Degree Of Genetic Differentiation Research Articles

RNA-Seq Transcriptome Analysis and Evolution of OsEBS, a Gene Involved in Enhanced Spikelet Number per Panicle in Rice.

Spikelet number per panicle (SNP) is one of the most important yield components in rice. Rice ENHANCING BIOMASS AND SPIKELET NUMBER (OsEBS), a gene involved in improved SNP and yield, has been cloned from an accession of Dongxiang wild rice. However, the mechanism of OsEBS increasing rice SNP is poorly understood. In this study, the RNA-Seq technology was used to analyze the transcriptome of wildtype Guichao 2 and OsEBS over-expression line B102 at the heading stage, and analysis of the evolution of OsEBS was also conducted. A total of 5369 differentially expressed genes (DEGs) were identified between Guichao2 and B102, most of which were down-regulated in B102. Analysis of the expression of endogenous hormone-related genes revealed that 63 auxin-related genes were significantly down-regulated in B102. Gene Ontogeny (GO) enrichment analysis showed that the 63 DEGs were mainly enriched in eight GO terms, including auxin-activated signaling pathway, auxin polar transport, auxin transport, basipetal auxin transport, and amino acid transmembrane transport, most of which were directly or indirectly related to polar auxin transport. Kyoto Encyclopedia of Genes and Genomes (KEGG) metabolic pathway analysis further verified that the down-regulated genes related to polar auxin transport had important effects on increased SNP. Analysis of the evolution of OsEBS found that OsEBS was involved in the differentiation of indica and japonica, and the differentiation of OsEBS supported the multi-origin model of rice domestication. Indica (XI) subspecies harbored higher nucleotide diversity than japonica (GJ) subspecies in the OsEBS region, and XI experienced strong balancing selection during evolution, while selection in GJ was neutral. The degree of genetic differentiation between GJ and Bas subspecies was the smallest, while it was the highest between GJ and Aus. Phylogenetic analysis of the Hsp70 family in O. sativa, Brachypodium distachyon, and Arabidopsis thaliana indicated that changes in the sequences of OsEBS were accelerated during evolution. Accelerated evolution and domain loss in OsEBS resulted in neofunctionalization. The results obtained from this study provide an important theoretical basis for high-yield rice breeding.

Small-scale population structure of eastern North Pacific harbour porpoises (Phocoena phocoena) indicated by molecular genetic analyses

Concern about the conservation and management of harbour porpoise (Phocoena phocoena) populations, which have experienced relatively large incidental fishery kills in localised areas throughout their range, has prompted research to better understand their population structure. Both mitochondrial and nuclear (microsatellites) DNA were used to examine the intra-specific structure of harbour porpoise inhabiting the eastern North Pacific Ocean. Null hypotheses of panmixia were tested after mitochondrial DNA (mtDNA) control region sequence data (402 base pairs; n = 249) and allele frequency data (9 polymorphic loci; n = 194) were sub-divided into geographic strata defined a priori. Strata were based on sampling discontinuities and not discontinuities in population distribution. The mtDNA and nuclear gene data revealed statistically significant genetic differentiation between most strata (a = 0.05) suggesting demographic independence of fairly small sub-units within the population. Since harbour porpoises are essentially continuously distributed in the eastern North Pacific, this degree of genetic differentiation was unexpected and needs to be considered in developing a sound management plan to protect them.

Genetic structure of Aedes albopictus (Diptera: Culicidae) populations in China and relationship with the knockdown resistance mutations

BackgroundMosquito control is needed to prevent dengue fever, which is mainly spread by Aedes albopictus in China. Application of insecticides is one of the main mosquito control methods; however, this approach can fail due to the knockdown resistance (kdr) gene mutation that causes decreased sensitivity to insecticides in Ae. albopictus. The kdr mutation patterns among different regions in China differ significantly. However, the underlying mechanism and factors that influence kdr mutation remain unclear. To explore the potential influence of genetic background on the development of insecticide resistance in Ae. albopictus, we analyzed the genetic structure of Ae. albopictus populations in China and its correlation with major kdr mutations.MethodsWe collected Ae. albopictus from 17 sites in 11 provinces (municipalities) across China from 2016 to 2021 and extracted the genomic DNA from individual adult mosquitoes. We selected eight microsatellite loci for genotyping, and based on microsatellite scores, we estimated intraspecific genetic diversity, population structure, and effective population size. The association between the intrapopulation genetic variation and F1534 mutation rate was evaluated by the Pearson correlation coefficient.ResultsBased on variation analysis of the microsatellite loci of 453 mosquitoes representing 17 populations throughout China, more than 90% of the variation occurred within individuals, whereas only about 9% of the variation occurred among populations, indicating that field populations of Ae. albopictus are highly polymorphic. The northern populations tended to belong to gene pool I (BJFT 60.4%, SXXA 58.4%, SDJN 56.1%, SXYC 46.8%), the eastern populations tended to belong to pool III (SH 49.5%, JZHZ 48.1%), and the southern populations tended to belong to three different gene pools. Moreover, we observed that the greater the fixation index (FST), the lower the wild-type frequency of F1534 of VSGC.ConclusionsThe degree of genetic differentiation among Ae. albopictus populations in China was low. These populations were divided into three gene pools, in which the northern and eastern pools are relatively homogeneous, while the southern gene pool is heterogeneous. The possible correlation between its genetic variations and kdr mutations is also noteworthy.Graphical

Genetic Diversity and Population Differentiation of a Chinese Endangered Plant Ammopiptanthus nanus (M. Pop.) Cheng f.

Ammopiptanthus nanus (M. Pop.) Cheng f. is a very important resource plant that integrates soil and water conservation, afforestation of barren mountains, and ornamental, medicinal, and scientific research functions and is also a critically endangered plant in China, remaining in only six small fragmented populations in the wild. These populations have been suffering from severe anthropomorphic disturbances, causing further losses in genetic diversity. However, its genetic diversity level and genetic differentiation degree among the fragmented populations are still unclear. Inthis study, DNA was extracted from fresh leaves from the remnant populations of A. nanus, and the inter-simple-sequence repeat (ISSR) molecular marker system was used to assess its level of genetic diversity and differentiation. The result was that its genetic diversity is low at both species and population levels, with only 51.70% and 26.84% polymorphic loci, respectively. The Akeqi population had the highest genetic diversity, whereas the Ohsalur and Xiaoerbulak populations had the lowest. There was significant genetic differentiation among the populations, and the value of the genetic differentiation coefficient (Gst) was as high as 0.73, while the gene flow value was as low as 0.19 owing to spatial fragmentation and a serious genetic exchange barrier among the populations. It is suggested that a nature reserve and germplasm banks should be established as soon as possible for elimination of the anthropomorphic disturbances, and mutual introductions between the populations and introduced patches of the species, such as with habitat corridors or stepping stones, should be performed simultaneously to improve the genetic diversity of the isolated populations for the conservation of this plant.

New insights into the genetic structure of the outbreak-prone bamboo grasshoppers

IntroductionThe genetic structure of species is shaped by natural (e.g., terrain, climate) and non-natural (e.g., human activities) factors. Geographical isolation and natural barriers are important causes of genetic structure formation of species. Here, we explored this issue in bamboo grasshopper, Ceracris kiangsu, which is an important pest that feeds on bamboo in East and Southeastern Asia.MethodsBased on 186 newly sequenced and 286 previously sequenced mitochondrial COI fragments, and 8 nuclear microsatellite loci, we examined the genetic diversity and population genetic structure of C. kiangsu.ResultsThe degree of genetic differentiation among populations was also high, and Mantel test showed that it was significantly correlated with geographical distance. Principal coordinate analysis and STRUCTURE results revealed two genetically different groups, a South China (S-China) Group and a Southeast Asia (SE-Asia) Group. Climate variables partly explained the population genetic structure. The demographic history and ABC showed that the S-China Group experienced population expansion, whereas the SE-Asia Group was consistently stable.DiscussionOur study demonstrates an obvious population structure maintained in this migratory insect and reveals the potential effect of past climatic change, geographical isolation, and ecological factors on the evolution of their genetic structure.

An expanded description, natural history, and genetic variation of the recently described cobra species Naja fuxi Shi et al., 2022

The morphological variation, extended distribution, and sequence divergence of a recently described of cobra Naja fuxiShi et al., 2022 captured from mountainous areas in Thailand are evaluated by using molecular and morphological analyses. We investigated the genetic variation and affinities of 72 specimens in the genus Naja by using mitochondrial DNA (cytochrome b and control region) and the nuclear DNA gene, C-mos. Morphological examination was conducted for 33 cobra specimens obtained from the northern, western, and north-eastern regions, and data on their natural history were gathered during field surveys. A high degree of genetic differentiation was shown to exist between the cobras collected from lowlands and those from mountainous areas. N. fuxi occurs in uplands bordering Thailand’s Central Basin, whereas the similar looking N. kaouthia Lesson, 1831 is more or less restricted to the lowlands. All phylogenetic and network analyses supported a distinct clade of N. fuxi from north, west, and, north-east regions. In addition, N. fuxi seems to exhibit a split between the north-eastern population and those from the north and west. The range of N. fuxi probably extends far into the mountainous areas of the neighbouring countries Myanmar, Laos, and Vietnam. Morphologically, N. fuxi in Thailand can be distinguished from all other cobra species in the adjacent Oriental Region. The speciation of cobras in Thailand likely reflects key events in the region’s geographical, climate and environmental history.

Population dynamics and genome-wide selection scan for dogs in Chernobyl

BackgroundNatural and anthropogenic disasters can have long-lasting impacts on the genetics and structure of impacted populations. The 1986 Chernobyl Nuclear Power Plant disaster led to extensive contamination of the local environment and the wildlife therein. Several ecological, environmental, and genetic studies reported various effects of this disaster on animal, insect, and plant species; however, little work has been done to investigate the genetics of the free-breeding dogs that occupy the Chernobyl Exclusion Zone (CEZ).ResultsWe define the population genetic structure of two groups of dogs that reside within the CEZ, one around the reactor site itself and another living within Chernobyl City. We found little evidence of gene flow and a significant degree of genetic differentiation between the two populations dogs, suggesting that these are two distinct populations despite occupying areas located just 16 km apart. With an FST-based outlier analysis, we then performed a genome-wide scan for evidence of directional selection within the dog populations. We found 391 outlier loci associated with genomic regions influenced by directional selection, from which we identified 52 candidate genes.ConclusionsOur genome scan highlighted outlier loci within or near genomic regions under directional selection, possibly in response to the multi-generational exposure faced. In defining the population structure and identifying candidate genes for these dog populations, we take steps towards understanding how these types of prolonged exposures have impacted these populations.

Genetic relationships among laboratory lines of the egg parasitoid Trissolcus japonicus from native and adventive populations

Candidate biological control agents of invasive insect pests are increasingly being found in new geographic regions as a result of unintentional introductions. However, testing the degree of genetic differentiation among adventive and native-range populations of these agents is rarely done. We used reduced-representation sequencing of genomic DNA to investigate the relationships among laboratory lines of Trissolcus japonicus (Ashmead) (Hymenoptera, Scelionidae), an egg parasitoid and biological control agent of the brown marmorated stink bug, Halyomorpha halys (Stål) (Hemiptera, Pentatomidae). We compared sequences from multiple adventive populations in North America (Canada, USA) and Europe (Switzerland) with populations sourced from part of its native range in China. We found considerably more genetic variation among lines sourced from adventive populations than among those within native populations. In the Pacific Northwest of North America (British Columbia, Canada and Washington State, USA), we found preliminary evidence of three distinct genetic clusters, two of which were highly dissimilar from all other lines we genotyped. In contrast, we found that other adventive lines with close geographic proximity (two from Ontario, Canada, three from Switzerland) had limited genetic variation. These findings provide a basis for testing biological differences among lines that will inform their use as biological control agents, and provide evidence to support a hypothesis of several independent introductions of T. japonicus in western North America from different source areas.

Photo-identification confirms that humpback whales (Megaptera novaeangliae) from eastern Australia migrate past New Zealand but indicates low levels of interchange with breeding grounds of Oceania

Recent photo-identification and genetic studies have identified at least five discrete breeding populations in Australia and Oceania: western Australia (D), eastern Australia (E (i)), New Caledonia (E (ii)), Tonga (E (iii)), French Polynesia and the Cook Islands (F). Also evident are low levels of intermingling among breeding populations consistent with the degree of genetic differentiation. Photo-identification has confirmed linkages between Area V feeding areas and eastern Australia breeding grounds and one genotype match has been reported between Area V feeding areas and Oceania breeding grounds. Recent abundance estimates show strong increases in the eastern Australian population, and some recovery in the New Caledonia and Tonga populations, but with little evidence of recovery at other known Oceania breeding grounds or New Zealand. Studies to date have provided no conclusive evidence of the migratory destination of humpback whales passing through New Zealand waters en route between Antarctic feeding areas and tropical breeding grounds. Photo-identification comparisons were undertaken between humpback whale fluke catalogues from eastern Australia (EA, 1315), Oceania east (OE, 513), Oceania west (OW, 166) and New Zealand (NZ, 13). Five matches were found between OE/OW, four matches between OW/EA and three matches between NZ/EA. The data are used to investigate and discuss the migratory destination and breeding ground migratory interchange of humpback whales travelling through New Zealand waters. The data confirm that humpback whales with site fidelity to eastern Australia migrate past New Zealand including through the Cook Strait and Foveaux Strait.

Mixed-stock analysis of humpback whales (Megaptera novaeangliae) on Antarctic feeding grounds

In understanding the impact of commercial whaling, it is important to estimate the mixing of low latitude breeding populations on Antarctic feeding grounds, particularly the endangered humpback whale populations of Oceania. This paper estimates the degree of genetic differentiation among the putative populations of Oceania (New Caledonia, Tonga, the Cook Islands and French Polynesia) and Australia (western Australia and eastern Australia) using ten microsatellite loci and mtDNA, assesses the power of the data for a mixed-stock analysis, determines ways to improve statistical power for future studies and estimates the population composition of Antarctic samples collected in 2010 south of New Zealand and eastern Australia. A large proportion of individuals could not be assigned to a population of origin (> 52%) using a posterior probability threshold of > 0.90. The mixed-stock analysis simulations however, produced accurate results with humpback whales reapportioned to their population of origin above the 90% threshold for western Australia, New Caledonia and Oceania grouped using a combined mtDNA and microsatellite dataset. Removing the Cook Islands, considered a transient region for humpback whales, from the simulation analysis increased the ability to reapportion Tonga from 86% to 89% and French Polynesia from 89% to 92%. Breeding ground sample size was found to be a factor influencing the accuracy of population reapportionment whereas increasing the mixture or feeding ground sample size improved the precision of results. The mixed-stock analysis of our Antarctic samples revealed substantial contributions from both eastern Australia (53.2%, 6.8% SE) and New Caledonia (43.7%, 5.5% SE) [with Oceania contributing 46.8% (5.9% SE)] but not western Australia. Despite the need for more samples to improve estimates of population allocation, our study strengthens the emerging genetic and non-genetic evidence that Antarctic waters south of New Zealand and eastern Australia are used by humpback whales from both eastern Australia and the more vulnerable breeding population of New Caledonia, representing Oceania.

Effects of Genetic Mutation Sites in ADR Genes on Modern Chickens Produced and Domesticated by Artificial Selection.

Associations between neurotransmitters, adrenergic receptor (ADR) mutations, and behaviors in chickens produced and domesticated by artificial selection remain unclear. This study investigates the association of neurotransmitters and ADR mutations with egg laying and cockfighting-behaviors associated with significantly different breeding backgrounds-in Shaver Brown and Shamo chickens. Accordingly, the whole sequences of nine ADR genes were determined, and nine amino acid-specific mutation sites from five genes (ADRα1A: S365G, ADRα1D: T440N, ADRα2A: D273E, ADRβ1: N443S, S445N, ADRβ3: R342C, Q404L, and P406S) were extracted. Evolutionary analysis showed that these mutations were not ancestrally derived. These results confirm that the mutations at these sites were artificially selected for domestication and are breed specific. NST population analysis confirmed a difference in the degree of genetic differentiation between the two populations in seven genes. The results further confirm differences in the degree of genetic differentiation between the two populations in Shaver Brown (ADRA1B and ADRA1D) and Shamo (ADRA1A and ADRA2B) chickens, indicating that the ADR gene differs between the two breeds. The effects of artificial selection, guided by the human-driven selection of desirable traits, are reflected in adrenaline gene mutations. Furthermore, certain gene mutations may affect domestication, while others may affect other traits in populations or individuals.

Genetic Diversity Analysis of Non-Heading Chinese Cabbage of Resistance to Clubroot Disease Based on SNP Molecular Markers

Clubroot disease is a kind of soil-borne disease that seriously infects Brassica species. In this study, we collected 121 varieties of non-heading Chinese cabbages. In order to better understand the genetic variation and to screen suitable clubroot disease-resistant parental material, we re-sequenced them to examine the population genetic structure, population genetic diversity, population differentiation index, and selective sweep based on SNPs. The mapping rate with the reference genome was high, and data quality analysis revealed that the sequencing quality was good. The annotated data indicated that intronic and intergenic areas held the majority of SNPs and indels. Four subgroups of 121 non-heading Chinese cabbages were identified using principal component analysis, phylogenetic tree, and genetic structure analysis. An examination of genetic diversity revealed that while selfing may happen in subgroups C and D, heterozygosity may exist in subgroups A and B. In subgroup B, self-fertilization is not possible. There was a moderate degree of genetic differentiation between subgroups B and C (Fst = 0.0744347). For genes in certain sweep regions, we also ran GO enrichment and KEGG enrichment analysis. Two disease resistance-related genes, BraA01g042910.3.5C and BraA06g019360.3.5C, were examined. These findings will serve as a theoretical foundation for developing novel, clubroot disease-resistant types of non-heading Chinese cabbages.

Genome‐wide RAD sequencing data suggest predominant role of vicariance in Sino‐Japanese disjunction of the monotypic genus Conandron (Gesneriaceae)

AbstractDisjunct distribution is a key issue in biogeography and ecology, but it is often difficult to determine the relative roles of dispersal vs. vicariance in disjunctions. We studied the phylogeographic pattern of the monotypic Conandron ramondioides (Gesneriaceae), which shows Sino‐Japanese disjunctions, with ddRAD sequencing based on a comprehensive sampling of 11 populations from mainland China, Taiwan Island, and Japan. We found a very high degree of genetic differentiation among these three regions, with very limited gene flow and a clear Isolation by Distance pattern. Mainland China and Japan clades diverged first from a widespread ancestral population in the middle Miocene, followed by a later divergence between mainland China and Taiwan Island clades in the early Pliocene. Three current groups have survived in various glacial refugia during the Last Glacial Maximum, and experienced contraction and/or bottlenecks since their divergence during Quaternary glacial cycles, with strong niche divergence between mainland China + Japan and Taiwan Island ranges. Thus, we verified a predominant role of vicariance in the current disjunction of the monotypic genus Conandron. The sharp phylogenetic separation, ecological niche divergence among these three groups, and the great number of private alleles in all populations sampled indicated a considerable time of independent evolution, and suggests the need for a taxonomic survey to detect potentially overlooked taxa.

Genetic diversity in - chilli (Capsicum annuum L.) based on microsatellite markers: An evaluation of Bangladeshi germplasm

Genetic diversity analysis is a pre-requisite to develop improve variety of any crop. Hence, 39 SSR markers were used to analyze the genetic diversity of local chilli cultivars. PCR-amplified microsatellite loci were shown to be polymorphic in all investigated cultivars. The locus, CAMS-647 produced the highest number of alleles (8) ranging in size from 188 to 279 bp. PIC values for 39 primers ranged from 0.099 for the locus Hpms 1-165 to 0.806 for the locus CAMS-679. All of the SSRs examined were informative in characterizing the genotypic variance of the samples while 12 were more informative with higher PIC values (> 0.6). There was a wide range of genetic diversity varied from 0.117 (HpmsE075) to 0.806 (CAMS-647), whereas the highest (1.713) and the lowest (0.205) value of Shannon’s Information Index was registered in the locus CAMS-679 and Hpms 1-165, respectively. There was a higher degree of genetic differentiation (0.927) and a lower amount of gene flow (0.010). Nei’s genetic distance (GD) varied from 0.100 to 0.990. Among 96 cultivars, 55 had distinct status in the dendrogram with higher GD values (> 0.6), while 41 cultivars showed a close relationship and yielded lower GD values.

High-throughput RNA sequencing and genetic structure studies of turnip mosaic virus infecting black and yellow mustard revealing emergence of world-B3 pathotype in India.

To study the evolution and host expansion of a TuMV for the first time in India using molecular population genetic framework. Here, we decipher the complete genome sequences of two TuMV world-B3 strains infecting yellow and black mustard in India through high-throughput RNA sequencing subjecting ribosomal RNA depleted mRNA isolated from leaves exhibiting puckering and mosaic symptoms with 100% incidence and high severity in the experimental field. The viral genomes of the two isolates were 9817 and 9829 nucleotides long. They featured two open reading frames (ORFs), one of which encoded a polyprotein comprised of 3164 amino acids and the other of which encoded a PIPO protein of 62 amino acids. The two TuMV strains from New Delhi region shared identity with the world-B pathotype and subpathotype world B3 showcasing its emergence first time in South Asia. In contrast, other isolates reported previously from South Asia were all Asian-BR pathotypes. According to our knowledge, this is the first instance of TuMV association with black mustard naturally. Their geographical prevalence justifies a lower degree of genetic differentiation and higher rate of gene flow calculated between the world-B and Asian-BR pathotypes. This study provides insights on population structuring, expansions and evolution, level of genetic heterogeneity and variability of worldwide prevalent isolates of TuMV which will further aid in understanding virus epidemiology and help prevent losses.

Analysis of genetic diversity among six dojo loach (Misgurnus anguillicaudatus) populations in the Pearl River Basin based on microsatellite and mitochondrial DNA markers

Due to environmental pollution and overfishing, the germplasm resources of wild loach (Misgurnus anguillicaudatus) have been degraded. To explore the genetic diversity of different geographical populations of loach in the Pearl River Basin, a total of 184 M. anguillicaudatus individuals from six dojo loach natural populations sampled from Yingde (Beijiang), Qingyuan (Beijiang), Liannan (Beijiang), Nanxiong (Dongjiang), Meizhou (Dongjiang), and Liuzhou (Liujiang) were investigated based on microsatellite DNA markers and mitochondrial DNA markers (cytb and D-loop). The results showed that a total of 71 alleles (Number of alleles, Na) were amplified in the six M. anguillicaudatus populations by 10 pairs of microsatellite primers. The average observed heterozygosity (Ho), expected heterozygosity (He), and polymorphic information content (PIC) among were 0.3892, 0.5101, and 0.4781, respectively. The average genetic differentiation coefficient (Fst) and number of migrants per generation (Nm) of the six M. anguillicaudatus populations were 0.3395 and 0.4863, respectively, indicating a low level of genetic exchange among the six populations and a high degree of genetic differentiation. Moreover, based on cytb, the number of haplotypes (h), the haplotype diversity (Hd), and nucleotide diversity (π) of the six M. anguillicaudatus populations were 34, 0.925, and 0.0539, respectively, and were 36, 0.879, and 0.0160 based on D-loop sequences. The Fst values among the six populations were 0.4963 (cytb) and 0.4833 (D-loop), and they all showed a high degree of genetic differentiation. The above results indicate that there is abundant genetic diversity of M. anguillicaudatus in the Pearl River Basin in China, and the fish could be used as excellent materials for breeding. The study provides a theoretical basis for the protection and utilization of M. anguillicaudatus natural resources in the Pearl River Basin of China.

The oceanographic isolation of the Ogasawara Islands and genetic divergence in a reef‐building coral

AbstractAimDue to their spatial isolation, oceanic islands are natural systems to study evolutionary divergence. The Ogasawara Islands belong to the most isolated archipelagos on Earth and are well‐known for their high terrestrial endemicity; however, less is known about the marine realm. Here, we analyse the degree of oceanographic isolation of the archipelago based on genetic data of a reef‐building coral and a biophysical dispersal model.LocationNorth‐Western Pacific (Ogasawara, Ryukyu, Daito Islands, Guam).TaxonGalaxea fascicularis L.MethodThree to 15 specimens were sampled at several sites in Ogasawara and its closest potential migration sources in southern Japan and the Mariana Islands (Guam) and RAD‐sequenced. 108 specimens from the common Pacific lineages ‘L’ (Ryukyu‐ and Daito Islands, Guam) and ‘Ogasawara’ (Ogasawara) were analysed with population genetics and demographic modelling. Oceanographic dispersal was investigated by inverse particle tracking using a Lagrangian particle advection simulation based on ROMS and applying biological dispersal parameters of G. fascicularis.ResultsThe G. fascicularis population in Ogasawara is genetically highly differentiated from the next closest reefs in the region and has diverged from the Ryukyu Islands under very little, asymmetric, eastward migration. Inverse particle tracking confirmed the oceanographic isolation of Ogasawara and showed that the islands are rarely but most likely reached by settlers from the Ryukyu Islands by long‐distance‐dispersal of exceptionally long‐lived larvae (>44 days), with no dispersal vice versa.Main conclusionsOgasawara is a dispersal sink location and the high degree of genetic differentiation in Galaxea has resulted from strong oceanographic isolation. This research highlights how oceanographic features impact species‐level genetic differentiation even in well‐dispersed taxa such as broadcast‐spawning corals, and they are likely even more pronounced in less vagile organisms. These findings suggest the Ogasawaran Archipelago should be considered an important priority for marine conservation, alongside its high importance for terrestrial conservation.

A new species of lotic breeding salamander (Amphibia, Caudata, Hynobiidae) from Shikoku, Japan.

BackgroundHynobius hirosei is a lotic-breeding salamander endemic to Shikoku Island in western Japan. Significant allozymic and morphological differences have been found among the populations of this species; however, the degree and pattern of intraspecific variation have not been surveyed using a sufficient number of samples.MethodsFor the taxonomic revision of H. hirosei, we conducted genetic and morphological surveys using samples collected throughout the distribution. Phylogenetic analysis using the cytochrome b region of mitochondrial DNA and population structure analysis using single nucleotide polymorphisms were conducted to evaluate the population structure within the species and the degree of genetic differentiation. Subsequently, a morphological survey based on multivariate and univariate analyses was performed to assess the morphological variation.ResultsGenetic analyses revealed three genetic groups (Tsurugi, Central, and Nanyo) within H. hirosei, with the Nanyo group distributed allopatrically from the others, and the Tsurugi and Central groups distributed parapatrically with the formation of a hybrid zone between them. The Nanyo group was morphologically distinguishable from the remaining samples, including the topotype of H. hirosei, based on a smaller body size and several ratio values of characters to snout-vent length, longer axilla-groin distance, shorter tail length, shorter internarial distance, longer upper eyelid length, and larger medial tail width. These results support the notion that the Nanyo group is an undescribed species. However, the remaining genetically differentiated groups could not be divided in the present study. Herein, we described the Nanyo group as a new species.

Genetic Variation among Varieties, Wild Species and Related Genera of Arecanut (Areca catechu L.) as Revealed by Microsatellite Markers

Studies on genetic diversity of crops are crucial for germplasm conservation and crop improvement programmes. Arecanut (Areca catechu L.) is one of the plantation crops that have been in cultivation since time immemorial in tropical regions of the world. In this investigation, molecular characterization and genetic diversity analysis was carried out among 20 arecanut genotypes comprising of 16 cultivated types (including 13 cultivated varieties, two dwarf hybrids and a natural mutant), two wild species (Areca triandra and Areca concinna) and two other genera (Normanbya normanbyii and Actinorhytis calapparia), maintained in the National Arecanut Gene Bank, Vittal, Karnataka State, India, by employing eight simple sequence repeat (SSR) markers. A total of 45 alleles were detected with most of the markers revealing five alleles or more. The number of alleles at each locus varied from 3 (AC07 and AC08) to 8 (AC23) with a mean of 5.62 alleles per locus. The polymorphism information content (PIC) value, which is a measure of polymorphism for a marker locus, varied from 0.46 (AC08) to 0.84 (AC01) among the SSR markers loci, the average being 0.70. The effective number of alleles per locus (Ne) ranged from 1.28 to 3.11 with a mean of 2.31. The marker AC07 had the lowest effective number of alleles per locus and the marker AC29 had the highest numbers of effective alleles. Shannon’s Information Index ranged from 0.43 (AC07) to 1.33 (AC23) with a mean of 0.97. The observed heterozygosity (Ho) values ranged from 0.25 to 1.00 with an average of 0.73. The expected heterozygosity (He) values ranged from 0.22 to 0.69 with an average of 0.54. The degree of genetic differentiation among the subpopulations (FST) ranged from 0.11 (AC06) to 0.66 (AC01) with a mean of 0.32. The gene flow (Nm) values ranged from 0.12 (AC01) to 1.96 (AC06) with a mean gene flow value of 0.52. The lowest gene flow value was observed in the marker AC01 and the highest gene flow was exhibited by AC06. The dendrogram constructed using similarity coefficient values, by following the Unweighted Pair Group Method with Arithmetic Mean (UPGMA), formed two major clusters with cluster I consisting of all the 16 cultivated varieties and 2 wild species, viz., Areca triandra and Areca concinna and the second major cluster comprised of related genera viz., Normanbya normanbyii and Actinorhytis calapparia. The highest genetic similarity was observed between the cultivated varieties, Kahikuchi and Mohitnagar and Nalbari and Sumangala, and the lowest similarity value of 0.33 was found between the related genera, Normanbya normanbyii, and the cultivated variety, Sreemangala.

Identification and genetic diversity analysis of Rickettsia in Dermacentor nuttalli within inner Mongolia, China

BackgroundThe genus Rickettsia contains the lineages spotted fever group (SFG), typhus group (TG), and transitional group (TRG). The spotted fever group Rickettsia (SFGR) is transmitted by ticks. The tick species Dermacentor nuttalli is considered the main vector carrying SFGR in Inner Mongolia. Studying the genetic diversity and population structure of Rickettsia is essential for developing effective control strategies and predicting evolutionary trends of Rickettsia.MethodsIn 2019 we collected 408 D. nuttalli in the Inner Mongolia Autonomous Region, detected the percentage of Rickettsia-positive specimens, and characterized the haplotypes. From the Rickettsia-positive ticks, the gltA and ompA genes were extracted, amplified, and sequenced.ResultsTen haplotypes of the gltA gene and 22 haplotypes of the ompA gene were obtained. The phylogenetic analysis showed that the haplotypes G1–G7 and G9 of the gltA gene cluster with Rickettsia raoultii, while G8 and G10 cluster with Rickettsia sibirica. Haplotypes O1–O15, O18 and O20–O22 of the ompA gene cluster with R. raoultii, while O16 and O19 cluster with R. sibirica. The average haplotype diversity was 0.3 for gltA and 0.7 for ompA. The average nucleotide diversity was greater than 0.05. Neutrality tests were nonsignificant for Tajima’s D results and Fu’s Fs results. The fixation index values (FST) showed that the degree of genetic differentiation between most sampled populations was small (FST < 0.05), whereas some populations showed a medium (FST > 0.05) or large (FST > 0.15) degree of differentiation. Analysis of molecular variance (AMOVA) revealed that the variation within populations was greater than that between populations. The mismatch analysis of Rickettsia showed double peaks.ConclusionsWe found two Rickettsia spp. (R. raoultii and R. sibirica). The high genetic disparity of Rickettsia allows for easy adaption to different environments. Genetic differentiation between populations is small, and Rickettsia populations do not show a geographically differentiated structure. The high rates of retention and infection of Rickettsia in D. nuttalli together with the animal husbandry exchange in Inner Mongolia gradually led to the harmonization of genetic characteristics of Rickettsia across various regions. Overall, the significant genetic diversity and geographical structure of Rickettsia in D. nuttalli are critical for SFGR control.Graphical