Molecular characterization of <i>Apis florea </i>(Hymenoptera: Apidae), An unsung pollinator of major horticultural crops

Genetic diversity is shaped by life history traits and environmental factors across the marine ecoregions of the world (MEOW), a condition that serves as a valuable framework to enhance our understanding of gene flow processes and identifying priority conservation centers among populations in different regions. We investigated the genetic and phylogenetic diversity of 13 decapod crustacean species distributed across the marine ecoregions of Brazil. We hypothesized that ecoregions act as barriers to gene flow, creating distinct population structures and varying genetic diversity levels. We examined how habitat type, bathymetry, geographical distribution, and larval development affect genetic diversity. Mitochondrial markers from 13 species of the four major decapod groups (Anomura, Brachyura, Caridea, and Penaeoidea) were analyzed using nucleotide diversity, haplotype networks, pairwise FST, and linear mixed-effects models (LMER). Results show no significant genetic structuring among ecoregions. Genetic diversity correlates with habitat type (P < 0.05), with species from less impacted areas, especially intertidal zones like rocky shores and estuaries, displaying higher diversity. Phylogenetic diversity (PD) and species richness (SR) varied, with the highest PD in eastern Brazil and the highest SR in southeastern Brazil. Intertidal zones showed the highest genetic diversity, likely due to their complex microhabitats and environmental variability. Our findings indicate that environmental and geographical barriers defined by the ecoregions do not significantly impede genetic connectivity among decapod crustaceans, which suggests that high dispersal potential of larval stages facilitates genetic flow across ecoregions. The results underscore the need for conservation strategies that consider the high genetic connectivity and diversity of marine species across broad spatial scales.

Abstract. Tapilatu ME, Wijayanti DP, Subagiyo, Sembiring A, Yusmalinda NLA, NIngsih EY, Malik MDA, Pertiwi NPD. 2023. Genetic diversity of wedgefishes and guitarfishes at landing sites in east Indonesia using Cytochrome Subunit I (COI). Biodiversitas 24: 3120-3127. Wedgefish and guitarfish are considered endangered and protected by law in Indonesia due to pressure from overexploitation. They are highly exploited because of their economic value. This condition impacts the decline in the number of populations to the value of genetic diversity. This study used mitochondrial DNA to assess the genetic diversity of wedgefishes and guitarfishes which landed in the eastern part of Indonesia. We found Rhynchobatus australiae (Whitley, 1939) to be the most common species (14 out of 26 sequenced samples), with Glaucostegus typus (Bennett, 1830) and Rhinobatos jimbaranensis (Last, White, & Fahmi, 2006) appearing infrequently. COI sequences were obtained from the NCBI database and utilized in the study to compare population differentiation. Among the R. australiae populations, the results showed that the genetic diversity (Hd) values from Papua, Bali, and Lombok were 1.00, 0.67, and 0.75, respectively. In Papua, G.typus populations showed genetic diversity values of 0.90. R. jimbaranensis from Bali showed a genetic diversity of 0.50. Papua populations indicated higher genetic diversity than Bali and Lombok populations. Furthermore, the analyses of pairwise FST values and AMOVA indicated moderate genetic divergence across reference populations of R. australiae and G. typus in this study. Based on this value, a cautious conservation strategy in optimizing fisheries management will be required to limit anthropogenic impacts.

We aimed to identify biotic and abiotic factors underlying genetic structure and diversity of reef fish around Cuba. For three species, Stegastes partitus, Haemulon flavolineatum and Acanthurus tractus, we investigated the effects of shared environmental factors, such as the geography of the Cuban Archipelago, and specific characteristics, such as life history traits, on genetic structure and diversity. Samples were collected at five locations around Cuba. For S. partitus and H. flavolineatum, mitochondrial DNA and microsatellite loci were examined, whereas only mitochondrial DNA polymorphism was analyzed for A. tractus. All three species showed high genetic diversity. Mismatch distribution analyses suggest past population expansion in all species, but at different times in each species. Haplotype network and population genetic analyses suggest that: (1) S. partitus went through a recent population bottleneck in the late Pleistocene, (2) H. flavolineatum went through a population bottleneck but earlier, in the mid-Pleistocene, and (3) A. tractus has had a large and stable population size with coalescence times that go back to the late Pliocene. Genetic polymorphism in H. flavolineatum and A. tractus is homogeneous throughout the archipelago, whereas there is significant genetic structure in S. partitus. Genetic differentiation among S. partitus populations is most likely the result of the combined effects of egg type and oceanic current patterns along the Cuban coast.

ABSTRACTThis study aims to expand the current knowledge on the distribution and genetic diversity of Kappaphycus malesianus, a commercially important carrageenophyte whose cultivation has been limited to the southern Philippines. By broadening the sampling range and using molecular phylogenetic approaches, it seeks to provide a comprehensive overview of the species' genetic structure and diversity in the Philippines. Specimens obtained from four regions across the country were examined for morphological characteristics and subjected to molecular analysis using mitochondrial (COI‐5P and cox2‐3 spacer), plastid (rbcL), and nuclear (SSU) markers. Genetic diversity and haplotype network analyses, along with Bayesian phylogenetic inference, were conducted to assess genetic variation, population structure, and evolutionary relationships among K. malesianus populations. These analyses revealed new wild K. malesianus populations in Luzon (Sorsogon) and Visayas (Northern Samar, Bohol, and Iloilo), revealing a broader distribution and greater morphological diversity than previously reported. Multiple novel haplotypes were identified, indicating high genetic diversity and a complex population structure shaped by historical gene flow and regional diversification. A key finding is the identification of KMAL‐G, a wild haplotype from Sorsogon and Northern Samar, which genetically links the farmed KMAL‐A to wild Tawi‐Tawi populations, suggesting unrecognized genetic connectivity across these distant regions. Additionally, the close genetic similarity of the unidentified Kappaphycus sp. (GUI1) to K. malesianus suggests potential conspecificity. Similarly, the high genetic affinity between K. malesianus and K. inermis suggests a possible species complex. Overall, these findings demonstrate that K. malesianus is more geographically widespread and genetically diverse than previously known. The discovery of novel haplotypes highlights the importance of continued genetic surveys for aquaculture improvement. These findings not only provide insights on the domestication history of K. malesianus but also advance our understanding of its genetic diversity and phylogeographic distribution in the Philippines.

Foxtail millet [Setaria italica (L.) P. Beauv.], an important crop of East Asia is known for its drought tolerance and was once an indispensible crop of vast rainfed areas in semi-arid regions in India. In India it is cultivated in Andhra Pradesh, Karnataka, Maharashtra, Tamil Nadu, Rajasthan, Madhya Pradesh, Uttar Pradesh and north eastern states. The grain finds use in several local recipes such as roti (bread), jaula, singal, sirol. Foxtail millet grain contains 12.3% protein, 4.7% fat, 60.6% carbohydrates, and 3.2% ash. The present study was conducted to analyse the genetic diversity among foxtail accessions from different states of India and a few exotic accessions using RAPD and ISSR techniques and identify diverse accessions for use in variety improvement programmes. A set of 125 foxtail millet accessions selected from 11 different agro-ecological regions of India were analyzed using random amplified polymorphic DNA (RAPD) and inter simple sequence repeat (ISSR) marker techniques. A total of 146 (115 RAPD and 31 ISSR) scoreable markers were generated with 16 RAPD and four ISSR primers. The dendrogram generated using Nei's genetic distances and principal component analyses revealed presence of two clusters and two subclusters in group I. The accessions from Andhra Pradesh, Karnataka, Maharashtra and Uttarakhand were more diverse since they were distributed in both the clusters. There was no clear geographical differentiation observable. The bootstrap support for the major groups identified was strong (above 80%) indicating good statistical support. The average value of Nei and Li's genetic distance was lowest (0.081) for accessions from West Bengal while the collections from Karnataka showed highest dissimilarity (average genetic distance = 0.239). The average genetic distance for all 125 accessions together was 0.177 indicating presence of only moderate genetic diversity in the collections. The analysis of molecular variance indicated that only 2.76% variation was explained by variations among the groups and 11.55% among populations within groups. However the percentage of variation observed within populations was high (85.68). The value of Fst was observed to be very low (0.028) indicating low differentiation of the accessions analysed. The population genetic analysis carried out indicates that highest number of alleles per locus (1.745 ± 0.438) was observed for Andhra Pradesh with 35 accessions. When four eco-geographic regions were considered, the southern region comprising AP, Karnataka and TN showed the highest number of alleles per locus (1.787 ± 0.411). The value of Gst was lowest for south (0.123) and highest for central west (0.455). This indicated that all the landraces from south share common alleles. The gene flow between the accessions from different regions was also observed to be high with the highest migration (3.557) recorded for south.

Honey bees are an important component of the agricultural ecosystem and provide valuable pollination service. Cultivation of annual ornamental flowering plants is being recognized as a suitable options to compensate for the loss of natural floral resources for conserving the declining population of the honey bee. The capitulum/ inflorescence of commonly grown annual ornamental flowers of the Asteraceae family differs in morphology. The morphology of flowers affects the abundance and diversity of bee species. Therefore, the present study was conducted with an aim to study the influence of commercially cultivated flowering plants of India (Calendula officinalis, Chrysanthemum indicum, Glebionis segetum, Tagetes patula and Tagetes erecta) on honey bee diversity and abundance in the hot semi-arid environment. The capitulum of these plant species differed significantly in length and diameter of the corolla tube. It was observed that dwarf (Apis florea) and giant (Apis dorsata) honey bee were the most common visitors, however, the abundance of both bee species was significantly different (P<0.01) on different plant species. Plants with relatively longer (15.25-18.9 mm) and wider corolla tube (Tagetes erecta and Tagetes patula) were visited by both the bee species. However, plants having short (5.0-6.5 mm) and narrow (1.0-1.33 mm) corolla tubes (Calendula officinalis, Chrysanthemum indicum, Glebionis segetum) were dominantly visited by only Apis florea. Therefore, the cultivation of Tagetes patula and Tagetes erecta may enhance the population and conservation of both Apis florea and Apis dorsata, while Calendula officinalis, Chrysanthemum indicum, and Glebionis segetum may only enhance the population of Apis florea in the arid and semi-arid zone of India. Key words: Flower size, Apis dorsata, Apis florea, arid region, foraging behavior

Glycyrrhiza uralensis is an endangered and national-protected medicinal plant species distributed in semi-arid and arid areas of North China. This study addresses the genetic diversity and relationship between populations in different habitats by amplified fragment length polymorphism (AFLP). The plant materials consisted of 50 individuals from 5 different populating areas of Chifeng (Inner Mongolia), Hengjinqi (Inner Mongolia), Minqin (Ganshu), Aletai (Xinjiang) and Kashi (Xinjiang). Eight AFLP primer combinations generated a total of 1025 bands with 52.7% polymorphism. Unweighted pair group method based on arithmetic average (UPGMA) analysis was performed on Jaccard’s similarity coefficient matrix. According to results, the genetic resources and diversity in wild populations of G. uralensis were rich (polymorphism = 54.3%, He = 0.1932). The polymorphism among populations was Chifeng > Hangjinqi > Minqin > Aletai > Kashi and the genetic diversity varied from 0.1794 - 0.2061 and was in the order of Minqin > Chifeng > Hangjinqi > Aletai > Kashi. Genetic diversity was significantly correlated with annual mean precipitation and soil pH. Aletai and Kashi populations had close genetic relationship, and so Minqin and Chifeng populations. Conservational efforts have to be strengthened for all populations of the plant species in different habitats. Key words: Genetic characteristic, plant population, liquorice, semi-arid and arid area, biodiversity conservation.

Based on clinical samples collected in China, we detected and reported 22 types for the first time in China, as well as three types for the first time in Asia, and reported their genetic characteristics and diversity. We identified a novel type of Rhinovirus (RV), A110, highlighting its unique genetic features. We annotated the genomic structure and serotype of all the existing RV sequences in the database, and four novel RV types were identified and their genetic diversity reported. Combined with the sequence annotation, we constructed a complete VP1 data set of RV and conducted the first large-scale evolutionary dynamics analysis of RV. Based on a high-quality data set, we conducted a comprehensive analysis of the guanine-cytosine (GC) content variations among serotypes of RVs. This study provides crucial theoretical support and valuable data for understanding RV's genetic diversity and developing antiviral strategies.

Leucinodes orbonalis is a destructive pest found throughout eggplant cultivating fields of Tamil Nadu, India. The genetic diversity and its population structure were investigated in this pest using mitochondrial cytochrome c oxidase subunit I (COI) gene sequences from 20 populations of L. orbonalis collected from various agro-climatic conditions. The study indicated almost no genetic diversity among various populations. The COI nucleotide sequence based haplotype analysis also revealed no significant genetic variation among various populations. However, haplotype network analysis with three clades was nearly matching with the structure of phylogenetic analysis that showed geographical separations induced distribution of some genetic variation. The PCA and nMDS Shephard’s plot analyses were also illustrated that the populations sampled were nearly matched with phylogenetic tree and haplotype network. This study on phylogeographical structure using the mitochondrial COI sequence diversity of L. orbonalis therefore suggested presence of few genetically distinct populations due to some specific habitat requirements.

Background Malaria is still a public health problem in Saudi Arabia specifically in the Jazan region. Plasmodium falciparum knob-associated histidine-rich proteins (PfKAHRPs) play an important role in cerebral malaria pathophysiology as well as pathogenesis of P. falciparum infections. The repeat region of PfKAHRP C-terminal interaction domain has been found to bind to the infected red blood cells and the vascular endothelium. Thus, this study aimed to assess the allelic variations, genetic diversity, and natural selection acting at the C-terminal PfKAHRP between parasite isolates from Saudi Arabia. Materials and Methods The PfKHARP C-terminal interaction domain was successfully PCR-amplified and sequence data from 441 clinical isolates from Saudi Arabia were obtained. The DnaSP v5.10 software was used to determine the genetic diversity, polymorphism, haplotype, and natural selection. Haplotype network analysis was constructed by using the median-joining method in the NETWORK version 5.0.0.1 software. Results Alignment and analysis of 441 C-terminal PfKAHRP-deduced amino acid sequences identified 5 genotypes (I–V) based on the decapeptide repeat arrangements (TKEASTSKEA, TKEASTSKGA, TKEASTTEGA, and TKEASTSKRA). Among the repeat types, Type I (49.43%, 218/441) was the most abundant in Saudi Arabia, followed by Type II (48.29%, 213/441). Overall, the nucleotide diversity in the PfKHARP C-terminal region was found to be low in Saudi Arabia (π = 0.00142); however, natural selection tests indicated positive selection (dN-dS = 1.64, P < 0.05) which was due to the variations within the repeat motifs. Genealogical relationship haplotype network of PfKAHRP from 4 different countries (i.e., Saudi Arabia, Iran, Burundi, and India) revealed 1 major shared haplotype cluster (H_1) with samples representative from all 4 countries (Saudi Arabia; n = 441, Burundi; n = 4, Iran; n = 13, and India; n = 1). Conclusion Since this is the first study to report on genetic diversity of C-terminal PfKAHRP interaction domain and the repeat motifs from clinical samples in Saudi Arabia, it will contribute towards the rational design of antiadhesion drug therapies for P. falciparum malaria.

Dwarf honey bees, Apis florea, and Apis andreniformis are known as the potential wild pollinator in Asia. Apis florea was introduced to Indonesia, West Asia, and Africa. Based on the cytochrome oxidase subunit 1 (COX1) gene, introduced A. florea in Iran is suggested to come from India. Although the databases of the dwarf honey bee COX1 gene are available in GenBank, however, the phylogeny analysis was focused on the restricted area. Thus, this study aims to evaluate the phylogenetic relationship and genetic diversity of dwarf honey bees based on the COX1 gene sequence from GenBank databases. The COX1 gene sequence databases are collected from NCBI. The genetic diversity and phylogenetic relationship are analyzed using MEGAX. Alignment of 530 bp COX1 gene of dwarf honey bee showed that there are 60 nucleotide variations between A. florea and A. andreniformis. Our analysis indicated that the genetic diversity between A. andreniformis is low (0-0.19%). On the other hand, there are 28 nucleotide variations between A. florea and eight nucleotide sites that are suggested as a marker to differentiate A. florea1 India+Egypt+Iran and A. florea2 Thailand+China with 1.7-3.4% genetic distance. The high genetic distance of A. florea is supported by the separation sub-clade of A. florea1 and A. florea2 in the phylogenetic tree.

The introduction of exotics is common in forestry, and majorly important species, like eucalypts, poplar, and Casuarina sp., occupy vast areas in the Indian subcontinent. Importantly, with the latest cost-effective sequencing techniques, genetic diversity research through molecular marker approaches on major exotics provides novel information for genetic improvement in economic traits with climatic adaptation. The study was carried out on Grevillea robusta to assess genetic relatedness and diversity among 228 genotypes belonging to five northwestern states in India. These genotypes were assayed using twelve simple sequence repeat (SSR) markers. A population structure analysis using structure software identified four major gene pool subgroups with clear-cut differences from each other. Principal coordinate analysis also supports the clustering patterns of the unweighted pair group method with arithmetic mean analysis. In the case of genetic diversity assessment, a total of seventy-three alleles were detected from twelve SSRs, with an average of 6.08 ± 0.71 per locus. Polymorphism information content ranged from 0.17 to 0.67 with a mean of 0.44 ± 0.045, indicating high levels of polymorphism across the genotypes. All the evaluated SSRs demonstrated moderate genetic diversity (observed heterozygosity = 0.31 ± 0.03; expected heterozygosity = 0.32 ± 0.03; and genetic differentiation = 0.295) among the sampled genotypes. These findings indicate significant genetic variability in the germplasm to warrant selection and have potential for a long-term tree improvement program of G. robusta in India. Study Implications: The study on population genetics of Grevillea robusta in exotic environments assessed probable gene pools, provenances, and genetic diversity in geographical distribution range of the species in the Indian scenario. The basic population genetic measures revealed the high diversity areas and probable seed zones of G. robusta in its exotic range. Importantly, the study will be helpful in the selection of candidate plus trees of G. robusta to further strengthen the genotype × environment interaction study for future breeding programs. Further, studying the genetic makeup for moderately diverse species offers valuable insights into evolutionary history, population dynamics, and ecological interactions, which may lead to conservation efforts and guidance for the management of trees such as G. robusta in their native and introduced regions.

Mangroves are ecologically important forest communities in tropical and subtropical coasts, the effective management of which requires understanding of their phylogeographic patterns. However, these patterns often vary among different species, even among ecologically similar taxa or congeneric species. Here, we investigated the levels and patterns of genetic variation within Lumnitzera consisting of two species (L. racemosa and L. littorea) with nearly sympatric ranges across the Indo-West Pacific (IWP) region by sequencing three chloroplast DNA regions (for both species) and genotyping 11 nuclear microsatellite loci (for L. littorea). Consistent with findings in studies on other mangrove species, we found that both L. racemosa and L. littorea showed relatively high genetic variation among populations but low genetic variation within populations. Haplotype network and genetic clustering analyses indicated two well-differentiated clades in both L. racemosa and L. littorea. The relationship between geographic and genetic distances and divergence time estimates of the haplotypes indicated that limited dispersal ability of the propagules, emergence of land barriers during ancient sea-level changes, and contemporary oceanic circulation pattern in the IWP influenced the current population structure of the two species. However, the position of genetic break was found to vary between the two species: in L. racemosa, strong divergence was observed between populations from the Indian Ocean and the Pacific Ocean possibly due to land barrier effect of the Malay Peninsula; in L. littorea, the phylogeographic pattern was created by a more eastward genetic break along the biogeographic barrier identified as the Huxley’s line. Overall, our findings strongly supported previous hypothesis of mangrove species divergence and revealed that the two Lumnitzera species have different phylogeographic patterns despite their close genetic relationship and similar current geographic distribution. The findings also provided references for the management of Lumnitzera mangroves, especially for the threatened L. littorea.

Understanding the genetic diversity and distribution patterns of seaweeds species is crucial for evaluating key regions of high genetic diversity. Identifying hotspots of high intraspecific diversity is an important step for developing conservation strategies. Grateloupia is a diverse genus of Rhodophyta, many of which are resource of numerous useful bioactive compounds; therefore, the genus is valuable target for conservation. The aim of this study is to examine the genetic diversity and population structure of two Grateloupia species, Grateloupia asiatica and Grateloupia jejuensis, with the understanding of the phylogeography of the Korean genetic diversity hotspot for two species. Plastid rbcL gene sequences of 134 specimens of G. asiatica and 112 specimens of G. jejuensis collected from the Korean coast were analyzed. We evaluated the number of haplotypes, genetic diversity (haplotype and nucleotide diversity), and haplotype networks of two species. Historical demographic was inferred by calculating neutrality tests and genetic differentiation was estimated using the fixation index, FST. Our results show that both species are generally similar in geographical distribution patterns, that is, relatively homogeneous with few haplotypes derived from the most frequent haplotype. The east coast of Korea is identified as a 'hotspot' with the highest genetic diversity for both species, whereas Jeju Island is identified as a 'cold spot' with the lowest genetic diversity for G. jejuensis. Analyses across most distribution ranges of the two species in Korea reveal low genetic and haplotype diversities, which could indicate that these two Grateloupia species have either experienced a historical lack of diversity or a recent reduction in diversity due to high gene flow. The low genetic diversity values found in the present study raise considerable concern about the conservation status of these two Grateloupia species and highlight the need to locate further hotspots of genetic diversity to strengthen their resilience against further decline.

Jewel beetles of the genus Sternocera are widely distributed across tropical regions, including Thailand and Lao PDR, where the green-legged S. aequisignata Saunders, 1866, and red-legged S. ruficornis Saunders, 1866, are commonly found. These jewel beetles have significant economic importance, as they are edible, and their iridescent wings are used to create jewelry, leading to high market demand and intensive harvesting. Additionally, their habitats are being rapidly destroyed, resulting in population decline. However, genetic information on these species remains limited. This study aims to investigate the genetic diversity of S. aequisignata and S. ruficornis from various localities in Thailand and Lao PDR using mitochondrial cytochrome c oxidase subunit 1 (CO1) and 16S ribosomal DNA (16S rDNA) sequences. High genetic diversity was observed, with 45 and 62 CO1 haplotypes and 35 and 28 16S rDNA haplotypes identified in S. aequisignata and S. ruficornis populations, respectively. Haplotype network and phylogenetic analyses clearly distinguish S. aequisignata from S. ruficornis. Based on CO1 sequences, S. aequisignata was divided into three distinct haplogroups (GG1-GG3). Haplogroup GG1 was the most widespread, occurring in both Thailand and Lao PDR, while haplogroups GG2 and GG3 were restricted to some localities in northern, western, and northeastern Thailand, as well as Lao PDR. These findings suggest the presence of cryptic diversity within S. aequisignata, with at least three genetically distinct groups. Further comprehensive studies on the biology, ecology, and genetic diversity of these jewel beetles across their distribution range are essential to better understand their evolutionary dynamics.