Genetic Distance Values Research Articles

Relationship analysis of FaPYR1 and FaCHS genes encoding fruit ripening of three species of strawberries (Fragaria spp.) fruit

Abstract. Aristya GR, Dyatama GR, Zuyyina C, Maulina NTA, Arif MF, Musthofa A, Kasiamdari RS. 2023. Relationship analysis of FaPYR1 and FaCHS genes encoding fruit ripening of three species of strawberries (Fragaria spp.) fruit. Biodiversitas 24: 87-97. The difference in the phenotypes characters and gene expressionof strawberries (Fragaria spp.) is influenced by changes in hormone signaling mechanisms to receptors due to the adaptation to various types of environments. Abscisic acid (ABA) is one of the phytohormones that plays a role in the growth and development of strawberries, response to environmental stress, and fruit ripening. One of the ABA receptors is the PYR1 protein which is encoded by FaPYR1 gene. ABA also plays a role in inducing the FaCHS gene associated with pigmentation in strawberry fruit. This study aimed to analyze the relationship between FaPYR1 and FaCHS gene sequences in three strawberry species encoding fruit ripening. The FaPYR1 (585-633 bp) and FaCHS (90-93 bp) genes from three strawberries species namely Fragaria moschata, Fragaria vesca L. 'Californica', and Fragariax ananassa 'Festival' were successfully amplified. The results of the gene family relationship analysis of FaPYR1 gene sequences showed a close relationship with the comparative three species to GenBank, with a genetic distance value of 0.01-0.02. Meanwhile, FaCHS gene sequences from three species of strawberries showed a close relationship with the comparable FaCHS gene sequence from GenBank, with a genetic distance of 0.1-0.2.

The assessment of genetic diversity and population structure of endemic Scutellaria yildirimlii (Lamiaceae) for conservation purposes

Scutellaria yildirimlii is an endangered perennial endemic species from Turkey and belongs to the family Lamiaceae, which has a high number of medicinal and aromatic plants. It is crucial to determine genetic diversity and population structure of this species for its conservation measures; therefore, 111 individuals from five natural populations of S. yildirimlii were investigated by using 15 inter simple sequence repeats (ISSR) primers. The percentage of polymorphic loci (PPL), Nei?s gene diversity (H), and Shannon?s information index (I) at the species and population-level were determined as 93.9%, 0.183, 0.292 and 56.5%, 0.158, 0.242, respectively. The analysis of molecular variance (AMOVA) showed that there is more genetic variation within populations (84%) than among populations (16%). Nei?s differentiation coefficient (GST = 0.144) was determined to be moderate, which was confirmed by the level of genetic differentiation among populations. Gene flow (Nm = 2.984) showed high genetic exchange among populations. Pairwise genetic distance values among populations ranged from 0.0219 to 0.0512. The Mantel test revealed a statistically significant positive correlation between genetic and geographical distance (r = 0.493, p < 0.001). The Unweighted Pair Group Method with Arithmetic Averages (UPGMA) dendrogram and Principal Coordinate Analysis (PCoA) showed similar results. STRUCTURE analysis (?K = 3) revealed that the K test yielded maximum peaks for 3 clusters. Based on the findings, measures for genetic conservation and management of this species were presented.

Comparative Mitogenomic Analysis Indicates Possible Cryptic Species in Lambis lambis (Gastropoda: Strombidae)

The spider-like strombid Lambis lambis is widely distributed in the Indo-Pacific region and possesses morphological diversity. In the present study, the complete mitochondrial genomes of two morphologically different specimens of L. lambis that were collected in Sanya (SY) and Zhaoshu (ZS) islands of the South China Sea (namely L. lambis-SY and L. lambis-ZS) were sequenced. They were also compared with that of L. lambis previously published and sampled from coastal waters of Quanfu (QF) Island of the South China Sea (namely L. lambis-QF). The newly sequenced mitochondrial genomes L. lambis-SY and L. lambis-ZS contained 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes, and several noncoding regions, indicating a similar pattern with respect to genome size, gene order, and nucleotide composition compared with that of L. lambis-QF. Although L. lambis-SY and L. lambis-ZS differed in shell morphology, the genetic distance between them was small. On the other hand, considerable genetic distance values were detected between L. lambis-QF and L. lambis-SY/L. lambis-ZS, suggesting that the former might be a possible cryptic species within L. lambis. The divergence of the cryptic lineage L. lambis-QF was dated to 4.6 Mya, falling in the lower Pliocene that corresponded to a paleoclimatic transition from cool to warm conditions. This study, therefore, suggests a correlation between paleoclimate change and speciation event.

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 (&gt; 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 (&gt; 0.6), while 41 cultivars showed a close relationship and yielded lower GD values.

COI gene analyses of the Daghestan pine vole (Microtus daghestanicus Shidlovsky, 1919) population from northeastern Turkey

Daghestan pine vole (Microtus daghestanicus Shidlovsky, 1919) is spread in Caucasia, Turkey and Northwestern Iran and distribution of this species is limited to Northeastern Anatolia in Turkey. Few molecular studies on M. daghestanicus have been performed so far, and it was analysed in this study with the mitochondrial cytochrome oxidase subunit I (COI) region and compared with other Terricola species (Microtus subterraneus and Microtus majori) and other Microtus species found in its distribution area (Microtus arvalis and Microtus mystacinus). For this purpose, mean genetic distance values and fixation index values were calculated. Also, Bayesian Inference tree and Median-joining network were constructed. The acquired results showed that M. daghestanicus was clearly separated in the Pleistocene Period and was closer to M subterraneus than M. majori in the subgenus Terricola.

Genetic diversity assessment by microsatellite markers in summer chilli (Capsicum annuum L.) genotypes of Bangladesh

Assessment of genetic diversity among different is a prerequisite for plant breeders in choosing potential parental lines. Ten genotypes of summer growing chilli including one released variety viz., BARI morich-2; one advanced line viz., SRC- 517 and eight local cultivars viz., IAH-160, IAH-164, AHM-206, AHM-217, AC-63, AC-312, RAI-67, and RI-1(6) were characterized with a view to explore genetic diversity within these genotypes based molecular markers. Using eight microsatellite (SSR) primers across 10 genotypes, a total of 30 alleles with an average number of 3.75 alleles per locus were found. The number of alleles detected varied form three (CAMS-864, CAMS-880, CAMS-885) to five (CAMS-647). The allele size ranged from 160 (CAMS-075) to 289 bp (CAMS-864). All most all sets of primers showed high polymorphism (PIC value ≥0.6) except CAMS-880 and CAMS-885 which suggesting the greater genetic diversity in the genotypes. Gene diversity ranged from 0.460 (CAMS-885) to 0.740 (CAMS-647) and the highest and lowest value of Shannon's Information Index was registered in the same locus with their average value of 1.174. Higher level of genetic differentiation (0.971) and lower level of gene flow value (0.007) which were indicative of the presence of diversity among the genotypes. The genotypes had distinct status in the dendrogram, because of variation in genetic distance values differed from 0.138 to 0.938. SAARC J. Agric., 20(2): 69-82 (2022)

Morpho-molecular characterization of napier (Pennisetum purpureum) fodder mutants through SSR markers

Napier (Pennisetum purpureum) fodder is an important fodder supporting livestock systems in Bangladesh. Using gamma irradiation we developed 48 Napier fodder mutants which were analyzed through morpho-molecular characterization. Among 48 Napier fodder mutants, 41 mutants were originated by applying radiation (20Gy, 30Gy, 40Gy and 50 Gy) on them. The Napier mutants showed variations in survival rate and fresh weight. The survival rate (0-75%) was observed, 20Gy treated plants produced higher fresh weight in Napier-2, Napier-3, Rokona, Markiron grasses; whereas, 30Gy treated plants produced higher fresh weight in Napier-1, Napier-4 and Pakchong. The total of the alleles found in molecular characterization were 17 and the mean number of allele per locus was 3.4. The PIC value ranged from 0.3047 to 0.6587 having an average of 0.4704 per locus. The highest gene diversity (0.7101) was observed in primer Xipes0093 and the lowest gene diversity (0.3750) was observed in primer PSMP2255, having an average diversity of 0.5286. Pair wise genetic distance values ranged (0.0-1.0) with highest between Napier-2 40 Gy vs (Napier-1control, Napier-2 20Gy Napier-2 30Gy), Napier -3 control, vs (Napier-1control, Napier-2 20Gy Napier-2 30Gy), Napier- 3 20Gy vs (Napier-1control, Napier-2 20Gy Napier-2 30Gy) ,(Napier-3 20Gy, Napier-3 30Gy Napier-1 20Gy, Napier-3 50Gy) vs (Napier -2 20Gy, Napier-3 control, Napier-3 20Gy) etc. The UPGMA displayed five major clusters including sub-clusters. Cluster 5 included the highest number of genotypes (21) and cluster 3 included the lowest number of genotypes (2). The results may be useful for future breeding program for Napier fodder development. SAARC J. Agric., 20(2): 105-119 (2022)

Haplotype and Genetic Analysis of 41 Y-STR Loci in the Wuwei Han Population from Gansu Province, China.

Y-Chromosomal short tandem repeat polymorphism (Y-STR) analysis plays an indispensable role in the identification of male individuals, population genetics, and biogeographic research. While profiles of many populations based on Y-STR markers in human genomes are ample, haplotype data for the Wuwei Han are still scarce. In this study, 2180 unrelated Wuwei Han male individuals residing in Gansu Province, China were collected and genotyped using the novel Microreader™ 40Y Plus ID system. Phylogenetic relationship reconstructions, multidimensional scaling (MDS), and heatmap analysis were performed based on the genetic distance (Rst) values between our studied population and other populations of the Ymax module in the Y-STR Haplotype Reference Database (YHRD). A total of 2129 unique haplotypes were obtained, and the haplotype diversity (HD) and discrimination capacity (DC) for the Wuwei Han were 0.9999 and 0.9931, respectively. Our results demonstrate that the Wuwei Han population had intimate genetic relationships with East Asians, especially the geographically close Han populations. Overall, this Y-Chromosomal assay gives valuable information about paternal lineages in male individual tracking and genealogical database construction.

First DNA barcode efficiency assessment for an important ingredient in the Amazonian ayahuasca tea: mariri/jagube, Banisteriopsis (Malpighiaceae)

Mariri or jagube (Banisteriopsis C. B. Rob.) is a vine of the Malpighiaceae family and is naturally found in the Brazilian Amazon. It is also an important ingredient of ayahuasca tea, which is used by some traditional, indigenous people and religious groups of Amazonian origin. Via DNA barcodes, this study aimed to evaluate the efficiency of six markers to access genetic diversity and use them in the identification of either ethnovarieties or species of Banisteriopsis used in the preparation of “ayahuasca” in the Amazon. The efficiency of three plastid genes (matK/trnK, ndhF, and rcbL) and three nuclear markers (MP3 and yage5 isolated in the present study and ITS—Internal Transcribed Spacer) were tested. For these six markers, a total of 4792 base pairs were sequenced. The plastid markers revealed that all the samples analyzed belong to the genus Banisteriopsis; however, they presented the lowest indices of genetic diversity and were not efficient for use in the identification of ethnovarieties. Nuclear DNA markers showed the highest levels of genetic diversity. The ITS showed the highest values of genetic distances between the identified lineages. This study demonstrates that the use of ITS for DNA barcoding was more efficient since the identified lineages showed correspondence with the ethnovarieties of Banisteriopsis spp. used in the preparation of ayahuasca. As such, we encourage new integrative studies like this one, which combines modern approaches and traditional knowledge, to contribute to the maintenance of traditional knowledge as well as the conservation of species.

Genetic diversity of Venturia inaequalis isolates from the scabs in apple trees in Gansu Province, China, using AFLP markers.

Apple scab is a serious disease that restricts the growth of cultivated apples. The objective of this study is to investigate the genetic variations and genetic structure of Venturia inaequalis in Gansu Province, China. 108 isolates of the pathogen V. inaequalis from the Jingning, Lingtai, Jingchuan, Xifeng, Ning and Maiji regions were collected, and their genetic diversity was analyzed using AFLP molecular marker technique. The results showed that genetic diversity was present among the isolates but was not statistically significant. Genetic distance values ranged from 0.0095 to 0.0762. Cluster analysis results showed that the 108 isolates could be divided into two clusters using a similarity coefficient of 0.69. A total of 104 isolates were contained in cluster I while four isolates were contained in Cluster II. From the AMOVA analysis, 98% of variations were observed within the same region, while 2% were observed across different regions. The analysis of population structure showed that 108 isolates had two common ancestors, with the Jingning isolates mainly being derived from the red ancestor. PCoA analysis showed that the Jingning isolates were independent to a certain extent. The different geographical location caused the genetic difference of the isolates. The genetic diversity of apple scab in Gansu Province is greatly aided by this work, which also offers a theoretical foundation for the use of molecular markers in assisted breeding to create novel resistant types.

First record of Grammatodinium (Dinophyceae) for the American Eastern Pacific coast: Morphological, molecular and ecological confirmation

Grammatodinium Li & Shin is a monospecific genus described from the Tongyeong Bay area in Korea. In the current study, we describe its presence in the American Eastern Pacific coast for the first time, particularly in Acapulco Bay, Mexico, using morphological, molecular and environmental data. Sequences generated in this study with SSU and LSU formed a monophyletic group with other sequences from GenBank belonging to Gr. tongyeonginum, the only species known for the genus; however, genetic distance values between this species and our specimens (8.5% SSU; 2.8% LSU) were equivalent or even greater than those reported in other genera of dinoflagellates. Our phylogeny clearly showed the relationship of Grammatodinium with the families Pyrocystaceae and Gonyaulacaceae. In our specimens, cells appeared individually and in colonies of up to 16 cells, which were observed mainly during the dry season, so they could be confused with Gymnodinium catenatum, a common dinoflagellate in Acapulco with which they can coexist and share their general appearance, but they are clearly differentiated by the presence of longitudinal furrows throughout the body and a yellowish-green coloration, both absent in Gymnodinium catenatum. Although our evidence strongly suggests the presence of a new species for the region, more detailed morphological examinations are needed to confirm this statement.

Redescription of immature stages of Culicoides paraensis (Goeldi) (Diptera: Ceratopogonidae), vector of the Oropouche virus

Oropouche fever is an emerging zoonotic disease caused by Oropouche virus (OROV). It has two distinct transmission cycles, with the anthropophilic biting midge Culicoides paraensis (Goeldi) (Diptera: Ceratopogonidae) being the primary vector in the urban cycle. Species identification of Culicoides typically has been carried out on the basis of morphological characters, but molecular tools applied to taxonomy can provide rapid and efficient methods to the identification of vector species. The aim of this work was to obtain the first DNA barcode for C. paraensis collected in Argentina and redescribe the larvae and pupae of this species. Nested PCR amplification was applied in this study to increase the DNA amplification, because the material was preserved in alcohol 70% for a long period of time. The immature stages of C. paraensis are fully described from material collected in Misiones province, Argentina. Both stages are compared with their most similar congeners. This COI sequence complements the identification based on morphological characters and the values of genetic distance between the analysed species show that this sequence is useful to discriminate between species of the Culicoides genus.

Characterization of mitochondrial genome of Indian Ocean blue-spotted maskray, Neotrygon indica and its phylogenetic relationship within Dasyatidae Family

The present study characterized complete mitochondrial genome of Blue-spotted maskray, Neotrygon indica and studied the evolutionary relationship of the species within the Dasyatidae family. The total length of the mitogenome was 17,974 bp including 37 genes and a non-coding control region. The average frequency of nucleotides in protein-coding genes was A: 29.1 %, T: 30.2 %, G: 13.0 % and C: 27.7 % with AT content of 59.3 %. The values of AT and GC skewness were −0.018 and −0.338, respectively. Comparative analyses showed a large number of average synonymous substitutions per synonymous site (Ks) in gene NADH4 (5.07) followed by NADH5 (4.72). High values of average number of non-synonymous substitutions per non-synonymous site (Ka) were observed in genes ATPase8 (0.54) and NADH2 (0.44). Genes NADH4L and NADH2 showed high interspecific genetic distance values of 0.224 ± 0.001 and 0.213 ± 0.002, respectively. Heat map analysis showed variation in codon usage among different species of the Dasyatidae family. The phylogenetic tree showed a sister relationship between the Dasyatinae and the Neotrygoninae subfamilies. Neotrygon indica formed as a sister species to the clade consisting of N. varidens and N. orientalis. Based on the present results, Neotrygon indica could have diverged from the common ancestor of the two latter in the Plio-Pleistocene. The present study showed distinct characteristics of N. indica from its congeners through comparative mitogenomics.

Analysis of genetic diversity among Chinese Cyclocybe chaxingu strains using ISSR and SRAP markers.

BackgroundCyclocybe chaxingu is an edible and medicinal fungal species commonly cultivated in China. The major problems currently facing by growers of C. chaxingu is the random labeling of strains and strains aging and degeneration. Therefore, an evaluation of genetic diversity is essential for the conservation and reproducing programs of this species.MethodsIn the present study, 24 widely cultivated strains were collected from the main producing areas of China, and the genetic diversity analysis was performed. DNA polymorphism among these Chinese C. chaxingu strains was analyzed using inter-simple sequence repeat (ISSR) and sequence-related amplified polymorphism (SRAP) markers.ResultsEight ISSR primers amplified a total of 75 DNA fragments of which 61 (81.33%) were polymorphic. Fifteen SRAP primer combinations amplified 166 fragments of which 132 (79.52%) were polymorphic. Cluster analysis showed that the C. chaxnigu strains fall into five groups with a genetic distance values ranging from 0.06 to 0.60 by ISSR analysis, while the SRAP analysis divided the test strains into four groups within the range of genetic distance from 0.03 to 0.57. The results of the present study reveal a high level of genetic diversity among the widely cultivated C. chaxingu strains.

Chloroplast Genome Analysis for Genetic Information and Authentication in Five Barleria Species.

In order to authenticate the genomic information of Barleria cristata L., B. lupulina Lindl., B. repens Nees, B. siamensis Craib, and B. strigosa Willd, cp genomes were investigated. They revealed a general structure with a total size of 151,997–152,324 bp. The genomes encoded a total of 131 genes, including 86 CDS, 37 tRNA, and 8 rRNA genes. Other details found were as follows: different numbers and types of SSRs; identical gene content, which is adjacent to the border regions, except for B. strigosa, that revealed a shorter ndhF gene sequence and lacked the ycf1 gene; slightly different genetic distance values, which can be used for species identification; three distinct gaps of nucleotide variations between the species located at the intergenic spacer regions of the LSC and CDS of the SSC; three effective molecular markers derived from divergent hotspot regions, including the ccsA-ndhD, ndhA-ndhH-rps15, and ycf1. The genetic relationships derived from the cp genome and the CDS phylogenetic trees of Barleria and the 13 genera in Acanthaceae and different families, Scrophulariaceae and Phrymaceae, showed similar results. The six Barleria species as monophyletic groups with inner and outer outgroups were found to have perfect discrimination. These results have helped to authenticate the five Barleria species and the six genera in Acanthaceae.

Molecular identification of ornamental loaches (Cypriniformes, Cobitoidei) of North East India using mitochondrial genes

North East (NE) India, referred as Biodiversity Hot Spot, is the natural habitat of a large variety of ornamental fishes. Among all the ornamental fishes available in NE India, Loaches are of great importance in the ornamental fish trade. In this study, 38 specimens from ten loaches species of North-eastern India are characterized using three mitochondrial genes i.e. cytochrome c oxidase subunit I (COI), 16S rRNA and cytochrome b (Cyt b). The average genetic distance values for all the three mitochondrial genes have increased gradually when moving up from species to genus to family levels. Among the genes, Cyt b gene showed relatively higher genetic distance values than mitochondrial 16S rRNA and COI genes. Some of the specimens of Botia and Lepidocephalichthys showed higher intraspecific genetic distance values compared to other specimens under analysis.

Molecular characterization and genotype distribution of thioester-containing protein 1 gene in Anopheles gambiae mosquitoes in western Kenya

BackgroundEvolutionary pressures lead to the selection of efficient malaria vectors either resistant or susceptible to Plasmodium parasites. These forces may favour the introduction of species genotypes that adapt to new breeding habitats, potentially having an impact on malaria transmission. Thioester-containing protein 1 (TEP1) of Anopheles gambiae complex plays an important role in innate immune defenses against parasites. This study aims to characterize the distribution pattern of TEP1 polymorphisms among populations of An. gambiae sensu lato (s.l.) in western Kenya.MethodsAnopheles gambiae adult and larvae were collected using pyrethrum spray catches (PSC) and plastic dippers respectively from Homa Bay, Kakamega, Bungoma, and Kisumu counties between 2017 and 2020. Collected adults and larvae reared to the adult stage were morphologically identified and then identified to sibling species by PCR. TEP1 alleles were determined in 627 anopheles mosquitoes using restriction fragment length polymorphisms-polymerase chain reaction (RFLP-PCR) and to validate the TEP1 genotyping results, a representative sample of the alleles was sequenced.ResultsTwo TEP1 alleles (TEP1*S1 and TEP1*R2) and three corresponding genotypes (*S1/S1, *R2/S1, and *R2/R2) were identified. TEP1*S1 and TEP1*R2 with their corresponding genotypes, homozygous *S1/S1 and heterozygous *R2/S1 were widely distributed across all sites with allele frequencies of approximately 80% and 20%, respectively both in Anopheles gambiae and Anopheles arabiensis. There was no significant difference detected among the populations and between the two mosquito species in TEP1 allele frequency and genotype frequency. The overall low levels in population structure (FST = 0.019) across all sites corresponded to an effective migration index (Nm = 12.571) and low Nei’s genetic distance values (< 0.500) among the subpopulation. The comparative fixation index values revealed minimal genetic differentiation between species and high levels of gene flow among populations.ConclusionGenotyping TEP1 has identified two common TEP1 alleles (TEP1*S1 and TEP1*R2) and three corresponding genotypes (*S1/S1, *R2/S1, and *R2/R2) in An. gambiae s.l. The TEP1 allele genetic diversity and population structure are low in western Kenya.

Biochemical and molecular characterization of some advanced mutant rice (Oryza sativa L.) Genotypes

Rice (Oryza sativa L.) is one of the main cereal crops in the world and the main staple food of Bangladesh. Amylose content of rice endosperm is the main chemical properties that contributes the eating and cooking quality. On the other hand, rice protein is the important source of nutrition of almost 50 per cent of the world’s population living on rice. A total of 12 rice genotypes including ten advanced mutant lines, one landrace namely Laxmidigha along with BRRI dhan49 was collected from Plant Breeding Division of Bangladesh Institute of Nuclear Agriculture (BINA), Mymensingh and Bangladesh Rice Research Institute (BRRI), Gazipur. The genotypes were analyzed to assess the amylose and protein content as well as their genetic diversity relationship. Among all the tested genotypes amylose content were ranged from 23.9-20.3% where highest amylose percentage was found for Magic-86 (25.6%). Protein content of the genotypes were ranged from 8.50-5.04%, where highest 8.86% protein was recorded for SSB-3. The highest gene diversity (0.81) was observed in RM519 marker and the lowest (0.28) was in RM111 marker. The PIC values ranged from 0.24-0.78 with a mean of 0.51. The highest Nei’s genetic distance value 0.87 was found in RM-16(N)-10 vs RM-40(C)-4-2-8 and the lowest value 0.18 was found in LD-200-1-3-3-8 vs LD-200-1-3-2-4. A dendogram was constructed using UPGMA system based on Nei’s similarity coefficient and six major clusters were obtained at 0.7 cut off. The genotypes showing diverse ranges of amylose and protein content tended to cluster together in the dendogram with some exceptions. SAARC J. Agric., 20(1): 41-53 (2022)

Phylogenetic diversity of water scorpions (Nepa spp., Insecta, Hemiptera)

Water scorpions belonging to the genus Nepa are predatory freshwater aquatic insects of the order Hemiptera. There are currently five accepted species, with a Holarctic distribution: N. cinerea (Eurasia and Northern Africa), N. sardiniensis (Sardinia and Corsica), N. anophthalma (endemic to Movile Cave, Romania), N. apiculata (North America) and N. hoffmanni (Eastern Asia). Mitochondrial and nuclear genetic markers indicate a correlation between genetic diversity and geographic distribution. Analyses also reveal a cryptic diversity in the Western Mediterranean basin, with specimens of the cinerea clade being assigned to the sardiniensis clade. The cave-adapted N. anophthalma is genetically closest to N. cinerea, suggesting surface populations of N. cinerea as possible ancestors. N. cinerea samples from three cave systems in Italy indicate various degrees of gene flow between surface and subterranean populations and an instance of a possible incipient speciation event. Despite the overlap in distribution range in mainland Eastern Asia between N. cinerea and N. hoffmanni, there is a high genetic distance between the two species. A similar value of genetic distance is found between N. cinerea and N. apiculata, but also between N. hoffmanni and N. apiculata, suggesting the assignment of N. hoffmanni and N. apiculata to different genera. The single species currently considered as stygobiotic, N. anophthalma, deserves more research to understand the timing of colonization of Movile groundwater by its surface ancestors.

DNA barcoding suggests new species for the Mansonia subgenus (Mansonia, Mansoniini, Culicidae, Diptera) in the area surrounding the Jirau hydroelectric dam, Porto Velho municipality, Rondônia state, Brazil

Previous studies have linked the construction of hydroelectric dams with increases in the density of mosquitoes, especially Mansonia. In Brazil, Mansonia mosquitoes are still poorly studied at the taxonomic, biological, ecological and epidemiological levels, and nothing is known about the genetic diversity and the cryptic speciation of the group. The current study analyzed the molecular taxonomy of Mansonia species captured in the area surrounding the Jirau hydroelectric dam, Rondônia state, Brazil. Samples were collected from fifteen locations between 2018 and 2019. Genomic DNA of the specimens was extracted, and the DNA barcode region of the Cytochrome Oxidase, subunit I gene was amplified with PCR and both DNA strands were sequenced. The dataset was analyzed using MEGA, Mr. Bayes and DnaSP software. The results provided COI sequences for 100 specimens collected in the area surrounding from Jirau hydroelectric dam. These belonged to five species of the Mansonia subgenus, identified morphologically as Mansonia humeralis, Mansonia amazonensis, Mansonia titillans, Mansonia dyari and Mansonia indubitans. Findings showed that the COI gene is an effective and accessible DNA barcode that provides a high-resolution tool for delimiting species within the subgenus Mansonia, with the tree construction (Bayesian Inference) well supported and non-overlapping intraspecific and interspecific (K2-P) genetic distance values. These findings also indicate the occurrence of cryptic speciation within M. dyari and near of M. titillans. This is the first study to apply molecular tools to the taxonomy of Mansonia species from Brazil.