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Siamese rosewood (Dalbergia cochinchinensis Pierre) is a highly valuable economic tree species in Thailand. This study investigated genetic diversity across 72 tree samples from 17 Thai locations using two genetic markers: the chloroplast maturase K (matK) gene and the nuclear internal transcribed spacer (ITS) region. Analysis of 48 matK and 65 ITS sequences revealed 34 (DcM1–DcM34) and 31 (DcI1–DcI31) haplotypes, respectively. The Saraburi province haplotype DcM10 exhibited the highest genetic divergence, differing by 25 mutational steps from other haplotypes. Phylogenetic analysis incorporating GenBank sequences from other Dalbergia species showed that matK sequences separated D. cochinchinensis into two distinct clades: Clade A, comprising most Thai samples, and Clade B, containing Saraburi samples grouped with sequences from Laos and Cambodia. In contrast, ITS analysis revealed a single monophyletic group. These findings have important applications for conservation strategies, particularly in prioritizing the genetically distinct Saraburi population for protection, and can inform breeding programs to maintain genetic diversity. Additionally, the identified genetic markers could be developed into tools for timber authentication to combat illegal logging, while the revealed population structure can guide reforestation efforts and international conservation collaboration with Laos and Cambodia. [ABSTRACT FROM AUTHOR]

A new pest of tomato, the South American tomato pinworm, Tuta absoluta (Meyrick, 1917) (Lepidoptera: Gelechiidae), was found in Kumamoto Prefecture, Japan in 2021. We examined the genetic variation in the DNA sequences of the mitochondrial cytochrome c oxidase subunit I (mtCOI) gene in 1039 individuals belonging to 39 countries including Japan. In the maximum likelihood phylogenetic tree and haplotype network, 19 haplotypes were detected in the world. Of those haplotypes, only one haplotype (Ta1) was detected from all 39 countries including neighboring countries and Japan. These results and some other information suggest that this species migrated from neighboring countries to Japan. Furthermore, we developed a Multiplex PCR using species-specific primers to discriminate T. absoluta from other gelechiid moth, Phthorimaea operculella (Zeller, 1873) (Lepidoptera: Gelechiidae). We could successfully identify the first instar larvae, fourth instar larvae, pupae, and adults of both species based on the differences in the length of amplicon bands. In addition, we were able to identify adults of both species collected from various prefectures. These results indicated that the Multiplex PCR developed in this study is useful to identify all developmental stages of both species collected in the fields. [ABSTRACT FROM AUTHOR]

Background: Haplotype networks are useful for investigating the genealogical relationships among haplotypes and have been extensively used in molecular evolution and population genetic studies. However, existing tools for visualizing haplotype networks lack comprehensive functionalities for data exploration and layout adjustments. Therefore, there is a need for a useful tool capable of constructing and visualizing haplotype networks, facilitating the exploration of data, particularly with datasets with large sample sizes. Results: We present HapNetworkView, a user-friendly tool that facilitates the construction and interactive visualization of haplotype networks, enabling users to explore haplotypes and mutation information effectively. HapNetworkView offers both automatic optimization and manual adjustment for haplotype network layouts. Additionally, HapNetworkView supports various input and output formats, as well as color customization. Conclusions: These comprehensive functionalities collectively satisfy various needs of users in haplotype network analysis, making HapNetworkView a valuable tool. [ABSTRACT FROM AUTHOR]

The severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) has evolved many high‐risk variants, resulting in repeated COVID‐19 waves over the past years. Therefore, accurate early warning of high‐risk variants is vital for epidemic prevention and control. However, detecting high‐risk variants through experimental and epidemiological research is time‐consuming and often lags behind the emergence and spread of these variants. In this study, HiRisk‐Detector a machine learning algorithm based on haplotype network, is developed for computationally early detecting high‐risk SARS‐CoV‐2 variants. Leveraging over 7.6 million high‐quality and complete SARS‐CoV‐2 genomes and metadata, the effectiveness, robustness, and generalizability of HiRisk‐Detector are validated. First, HiRisk‐Detector is evaluated on actual empirical data, successfully detecting all 13 high‐risk variants, preceding World Health Organization announcements by 27 days on average. Second, its robustness is tested by reducing sequencing intensity to one‐fourth, noting only a minimal delay of 3.8 days, demonstrating its effectiveness. Third, HiRisk‐Detector is applied to detect risks among SARS‐CoV‐2 Omicron variant sub‐lineages, confirming its broad applicability and high ROC‐AUC and PR‐AUC performance. Overall, HiRisk‐Detector features powerful capacity for early detection of high‐risk variants, bearing great utility for any public emergency caused by infectious diseases or viruses. [ABSTRACT FROM AUTHOR]

Snail-eating turtles (Malayemys spp.) are freshwater turtles native to mainland Southeast Asia. Three snail-eating turtle species (Malayemys khoratensis, Malayemys macrocephala, and Malayemys subtrijuga) were previously reported in Thailand. Before the present study, information on the distribution of snail-eating turtles in northeastern and eastern Thailand was limited, and a question arose regarding the distribution range of the new species, Malayemys khoratensis. From 2018 to 2020, we surveyed and collected data on the morphological traits of 109 snail-eating turtles along with 60 blood samples from 23 out of 27 provinces across northeastern and eastern Thailand. We found that both M. khoratensis and M. subtrijuga occur in northeastern Thailand. The distribution of M. khoratensis is in the Chi River Basin and upper Mun River Basin to the Mekong River. while the distribution of M. subtrijuga is from the lower Mun River to the Mekong River. Malayemys macrocephala occur in eastern Thailand and were found in 2 large provinces (Nakhon Ratchasima and Udon Thani) in northeastern Thailand. Based on morphological characteristics known to distinguish these species, 28 of the sampled individuals from areas in lower Mun River basin could not be assigned to any of the 3 species. Therefore, we reconstructed the phylogenetic relationships of 26 of these samples as well as other samples from known species based on 2 mitochondrial genes (Cyt b and ND4). Results based on mtDNA data indicated that the turtles in the unknown group belonged to 1 of the 3 clades corresponding to M. khoratensis, M. macrocephala, and M. subtrijuga. This result confirms that the unknown group does not represent a novel species within the genus Malayemys. However, it also indicates a discordance between the genetic and morphological characteristics of the turtles, highlighting the complexity of species identification within the genus Malayemys. [ABSTRACT FROM AUTHOR]

Many species of shark are threatened with extinction, a consequence of overfishing to supply the shark fin and meat trade, or through bycatch. While the shark fin trade is comparatively well understood and documented, the trade in shark meat is remains understudied, even though it is larger than the fin trade in terms of value and volume. The species composition of the shark meat trade along with their geographic origin of capture remains largely unknown; this is problematic because it makes the design of effective conservation measures to prevent the overexploitation of sharks and the associated loss of biodiversity challenging. Our work here is the first to comprehensively survey of the shark meat trade in retail establishments from a region of the world that has global significance in the shark product trade. It suggests that local fishing pressure on one or few stocks or populations, rather than complex international supply chains support the trade in shark meat products destined for human consumption. Importantly, it provides a critical assessment and documentation of the species involved. This work has relevance in our efforts to protect sharks and arrest the ongoing biodiversity crisis. [ABSTRACT FROM AUTHOR]

Introduction: Malayemys khoratensis is a freshwater turtle species endemic to northeastern Thailand and Lao PDR. While M. khoratensis is relatively common and widespread in Thailand, its population size and demographic trends remain largely unknown, as direct population estimates are lacking. This species faces significant threats from consumption, exploitation, and trade. Therefore, this study aims to investigate the genetic diversity, population structure, and demographic trends of M. khoratensis in northeastern Thailand, using two mitochondrial DNA genes, Cyt b and ND4. Method: We grouped the turtles based on three major river basins in northeastern Thailand: Mun, Chi, and Northeast Mekong to assess population structure and test the isolation-by-basin hypothesis. The Cyt b and ND4 genes of 49 M. khoratensis individuals across 15 provinces in Thailand were sequenced, and 15 sequences from a previous study of Ihlow et al. (2016) were included into the analyses. We constructed a haplotype network from the concatenated sequences and analyzed the population structure with the analysis of molecular variance (AMOVA). Additionally, we used a Bayesian Skyline plot (BSP) analysis to estimate the effective female population size and explore the demographic history of this species. Results: Our analysis identified 13 unique haplotypes defined by 26 polymorphic sites from 64 samples. The total haplotype diversity for M. khoratensis was 0.819, while nucleotide diversity was 0.0031. The haplotype network and AMOVA revealed no distinct population structure among the river basins, suggesting gene flow across these regions. The BSP estimated a stable effective female population size of approximately 130,000 individuals since around 100,000 years ago (late Pleistocene). Conclusion: Our findings indicated no significant population structure by river basin, which may be due to natural movement between basins or potential human-mediated translocations linked to the turtle trade. The demographic trend of M. khoratensis appears to have been stable over time. However, given the ongoing exploitation of this species, we recommend regular monitoring of population trends to support its long-term survival. [ABSTRACT FROM AUTHOR]

Background: Understanding the processes that influence distribution of organisms is a major goal in evolutionary biology. Speciation in freshwater fishes is mainly associated with the "island-like" model of evolution, in which the formation of land barriers between different hydrographic basins interrupts gene flow and promotes isolation. Freshwater fish therefore provide an excellent model system for macro- and micro-evolutionary studies. The Mesa Silverside, Chirostoma jordani, is one of the most widespread freshwater fish species in the Mexican Plateau, a geologically complex physiographic region with a long history of genesis, destruction and compartmentalization of hydrographic basins that has promoted the dispersal and isolation of freshwater fishes. Methods: We used mitochondrial (Cytb and D-loop) and nuclear (first intron of the ribosomal protein S7) data and used phylogeographic and coalescent based methods to elucidate the evolutionary history of C. jordani throughout its distributional range on the Mexican Plateau. Results: The results obtained in the present study revealed that C. jordani consists of two main genetic groups with geographical correspondence. Clade I occur exclusively in north-western basin and shows population structure. Clade II is widely distributed across the west, central and eastern basins without population structure. The split between these two main clades was estimated at 1.4 Mya. This cladogenetic event may be associated with the allopatric process promoted by the fragmentation and compartmentalization of hydrographic basins induced by the geological and climatic history of the Mexican Plateau. [ABSTRACT FROM AUTHOR]

AbstractThe Ribbontail stingray Taeniura lymma is an economically important fish and attractive species for the aquarium trade industry. Overfishing, habitat degradation, and pollution, however, pose a threat to this species. This study used partial mitochondrial cytochrome oxidase subunit I (COI) sequences (603 base pairs long) from 96 samples of T. lymma collected at five fish-landing sites (Deep Sea-Tanga, Malindi-Unguja, Kaole-Bagamoyo, Kivukoni-Dar es Salaam, and Bandarini-Mtwara) located along the coast of Tanzania to determine the species’ genetic diversity, population genetic structure, and demographic history. The findings revealed an average nucleotide diversity of 0.24 ± 0.16% and a haplotype diversity of 0.75 ± 0.04. Nucleotide and haplotype diversities were relatively low at Kaole-Bagamoyo compared to the other studied localities. An Analysis of Molecular Variance (AMOVA) indicated limited but statistically significant genetic differences among populations (Overall FST = 0.09, p < 0.01). Pairwise AMOVA revealed genetic difference between the Deep Sea-Tanga population and all other populations studied with exception of Malindi-Unguja. Analyses of mismatch distribution, demographic history, and a haplotype network support a scenario of historical population expansion in the studied species. Immediate effort is required to protect population exhibiting low genetic diversity in this commercially important ray. [ABSTRACT FROM AUTHOR]

Astylus atromaculatus Blanchard, 1843 (Coleoptera: Melyridae) is a pollinivorous beetle native to southern South America, which has invaded South Africa more than a century ago. Adults and/or larvae may occasionally damage flowers, seeds, and seedlings of various crops. Severe cattle intoxication has also been reported in Argentina, Uruguay, and South Africa following consumption of alfalfa and forage grasses infested with A. atromaculatus. Despite its economic impact, essential genetic information is lacking for this species. The present paper provides the first DNA barcode reference sequences for A. atromaculatus based on the standard 5’ fragment (658 bp) of the cytochrome c oxidase subunit I gene. The sequences obtained exhibited pairwise distances of ≤ 1.82% among them, and ~ 90% nucleotide identity with the homologous gene fragment in the morphologically similar Astylus variegatus Germar, 1824. The use of this molecular marker to explore the intraspecific variability of A. atromaculatus in central Argentina showed 21 different haplotypes, out of 32 individuals analyzed. A very high haplotype diversity (Hd = 0.962 ± 0.019) and a moderate nucleotide diversity (π = 0.00778 ± 0.00079) were recorded. The haplotype network displayed a diffuse structure due to the abundance of singletons and possible missing haplotypes, with the most common haplotype comprising only 15.6% of the specimens collected. Future research with increased sampling size and geographic coverage will allow for a better understanding of the population genetics of this pest, and consequently, for developing efficient management practices. [ABSTRACT FROM AUTHOR]

Flowering time of crops is critical for maximizing yield, quality and regional adaptability under target environments. In rice, Heading date 3a (Hd3a) and Rice Flowering Locus T 1 (RFT1) proteins are the key factors of flowering time regulation in the florigen activation complex. However, effects of hd3a and rft1 mutations on the flowering time under long-day conditions are not clear. In this study, we generated single and double mutants of Hd3a and RFT1 in japonica varieties Shen Nong 9816 (SN9816) background, termed hd3a-SNs, rft1-SNs and doub-SNs, by using CRISPR/Cas9 system. The flowering time of hd3a-SN mutants was similar to wild-type (WT); but mutations of RFT1 delayed flowering time by 11 to 14 days comparing to WT under nature long day (NLD) conditions. Double mutants of Hd3a and RFT1 (doub-SNs) exhibited an extremely late flowering phenotype, and they did not flower up to 365 days after regeneration under either NLD or short-day conditions. The leaf emergency rate of RFT1 mutants was similar to WT, suggesting that the late flowering phenotype of rft1-SNs was caused by delayed floral transition, but not by retarded growth. The expression of the key floral organ identity genes was significantly decreased in rft1-SN and doub-SN mutants, resulting in late flowering phenotypes. The expression profiles, evolution and haplotypes of Hd3a and RFT1 was also analyzed. Our studies provide insight into the potential utilization of Hd3a and RFT1 gene resources to improving growth period and regional adaptability in rice breeding. [ABSTRACT FROM AUTHOR]

Sound management of coastal resources is based on science-based decisions. Bottlenose dolphins are found around Puerto Rico; however, limited information exists on the ecology, behavior, sex ratio, distribution patterns, and population structure presenting, challenges in managing the bottlenose dolphin as defined in the Marine Mammal Protection Act of 1972. We sequenced the mitochondrial control region (mtDNA-CR) of 27 live and 11 stranded dolphins from Puerto Rico, five stranded dolphins from Guadeloupe and included sequences from the North Atlantic and the Pacific Ocean. Our genetic data from the new samples indicates the presence of distinct genetic lineages (inshore—represented by coastal individuals) and worldwide-distributed form (represented by both coastal and offshore individuals) in Puerto Rico. DNA divergence between inshore/coastal and offshore haplotypes ranged from 4.34 to 6.58%. All haplotypes from Puerto Rico have been previously reported from the Caribbean and North Atlantic. Genetic analysis yielded a complex population structure without a clear geographic signal; an expected result from a highly mobile marine mammal. A clade consisting exclusively of coastal dolphins of the Caribbean and the western North Atlantic was recovered. Offshore haplotypes from the eastern and western North Atlantic were generally clustered with offshore haplotypes of the Caribbean. Coastal and offshore haplotypes from the Pacific differed from those from the Atlantic. When we partitioned the data by form (coastal vs. offshore) and ocean (Atlantic vs. Pacific), we detected significant population differentiation (FST = 0.4089), indicating limited gene flow between forms and across oceans. [ABSTRACT FROM AUTHOR]

Opuntia ficus-indica, commonly known as prickly-pear, tuna, or nopal, is a cactus species of economic significance. It is widely cultivated for its fruits and cladodes, used as both fodder and human food. The species would have been domesticated in pre-Hispanic Mexico. In Argentina, two forms are present: the horticultural (spineless, f. ficus-indica) and the wild (spiny, f. amyclaea) forms. The presence/absence of spines would be a genetically controlled trait; thus, the species would have been introduced more than once in our country. A molecular and cytogenetic study was conducted to characterize the genetic variability, infer the source of introduction in Argentina, and explore the relationship between morphotypes. Most spine samples had the Q16-H1 haplotype, except for samples from Mexico, Santiago del Estero, and Catamarca. Samples from Salta, Santiago del Estero, and Catamarca showed morphological differences from O. ficus-indica. The cytological analysis revealed that most populations are octoploid, except for one diploid population from Mexico. Although the number of individuals from Mexico was low, haplotype diversity and number of diploid individuals was higher in that country than in Argentina. The occurrence of a single haplotype of the species associated with both spineless and spiny forms in Argentina reveals a single introduction event and its subsequent dispersion mainly through asexual reproduction. The haplotype diversity found in Argentina is probably due to hybrids between O. ficus-indica and Opuntia species native to this country. [ABSTRACT FROM AUTHOR]

Two isidiate species, Sticta arenosella and S. cellulosa , are reported from South America for the first time and the former species also as new to Southern Hemisphere. Sticta arenosella was found in Chile and S. celulosa in Bolivia. The identification of both species was confirmed by sequencing of the nuITS rDNA marker, a universal barcode of fungi, and the haplotype network analyses. Specimen of S. celulosa possess sparse apothecia, which previously have not been observed in this species.

The hypervariable region (HVR) in the control region of the mitochondrial DNA has frequently been used for population genetics and phylogeographic studies because of its highly variable nature. Although the HVR is beneficial for evaluating recent evolutionary history, including population demography, recent studies have implied the incidence of homoplasy in this region. To assess the accuracy of relying solely on the HVR for population genetics studies, molecular evolutionary analysis of the HVR, NADH-dehydrogenase subunit 2 (ND2), and cytochrome b genes were performed using 120 individuals of marbled flounder Pseudopleuronectes yokohamae. The HVR exhibited the highest genetic variability among the three regions, with sites showing high site-specific substitution rates. Considering the reticulate haplotype network structure and evolutionary linkages between regions, homoplastic mutations were indicated in the HVR in addition to ND2, underestimating genetic diversity. We found that homoplasy was less likely to affect coalescent-based demographic inferences in the population; however, there is still a potential risk of misinterpretation of population demography when solely using the HVR owing to its hypervariable nature. Collectively, we suggest analyzing other regions in addition to the HVR in fish population genetic research to improve accuracy and eliminate biases caused by homoplasy. [ABSTRACT FROM AUTHOR]

Analysis of genetic divergence in published mitochondrial DNA barcodes from 'juniper' and 'cedar' hairstreaks, Callophrys gryneus (Hübner) and Callophrys muiri (Hy. Edwards), together with a comparison of phenotypic differences in populations from North America, have been used to address the long-standing controversy regarding subspecies and species assignments in this confusing group of hairstreaks. The most recent view holds that C. gryneus is a single polytypic species comprising 11 nominal subspecies and that C. muiri from California is a valid species. An alternative view subdivides C. gryneus into three nominal species, C. gryneus (s.s.), Callophrys siva and Callophrys nelsoni, each with several named subspecies, and retains C. muiri as a full species. Haplotype networks, phylogenetic analysis and analysis of molecular variance of barcodes provided evidence supporting the subspecies scenario. However, barcodes from closely related congeners of C. gryneus (s.l.) revealed pairwise genetic divergences that would also support elevating three subspecies (C. g. castalis, C. g. siva and C. g. nelsoni) to full species. The barcode data also raise the question of whether C. muiri warrants full species status. Larval host plant preference as a possible driver of genetic differentiation in western populations of this group is also discussed briefly. [ABSTRACT FROM AUTHOR]

The Eichwald Toad, Bufo eichwaldi is one of the endemic amphibians distributed throughout Hyrcanian forests, marshes, wetlands, and streams in the north of Iran and the south of Azerbaijan. Populations of B. eichwaldi have previously been studied based on a few molecular and morphological data. Here, we undertake taxonomic and phylogenetic analyses based on morphological and morphometric features for 56 specimens of B. eichwaldi from Iran, and mitochondrial cyt b marker for 20 specimens from the whole species range in the west and east Caspian Sea lowland. Molecular analyses based on 794 bp of cyt b gene demonstrated two clusters: the east Caspian Sea lowland (A1) and the west Caspian Sea lowland (A2) clusters. Univariate analyses indicated six out of 25 morphometric variables in male B. eichwaldi specimens from the east (A1) are significantly different from male specimens of B. eichwaldi from the west Caspian Sea (A2; P≤0.05). Females have been also significantly different between two clusters in one character (distance between lids; P≤0.05). Sexual size dimorphism was also significantly different within and between populations in some variables. However, the PCA analyses show no differentiation among B. eichwaldi populations in the east and west Caspian Sea lowland. Based on p-distance parameter, the east and west groups showed a low level of genetic differentiation (0.2%). [ABSTRACT FROM AUTHOR]

Equine rhinitis A (ERAV) and B (ERBV) viruses are respiratory pathogens with worldwide distribution. The current study aimed to determine the frequency of infection of ERAV and ERBV among horses and foals at Polish national studs, and to determine genetic variability within the viruses obtained. Virus-specific quantitative RT-PCR assays targeting a 5′ untranslated region were used to screen nasal swabs collected from 621 horses at 16 national horse studs from throughout Poland, including 553 healthy horses and 68 horses with respiratory disease. A partial DNA polymerase gene was amplified and sequenced from the qRT-PCR-positive samples. The obtained sequences were analysed using phylogeny and genetic network analysis. None of the nasal swabs were positive for ERAV, whereas ERBV was found in 11/621 (1.78%) samples collected from 10 healthy horses and one foal affected by respiratory disease. Partial DNA polymerase gene sequence variability was correlated with individual horses and studs from which samples were collected when only Polish sequences were analysed, but there was no correlation between country of origin and ERBV sequence when Polish and international sequences were included in the network. The report presents the first detection of ERBV in Poland. [ABSTRACT FROM AUTHOR]

Hyalomma anatolicum, an Anatolian hard tick is a well-recognized vector involved in the transmission of various pathogens to animals and humans. The present study elucidated the population structure and haplotype network of H. anatolicum based on the mitochondrial large subunit ribosomal RNA (16S rRNA) gene sequence. The population structure and haplotype network analysis of 75 sequences archived in the GenBank, including the 15 sequences generated herein, yielded 24 haplotypes. Haplotype 1 (Hap_1) was the predominant haplotype consisting of 45 sequences from India, China, Pakistan, Turkey, Egypt, Iraq, and Tajikistan. The complete haplotype network exhibited a stellate conformation, highlighting a recent population expansion. The overall dataset, together with the sequences corresponding to India, China, and Pakistan, showed a high haplotype (0.638 ± 0.065, 0.671 ± 0.103, 0.753 ± 0.099, and 0.854 ± 0.061, respectively) and low nucleotide (0.00407 ± 0.00090, 0.00525 ± 0.00196, 0.00680 ± 0.00233, and 0.00453 ± 0.00056, respectively) diversity, further emphasized a recent population expansion. The neutrality indices including Tajima’s D, Fu and Li’s D, and Fu and Li’s F for the complete dataset (− 2.661, − 6.008, and − 5.649, respectively) as well as for the sequences from India (− 2.223, − 3.414, and − 3.567, respectively) were negative, suggesting deviation from neutrality and a recent population expansion. The present study provided novel insights into the population structure and haplotype networks of H. anatolicum based on the mitochondrial 16S rRNA gene, and the different tests inferred a low genetic differentiation and suggested a recent population expansion of this economically important tick species. [ABSTRACT FROM AUTHOR]

Micranthes nelsoniana possesses multiple different variants and numerous chromosomes. Based on the internal transcribed spacer (ITS) and chloroplast (cp)DNA sequences, the phylogeography of M. nelsoniana and its relatives in Northeast Asia was investigated, with extensive sampling around the Kuril Islands. The Arctic–Asian continent and a clade of marginal islands were the two main groupings that comprised the ITS phylogenetic tree. The island clade was separated into five well-supported clades: Kamchatka and Hokkaido highlands, Kuril–Aleutian Islands, southern Kuril Islands, Japanese archipelago, and Primorye region. Micranthes fusca was found in Japan and in the southern Kuril Islands. It is a separate species that created several types of hybrids between M. nelsoniana in the centre of the Kuril Islands based on a comparison of the ITS and cpDNA networks. Micranthes nelsoniana and M. ohwii appear to have hybridized in the northern Kuril Islands. Cytological investigation on the local species of M. nelsoniana showed that the chromosomal numbers are: 2 n  = 24, 26, 28, 30, 50, and 80. Among them, two usual numbers to this area, 2 n  = 24 and 50, appear to encourage interspecific gene exchange. The genomes of Hokkaido plants with high chromosome counts were cloned, revealing that they contained genes of both continental and marginal origins. This study revealed the crucial role of marginal islands along Northeast Asia in the genetic diversity of M. nelsoniana and related species. [ABSTRACT FROM AUTHOR]

Two isidiate species, Sticta arenosella and S. cellulosa, are reported from South America for the first time and the former species also as new to the Southern Hemisphere. Sticta arenosella was found in Chile and S. cellulosa in Bolivia. The identification of both species was confirmed by sequencing of the nuITS rDNA marker, a universal barcode of fungi, and the haplotype network analyses. Specimens of S. cellulosa possess sparse apothecia, which previously have not been observed in this species. [ABSTRACT FROM AUTHOR]

Background Understanding the processes that influence distribution of organisms is a major goal in evolutionary biology. Speciation in freshwater fishes is mainly associated with the “island-like” model of evolution, in which the formation of land barriers between different hydrographic basins interrupts gene flow and promotes isolation. Freshwater fish therefore provide an excellent model system for macro- and micro-evolutionary studies. The Mesa Silverside, Chirostoma jordani, is one of the most widespread freshwater fish species in the Mexican Plateau, a geologically complex physiographic region with a long history of genesis, destruction and compartmentalization of hydrographic basins that has promoted the dispersal and isolation of freshwater fishes. Methods We used mitochondrial (Cytb and D-loop) and nuclear (first intron of the ribosomal protein S7) data and used phylogeographic and coalescent based methods to elucidate the evolutionary history of C. jordani throughout its distributional range on the Mexican Plateau. Results The results obtained in the present study revealed that C. jordani consists of two main genetic groups with geographical correspondence. Clade I occur exclusively in north-western basin and shows population structure. Clade II is widely distributed across the west, central and eastern basins without population structure. The split between these two main clades was estimated at 1.4 Mya. This cladogenetic event may be associated with the allopatric process promoted by the fragmentation and compartmentalization of hydrographic basins induced by the geological and climatic history of the Mexican Plateau.

Introduction Malayemys khoratensis is a freshwater turtle species endemic to northeastern Thailand and Lao PDR. While M. khoratensis is relatively common and widespread in Thailand, its population size and demographic trends remain largely unknown, as direct population estimates are lacking. This species faces significant threats from consumption, exploitation, and trade. Therefore, this study aims to investigate the genetic diversity, population structure, and demographic trends of M. khoratensis in northeastern Thailand, using two mitochondrial DNA genes, Cyt b and ND4. Method We grouped the turtles based on three major river basins in northeastern Thailand: Mun, Chi, and Northeast Mekong to assess population structure and test the isolation-by-basin hypothesis. The Cyt b and ND4 genes of 49 M. khoratensis individuals across 15 provinces in Thailand were sequenced, and 15 sequences from a previous study of Ihlow et al. (2016) were included into the analyses. We constructed a haplotype network from the concatenated sequences and analyzed the population structure with the analysis of molecular variance (AMOVA). Additionally, we used a Bayesian Skyline plot (BSP) analysis to estimate the effective female population size and explore the demographic history of this species. Results Our analysis identified 13 unique haplotypes defined by 26 polymorphic sites from 64 samples. The total haplotype diversity for M. khoratensis was 0.819, while nucleotide diversity was 0.0031. The haplotype network and AMOVA revealed no distinct population structure among the river basins, suggesting gene flow across these regions. The BSP estimated a stable effective female population size of approximately 130,000 individuals since around 100,000 years ago (late Pleistocene). Conclusion Our findings indicated no significant population structure by river basin, which may be due to natural movement between basins or potential human-mediated translocations linked to the turtle trade. The demographic trend of M. khoratensis appears to have been stable over time. However, given the ongoing exploitation of this species, we recommend regular monitoring of population trends to support its long-term survival.

Abstract Biomphalaria straminea is one of the three snails that act as the intermediate hosts of Schistosoma mansoni and is responsible for maintaining high rates of schistosomiasis in some areas of northeastern Brazil. The principal morphological characteristic of B. straminea is the marked vaginal wrinkling, although it is also present in congeneric species, a group known as the B. straminea complex. Based on the morphological and molecular analyses, we investigated the intraspecific variation of B. straminea. The specimens were obtained from 10 sites in Brazil, and the shells were analyzed, as well as 16 morphological structures of the reproductive system. The COI and ITS2 sequences were used for phylogenetic analysis, genetic divergence, and haplotype network (COI). We observed a large intraspecific variation in the morphological structures examined. The genetic divergence also demonstrated significant intraspecific variability in B. straminea: 0–3% in ITS2 sequences, and 0–6% in COI sequences. Analysis of the distribution of COI haplotypes recovered 16 haplotypes and haplotype diversity of 0.9088. These results indicate phenotypic variability that is not constrained to a locality or strictly controlled genetically by B. straminea, which may have driven a misidentified of these species.

Abstract The COVID-19 pandemic has profoundly affected all aspects of our lives. Through real-time monitoring and rapid vaccine implementation, we succeeded in suppressing the spread of the disease and mitigating its consequences. Finally, conclusions can be summarized and drawn. Here, we use the example of Poland, which was seriously affected by the pandemic. Compared to other countries, Poland has not achieved impressive results in either testing or vaccination, which may explain its high mortality (case fatality rate, CFR 1.94%). Through retrospective analysis of data collected by the COVID-19 Data Portal Poland, we found significant regional differences in the number of tests performed, number of cases detected, number of COVID-19-related deaths, and vaccination rates. The Masovian, Greater Poland, and Pomeranian voivodeships, the country’s leaders in vaccination, reported high case numbers but low death rates. In contrast, the voivodeships in the eastern and southern parts of Poland (Subcarpathian, Podlaskie, Lublin, Opole), which documented low vaccination levels and low case numbers, had higher COVID-19-related mortality rates. The strong negative correlation between the CFR and the percentage of the population that was vaccinated in Poland supports the validity of vaccination. To gain insight into virus evolution, we sequenced more than 500 genomes and analyzed nearly 80 thousand SARS-CoV-2 genome sequences deposited in GISAID by Polish diagnostic centers. We showed that the SARS-CoV-2 variant distribution over time in Poland reflected that in Europe. Haplotype network analysis allowed us to follow the virus transmission routes and identify potential superspreaders in each pandemic wave.

Ocypode Weber, 1795 (Brachyura: Ocypodidae) is popularly known as ghost crab, and encompasses 21 valid species, including Ocypode quadrata (Fabricius, 1787). This species has wide distribution along the Atlantic coast of America, from the USA (Massachusetts) to Brazil (Rio Grande do Sul), Central America, and Antilles. Such distribution, along with some biological characteristics of its life cycle and the presence of geographic barriers, could lead to genetic structuring. Herein, we evaluate the hypothesis of the presence of geographic barriers using COI and 16S partial gene fragments. The Maximum Likelihood tree suggests the monophyly of O. quadrata, while the values of intraspecific genetic distance along with the star-shaped haplotype network suggested a lack of genetic structure in Brazilian, Panama, and French Guiana populations, probably caused by larval dispersion. USA and Mexico populations may be a new lineage, but we cannot say it with few sequences and with no morphological characters.

The fluke Clinostomum complanatum, a parasite of piscivorous birds, but also reptiles and rarely mammals, has established several foci in the western Palaearctic regions. Previous studies pointed out the complicated taxonomy of the genus, but broader population genetic analysis of C. complanatum has not yet been carried out. The aim of this study was to determine the structure, intraspecific variability, and diversity of mitochondrial cox1 haplotypes of C. complanatum from different localities in Slovakia (Danube floodplain forests) and Italy (Emilia-Romagna and Tuscany), as well as to evaluate the interrelationships among populations from Europe, the Middle East, and North Africa. The genetic structure of C. complanatum from Slovakia and Italy was represented by a great number of haplotypes, showing stable populations with high intraspecific diversity. The haplotypes of samples from other localities (Romania, Turkey, Egypt, and Iran) showed possible gene flow among the populations from Central Europe down to the Mediterranean region, North Africa, and the Middle East. The genetic homogeneity of these samples can be linked to the distribution and migratory routes of the definitive hosts, aquatic piscivorous birds, mainly herons and cormorants, that spread parasite eggs among the continents.

The COVID-19 pandemic has profoundly affected all aspects of our lives. Through real-time monitoring and rapid vaccine implementation, we succeeded in suppressing the spread of the disease and mitigating its consequences. Finally, conclusions can be summarized and drawn. Here, we use the example of Poland, which was seriously affected by the pandemic. Compared to other countries, Poland has not achieved impressive results in either testing or vaccination, which may explain its high mortality (case fatality rate, CFR 1.94%). Through retrospective analysis of data collected by the COVID-19 Data Portal Poland, we found significant regional differences in the number of tests performed, number of cases detected, number of COVID-19-related deaths, and vaccination rates. The Masovian, Greater Poland, and Pomeranian voivodeships, the country's leaders in vaccination, reported high case numbers but low death rates. In contrast, the voivodeships in the eastern and southern parts of Poland (Subcarpathian, Podlaskie, Lublin, Opole), which documented low vaccination levels and low case numbers, had higher COVID-19-related mortality rates. The strong negative correlation between the CFR and the percentage of the population that was vaccinated in Poland supports the validity of vaccination. To gain insight into virus evolution, we sequenced more than 500 genomes and analyzed nearly 80 thousand SARS-CoV-2 genome sequences deposited in GISAID by Polish diagnostic centers. We showed that the SARS-CoV-2 variant distribution over time in Poland reflected that in Europe. Haplotype network analysis allowed us to follow the virus transmission routes and identify potential superspreaders in each pandemic wave. [ABSTRACT FROM AUTHOR]

Background & objectives Genetic analysis of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) strains circulating in India during 2020-2022 was carried out to understand the evolution of potentially expanding and divergent clades. Methods SARS-CoV-2 sequences (n=612) randomly selected from among the sequences of samples collected through a nationwide network of Virus Research Diagnostic Laboratories during 2020 (n=1532) and Indian sequences available in Global Initiative on Sharing All Influenza Data during March 2020-March 2022 (n=53077), were analyzed using the phylo-geo haplotype network approach with reference to the Wuhan prototype sequence. Results On haplotype analysis, 420 haplotypes were revealed from 643 segregating sites among the sequences. Haplotype sharing was noted among the strains from different geographical regions. Nevertheless, the genetic distance among the viral haplotypes from different clades could differentiate the strains into distinct haplo groups regarding variant emergence. Interpretation & conclusions The haplotype analysis revealed that the G and GR clades were co-evolved and an epicentrefor the evolution of the GH, GK and GRA clades. GH was more frequently identified in northern parts of India than in other parts, whereas GK was detected less in north India than in other parts. Thus, the network analysis facilitated a detailed illustration of the pathways of evolution and circulation of SARS-CoV-2 variants. [ABSTRACT FROM AUTHOR]

Here, we characterise the standard “Folmer region” of the mitochondrial cytochrome c oxidase subunit 1 (CO1) marker and a fragment of nuclear 28S marker in four species of the Jaera albifrons complex. Jaera albifrons (Leach, 1814), Jaera ischiosetosa Forsman, 1949, Jaera praehirsuta Forsman, 1949, and Jaera forsmani Bocquet, 1950 were collected from localities on the Norwegian coast and identified with morphological characters. We compared DNA sequences with sequences available in GenBank and BOLDsystems and calculated haplotype networks and interspecific versus intraspecific genetic distances. These analyses revealed low interspecific genetic distance (CO1 0.00–1.57%, 28S 0.00–0.39%) and extensive haplotype sharing between J. albifrons group species and specimens from both sides of the North Atlantic for both CO1 and 28S. Genetic distances between J. albifrons group species and other Jaera species, however, exceeded 29% for both CO1 and 28S, with no haplotype sharing. These assessments, together with taxonomically unconstrained analyses with software ABGD and ASAP, show that these markers are unable to distinguish between the J. albifrons group of morphospecies. The sequences do, however, clearly identify J. albifrons species complex from other Jaera species. Thus, a likely hypothesis is that taxa in this complex represent a single species. Our results corroborate previous finds where discordance between mitochondrial gene clusters, AFLP, and other data highlights the potential conflict between different “species criteria” and the well-established distinction between gene trees and species trees. In operational terms, common protocols for metabarcoding will potentially underestimate sympatric species diversity with cases like the J. albifrons complex, if the members of this complex indeed represent different species. [ABSTRACT FROM AUTHOR]

Ocypode Weber, 1795 (Brachyura: Ocypodidae) is popularly known as ghost crab, and encompasses 21 valid species, including Ocypode quadrata (Fabricius, 1787). This species has wide distribution along the Atlantic coast of America, from the USA (Massachusetts) to Brazil (Rio Grande do Sul), Central America, and Antilles. Such distribution, along with some biological characteristics of its life cycle and the presence of geographic barriers, could lead to genetic structuring. Herein, we evaluate the hypothesis of the presence of geographic barriers using COI and 16S partial gene fragments. The Maximum Likelihood tree suggests the monophyly of O. quadrata, while the values of intraspecific genetic distance along with the star-shaped haplotype network suggested a lack of genetic structure in Brazilian, Panama, and French Guiana populations, probably caused by larval dispersion. USA and Mexico populations may be a new lineage, but we cannot say it with few sequences and with no morphological characters. [ABSTRACT FROM AUTHOR]

Determining the genetic diversity and source rookeries of sea turtles collected from feeding grounds can facilitate effective conservation initiatives. To ascertain the genetic composition and source rookery, we examined a partial sequence of the mitochondrial control region (CR, 796 bp) of 40 green turtles (Chelonia mydas) collected from feeding grounds around the Korean Peninsula between 2014 and 2022. We conducted genetic and mixed-stock analyses (MSA) and identified 10 CR haplotypes previously reported in Japanese populations. In the haplotype network, six, three, and one haplotype(s) grouped with the Japan, Indo-Pacific, and Central South Pacific clades, respectively. The primary rookeries of the green turtles were two distantly remote sites, Ogasawara (OGA) and Central Ryukyu Island (CRI), approximately 1,300 km apart from each other. Comparing three parameters (season, maturity, and specific feeding ground), we noted that OGA was mainly associated with summer and the Jeju Sea, whereas CRI was with fall and the East (Japan) Sea ground. The maturity did not show a distinct pattern. Our results indicate that green turtles in the feeding grounds around the Korean Peninsula originate mainly from the Japan MU and have genetic origins in the Japan, Indo-Pacific, and Central South Pacific clades. Our results provide crucial insights into rookeries and MUs, which are the focus of conservation efforts of the Republic of Korea and potential parties to collaborate for green turtle conservation. [ABSTRACT FROM AUTHOR]

Abstract Background Plasmodium vivax Duffy binding protein (PvDBP) is a merozoite surface protein located in the micronemes of P. vivax. The invasion of human reticulocytes by P. vivax merozoites depends on the parasite DBP binding domain engaging Duffy Antigen Receptor for Chemokine (DARC) on these red blood cells (RBCs). PvDBPII shows high genetic diversity which is a major challenge to its use in the development of a vaccine against vivax malaria. Methods A cross-sectional study was conducted from February 2021 to September 2022 in five study sites across Ethiopia. A total of 58 blood samples confirmed positive for P. vivax by polymerase chain reaction (PCR) were included in the study to determine PvDBPII genetic diversity. PvDBPII were amplified using primers designed from reference sequence of P. vivax Sal I strain. Assembling of sequences was done using Geneious Prime version 2023.2.1. Alignment and phylogenetic tree constructions using MEGA version 10.1.1. Nucleotide diversity and haplotype diversity were analysed using DnaSP version 6.12.03, and haplotype network was generated with PopART version 1.7. Results The mean age of the participants was 25 years, 5 (8.6%) participants were Duffy negatives. From the 58 PvDBPII sequences, seven haplotypes based on nucleotide differences at 8 positions were identified. Nucleotide diversity and haplotype diversity were 0.00267 ± 0.00023 and 0.731 ± 0.036, respectively. Among the five study sites, the highest numbers of haplotypes were identified in Arbaminch with six different haplotypes while only two haplotypes were identified in Gambella. The phylogenetic tree based on PvDBPII revealed that parasites of different study sites shared similar genetic clusters with few exceptions. Globally, a total of 39 haplotypes were identified from 223 PvDBPII sequences representing different geographical isolates obtained from NCBI archive. The nucleotide and haplotype diversity were 0.00373 and 0.845 ± 0.015, respectively. The haplotype prevalence ranged from 0.45% to 27.3%. Two haplotypes were shared among isolates from all geographical areas of the globe. Conclusions PvDBPII of the Ethiopian P. vivax isolates showed low nucleotide but high haplotype diversity, this pattern of genetic variability suggests that the population may have undergone a recent expansion. Among the Ethiopian P. vivax isolates, almost half of the sequences were identical to the Sal-I reference sequence. However, there were unique haplotypes observed in the Ethiopian isolates, which does not share with isolates from other geographical areas. There were two haplotypes that were common among populations across the globe. Categorizing population haplotype frequency can help to determine common haplotypes for designing an effective blood-stage vaccine which will have a significant role for the control and elimination of P. vivax.

Coral-dwelling gall crabs (Cryptochiridae) are common inhabitants of scleractinian corals. Several species have been described as new in recent years, including Lithoscaptus doughnut, which was described from Hong Kong based on a single female retrieved from the coral Plesiastrea peroni. Here we extend the distribution range of L. doughnut with nine additional localities throughout the Indo-West Pacific, from the Red Sea to the Coral Triangle and Japan. We describe a male specimen of L. doughnut for the first time, based on a specimen from Malaysia, and provide photographs of life and preserved material. Haplotype networks based on COI mtDNA (n = 12) and 16 rRNA sequences (n = 12) were created. We retrieved eleven COI haplotypes and six 16S haplotypes, however no clear geographic distribution pattern was discerned. Intraspecific variation in L. doughnut was 1.4% for COI and 0.2% for 16S. Lastly, the first colour photos and records of associated parasites of this species are provided.

The first records of Parmelia ernstiae from Madeira, as well as the new localities of P. encryptata from Poland and P. sulcata from Chile, are presented. All records are confirmed by molecular data, BLAST search, and haplotype network analysis of the nucITS rDNA sequences. The discussion on the morphology and secondary chemistry of all three species is provided with notes on their distribution and similar taxa. Parmelia encryptata is a rarely reported cryptic species that is morphologically indistinguishable from P. sulcata , and its identification requires molecular data. New localities of P. encryptata from northern Poland suggest that the taxon may be widespread in the country and not confined to large forests but also present in open areas on free-standing trees. Moreover, a new nucITS rDNA haplotype of the species is reported. Parmelia ernstiae is a near-cryptic species, morphologically and chemically very similar to P. saxatilis and P. serrana . Two specimens of the species from Madeira have sublinear lobes with marginal and laminal isidia, unlike most specimens of P. ernstiae, having short, broad lobes with laminal isidia, and thus are morphologically closer to P. saxatilis in lobe shape and to P. serrana in placement of isidia. However, the BLAST search and haplotype analysis of nucITS rDNA sequences placed these specimens in P. ernstiae . Parmelia sulcata , a common species in the Northern Hemisphere, is rare elsewhere, and only two records confirmed by molecular data were known from South America. The nucITS rDNA haplotype of two new and two previous records of the species represent the most common haplotype of the species known from the Northern Hemisphere.

Determining the genetic diversity and source rookeries of sea turtles collected from feeding grounds can facilitate effective conservation initiatives. To ascertain the genetic composition and source rookery, we examined a partial sequence of the mitochondrial control region (CR, 796 bp) of 40 green turtles (Chelonia mydas) collected from feeding grounds around the Korean Peninsula between 2014 and 2022. We conducted genetic and mixed-stock analyses (MSA) and identified 10 CR haplotypes previously reported in Japanese populations. In the haplotype network, six, three, and one haplotype(s) grouped with the Japan, Indo-Pacific, and Central South Pacific clades, respectively. The primary rookeries of the green turtles were two distantly remote sites, Ogasawara (OGA) and Central Ryukyu Island (CRI), approximately 1,300 km apart from each other. Comparing three parameters (season, maturity, and specific feeding ground), we noted that OGA was mainly associated with summer and the Jeju Sea, whereas CRI was with fall and the East (Japan) Sea ground. The maturity did not show a distinct pattern. Our results indicate that green turtles in the feeding grounds around the Korean Peninsula originate mainly from the Japan MU and have genetic origins in the Japan, Indo-Pacific, and Central South Pacific clades. Our results provide crucial insights into rookeries and MUs, which are the focus of conservation efforts of the Republic of Korea and potential parties to collaborate for green turtle conservation.

The taxonomic history of nominal subspecies of Danaus gilippus is reviewed. The historical record together with analysis of both morphological and molecular characters suggest that the current infraspecific nomenclature is in need of revision. The absence of DNA barcode differences and lack of consistent morphological differences in wing maculation in western and eastern populations in continental North America currently assigned to subspecies D. g. thersippus and D. g. berenice, respectively, raise the possibility that only a single subspecies, D. g. berenice, should be recognized. Recently published isotopic evidence for connectivity between eastern and western populations of D. gilippus, and potential ecological consequences of the relatively low numbers present in the spring and summer breeding range of the eastern migratory populations of the monarch, Danaus plexippus, are briefly discussed. [ABSTRACT FROM AUTHOR]

Coral-dwelling gall crabs (Cryptochiridae) are common inhabitants of scleractinian corals. Several species have been described as new in recent years, including Lithoscaptus doughnut, which was described from Hong Kong based on a single female retrieved from the coral Plesiastrea peroni. Here we extend the distribution range of L. doughnut with nine additional localities throughout the Indo-West Pacific, from the Red Sea to the Coral Triangle and Japan. We describe a male specimen of L. doughnut for the first time, based on a specimen from Malaysia, and provide photographs of life and preserved material. Haplotype networks based on COI mtDNA (n = 12) and 16 rRNA sequences (n = 12) were created. We retrieved eleven COI haplotypes and six 16S haplotypes, however no clear geographic distribution pattern was discerned. Intraspecific variation in L. doughnut was 1.4% for COI and 0.2% for 16S. Lastly, the first colour photos and records of associated parasites of this species are provided. [ABSTRACT FROM AUTHOR]

Background: Plasmodium vivax Duffy binding protein (PvDBP) is a merozoite surface protein located in the micronemes of P. vivax. The invasion of human reticulocytes by P. vivax merozoites depends on the parasite DBP binding domain engaging Duffy Antigen Receptor for Chemokine (DARC) on these red blood cells (RBCs). PvDBPII shows high genetic diversity which is a major challenge to its use in the development of a vaccine against vivax malaria. Methods: A cross-sectional study was conducted from February 2021 to September 2022 in five study sites across Ethiopia. A total of 58 blood samples confirmed positive for P. vivax by polymerase chain reaction (PCR) were included in the study to determine PvDBPII genetic diversity. PvDBPII were amplified using primers designed from reference sequence of P. vivax Sal I strain. Assembling of sequences was done using Geneious Prime version 2023.2.1. Alignment and phylogenetic tree constructions using MEGA version 10.1.1. Nucleotide diversity and haplotype diversity were analysed using DnaSP version 6.12.03, and haplotype network was generated with PopART version 1.7. Results: The mean age of the participants was 25 years, 5 (8.6%) participants were Duffy negatives. From the 58 PvDBPII sequences, seven haplotypes based on nucleotide differences at 8 positions were identified. Nucleotide diversity and haplotype diversity were 0.00267 ± 0.00023 and 0.731 ± 0.036, respectively. Among the five study sites, the highest numbers of haplotypes were identified in Arbaminch with six different haplotypes while only two haplotypes were identified in Gambella. The phylogenetic tree based on PvDBPII revealed that parasites of different study sites shared similar genetic clusters with few exceptions. Globally, a total of 39 haplotypes were identified from 223 PvDBPII sequences representing different geographical isolates obtained from NCBI archive. The nucleotide and haplotype diversity were 0.00373 and 0.845 ± 0.015, respectively. The haplotype prevalence ranged from 0.45% to 27.3%. Two haplotypes were shared among isolates from all geographical areas of the globe. Conclusions: PvDBPII of the Ethiopian P. vivax isolates showed low nucleotide but high haplotype diversity, this pattern of genetic variability suggests that the population may have undergone a recent expansion. Among the Ethiopian P. vivax isolates, almost half of the sequences were identical to the Sal-I reference sequence. However, there were unique haplotypes observed in the Ethiopian isolates, which does not share with isolates from other geographical areas. There were two haplotypes that were common among populations across the globe. Categorizing population haplotype frequency can help to determine common haplotypes for designing an effective blood-stage vaccine which will have a significant role for the control and elimination of P. vivax. [ABSTRACT FROM AUTHOR]

The present study was aimed to determine the phylogenetic relationship, haplotype network, and demographic dynamics of H. felis infecting the endangered Asiatic lions in Gir National Park, Gujarat, India, on the basis of partial 18S rRNA gene. The phylogenetic analysis based on the partial 18S rRNA gene sequences of H. felis exhibited the presence of two distinct genotypes of H. felis (HfG1 and HfG2) infecting the Indian wild felids, viz., the Asiatic lion, Royal Bengal tiger, and Indian leopard. The HfG1 and HfG2 genotypes exhibited 97.6–100% and 99.7–100%, and 96.9–98.7% nucleotide identity within and between themselves, respectively. The HfG1 genotype exhibited a higher genetic diversity as compared to HfG2. A total of 22 molecular signatures were identified in the 18S rRNA gene between these genotypes. Further, analysis of a total 67 sequences of H. felis (13 different host species from 13 countries of Africa, South America, Asia, and Europe) that were downloaded from GenBankTM, generated 30 haplotypes. Among all the haplotypes, Hap_17 (h=12) was the most frequent followed by Hap_12 (h=09) and Hap_4 (h=05). Out of 13 location-wise populations, India (h=12) shared the highest number of haplotypes followed by Japan (h=08), and the least number of haplotypes were found in Hungary (h=02). Population dynamics study involving neutrality tests and mismatch distribution, and genetic differentiation indices, revealed the presence of phylogeographic population structure and a constant population size indicating a uniform gene flow among the populations worldwide. In conclusion, a high genetic diversity along with the presence of two distinct genotypes of H. felis were observed on the basis of 18S rRNA gene sequence analysis. [ABSTRACT FROM AUTHOR]

In the early twentieth century, European mouflon was introduced in Croatia, while all introductions in Slovenia occurred in the 1950s and 1960s. Although majority of the introductions were historically documented, occasional cases involving individuals of unknown origin have likely contributed to a mixed genetic pool in established colonies. To understand the impact of past management and the potential founder effects on contemporary mouflon populations, we performed the first genetic study of the species in these two countries. Utilising next-generation sequencing of both mitochondrial control region (mtDNA CR) and major histocompatibility complex (MHC DRB exon 2), our study scrutinises the genetic diversity and structure of these populations. Additionally, the origins and genetic variability of mouflon in Croatia and Slovenia were compared with reference samples from Czech Republic, Sardinia (Italy), and Corsica (France). The mtDNA haplotype network showed that the majority of mouflon from Slovenia are closely related to mouflon from Sardinia, and only few shared the same haplotypes with mouflon from Croatia. Some mouflon from mainland Croatia share identical or closely related haplotypes with individuals from the initially established population in this country (on the Brijuni Archipelago), while others belong to a distinctly different cluster. We found five MHC alleles previously reported for mouflon in Europe, and genetic diversity was similar in both studied countries. We observed an excess of the Ovar-DRB1*07012/*07012 genotype, and only a few individuals exhibited the advantageous genotypes for parasite infection (Ovar-DRB1*0114 allele and Ovar-DRB1*0324/*0114 genotype). Genetic data showed that the population origins are generally in agreement with the written historical records, although we found signals of release of extra individuals into certain colonies. [ABSTRACT FROM AUTHOR]

The land snail Elona quimperiana is listed in annexes II and IV of the Europe Habitats Directive. In this study, phylogenetic relationships between populations of this protected species from its whole distribution range were reconstructed based on the sequencing of two mtDNA gene fragments (COI and 16S rRNA) and one nDNA gene fragment (ITS2). Haplotype networks were also generated for the COI and 16S rRNA gene fragments. Results yielded three main intraspecific phylogroups, here designated as the lineages Brittany-Spain, Basque, and Navarre-Rioja. This last lineage had not been identified previously. Genetic distances between the three main phylogroups suggest they could have originated by allopatric fragmentation before the Last Glacial Maximum, and then separately evolved in three refugia in the Iberian Peninsula. We here propose that each phylogroup is considered an Evolutionarily Significant Unit. Through extended sampling, we were able to delimit the geographic distribution of all three lineages. Our genetic results support post-glacial colonization of this species from the north-eastern Iberian Peninsula to Brittany in NW-France as proposed previously, and rule out its recent anthropic introduction.

Oxalis section Palmatifoliae (wood sorrel) includes five species that are well differentiated morphologically. A previous population study in one of the species (O. laciniata) suggested a complex phylogeographic history and highlighted the need to explore the genetic variability of all the species in the section. Thus, we performed a population level study of the five species to (1) determine the population structure within and among species, (2) model their current and paleoclimatic distributions, and (3) assess the historical processes that influenced their current genetic and morphological variation. We generated inter-simple sequence repeat (ISSR) polymorphism data and DNA sequences for the plastid region trnH-psbA and used those data to obtain a haplotype network, and used georeferenced coordinates and Maxent to obtain present and past species distribution models. Our major results included: 1) ISSR data showed a significant level of genetic differentiation among the five species and a degree of admixture within species; 2) plastid region trnH-psbA shows that one haplotype is the most frequent and widespread among all the species; 3) modelling of species present distributions showed different climatic variables for each species, whereas modelling of past distribution scenarios suggests broader distributions of all species. [ABSTRACT FROM AUTHOR]

The orb-weaving spider Argiope trifasciata (Forsskål, 1775) was scientifically described in Egypt while it has been considered native to North America. The aim of this study was to analyse the phylogenetic relationships of the Egyptian population and shed light on its introduction and migration history. The COX1 gene (mtDNA) of 49 samples from Egypt and Cyprus was analysed with 168 additional COX1 sequences available in GenBank and BOLD originating from nineteen other countries. Selected ecological parameters were also studied in an Egyptian desert habitat for comparison with North American populations. We found that spiders oriented their webs in relation to the sun's position (South and South-East) most likely to regulate their body temperature. The life cycle of A. fasciata in Egypt was found to be extended from what has been reported from other populations, partly possible because some individuals may survive throughout the winter. The phylogenetic analysis revealed that the sequences from Egypt and Cyprus clustered with Afro-Eurasian populations. Thirty haplotypes were found in Egypt and Cyprus of which 21 were unique. The analysis further revealed that the nearest American COX1 sequence was separated by 18 mutations. The high COXI divergence (5.1%) as well as the low gene flow (Fst = 0.75) between Afro-Eurasian and American populations, indicated that A. trifasciata has not been recently dispersed from America to Africa and other continents, but the genetic isolation was estimated to have happened around 2.04 My ago. If these spiders represent unique species or subspecies will need further research. [ABSTRACT FROM AUTHOR]

The major plant pest fall armyworm (FAW), Spodoptera frugiperda, is native to the Americas and has colonized Africa and Asia within the Eastern hemisphere since 2016, causing severe damage to multiple agricultural crop species. However, the genetic origin of these invasive populations requires more in‐depth exploration. We analysed genetic variation across the genomes of 280 FAW individuals from both the Eastern hemisphere and the Americas. The global range‐wide genetic structure of FAW shows that the FAW in America has experienced deep differentiation, largely consistent with the Z‐chromosomal Tpi haplotypes commonly used to differentiate 'corn‐strain' and 'rice‐strain' populations. The invasive populations from Africa and Asia are different from the American ones and have a relatively homogeneous population structure, consistent with the common origin and recent spreading from Africa to Asia. Our analyses suggest that north‐ and central American 'corn‐strain' FAW are the most likely sources of the invasion into the Eastern hemisphere. Furthermore, evidence based on genomic, transcriptomic and mitochondrial haplotype network analyses indicates an earlier, independent introduction of FAW into Africa, with subsequent migration into the recent invasive population. [ABSTRACT FROM AUTHOR]

The results of studies of the morphology and genetics of the Baikal subendemic (Harpacticella inopinata Sars, 1908 harpacticoid) are presented. The collections of 1969 and 2017–2022 from the southern part of Lake Baikal and the Yenisei River within the city of Krasnoyarsk are used as material. It is demonstrated that morphological variability within the species is most pronounced in the structure of the antenna exopodite and the number of pores and sensilla on the integument of thoracic somites. The genetic variability of the studied H. inopinata sample is described by three clades with an average distance between them of 0.24; genetic distances between individuals within the detected genetic groups do not exceed 0.005. It is found that H. inopinata from geographically distant habitats (Lake Baikal and the Yenisei River) form a single morphological and genetic group. The analysis of genetic diversity of H. inopinata confirms the relatively recent Baikal origin of the species in the Yenisei River, probably associated with an anthropogenic invasion. [ABSTRACT FROM AUTHOR]

From June 7th to 11th, 2023, eight cases of Mpox were identified in Guangzhou, China. This is the first report of multiple local sporadic cases after the imported case in Chongqing, China. Epidemiological investigation revealed that these cases had no history of international travel and no connections with each other. Haplotype network and phylogenetic analyses indicated that the possible origin is likely from Japan, although the direct origin may remain uncertain due to limited genomic sequences and sampling bias in GISAID. The three Guangzhou sequences have accumulated several novel mutations, suggesting the local transmission of Mpox may have been ongoing for some time. Based on the daily cases during the early stage of Mpox outbreak in four other countries, the number of possible infected cases in Guangzhou is inferred to be more than 300, suggesting that swift and efficient control measures must be implemented to mitigate the risk of a potential epidemic.

The present study aimed to investigate an outbreak of Theileria annulata (T. annulata) infection in an organized dairy cattle farm in Madhya Pradesh, India, using clinical and molecular techniques. Following the deaths of two crossbred cattle in March 2021, 43 blood samples were collected from infected and apparently healthy animals and examined by blood smear and polymerase chain reaction (PCR) techniques. The blood smear examination showed that 23.25% of samples were positive for Theileria organisms, while conventional PCR targeting the 18S ribosomal RNA (18S rRNA) and T. annulata merozoite surface antigen-1 (TAMS-1) genes revealed that 32.55% of samples were positive for T. annulata. PCR targeting cytochrome b (Cytb) gene showed 46.51% of samples were positive for T. annulata. Haematological analysis confirmed clinical signs of infection in affected animals, which were treated with buparvaquone @ 2.5 mg/kg body weight intramuscularly along with supportive medicine. Two 18S rRNA gene amplicons were sequenced and analysed in a phylogenetic tree and haplotype network with 54 Indian and 38 foreign sequences. The phylogenetic tree revealed two groups with a high posterior probability and bootstrap value, while the haplotype network revealed 35 haplotypes, with haplotype 1 (H1) being the most abundant and several single haplotypes clustering around it, indicating fast and widespread expansion. Genetic diversity indices and neutrality tests confirmed that the population was expanding. These studies highlight the significance of prompt and precise diagnosis and management of T. annulata outbreaks and provide insights into its evolutionary history and population dynamics of T. annulata in India, which could aid improving disease preventive and control strategies. [ABSTRACT FROM AUTHOR]

Sthenoteuthis oualaniensis is known for its complex population structure with three major transoceanic forms (viz. middle‐sized, dwarf, and giant forms) whose taxonomic status has been disputed for decades. This integrated taxonomic study examines these prevenient morphotypes gathered on cruises in the Indian Ocean to ascertain their status in the evolutionary history of the species. Molecular analyses employing mitochondrial (COI, ND2) and nuclear (H3) markers revealed four genetically distinct and novel lineages of the species in the Indian Ocean, representing three morphotypes from the Arabian Sea and one from the Southern Indian Ocean. The mitochondrial‐based phylograms revealed two distinct clades in the species: "dwarf forms + giant form" and "middle‐sized forms," which further branch into geographically structured evolutionary units. Species delimitation analyses recovered five distinct clades, namely, the Arabian Sea giant and dwarf forms, Equatorial, Eastern Typical, and Other Middle‐sized forms, representing the consensus molecular operational taxonomic units. H3 being heterozygous could not resolve the phylogeny. Haplotype network and AMOVA analysis of mtDNA genes indicated explicit phylogeographic structuring of haplotypes, whereas these outputs and PCA results were incongruent with the morphological grouping. Phenetic features distinguishing the morphotypes were sometimes plastic and mismatched with the genotypes. The giant form was genetically close to the dwarf forms, contradicting the earlier notion that it descended from the middle‐sized form. It may be assumed that the dwarf form evolved following sympatric speciation and adaptation to warm equatorial waters, while the focal features of the Western Arabian Sea guide toward allopatric speciation of the giant form. [ABSTRACT FROM AUTHOR]