporated new samples, with an emphasis on secondary contact zones. Results obtained from a full dataset of 392 individuals (356,874 bp; 24,192 SNPs) were compared with those obtained after excluding substantially admixed individuals (n = 95; 835,467 bp; 51,557 SNPs) to explore the consequences of introgression on phylogenetic inference and taxonomic arrangement of subspecies. We found conflicting phylogenetic placements for taxa represented by many admixed individuals (identified by clustering ancestries). In contrast, a time-calibrated tree constructed without hybrids largely agrees with previous phylogenetic hypotheses. Within S. atra, we found paraphyly of S. atra atra, suggesting an additional candidate subspecies. Within S. infraimmaculata, two lineages are assignable to known subspecies and we additionally identified a third, deeply diverged lineage sampled near the Turkish/Syrian border. In S. algira, we found limited admixture between the subspecies S. a. tingitana and S. a. splendens despite their geographic proximity. Finally, within S. salamandra, we detected significant levels of hybridization between subspecies, which blurred their phylogenetic relationships, although the removal of admixed samples in subset analyses clarified the situation in most cases. Monophyly was recovered for subspecies that were previously found paraphyletic, including S. s. salamandra, S. s. gallaica, and S. s. fastuosa. Salamandra s. "alfredschmidti" was confirmed to be a junior synonym of S. s. bernardezi. Previously disputed subspecies, like S. s. "molleri" and S. s. "hispanica", correspond to separated lineages but are affected by admixture with other lineages. Further newly identified candidate subspecies in S. salamandra included a southern lineage within S. s. wer-neri and a western lineage within S. s. bernardezi. Finally, we re-evaluate the status of recognized subspecies in Salamandra, based on evidence from multiple delimitation criteria. Given that the evolutionary history could not be resolved for all subspecies, we highlight taxa within Salamandra that warrant further molecular examination and taxonomic revision, notably within the S. s. gallaica/"molleri"/bejarae complex. This study illustrates the impact of hybridization in phylogenetic analyses and its downstream effects in the identification of conservation units and their naming in the Linnean classification. [ABSTRACT FROM AUTHOR]

Revealing phylogeographic structure is important for accurate subspecies delineation and understanding a species' evolutionary history. In leopards (Panthera pardus), there are currently nine subspecies recognized. On the African continent, only one subspecies occurs (P. p. pardus), although mitochondrial DNA from historical samples suggests the presence of three putative continental clades: (1) West Africa (WA), (2) Central Africa (CA), and (3) Southern Africa (SA). So far, whole genome data did not recover this phylogeographic structure, although leopards in the southern periphery of their distribution range in Africa have not yet been investigated in detail. The Mpumalanga province of South Africa is of particular interest, as here, the CA and the SA clade possibly meet. The aim of this study was to characterize the first mitogenomes of African leopards from Mpumalanga, to help clarifying how South African leopards fit into continental patterns of genetic differentiation. Complete mitogenomes from nine leopards, including a strawberry leopard, were assembled de novo and included in phylogenetic analysis, in combination with 32 publicly available mitogenomes. Bayesian inference and maximum likelihood analyses identified two deeply diverged putative clades within South Africa, which were more genetically distinct than two subspecies in Asia. The clades dated back to 0.76-0.86 million years ago, indicating that they originated during the climatically unstable Mid-Pleistocene, as seen in other large mammals. The Pleistocene refuge theory states that the maintenance of savanna refugia in East and Southern Africa promoted the divergence between populations. As such, leopards may reflect the unique climatic history of southern Africa, which has resulted in eminent and endemic genetic diversity. [ABSTRACT FROM AUTHOR]

The aim of this study is to investigate the chemical composition of ethanol, acetone extracts and essential oil of the roots and aerial parts of Sanguisorba minor subsp. muricata. Flavonoids and phenolic acids were identified as the main components in the studied extracts herein. Rutin and quercetin-3-sophoroside were found to be dominant flavonoids in both extracts. Although it was observed that the determined chemical compositions of the essential oil obtained from the aerial parts and roots of the plant species were quite different from the data obtained by Headspace measurement, as expected, the essential oils obtained from the species were found to be rich in mainly monoterpene hydrocarbons and oxygenated monoterpenes. While salicylaldehyde, carvacrol and linalool were determined as the main components in the essential oil obtained from the aerial parts of the species, the main components in the essential oil obtained from the roots were observed as borneol, myrtenol and a-campholenol. [ABSTRACT FROM AUTHOR]

Based on the study of freshly-collected material and old museum specimens, we have solved a decades-old riddle surrounding the name Onychoglomeris herzogowinensis (Verhoeff, 1898). The southern Dinaric coastal species Glomeris herzogowinensis Verhoeff, 1898 is revived, while Onychoglomeris herzogowinensis australis Attems, 1935 and O. h. media Attems, 1935, are treated here as full species after returning the specific name to Glomeris Latreille, 1902, O. australis Attems, 1935, stat. nov. and O. media Attems, 1935, stat. nov. Besides the designation of lectotypes, we provide comprehensive illustrations, diagnoses, detailed remarks and a distribution map for all three species. In addition, DNA barcoding provided COI sequences for Glomeris herzogowinensis and Onychoglomeris australis stat. nov., along with the first barcoding data of one additional species of Onychoglomeris Verhoeff, 1906, O. ferraniensis Verhoeff, 1909 and two Glomeris species, the Balkan G. balcanica Verhoeff, 1906 and the trans-Adriatic G. pulchra Koch, 1847. The significance of historical specimens from natural history museums is briefly discussed. [ABSTRACT FROM AUTHOR]

Conservation is prioritized based on accepted taxa. As a consequence, a conservation incentive exists to emphasize inter‐population differences to define taxa, potentially leading to taxonomic inflation. But stressing the uniqueness of threatened populations has the side effect of hindering conservation actions that promote inter‐population gene flow, such as genetic rescue. These actions may be of critical importance for severely inbred populations involved in extinction vortices, for which an inflated taxonomy can become a conservation trap. Here, we exemplify this scenario with the western capercaillie (Tetrao urogallus, Phasianidae) population in the Cantabrian Mountains, described and legally listed as a subspecies not supported by recent molecular data. The Cantabrian capercaillie population is Critically Endangered after a long‐lasting decline and a recent demographic collapse. It shows clear signs of inbreeding depression, including striking clutch size decreases as well as reduced hatchability and chick survival. This critical situation could be alleviated through a genetic rescue, but this possibility is hindered by inertias rooted in the putative uniqueness of the Cantabrian capercaillie. It had been previously argued that poor taxonomy could hamper conservation, through the oblivion of populations deserving, but not having, a taxonomic status. We show that taxonomic inflation can also become an obstacle for effective conservation. [ABSTRACT FROM AUTHOR]

Global change is affecting insect populations worldwide as species declines have been reported from different areas of the planet.Novel approaches such as the identification of Key Biodiversity Areas (KBAs) could detect areas of high biodiversity value for insect populations. The KBA approach relies on standardised criteria to identify important sites for biodiversity persistence. The application of such criteria to large numbers of species would significantly accelerate the KBA mapping process.A systematic application of KBA criteria has not been tested on insects, and very little is known about the efficiency and limits of such methodology.We applied four KBA criteria in Italy to 28 species/subspecies of bumblebees and identified potential KBAs for one species and three subspecies. Potential KBAs are only partially nested within current Italian KBAs and the protected areas network. When compared with potential KBAs of vertebrate species identified with the same methodology, the degree of nesting is only 12%.Our results provide evidence of a tendency of the KBA network to expand as more species are assessed, raising questions about the ability of the criteria to detect areas that truly are key for biodiversity and not just for specific taxa. We also highlight issues regarding the use of KBA criteria on insects, such as data availability and the use of subspecies. Further large‐scale assessments of KBAs will reveal the true potential of application of the KBA approach for insect conservation, and whether it actually may slow down the loss of important units of their extraordinary diversity. [ABSTRACT FROM AUTHOR]

The increased availability of quality genomic data has greatly improved the scope and resolution of our understanding of the recent evolutionary history of wild species adapted to extreme environments and their susceptibility to anthropogenic impacts. The guanaco (Lama guanicoe), the largest wild ungulate in South America, is a good example. The guanaco is well adapted to a wide range of habitats, including the Sechura Desert, the high Andes Mountains to the north, and the extreme temperatures and conditions of Navarino Island to the south. Guanacos also have a long history of overexploitation by humans. To assess the evolutionary impact of these challenging habitats on the genomic diversity, we analyzed 38 genomes (∼10 to 16×) throughout their extensive latitudinal distribution from the Sechura and Atacama Desert to southward into Tierra del Fuego Island. These included analyses of patterns of unique differentiation in the north and geographic region further south with admixture among L. g. cacsilensis and L. g. guanicoe. Our findings provide new insights on the divergence of the subspecies ∼800,000 yr BP and document two divergent demographic trajectories and to the initial expansion of guanaco into the more southern portions of the Atacama Desert. Patagonian guanacos have experienced contemporary reductions in effective population sizes, likely the consequence of anthropogenic impacts. The lowest levels of genetic diversity corresponded to their northern and western limits of distribution and some varying degrees of genetic differentiation. Adaptive genomic diversity was strongly linked with environmental variables and was linked with colonization toward the south followed by adaptation. [ABSTRACT FROM AUTHOR]

The article offers information on observations of the second generation of the butterfly species Papilio machaon L. in the Norfolk Broads. Topics include the general description of the British subspecies britannicus Seitz of Papilio machaon L., which is typically described as partially bivoltine, with adults usually flying from mid-May to early July.

Morphological variation is common within widely distributed plant species and often raises interesting taxonomic and evolutionary questions. We sampled eight typical inland populations and two coastal dwarf populations of Banksia occidentalis to assess whether the coastal variant warrants taxonomic recognition. Genomic (single nucleotide polymorphisms) and morphometric analyses were undertaken to assess the variation within and between variants. Genetically, the coastal populations were more closely related to geographically adjacent populations of the typical variant than they were to each other, indicating that each coastal population has originated independently. Morphologically, the coastal populations also did not represent a cohesive phenotypic group, with both falling outside the range of variation for the typical variant, but also not overlapping each other. Wide morphological, but not genomic, variation was identified along a coastal–inland transect. Combined, these data indicate that the morphological variation in these coastal populations is the result of parallel ecotype evolution from experiencing similar environmental conditions and does not represent the diversification of a distinct evolutionary lineage that would have warranted taxonomic recognition. Our study highlights the consequences of strong selection pressures in marginal environments and provides fascinating insight to the long evolutionary history of the flora in this ancient Australian landscape. [ABSTRACT FROM AUTHOR]

Predicting the effects of global environmental changes on species distribution is a top conservation priority, particularly for large carnivores, that contribute to regulating and maintaining ecosystems. As the most widespread and adaptable large felid, ranging across Africa and Asia, leopards are crucial to many ecosystems as both keystone and umbrella species, yet they are threatened across their ranges. We used intraspecific species distribution models (SDMs) to predict changes in range suitability for leopards under future climate and land‐use change and identify conservation gaps and opportunities. We generated intraspecific SDMs for the three western leopard subspecies, the African, Panthera pardus pardus; Arabian, Panthera pardus nimr; and Persian, Panthera pardus tulliana, leopards, and overlapped predictions with protected areas (PAs) coverage. We show that leopard subspecies differ in their environmental associations and vulnerability to future changes. The African and Arabian leopards are predicted to lose ~25% and ~14% of their currently suitable range, respectively, while the Persian leopard is predicted to experience ~12% range gains. We found that most areas predicted to be suitable were not protected, with only 4%–16% of the subspecies' ranges falling inside PAs, and that these proportions will decrease in the future. The highly variable responses we found between leopard subspecies highlight the importance of considering intraspecific variation when modelling vulnerability to climate and land‐use changes. The predicted decrease in proportion of suitable ranges falling inside PAs threatens global capacity to effectively conserve leopards because survival rates are substantially lower outside PAs due to persecution. Hence, it is important to work with local communities to address negative human‐wildlife interactions and to restore habitats to retain landscape connectivity where PA coverage is low. On the other hand, the predicted increase in range suitability across southern Europe presents opportunities for expansion outside of their contemporary range, capitalising on European rewilding schemes. [ABSTRACT FROM AUTHOR]

Coriariaceae are a small plant family of 14–17 species and subspecies that currently have a global but disjunct distribution. All species can form root nodules in symbiosis with diazotrophic Frankia cluster-2 strains, which form the earliest divergent symbiotic clade within this bacterial genus. Studies on Frankia cluster-2 mostly have focused on strains occurring in the northern hemisphere. Except for one strain from Papua New Guinea, namely Candidatus Frankia meridionalis Cppng1, no complete genome of Frankia associated with Coriaria occurring in the southern hemisphere has been published thus far, yet the majority of the Coriariaceae species occur here. We present field sampling data of novel Frankia cluster-2 strains, representing two novel species, which are associated with Coriaria arborea and Coriaria sarmentosa in New Zealand, and with Coriaria ruscifolia in Patagonia (Argentina), in addition to identifying Ca. F. meridionalis present in New Zealand. The novel Frankia species were found to be closely related to both Ca. F. meridionalis, and a Frankia species occurring in the Philippines, Taiwan, and Japan. Our data suggest that the different Frankia cluster-2 species diverged early after becoming symbiotic circa 100 million years ago. [ABSTRACT FROM AUTHOR]

The taxonomic status and interspecies relationships of hares (genus Lepus) in Xinjiang, China, remain ambiguous owing to extremely similar external morphologies, introgressive hybridization between species and a lack of molecular genetic records. In this study, a total of 154 hare specimens were used to clarify their taxonomic status. Based on multiple lines of evidence, including observations and comparisons of external morphological characteristics, skull morphometrics and genome‐wide single nucleotide polymorphism (SNP) datasets, four hare species were recognised. Lepus yarkandensis and Lepus timidus, which have obvious morphological characteristics, were identified as two distinct species, as previously reported. Combining the integrated morphological and molecular datasets with the relevant literature, we proposed suggestions on the classification of the more controversial hares. Due to molecular and morphological similarities, hares in northern and central Xinjiang were divided into two subspecies of Lepus tolai, namely, Lepus tolai lehmanni and Lepus tolai centrasiaticus. Despite similar external morphological characters, hares in the southwest Pamir Plateau and its surroundings can be distinguished from L. tolai by differences in skull morphology and genetic divergence and were, therefore, considered a subspecies of Lepus tibetanus, Lepus tibetanus pamirensis. Furthermore, we found that hybridization and introgression occurred between sympatric or parapatric hares, especially between L. yarkandensis and L. tibetanus pamirensis, L. yarkandensis and L. tolai centrasiaticus, and L. tolai lehmanni and L. timidus. [ABSTRACT FROM AUTHOR]

Crassostrea ariakensis (Fujita, 1913) is one of the most important economic and ecological oysters that is naturally distributed along the coast of Asia, separated by the Yangtze River estuary. They are usually compared as different populations, while there is no consensus on whether C. ariakensis in northern and southern areas should be considered as two species or subspecies. Here, we analyzed morphological characteristics, COI, 16s rRNA, mitogenome sequences, and species delimitation analysis (ASAP and PTP) to resolve the intraspecific taxonomic status of the C. ariakensis. Phylogenetic and ASAP analysis highlight that C. ariakensis was divided into N-type and S-type. PTP was unable to differentiate between the two types of C. ariakensis. The divergence time of N-type and S-type C. ariakinsis is estimated to be 1.6 Mya, using the relaxed uncorrelated lognormal clock method. Additionally, significant morphological differences exist between the two groups in terms of the adductor muscle scar color. Despite these differences, the COI (0.6%) and 16S rRNA (0.6%) genetic distance differences between N-type and S-type C. ariakensis has not yet reached the interspecific level. These results suggest that N-type and S-type C. ariakensis should be treated as different subspecies and renamed as C. ariakensis ariakensis subsp. nov and C. ariakensis meridioyangtzensis subsp. nov. [ABSTRACT FROM AUTHOR]

Summary: Rice yellow mottle virus (RYMV) causes one of the most devastating rice diseases in Africa. Management of RYMV is challenging. Genetic resistance provides the most effective and environment‐friendly control. The recessive resistance locus rymv2 (OsCPR5.1) had been identified in African rice (Oryza glaberrima), however, introgression into Oryza sativa ssp. japonica and indica remains challenging due to crossing barriers. Here, we evaluated whether CRISPR/Cas9 genome editing of the two rice nucleoporin paralogs OsCPR5.1 (RYMV2) and OsCPR5.2 can be used to introduce RYMV resistance into the japonica variety Kitaake. Both paralogs had been shown to complement the defects of the Arabidopsis atcpr5 mutant, indicating partial redundancy. Despite striking sequence and structural similarities between the two paralogs, only oscpr5.1 loss‐of‐function mutants were fully resistant, while loss‐of‐function oscpr5.2 mutants remained susceptible, intimating that OsCPR5.1 plays a specific role in RYMV susceptibility. Notably, edited lines with short in‐frame deletions or replacements in the N‐terminal domain (predicted to be unstructured) of OsCPR5.1 were hypersusceptible to RYMV. In contrast to mutations in the single Arabidopsis AtCPR5 gene, which caused severely dwarfed plants, oscpr5.1 and oscpr5.2 single and double knockout mutants showed neither substantial growth defects nor symptoms indicative lesion mimic phenotypes, possibly reflecting functional differentiation. The specific editing of OsCPR5.1, while maintaining OsCPR5.2 activity, provides a promising strategy for generating RYMV‐resistance in elite Oryza sativa lines as well as for effective stacking with other RYMV resistance genes or other traits. [ABSTRACT FROM AUTHOR]

Optical spectra of few-layer transition metal dichalcogenide semiconductors reveal several transitions whose character and origins continue to be debated. We have studied hBN encapsulated few-layer MoS2 films using electroreflectance (ER) spectroscopy. Two strong features are seen in the reflectance spectrum of trilayer MoS2 around the ground state A–exciton transition. In ER, the corresponding features show opposite phase response to the applied voltage. Evidence from first principles ER line shape simulation and photoluminescence spectroscopy suggests that these two features are likely to be A 1 s exciton subspecies proposed earlier, whose energy depends on which layer the electron–hole pair is located in. The first excited state A 2 s exciton transition is also identifiable in ER. Through the two-dimensional hydrogenic exciton model, it enables an approximate estimation of the exciton binding energy Eb. The increase in Eb with decreasing film thickness, which originates from reduced dielectric screening, is phenomenologically analyzed through a film thickness and capping material dependent effective dielectric constant. Extending this idea, we show that the A 1 s exciton is mostly confined to a single S–Mo–S layer, as predicted by theory. An inter-layer (IL) exciton is expected in bilayer and thicker 2H-MoS2 films. However, we show that there can be bilayer films where the IL exciton is absent, which may be related to increased carrier concentration. [ABSTRACT FROM AUTHOR]

Background: Taxonomic classification of reads obtained by metagenomic sequencing is often a first step for understanding a microbial community, but correctly assigning sequencing reads to the strain or sub-species level has remained a challenging computational problem. Results: We introduce Mora, a MetagenOmic read Re-Assignment algorithm capable of assigning short and long metagenomic reads with high precision, even at the strain level. Mora is able to accurately re-assign reads by first estimating abundances through an expectation-maximization algorithm and then utilizing abundance information to re-assign query reads. The key idea behind Mora is to maximize read re-assignment qualities while simultaneously minimizing the difference from estimated abundance levels, allowing Mora to avoid over assigning reads to the same genomes. On simulated diverse reads, this allows Mora to achieve F1 scores comparable to other algorithms while having less runtime. However, Mora significantly outshines other algorithms on very similar reads. We show that the high penalty of over assigning reads to a common reference genome allows Mora to accurately infer correct strains for real data in the form of E. coli reads. Conclusions: Mora is a fast and accurate read re-assignment algorithm that is modularized, allowing it to be incorporated into general metagenomics and genomics workflows. It is freely available at https://github.com/AfZheng126/MORA. [ABSTRACT FROM AUTHOR]

Background: Contagious caprine pleuropneumonia (CCPP) is a fatal WOAH-listed, respiratory disease in small ruminants with goats as primary hosts that is caused by Mycoplasma capricolum subspecies capripneumoniae (Mccp). Twelve CCPP outbreaks were investigated in 11 goat herds and a herd of captive Arabian sand gazelle (Gazella marica) in four Omani governorates by clinical pathological and molecular analysis to compare disease manifestation and Mccp genetic profiles in goats and wild ungulates. Results: The CCPP forms in diseased and necropsied goats varied from peracute (5.8%), acute (79.2%) and chronic (4.5%) while all of the five necropsied gazelles showed the acute form based on the clinical picture, gross and histopathological evaluation. Colonies of Mccp were recovered from cultured pleural fluid, but not from lung tissue samples of one gazelle and nine goats and all the isolates were confirmed by Mccp-specific real time PCR. Whole genome-single nucleotide polymorphism (SNP) analysis was performed on the ten isolates sequenced in this study and twenty sequences retrieved from the Genbank database. The Mccp strains from Oman clustered all in phylogroup A together with strains from East Africa and one strain from Qatar. A low variability of around 125 SNPs was seen in the investigated Omani isolates from both goats and gazelles indicating mutual transmission of the pathogen between wildlife and goats. Conclusion: Recent outbreaks of CCPP in Northern Oman are caused by Mccp strains of the East African Phylogroup A which can infect goats and captive gazelles likewise. Therefore, wild and captive ungulates should be considered as reservoirs and included in CCPP surveillance measures. [ABSTRACT FROM AUTHOR]

Understanding the forces that shape population genetic structure is fundamental both for understanding evolutionary trajectories and for conservation. Many factors can influence the geographic distribution of genetic variation, and the extent to which local populations differ can be especially difficult to predict in highly mobile organisms. For example, many species of seabirds are essentially panmictic, but some show strong structure. Pigeon Guillemots (Cepphus columba; Charadriiformes: Alcidae) breed in small colonies scattered along the North Pacific coastline and feed in shallow nearshore waters year‐round. Given their distribution, gene flow is potentially lower and population genetic structure is stronger than in most other high‐latitude Northern Hemisphere seabirds. We screened variation in the mitochondrial control region, four microsatellite loci, and two nuclear introns in 202 Pigeon Guillemots representing three of five subspecies. Mitochondrial sequences and nuclear loci both showed significant population differences, although structure was weaker for the nuclear loci. Genetic differentiation was correlated with geographic distance between sampling locations for both the mitochondrial and nuclear loci. Mitochondrial gene trees and demographic modeling both provided strong evidence for two refugial populations during the Pleistocene glaciations: one in the Aleutian Islands and one farther east and south. We conclude that historical fragmentation combined with a stepping‐stone model of gene flow led to the relatively strong population differentiation in Pigeon Guillemots compared to other high‐latitude Northern Hemisphere seabird species. Our study adds to growing evidence that Pleistocene glaciation events affected population genetic structure not only in terrestrial species but also in coastal marine animals. [ABSTRACT FROM AUTHOR]

Traditional Dipodomys (sub)species identification uses geography, phenotype, and external/skull measurements. Such measurements are correlated with size and thus redundant. I assessed the value of scaled cranial shape, based on two‐dimensional landmarks (analyzed using geometric morphometric methods) in distinguishing Dipodomys taxa, and in summarizing their variation. My dataset includes 601 adult specimens from 20 species (49 operational taxonomic units ‐ OTUs) across 190 localities. Cranial shape was highly useful in classifying Dipodomys taxa without considering geography. The auditory bulla was the most variable region—taxa differed in its hypertrophy, accompanied by different degrees of nearby structure crowding. Cranial shape was weakly allometric, with no significant sexual dimorphism. Weak size dimorphism was detected. (Sub)specific taxonomy is not reflective of shape variation, as the number of subspecies per species is not associated with disparity. Shape had significant phylogenetic signal, but subspecies did not always cluster with conspecifics and species did not always cluster according to phylogenetic relationship/taxonomy. Shape variation was correlated with climate, and species differed in morphological disparity and degree of specialization, which may contribute to divergence in shape variation patterns from phylogeny. D. deserti was the most specialized species, diverging greatly from the genus mean; D. heermanni was the least specialized. This study provides new insights into morphological variation of North American keystone species, several of conservation interest, for example, D. heermanni berkeleyensis, D. h. dixoni, D. nitratoides brevinasus, and D. n. nitratoides. [ABSTRACT FROM AUTHOR]

Mycobacterium orygis, a subspecies of the Mycobacterium tuberculosis complex (MTBC), has emerged as a significant concern in the context of One Health, with implications for zoonosis or zooanthroponosis or both. MTBC strains are characterized by the unique insertion element IS 6110, which is widely used as a diagnostic marker. IS 6110 transposition drives genetic modifications in MTBC, imparting genome plasticity and profound biological consequences. While IS 6110 insertions are customarily found in the MTBC genomes, the evolutionary trajectory of strains seems to correlate with the number of IS 6110 copies, indicating enhanced adaptability with increasing copy numbers. Here, we present a comprehensive analysis of IS 6110 insertions in the M. orygis genome, utilizing ISMapper, and elucidate their genetic consequences in promoting successful host adaptation. Our study encompasses a panel of 67 paired-end reads, comprising 11 isolates from our laboratory and 56 sequences downloaded from public databases. Among these sequences, 91% exhibited high-copy, 4.5% low-copy, and 4.5% lacked IS 6110 insertions. We identified 255 insertion loci, including 141 intragenic and 114 intergenic insertions. Most of these loci were either unique or shared among a limited number of isolates, potentially influencing strain behavior. Furthermore, we conducted gene ontology and pathway analysis, using eggNOG-mapper 5.0, on the protein sequences disrupted by IS 6110 insertions, revealing 63 genes involved in diverse functions of Gene Ontology and 45 genes participating in various KEGG pathways. Our findings offer novel insights into IS 6110 insertions, their preferential insertion regions, and their impact on metabolic processes and pathways, providing valuable knowledge on the genetic changes underpinning IS 6110 transposition in M. orygis. [ABSTRACT FROM AUTHOR]

We present the first description of the nest and egg of the Long-billed Forest-warbler Artisornis moreaui recently discovered in Nilo Nature Forest Reserve, Tanzania. Two subspecies are recognised: the nominate one, endemic to East Usambara Mountains in northeastern Tanzania, and sousae, endemic to the Njesi Highlands in northern Mozambique. Both are treated as distinct species by BirdLife International, which has classified the first as Critically Endangered, and the second as Endangered. Before this discovery, breeding information had been limited to observations of fledglings. Because in the East Usambaras A. moreaui shares habitat with its putative sisterspecies, Red-capped Forest-warbler A. metopias, we also provide additional information on the nesting of this species. Although the nests of the two species can be difficult to differentiate, their eggs are distinct. The markings on the egg of A. metopias are spread over the entire surface, while on the egg of A. moreaui the markings are concentrated at the broad end. [ABSTRACT FROM AUTHOR]

The harbour seal Phoca vitulina is a ubiquitous pinniped species found throughout coastal waters of the Northern Hemisphere. Harbour seal impacts on ecosystem dynamics may be significant due to their high abundance and food web position. Two subspecies exist in North America, P. v. richardii in the Pacific Ocean and P. v. vitulina in the Atlantic. Strong natal philopatry of harbour seals can result in fine‐scale genetic structure and isolation by distance. Management of harbour seals is expected to benefit from improved resolution of seal population structure and dynamics. Here, we use genotyping‐by‐sequencing to genotype 146 harbour seals from the eastern Pacific Ocean (i.e. British Columbia (BC), Oregon and California) and the western Atlantic Ocean (i.e. Québec, Newfoundland and Labrador). Using 12,742 identified variants, we confirm the recently identified elevated genetic diversity in the eastern Pacific relative to the western Atlantic and greatest differentiation between the subspecies. Further, we demonstrate that this is independent of reference genome bias or other potential technical artefacts. Coast‐specific analyses with 8933 and 3828 variants in Pacific and Atlantic subspecies, respectively, identify divergence between BC and Oregon–California, and between Québec and Newfoundland–Labrador. Unexpected PCA outlier clusters were observed in two populations due to cryptic relatedness of individuals; subsequently, closely related samples were removed. Admixture analysis indicates an isolation‐by‐distance signature where Oregon seals contained some of the BC signature, whereas California did not. Additional sampling is needed in the central and north coast of BC to determine whether a discrete separation of populations exists within the region. [ABSTRACT FROM AUTHOR]

The Gram-negative bacterium Xylella fastidiosa (Xf) was originally found in the Americas, but has now been identified in more than 20 countries across America, Asia, and Europe. This plant pathogen is currently listed as a priority pest in Europe due to its socio-economic and ecological impacts. Within the three Xf subspecies fastidiosa, multiplex and pauca, subsp. multiplex displays a notably wider range of host plants than the other two subspecies. Comparative genomics may allow determination of how Xf subsp. multiplex adapts to new and diverse hosts and environments, so it is important that more genomes of this subspecies are defined. Twelve complete closed genomes sequences of Xf subsp. multiplex were obtained using a hybrid assembly approach combining Illumina and Oxford Nanopore technologies. The combined use of Canu and Unicycler assemblers enabled identification and closure of several plasmid sequences with high similarity to other plasmids described in strains of Xf subsp. fastidiosa and subsp. pauca. The analysis also revealed prophage sequences and contigs outside the chromosomes, annotated as phages. These new genomes, in conjunction with those existing in GenBank, will facilitate exploration of the evolutionary dynamics of Xf subsp. multiplex, its host adaptation mechanisms, and the potential emergence of novel strains of this important plant pathogen. [ABSTRACT FROM AUTHOR]