Pairwise Genetic Distances Research Articles

Molecular transmission clusters in newly HIV-1 diagnosed migrants in Portugal from 2014 to 2019

Abstract Background Portugal has an important HIV burden with a total of 804 diagnosed cases in 2022. Migrants remain a significant source of HIV infections, with 45% of newly reported cases. We aimed to evaluate the characteristics of HIV-1 molecular transmission clusters (MTCs) among migrants followed in Portugal, diagnosed between 2014 and 2019. Methods 265 migrants, newly HIV-1 diagnosed were included in the BESTHOPE project with clinical, socio-behavioral and genomic data. Pol nucleotide-based phylogenetic analyses were used to infer HIV-1 MTC. Those were constructed using ClusterPickerGUI_1.2.3 considering SH-aLRT higher than 90 of branch support and a pairwise genetic distance of ≤ 4.5. Logistic regression analyses were used to examine the relationship between the sociodemographic and clinical data associated with HIV-1 clustering. Results 66.8% of the migrants included in the study were males with a median age at diagnosis of 36.0 years old (IQR:29-45). Most migrants were from African countries (50.6%) followed by Brazil (39.6%). Sixty-eight (33%) of the migrants were included in clusters. Being in cluster was significantly associated with region of origin, with individuals from South America more likely to be in cluster (OR = 14.85, 95%CI:1.52-144.79), compared to individuals from Africa; with transmission route, with men who have sex with men (MSM) more likely to be in cluster (OR = 23.52, 95%CI:2.35-235.10), compared to the heterosexuals and with subtype, with subtypes B less likely to be in cluster (OR = 0,017, 95%CI:0,001-0,254) compared with subtype non-B. Conclusions Migrants HIV transmission clusters in Portugal are associated with specific health determinants, such as region of origin, transmission route and subtype. Targeted prevention health strategies are needed to mitigate transmission of HIV within this population. Funded by FCT to GHTM - UID/04413/2020 and LA-REAL - LA/P/0117/2020; BESTHOPE (HIVERA:249697); and MARVEL (PTDC/SAU-PUB/4018/2021). Key messages • HIV transmission clusters in migrant are associated with their region of origin, transmission route and subtype. • Targeted prevention health strategies are needed for the migrant population.

Genetic Diversity Losses in Mantis Shrimp Oratosquilla oratoria Offspring Created for Supportive Releases Using an Ecological Breeding in Earthen Pond Method

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

Influence of Sires on Population Substructure in Dülmen Wild Horses.

The objectives of the present study were to analyze the influence of the stallions employed in the Dülmen wild horses on the genetic diversity and population substructure using Bayesian cluster analysis. The Dülmen wild horse is maintained as a unique horse population exposed to the natural conditions all year round in the Merfelder Bruch near Dülmen in Westphalia, Germany. Stallions selected for breeding have to prove their abilities to survive under this harsh environment. We used multilocus genotypic information from a set of 29 autosomal microsatellites to determine the paternity of 185 male foals sired by nine stallions. As females could not be sampled, we could not make inferences on all yearlings and test whether there are differences in the genetic population parameters between both sexes. The mean number of progeny was 19.92 with a range of 2-32, caused by the length of the service period per stallion. The average observed and unbiased expected heterozygosity was 0.688 and 0.631, the mean number of alleles was 4.448, and Wright's FIS was -0.173. Pairwise genetic distances (FST and Nei's unbiased genetic distances) were significant and varied between 0.038 to 0.091 and 0.085 to 0.290, respectively. Neighbor-joining dendrogram plots clustered a large proportion of the paternal progeny groups in different branches. Posterior Bayesian analyses using seven paternal half-sib groups with 10-74 members supported a maximum of six clusters, with two paternal progeny groups not differing, and a median of five clusters, with two groups of two sires each falling into the same clusters. When sires were employed in non-consecutive years, progeny from these different years of the same sires were grouped in the same cluster, whereas the progeny of one sire from two consecutive years were in different clusters. We were able to distinguish male progeny from Dülmen wild horse stallions and to show the effects of stallion use on the genetic substructure in the Dülmen wild horse herd. In conclusion, the analyses showed the genetic potential of the Dülmen wild horse stallions to maintain a high genetic diversity and also the effects in which breeding seasons and for how long stallions are used to sire foals. The selection of stallions may be sensitive for the further development of genetic diversity and preserve this closed population as a valuable resource for further studies on the evolution of the horse.

A new species within the Enteromius kerstenii complex (Actinopterygii, Cyprinidae, Smiliogastrinae) from south-western Ethiopia

A new species of small-sized smiliogastrin barb, Enteromius gamo sp. nov., is described from tributaries to lakes Abaya and Chamo in south-western Ethiopia. The new species belongs to a readily diagnosable group commonly identified as E. kerstenii, exhibiting a thickened and serrated last unbranched ray in the dorsal fin, a low number of scales in the lateral series (≤ 27), and a yellow, orange or reddish blotch on operculum. Pairwise genetic distances between the new species from Ethiopia and specimens of E. kerstenii from close to the type locality in north-eastern Tanzania were 7.5–8.3 % (COI) and 8.9–10.1 % (cytb). Enteromius gamo sp. nov. is morphologically distinguished from E. kerstenii and all examined congeners from Tanzania, Kenya, and Uganda primarily by short anterior (15.8–35.1 %, mean 27.4 %, of snout length) and posterior (63.2–95.7 %, mean 81.0 %, of snout length) barbels. The new species is known only from wetlands and side channels of rivers (Hare, Sile, and Sago) along the western shores of lakes Abaya and Chamo.

Genomic and Spatial Analysis on the Recent Transmission of Mycobacterium tuberculosis in Eastern China: A 10-Year Retrospective Population-Based Study.

Understanding the mode of Mycobacterium tuberculosis (M. tuberculosis) transmission is crucial for disease prevention and control. Compared to traditional genotyping methods, whole genome sequencing (WGS) provides higher resolution and comprehensive genetic information, enabling the tracing of infection sources and determining of transmission routes to resolve extensive tuberculosis (TB) outbreaks. We conducted a ten-year study on the transmission of M. tuberculosis in a population in eastern China. We selected Lianyungang, an eastern city in China, as the study site. Patients diagnosed with active pulmonary TB from 2011 to 2020 were enrolled as the study subjects. We isolated and sequenced 2252 M. tuberculosis. Strains with pairwise genetic distances of less than 12 single nucleotide polymorphisms were defined as genomic clusters and which were considered recent transmissions. Kernel density estimation and K-function analysis were applied to explore the spatial distribution of recently transmitted strains. After excluding non-tuberculous mycobacteria and duplicated samples, 2114 strains were included in the final analysis. These strains comprised lineage 2 (1593, 75.35%) and 4 (521, 24.65%). There were 672 clustered strains, with a recent transmission rate of 31.79%. The logistic regression model showed that the risk of recent transmission was high in students [adjusted odds ratio (aOR): 2.68, 95% confidence interval (CI): 1.63-4.49, P<0.001] and people infected with L2.2.1 strains (aOR: 1.59, 95% CI: 1.20-2.12). Higher spatial aggregation of TB transmission has been concentrated in Haizhou, Donghai, and Guanyun for the past 10 years. Three outbreaks affecting 46 patients were spatially spaced, with 11 to 23 persons each. Different groups exhibited varying geographic distances between the initial and later cases. There are areas with a high risk of transmission for M. tuberculosis in the research site, and the risk varies among different populations. Accurate prevention strategies targeted at specific regions and key populations can help curb the prevalence of TB.

Dimensionality reduction distills complex evolutionary relationships in seasonal influenza and SARS-CoV-2.

Public health researchers and practitioners commonly infer phylogenies from viral genome sequences to understand transmission dynamics and identify clusters of genetically-related samples. However, viruses that reassort or recombine violate phylogenetic assumptions and require more sophisticated methods. Even when phylogenies are appropriate, they can be unnecessary or difficult to interpret without specialty knowledge. For example, pairwise distances between sequences can be enough to identify clusters of related samples or assign new samples to existing phylogenetic clusters. In this work, we tested whether dimensionality reduction methods could capture known genetic groups within two human pathogenic viruses that cause substantial human morbidity and mortality and frequently reassort or recombine, respectively: seasonal influenza A/H3N2 and SARS-CoV-2. We applied principal component analysis (PCA), multidimensional scaling (MDS), t-distributed stochastic neighbor embedding (t-SNE), and uniform manifold approximation and projection (UMAP) to sequences with well-defined phylogenetic clades and either reassortment (H3N2) or recombination (SARS-CoV-2). For each low-dimensional embedding of sequences, we calculated the correlation between pairwise genetic and Euclidean distances in the embedding and applied a hierarchical clustering method to identify clusters in the embedding. We measured the accuracy of clusters compared to previously defined phylogenetic clades, reassortment clusters, or recombinant lineages. We found that MDS embeddings accurately represented pairwise genetic distances including the intermediate placement of recombinant SARS-CoV-2 lineages between parental lineages. Clusters from t-SNE embeddings accurately recapitulated known phylogenetic clades, H3N2 reassortment groups, and SARS-CoV-2 recombinant lineages. We show that simple statistical methods without a biological model can accurately represent known genetic relationships for relevant human pathogenic viruses. Our open source implementation of these methods for analysis of viral genome sequences can be easily applied when phylogenetic methods are either unnecessary or inappropriate.

Intra- and inter-subtype HIV diversity between 1994 and 2018 in southern Uganda: a longitudinal population-based study.

There is limited data on human immunodeficiency virus (HIV) evolutionary trends in African populations. We evaluated changes in HIV viral diversity and genetic divergence in southern Uganda over a 24-year period spanning the introduction and scale-up of HIV prevention and treatment programs using HIV sequence and survey data from the Rakai Community Cohort Study, an open longitudinal population-based HIV surveillance cohort. Gag (p24) and env (gp41) HIV data were generated from people living with HIV (PLHIV) in 31 inland semi-urban trading and agrarian communities (1994-2018) and four hyperendemic Lake Victoria fishing communities (2011-2018) under continuous surveillance. HIV subtype was assigned using the Recombination Identification Program with phylogenetic confirmation. Inter-subtype diversity was evaluated using the Shannon diversity index, and intra-subtype diversity with the nucleotide diversity and pairwise TN93 genetic distance. Genetic divergence was measured using root-to-tip distance and pairwise TN93 genetic distance analyses. Demographic history of HIV was inferred using a coalescent-based Bayesian Skygrid model. Evolutionary dynamics were assessed among demographic and behavioral population subgroups, including by migration status. 9931 HIV sequences were available from 4999 PLHIV, including 3060 and 1939 persons residing in inland and fishing communities, respectively. In inland communities, subtype A1 viruses proportionately increased from 14.3% in 1995 to 25.9% in 2017 (P < .001), while those of subtype D declined from 73.2% in 1995 to 28.2% in 2017 (P < .001). The proportion of viruses classified as recombinants significantly increased by nearly four-fold from 12.2% in 1995 to 44.8% in 2017. Inter-subtype HIV diversity has generally increased. While intra-subtype p24 genetic diversity and divergence leveled off after 2014, intra-subtype gp41 diversity, effective population size, and divergence increased through 2017. Intra- and inter-subtype viral diversity increased across all demographic and behavioral population subgroups, including among individuals with no recent migration history or extra-community sexual partners. This study provides insights into population-level HIV evolutionary dynamics following the scale-up of HIV prevention and treatment programs. Continued molecular surveillance may provide a better understanding of the dynamics driving population HIV evolution and yield important insights for epidemic control and vaccine development.

Genetic Diversity and Population Structure of Dülmen Wild, Liebenthal and Polish Konik Horses in Comparison with Przewalski, Sorraia, German Draught and Riding Horses.

The objective of the present study was to analyze the genetic diversity, individual-based assessment of population structure, and admixture in the Dülmen wild horse population in comparison to warmblood, coldblood, and primitive horse populations. The Dülmen wild horse is kept as a unique horse population in the Merfelder Bruch near Dülmen in Westphalia, Germany, and since 1856 has been managed by the Dukes of Croÿ. The Dülmen wild horse population is exposed to the natural conditions of the Merfelder Bruch all year round without human interventions for feeding and veterinary care. In the present study, genetic diversity was estimated for 101 Dülmen wild horses using multilocus genotypic information from a set of 29 autosomal microsatellites and compared with 587 horses from 17 different horse populations. Dülmen wild horses maintained a high degree of genetic diversity, with an average observed heterozygosity of 0.68, a mean number of 6.17 alleles, and heterozygote deficit of -0.035. Pairwise genetic distances (FST, Nei's standard, and Cavalli-Sforza distances) were closest to German coldblood breeds, Polish Konik, and Icelandic horses and most divergent from Sorraia and Przewalski's horses. Neighbor joining dendrogram and PCA plots showed a clear distinction of Dülmen wild horses from other populations, particularly from Przewalski horses. Posterior Bayesian analysis confirmed clear differentiation from other horse populations without an admixture pattern and a high membership index (0.92). It was possible to distinguish Dülmen wild horses from Dülmen and Polish Konik horses. In conclusion, Dülmen wild horses show a notable separation from other German horse breeds and primitive horse populations and may serve as a resource to study evolution of equine domestication.

Asian Mus musculus: subspecies divergence, genetic diversity, and historical biogeography

Abstract The House Mouse, Mus musculus, is a model organism that has greatly contributed to evolutionary research. Despite its significance, there remain gaps in our understanding of its phylogeography and population genetic structure in Asian regions. This comprehensive study aims to elucidate the evolutionary history, genetic diversity, and distribution patterns of M. musculus. A diverse data set of 281 M. musculus samples was collected from across Asia, covering 101 localities in 19 countries. Phylogenetic analysis using Cytochrome b and D-Loop region unveiled well-supported lineages. These lineages correspond to: M. m. musculus, M. m. domesticus, M. m. castaneus, and M. m. bactrianus. Also, validity of M. m. bactrianus was questioned. The analysis suggests a monophyletic origin of these subspecies approximately 0.59 million years ago (Mya), followed by 2 main lineages—one consisting of M. m. domesticus (~0.59 Mya) and the other comprising M. m. castaneus, M. m. bactrianus, and M. m. musculus (~0.56 Mya). Genetic diversity varied among subspecies, with M. m. domesticus exhibiting the highest diversity due to its extensive global distribution and M. m. bactrianus exhibiting the lowest diversity due to restriction in southwest Asia. Pairwise genetic distances and Fst values confirmed significant genetic differentiation among the subspecies, underlining their historical isolation. Additionally, a Mantel test indicated that geographical distance played a pivotal role in shaping genetic differentiation. Demographic analysis revealed evidence of population expansions in M. m. domesticus, M. m. musculus, and M. m. castaneus, while M. m. bactrianus showed characteristics of neutral selection and genetic drift. Species distribution modeling, assessing both Current Conditions and the Last Glacial Maximum, indicated habitat shifts and losses during glacial periods, particularly in the eastern and northern regions of Asia. However, each subspecies displayed unique responses to climatic changes, reflecting their distinct ecological adaptations. Historical biogeography analysis pointed to complex origins and a network of dispersal and vicariance events that led to the contemporary distribution of subspecies. Deserts and xeric shrublands emerged as critical areas for diversification and speciation. This study contributes to our understanding of the phylogeography and population genetics of M. musculus in Asia, highlighting the significance of geographical factors and climatic fluctuations in shaping its evolutionary history and genetic diversity.

Y-chromosome analysis recapitulates key events of Mediterranean populations

The remarkable geographical situation of the Mediterranean region, located between Europe, Africa, and Asia, with numerous migratory routes, has made this area a crucible of cultures. Studying the Y-chromosome variability is a very performant tool to explore the genetic ancestry and evaluate scenarios that may explain the current Mediterranean gene pool. Here, six Mediterranean populations, including three Balearic Islands (Ibiza, Majorca, and Minorca) and three Southern Italian regions (Catanzaro, Cosenza, and Reggio di Calabria) were typed using 23 Y-STR loci and up to 39 Y-SNPs and compared to geographically targeted key reference populations to explore their genetic relationship and provide an overview of Y-chromosome variation across the Mediterranean basin. Pairwise RST genetic distances calculated with STRs markers and Y-haplogroups mirror the West to East geographic distribution of European and Asian Mediterranean populations, highlighting the North-South division of Italy, with a higher Eastern Mediterranean component in Southern Italian populations. In contrast, the African populations from the Southern coast of the Mediterranean clustered separately. Overall, these results support the notion that migrations from Magna Graecia or the Byzantine Empire, which followed similar Neolithic and post-Neolithic routes into Southern Italy, may have contributed to maintaining and/or reinforcing the Eastern Mediterranean genetic component in Southern Italian populations.

First Insight into the Phylogenetic Diversity of Bovicola caprae Infesting Goats of Different Agro-climatic Locations in India.

Bovicola caprae is an important obligate ectoparasite of goats worldwide including India. The present study aimed at the molecular confirmation, phylogenetics and population structure analyses of B. caprae infesting goats of three different agro-climatic locations in India, by targeting the mitochondrial cytochrome C oxidase subunit 1 (cox1) genetic marker. The phylogenetic tree exhibited the presence of two different lineages of B. caprae. The sequences generated herein clustered in lineage 2 along with theGenBank™ archived sequences from China and Iran. The sequences generated herein also showed the circulation of sub-lineages of B. caprae in India based on the analysis of pairwise genetic distances between sequences and median-joining haplotype network. The population structure analyses revealed low nucleotide (0.00353 ± 0.00291 and 0.02694 ± 0.00363) and high haplotype (0.667 ± 0.314 and 0.618 ± 0.104) diversities for the present study isolates as well as for the complete dataset, respectively, which evinced a recent demographic expansion. High genetic differentiation (FST value = 0.97826) and low gene flow (Nm = 0.00556) were also recorded in the different lineages/populations. In conclusion, the present study addressed the research gap and provided the first insight into the phylogenetics of the goat louse B. caprae and highlighted the circulation of sub-lineages of the ectoparasite in India.

Tiwaripotamon keeae sp. nov. (Crustacea: Decapoda: Potamidae), a new miniature species of freshwater crab from the China-Vietnam border in Napo, Guangxi

A new miniature species of freshwater crab from the genus Tiwaripotamon Bott, 1970 (Potamidae), is described from a montane karst area in southern Napo, at the China-Vietnam border. It is the twelfth known species of the genus, and is also the smallest known, with the largest adult specimen observed barely exceeding 20 mm in carapace width. Apart from the small size, features of the eyes, carapace and ambulatory legs further set Tiwaripotamon keeae sp. nov. apart from its congeners. Pairwise genetic distances of the mitochondrial cytochrome oxidase subunit I (COI) gene also support it as a distinct species.

Genetic Links between Reproductive Traits and Amino Acid Pairwise Distances of Swine Leukocyte Antigen Alleles among Mating Partners in Microminipigs.

Previously, we found that a greater dissimilarity in swine leukocyte antigen (SLA) class I and class II alleles between mating partners resulted in increased farrowing rates in a highly inbred population of Microminipigs (MMPs). In this follow-up study, we have analyzed the effects of dissimilarity in SLA alleles between mating partners for seven different reproductive traits, including litter size and the number of stillborn and live or dead weaned piglets. We determined the relationships among reproductive traits within each mating event and the amino acid distances of SLA alleles as markers of diversity between mating partners. Our results indicate that mating partners with greater amino acid pairwise genetic distances in the SLA-1 class I gene or DQB1 class II gene alleles were associated with significantly larger litter sizes and higher numbers of live piglets at birth and weaning. Also, partners with greater pairwise distances in the SLA-2 class I gene alleles exhibited fewer pre-weaning deaths. These findings suggest that the dissimilarity in SLA class I and class II alleles between mating partners may affect not only farrowing rates but also other key reproductive traits such as litter size and improved piglet survival rates. Consequently, SLA alleles could serve as valuable genetic markers for selecting mating partners in breeding programs and for conducting epistatic studies on various reproductive traits in MMPs.

Genetic landscape of the people of Bangladesh depicted with 17 Y-Chromosome-Specific microsatellites

Seventeen microsatellite loci from the non-recombining region of the human Y chromosome were typed using AmpFlSTR® Yfiler® PCR amplification systems in 404 male subjects belonging to the three largest ethnic groups in Bangladesh. A total of 150 haplotypes from the Chakma, 144 from the Tripura, and 110 from the Khasia were detected with a corresponding discrimination capacity of 73.885%, 65.563%, and 81.250%, respectively. The highest allele frequency of 0.828 was detected in DYS391 locus in the Tripuras, while the lowest allele frequency of 0.009 was detected at the same locus for the Chakma population. The highest gene diversity (0.964) was observed at DYS385a/b locus in the Khasias, while the lowest gene diversity (0.301) was detected at DYS391 locus in Tripuras population. The overall haplotype diversity for the studied populations was 0.986141. Both the Neighbour-Joining tree and pairwise genetic distances showed that Chakma lies closer to a clade consisting of Tripuras (Khagrachari, Bangladesh) and Tripuri (Tripura, India). In contrast, the Khasias demonstrated a close affinity with the Oraon (Chhattisgarh, India), followed by the Santals. The Y-STR haplotype matching probabilities within and between populations demonstrated that the Chakma, Tripura, and Khasia were 100% genetically distinct. The studied ethnic populations exhibited higher frequency for haplogroups L and Q as opposed to haplogroups R1a, H, and L found in the mainstream Bengali population. The Median-joining networking showed haplogroups L and R1a have the most compact clustering within populations, followed by haplogroups Q and H. The presence of haplogroup R1a suggests that Bengali may have originated through west-to-east migration, whereas haplogroups L and Q distribution in the studied tribes reveal a very significant affinity with the South-East Asian populations and may have shared a common ancestral origin with the Mongoloid stock populations. Bioresearch Commu. 10(2): 1482-1488, 2024 (July)

First record of Garra kempi Hora, 1921 (Cypriniformes: Cyprinidae) from Lohandra River of Nepal

Nepal holds a high ichthyofaunal diversity, nevertheless, the molecular study of Nepalese fish is still in its early stages. The first record of a cyprinid fish species the Garra kempi Hora, 1921 for Nepal was reported from eastern Nepal’s Lohandra River. Both morphology and molecular data affirmed the existence of G. kempi in Nepal’s aquatic system. This species was previously reported from China (Tibet) and northern India. The maximum likelihood phylogenetic analysis and pairwise genetic distance based on Kimura 2 parameters using cytochrome oxidase subunit 1 (COI) segment sequences (665 bp) also confirmed the identity of the species as G. kempi. The COI sequences of specimens from Nepal formed a monophyletic clade with the sequence of G. kempi from northeastern India and the two contained a pairwise genetic distance of 1.8% only. The new record of G. kempi from Nepal warrants a detailed ichthyofaunal survey for documenting the fish diversity in Nepal.

Description of a new species of Andricus Hartig, 1840 (Hymenoptera: Cynipidae: Cynipini) from China

A new species of gall wasp, Andricus wugangensis Zeng, Liu, &amp; Zhu sp. nov. is described and illustrated herein from Hunan Province, China. The new species is most similar to A. wuhanensis Ide, Abe, Su &amp; Zhu and A. xishuangbanaensis Melika &amp; Tang in morphology but can be easily distinguished by having 1) a large V-shaped carina on the lower face and 2) a broad transverse depression spanning the region between the inner margin of the eyes on the upper face. The results of a phylogenetic analysis and pairwise genetic distance comparison, based on COI sequences, were consistent with the conclusion of the comparative morphological assessment of the similar species: A. wuganensis, A. wuhanensis and A. xishuangbanaensis, although the morphological differences are more obvious than the small genetic distance of the COI sequences, which is 4.3% and 3% between the new species and A. wuhanensis and A. xishuangbanaensis, respectively. Additionally, a taxonomic key to the known species of Andricus from China is provided.

Two new species of groundwater-inhabiting amphipods belonging to the genus Niphargus (Arthropoda, Crustacea), from Iran

In Iran, the Elburz and Zagros Mountain ranges include substantial karst regions housing numerous aquifers and groundwater resources. Niphargus Schiødte, 1849, a diverse subterranean amphipod genus, inhabits Western Palearctic groundwater environments, with Iran marking the eastern limit of its distribution. This study examined specimens collected from springs along the Elburz and Zagros Mountains, revealing two distinct taxonomic units through a combination of morphological observations and molecular analyses, utilizing COI and 28S rDNA genes. N. elburzensissp. nov. is characterized by produced epimeral plates I to III; a telson lobe with five distal, two lateral, and one mesial spine each, a rectangular shape of gnathopod II propodi with two L-setae on palmar corner and maxilla I outer plate spines with 2-2-1-1-3-0-1 denticles. N. zagrosensissp. nov. is distinguished by a triangular shape gnathopod II propodi, pereopod VI longer than pereopod VII, maxilliped outer plate less than half of palp article 2, and uropod III distal article exceeding 80% of the proximal article. Pairwise genetic distances between N. elburzensissp. nov. and other species ranged from 10.70% (N. fiseri) to 23.48% (N. daniali) for COI gene and 1.56% (N. urmiensis) to 10.98% (N. daniali) for 28S gene. Also, N. zagrosensissp. nov. exhibited COI gene distances from 5.73% (N. alisadri) to 20.66% (N. daniali) and from 0.13% (N. alisadri) to 11.36% (N. daniali) for 28S gene distances. Bayesian analysis suggests that the two newly discovered species are part of the expansive local Iranian clade. These species are supported phylogenetically by separate and independent lineages, as indicated by high bootstrapping values.

Genetic diversity in Pima (Gossypium barbadense L.) and advanced interspecific hybrids (Gossypium hirsutum x Gossypium barbadense) of cotton germplasm in Ethiopia

This study was conducted to assess the genetic diversity in Pima (Gossypium barbadense L.) and advanced interspecific hybrids (G. hirsutum L. x G. barbadense L.) of cotton germplasm in Ethiopia. A total of 26 germplasm were genotyped using 26 polymorphic simple sequence repeat (SSR) markers. A total of 165 polymorphic loci, with a range of 3 to 13 alleles and a mean of 6.35 per marker were detected. About 11% of total alleles were unique alleles in 11 germplasm. The gene diversity varied from 0.39 to 0. 89, while the heterozygosity was in the range of 0 to 1.00. Furthermore, the polymorphic information content of the markers varied from 0.37 (BNL1417) to 0.88 (BNL1672) with an average of 0.68. Among the complete panel of cotton germplasm used in this study, the pairwise genetic distance ranged from 0.08 to 0.94, with an overall mean of 0.61. The UPGMA cluster analysis grouped the Pima cotton germplasm into two cluster groups and the advanced interspecific hybrid cotton germplasm makes one cluster. Principal coordinate analysis indicates that the first three most informative principal coordinates explained 68.4% of the genetic variation. The result evidenced very low to high genetic dissimilarity and overall, a considerable genetic diversity among and within germplasm which could be used to further broaden the genetic base and to enlarge the number of available cotton germplasm.

Oxynoemacheilus fatmae, a new species from the Güzelhisar Stream in the Aegean Sea basin, Türkiye (Teleostei: Nemacheilidae).

Oxynoemacheilus fatmae, a new species, is found in the Güzelhisar Stream in the northern Aegean Sea basin. It is differentiated from all other species of Oxynoemacheilus in the northern Aegean Sea and adjacent basins by having four to eight irregularly shaped narrow black bars on the posterior part of flank, and anterior parts of the flank with a marbled pattern. O. fatmae is differentiated from the closest species Oxynoemacheilus theophilii by having 14 fixed diagnostic nucleotide substitution sites, and the pair-wise genetic distance is 2.22%. It further differs from O. theophilii by having a slenderer body (body at dorsal-fin origin: 15%-17% standard length [SL] vs. 17%-18%), a slenderer caudal peduncle (10%-12% SL vs. 12%-13%), a more forked caudal fin (length of middle caudal-fin lope: 16%-19% SL vs. 19%-23%), and the absence the dorsal and ventral adipose crests on the caudal peduncle behind the vertical of the posterior anal-fin base (vs. present). Three species delimitation tests (assemble species by automatic partitioning (ASAP), automatic barcode gap discovery (ABGD) and generalized mixed yule-coalescent (GMYC)) and phylogenetic analyses reinforce the validity of O. fatmae as a distinct species.

Similar looking sisters: A new sibling species in the Pristimantis danae group from the southwestern Amazon basin (Anura, Strabomantidae)

We describe a new frog species that is the sibling of Pristimantis reichlei. These two sister species inhabit the Amazonian lowlands and adjacent foothills of the Andes, from central Bolivia to central Peru. Pristimantis reichlei occurs from central Bolivia to southern Peru (Alto Purús National Park), while the new species occurs from northern Bolivia (Departamento Pando) to Panguana in central Peru (Departamento Huánuco), at elevations between 220 and 470 m a.s.l. In spite of their morphological crypsis, these siblings occur in syntopy without evidence of interbreeding (in the Alto Purús area) and are recovered as reciprocally monophyletic. Their uncorrected pairwise genetic distances in the 16S rRNA gene range from 9.5–13.5%, and their advertisement calls differ in both qualitative and quantitative traits. Moreover, our study found uncorrected pairwise distances within the new species of up to 5.0% and up to 9.3% within P. reichlei. We therefore cannot rule out the possible existence of hybrids or additional species-level lineages hidden in this complex. Furthermore, we found another potential pair of sibling species composed of P. danae and an unnamed lineage, with divergences of 9.4% in the 16S gene, whose in-depth analysis and taxonomic treatment are pending future revision. With the new nominal species, the Pristimantis danae species group now includes 20 species, distributed across the upper Amazon basin and in the eastern Andes, from western Brazil to Bolivia and Peru. Our study, together with an increasing number of other studies, indicates that sibling species are far from being rare among Amazonian amphibians and that species resolution remains low even for groups that have received considerable attention in recent years.