Genetic Distance Values Research Articles

Molecular characterization of soybean (glycine max) accessions from the international collection of the plant gene resources of Canada: germplasm identification

ABSTRACT Soybean (Glycine max) is one of the most important crops in the world in terms of total production and usage. Evaluation of gene bank accessions such as the international collections of soybean (Glycine max) of the Plant Gene Resources of Canada has not been undertaken at the molecular level. The main objectives of the present study were to 1) determine the level of genetic variation and distance among G. max accessions from the international collections of the Plant Gene Resources of Canada and 2) develop and characterize accession-diagnostic inter simple sequence repeat (ISSR) and sequence-characterized amplified region (SCAR) markers that can be used in soybean molecular breeding programs. Genomic DNAs from 108 soybeans (G. max) accessions from 11 different countries were analyzed using ISSR primers. The levels of polymorphic loci detected were in general moderate varying from 29% to 52%. Overall, 82% of genetic distance values among accessions were above 0.40 based on ISSR analysis. This suggests that the genetic diversity among and within soybean accessions might not be as low as other studies have demonstrated. The soybean accessions from the Netherlands, China, France, and Sweden were the least genetically variable. The dendrograms constructed with ISSR data revealed that the South Korean accessions formed an out-group. The ISSR markers successfully distinguished soybean accessions within each group (country). In fact, several accession-diagnostic markers were identified in each of the 11 groups. They represent useful tools in soybean molecular breeding programs. One accession-diagnostic marker was cloned, sequenced, and converted to a SCAR marker.

Phylogenetic Analysis of Rasbora spp. Based on the Mitochondrial DNA COI gene in Harapan Forest

Harapan forest is the remaining lowland tropical forest in Sumatra which represents about 20 percent of the biodiversity on the island of Sumatra. There are several Rasbora species found in the Sungai Kapas Tengah River Refuge in the Harapan Jambi Forest that the relationship is not yet known.This research aims to know kinship and genetic distance several species of Rasbora from Sungai Kapas Tengah, Hutan Harapan Jambi. The method in this research using secondary data from the NCBI website ((National Center for Biotechnology Information). The data taken, namelynucleotide sequence from the Cytochrome Oxidase I (COI) gene in mitochondrial DNA. The Rasbora species analyzed were Rasbora from identification results in the Sungai Kapas Tengah River Refuge, Harapan Jambi Forest, consisting of, Rasbora bankanensis, R. caudimaculata, R. cf. sumatrana, R. dusonensis, R. elegans, R. sumatrana, and R. trilineata. Based on phylogenetic analysis, the location of the branch length in each Rasbora species, the closest kinship is owned byR. sumatrana and R. elegans species. Based on the results of genetic distance analysis, the closest genetic distance was the species R. elegans and R. sumatrana, with a distance value of 0.023 (2.3%). While the farthest genetic distance between R. bankanensis and R. caudimaculata, with a distance value of 0.172 (17.2%).Based on research results It can be concluded that R. bankanensis has a greater kinship and genetic distance value than other Rasbora species, so that this species forms a separate group. Meanwhile, 5 other species have kinship and the value of close genetic distance so that these species are united in the same group. For future researchers, it is hoped that some additional families of fish species will be analyzed for phylogenetic analysis in Sungai Kapas, Hutan Harapan Jambi, so that they can find out the relationship of several other species.

Identification of Target Chicken Populations by Machine Learning Models Using the Minimum Number of SNPs.

Simple SummaryClassifying a target population at the genetic level can provide important information for the preservation and commercial use of a breed. In this study, the minimum number of markers was used in combination, to distinguish target populations based on high-density single nucleotide polymorphism (SNP) array data. Subsequently, a genome-wide association study for filtering target-population-specific SNPs between the case and control groups and principal component analysis with machine learning algorithms could be used to explore various combinations with the minimum number of markers. In addition, the optimal combination of SNP markers was able to produce stable results for the target population in verification studies, in which samples were analyzed.A marker combination capable of classifying a specific chicken population could improve commercial value by increasing consumer confidence with respect to the origin of the population. This would facilitate the protection of native genetic resources in the market of each country. In this study, a total of 283 samples from 20 lines, which consisted of Korean native chickens, commercial native chickens, and commercial broilers with a layer population, were analyzed to determine the optimal marker combination comprising the minimum number of markers, using a 600 k high-density single nucleotide polymorphism (SNP) array. Machine learning algorithms, a genome-wide association study (GWAS), linkage disequilibrium (LD) analysis, and principal component analysis (PCA) were used to distinguish a target (case) group for comparison with control chicken groups. In the processing of marker selection, a total of 47,303 SNPs were used for classifying chicken populations; 96 LD-pruned SNPs (50 SNPs per LD block) served as the best marker combination for target chicken classification. Moreover, 36, 44, and 8 SNPs were selected as the minimum numbers of markers by the AdaBoost (AB), Random Forest (RF), and Decision Tree (DT) machine learning classification models, which had accuracy rates of 99.6%, 98.0%, and 97.9%, respectively. The selected marker combinations increased the genetic distance and fixation index (Fst) values between the case and control groups, and they reduced the number of genetic components required, confirming that efficient classification of the groups was possible by using a small number of marker sets. In a verification study including additional chicken breeds and samples (12 lines and 182 samples), the accuracy did not significantly change, and the target chicken group could be clearly distinguished from the other populations. The GWAS, PCA, and machine learning algorithms used in this study can be applied efficiently, to determine the optimal marker combination with the minimum number of markers that can distinguish the target population among a large number of SNP markers.

Development of 23 novel microsatellite markers of Amomum tsao-ko (Zingiberaceae) based on restriction-site-associated DNA sequencing.

Amomum tsao-ko (Zingiberaceae) is a traditional Chinese medicine and condiment, and an important economic crop in the tropical forest of southwest China. However, few simple sequence repeat (SSR) markers are available in A. tsao-ko, which is hindering genetic research in this species. The aim of this study was to develop and characterize microsatellite markers for A. tsao-ko using restriction-site-associated DNA sequencing. A total of 115,482 microsatellites were identified using MISA software, and 13,411 SSR primer pairs were designed. 100 pairs of SSR primers were selected at random and used to evaluate polymorphisms among 4 A. tsao-ko samples. Finally, 23 pairs of SSR primers with clear bands and obvious polymorphism were selected for genetic diversity analysis of 72 A. tsao-ko accessions. The number of alleles and effective number of alleles per locus ranged from 2 to 6 and from 1.315 to 3.776, respectively. The observed heterozygosity ranged from 0.208 to 0.779, and the expected heterozygosity was from 0.239 to 0.735. The average values of the polymorphic information content were 0.454. Hardy–Weinberg equilibrium (HWE) analysis showed that 10 loci significantly deviated from HWE (P < 0.05). The pairwise FST and genetic distance values revealed low levels of genetic differentiation and high genetic similarity among six A. tsao-ko populations. These microsatellite markers developed will provide a valuable tool for further germplasm characterization, genetic diversity, and breeding studies in A. tsao-ko.Supplementary InformationThe online version contains supplementary material available at 10.1007/s11033-020-06127-6.

Evaluation of the Hepato- and Neuroprotective Effect of Chemical Constituents in Saussurea costus Extract Against the Toxicity Induced by Chloropyrofos Ethyl in Rats

The health hazardous occurred in both human and animals as a result of the continuous misuse of pesticides drives the researchers for looking about the solution. Natural plant extracts contain active phyto-constituents with antioxidant potency enables them to inhibit production of the free radicals that induce damage of the cells. The present study aimed to reveal efficiency of Saussurea costus (S. costus) extract against the hepato- and neurotoxicity induced by Chloropyrifos ethyl (CPF) in experimental animals (rats). The gas chromatography / mass spectrometer (GC/MS) that used for analyzing the active constituents in S. costus extract showed that the extract contains 11 potent active compounds and Dehydrocostuslactone represents about 77.37% and considered as the most dominant compound in the extract. Both of CPF and S. costus extract were studied on the rats that were divided into 6 groups as the following: Group 1 (control) received distilled water orally. Groups 2&3 (S. costus extract treated groups) received S. costus extract orally at a dose of 0.25 and 0.50 ml, respectively. Group 4 (CPF injected group) was injected with CPF at a dose of 3 mg/kg.bw. Groups 5&6 (CPF + S. costus extract group) injected with CPF then treated with S. costus extract at two tested doses respectively. The most hematological and biochemical measurements declined significantly (P≤0.05) in CPF injected group. S. costus extract restored all tested parameters towards the control values. Moreover, the electrophoretic isoenzyme showed that the physiological alterations occurred in the esterases (ESTs) as a result of CPF injection were represented by hiding normal EST types associated with existence of abnormal ones. Therefore, the similarity index (SI%) and genetic distance (GD%) values were altered with α-EST (SI=80.00%; GD=20.00%) and β-EST (SI=50.00%; GD=50.00%) patterns in CPF injected group. The S. costus extract at a dose of 0.5 ml restored integrity of these isoenzymes pattern by restoring the absent types with hiding the abnormal ones. Therefore, this group became physiologically similar to control group (SI=100.00%; GD=0.00%). These results were supported by histopathological examination for the target organs (brain, liver and kidney) that were affected by CPF and the S. costus extract improved architecture of these organs and restored their histopathological integrity to normal structure.

Molecular Detection and Genetic Identification of Wolbachia Endosymbiont in Wild-Caught Culex quinquefasciatus (Diptera: Culicidae) Mosquitoes from Sumatera Utara, Indonesia

The genetic identity of Wolbachia endosymbiont in wild-caught Culex quinquefasciatus was determined for the first time in Indonesia. A total of 314 Cx. quinquefasciatus were examined for Wolbachia by PCR assay targeting the Wolbachia surface protein (wsp) gene. The prevalence of Wolbachia infection was detected in 29.94% of Cx. specimens (45.86% female and 8.27% male). The group-specific infection was detected with an infection rate of 0.32%, 28.98%, and 0.64% in groups A, B, and A&B, respectively. Phylogenetic analysis revealed all Wolbachia strains from Indonesia were genetically affiliated to the supergroup A and B with the high sequence similarity of 97.9-100% and 99.7-100%, respectively. Phylogenetic relationships can be easily distinguished by neighbor-joining analysis and were congruent by maximum likelihood method. The genetic distance (GD) values of intra- and inter-group analysis indicated a lower level (GD < 0.007 for group A and GD < 0.003 for group B) within the Indonesia strains and a higher level (GD > 1.125 for group A and GD > 1.129 for group B) as compared with other Wolbachia strains. Our results provide the first genetic identification of Wolbachia endosymbiont in Cx. quinquefasciatus collected from Indonesia, and the phylogenetic analysis revealed a new discovery of group A Wolbachia in wild-caught Cx. quinquefasciatus mosquitoes.

Phylogenetic study of Sumatran Microhyla heymonsi Vogt, 1911 (Anura: Microhylidae) based on 16S rRNA mitochondrial gene

Microhyla heymonsi is a species that has a very wide distribution, ranging from Taiwan, China, India, Indochina, Peninsular Malaysia, to Sumatra. Species with a very wide distribution often contain cryptic species due to the geographical barrier resulting in reproductive isolation, gene mutation, and evolution. This study aims to determine the phylogenetic relationship between M. heymonsi species from Sumatra and outside Sumatra, as well as the value of genetic distance between the two groups of species. The genetic distance threshold as a species delimitation is 3 %. DNA sequences were obtained through the process of DNA barcoding and then phylogenetic studies were performed through analysis of Unweighted Pair Group Method with Arithmatic Mean, Neighborhood Joining, Maximum Likelihood, and Bayesian Inference. The results show that the M. heymonsi species from Sumatra form a large single clade on the phylogenetic tree of all analytical methods with significant bootstrap values. The genetic distance value of M. heymonsi Sumatra with M. heymonsi Singapore and Malaysia is still below 3 %. The genetic distance values between M. heymonsi Sumatra and M. heymonsi Thailand, Myanmar, Vietnam and China have exceeded 3 %.

Molecular characterization and genetic relationships of seven piranha species of the genera Serrasalmus and Pygocentrus (Characiformes: Serrasalmidae) from Paraná-Paraguay, São Francisco and Tocantins River basins in Brazil.

Genetic and phylogenetic relationships among seven piranha species of the genera Serrasalmus and Pygocentrus from the Paraná-Paraguay, São Francisco and Tocantins River basins were evaluated in the present study by partial sequences of two mitochondrial genes, Cytochrome b and Cytochrome c Oxidase I. Phylogenetic analysis of Maximum-Likelihood and Bayesian inference were performed. Results indicated, in general, greater genetic similarity between the two species of Pygocentrus (P. nattereri and P. piraya), between Serrasalmus rhombeus and S. marginatus and between S. maculatus, S. brandtii and S. eigenmanni. Pygocentrus nattereri, S. rhombeus and S. maculatus showed high intraspecific genetic variability. These species have each one, at least two different mitochondrial lineages that, currently, occur in sympatry (S. rhombeus) or in allopatry (P. nattereri and S. maculatus). Species delimitation analysis and the high values of genetic distances observed between populations of S. rhombeus and of S. maculatus indicated that each species may corresponds to a complex of cryptic species. The non-monophyletic condition of S. rhombeus and S. maculatus reinforces the hypothesis. The geographic distribution and the genetic differentiation pattern observed for the piranha species analyzed herein are discussed regarding the geological and hydrological events that occurred in the hydrographic basins.

42 Genetic differentiation of Russian goats and wild relatives based on microsatellite loci

Abstract Goat breeding is a traditional livestock industry for many regions of Russia. Due to unpretentiousness and high adaptive qualities, the Karachai, Dagestan wool and Dagestan down breeds are widespread in the North Caucasus. Moreover, their uniqueness is determined by sharing a common habitat with their wild relatives, West Caucasian and Dagestani turs, thus forming hybrid zones. The aim of the research was to study allele pool and interbreed differentiation of domestic goat breeds and wild relatives by microsatellites. Research was performed based on 16 loci on the ABI 3130xl analyzer. Population genetic characteristics were calculated in GenAlEx 6.5, and the phylogenetic tree was constructed in Populations 1.2.30 and SplitsTree 4.14.5. The sample collection included goat breeds (n = 226): Karachai (KRCH), Dagestan down (DAGD), Dagestan wool (DAGW) (North Caucasus), Soviet wool (SOVW) (Siberia), Orenburg (OREN) (South Ural), and wild goats (n = 72). Wild goats comprised mountain goats: Siberian goats (Capra sibirica) from the Altai, Tajikistan, Kyrgyzstan and the Himalayas; bezoar goats (Capra aegagrus) from Turkey and Pakistan; and tur (Capra caucasica) from the West Caucasus (Kuban), Central Caucasus, and East Caucasus (Dagestan). The Karachai breed was characterized by the highest level of genetic diversity: the average number of alleles per locus (NA) and allelic richness (AR) were 9,154 and 7,713, respectively, while these indices varied from 6,538 to 7,538 and from 6,425 to 7,538 (Table 1) in other breeds, respectively. The values of genetic distances showed differentiation of Karachai, Dagestan down and Dagestan wool breeds from Orenburg and Soviet wool breeds (Table 2). The formation of three clusters was established. The first one included subspecies of the Caucasian tur, the second one comprised Siberian goats, and the third contained domestic goats. Bezoar goats were in the root of the third cluster that confirmed their participation as an ancestral form of domestic goats.

Molecular detection and genetic identification of Wolbachia endosymbiont in Rhipicephalus sanguineus (Acari: Ixodidae) ticks of Taiwan.

The genetic identity of Wolbachia endosymbiont in Rhipicephalus sanguineus ticks was determined for the first time in Taiwan. In total 1004 Rh. sanguineus ticks were examined for Wolbachia by polymerase chain reaction assay targeting the Wolbachia surface protein (wsp) gene. The prevalence of Wolbachia infection was detected in nymphs, females, and males with an infection rate of 55.8, 39.8, and 44%, respectively. The phylogenetic relationships were analyzed by comparing the sequences of wsp gene obtained from 60 strains of Wolbachia representing 11 strains of supergroup A and 10 strains of supergroup B. In general, seven major clades of supergroup A and six major clades of supergroup B can be easily distinguished by neighbour-joining analysis and were congruent by maximum likelihood method. All these Wolbachia strains of Taiwan were genetically affiliated to supergroups A and B with high sequence similarity of 98.3-100% and 98.6-100%, respectively. Intra- and inter-group analysis based on the genetic distance (GD) values indicated a lower level (GD < 0.017) within the group A strains of Taiwan compared with the group B (GD > 0.576) of other Wolbachia strains, as well as a lower level (GD < 0.062) within the group B strains of Taiwan compared with the group A (GD > 0.246) of other Wolbachia strains. Our results provide the first genetic identification of Wolbachia endosymbiont in Rh. sanguineus ticks collected from Taiwan, and detection of Wolbachia in male and nymphal ticks may imply the possible mechanism of transstadial transmission in Rh. sanguineus ticks.

Pattern and magnitude of genetic diversity in Pinus gerardiana wall. Populations

Twelve populations of Pinus gerardiana in North- west Himalayas of India were analysed for isozyme variation based on the seven enzyme systems. In isozyme analysis, of the 16 gene loci identified for the assayed seven enzyme, six loci under six enzyme systems were polymorphic. Only one enzyme system i.e. GDH does not show any polymorphic loci. The mean number of alleles per locus was 1.48 and mean expected heterozygosity was 15%. The gene pool allelic differentiation among the populations varied from 38.2% to 45. 2% whereas gene pool genotypic differentiation varied from 52% to 60%. For all possible pairs of populations Nei’s genetic distance values averaged 0.0021.The value of differentiation observed in the study could be attributed to the adaptive mechanism to the microenvironment shows high level of polymorphism.

Short Communication: The mitochondrial cytochrome c oxidase subunit I (COI) for identification of batoids collected from landed sites in Medan, Indonesia

Abstract. Lubis K, Sudibyo M, Farajallah A, Hanim N. 2020. Short Communication: The mitochondrial cytochrome c oxidase subunit I (COI) for identification of batoids collected from landing sites in Medan, Indonesia. Biodiversitas 21: 5414-5421. Batoids are member of Elsamoranch subclass which consist of many species. Most of batoids species are overexploited, especially in Medan Indonesia. Up to presents, the information about diversity of rays on the east coast of North Sumatra, Indonesia was very limited. Therefore, this research aimed to investigate the diversity of rays on the east coast of North Sumatra. We examined the morphological trait of 82 individuals of batoid from three landing sites on the east coast of North Sumatra, namely: Tanjung Balai, Belawan, and Percut, then identify its species based on determination key. After that, we collected pectoral muscle tissue from an individual in each species which successfully identified to extract its genomic DNA. Molecular based identification was carried out by using DNA fragment form COI gene. The successfully amplificated COI gene DNA fragment then was sequenced and analyzed. Based on morphological trait, we successfully identifying nine species of batoid, which is Maculabatis gerrardi, Gymnura poecilura, Dasyatis zugei, Brevitrygon heterura, Neotrygon kuhlii, Hemitrygon bennettii, Rhinobatos jimbaranensis, Rhinoptera javanica, and Taeniura lymma. The result of identification based on COI gene DNA fragment was in congruent with morphological-based identification based on data BLAST-N and genetic distance value within same species. The nucleotide diversity within same species ranged from 0-15 nucleotide variants.

GENETIC OF Panulirus versicolor LOBSTER IN CENDRAWASIH BAY PAPUA AND LOMBOK WATERS WEST NUSA TENGGARA

The purpose of this study was to determine the level of diversity and genetic relationship of Panulirus versicolor lobsters in Cenderawasih Bay and Lombok waters based on the cytochrome oxidase I (COI) gene. The results showed the level of genetic diversity of the two populations was very high and generally did not differ greatly between populations. We identified 6 haplotypes for P. versicolor lobster populations from Cenderawasih Bay and 7 haplotypes for P. versicolor lobster populations from Lombok waters. Network analysis shows that several P. versicolor lobster individuals from the Cendeawasih Bay and Lombok waters had similar haplotypes. The population of Cenderawasih Bay with Lombok waters was closely related to the average genetic distance value P-distance 0.005 (s.d 0.001) and the results of phylogenetic tree reconstruction showed that the two populations of P. versicolor lobsters form a monophyletic clade (close relatives).

Rapid size change associated with intra-island evolutionary radiation in extinct Caribbean \u201cisland-shrews\u201d

BackgroundThe Caribbean offers a unique opportunity to study evolutionary dynamics in insular mammals. However, the recent extinction of most Caribbean non-volant mammals has obstructed evolutionary studies, and poor DNA preservation associated with tropical environments means that very few ancient DNA sequences are available for extinct vertebrates known from the region’s Holocene subfossil record. The endemic Caribbean eulipotyphlan family Nesophontidae (“island-shrews”) became extinct ~ 500 years ago, and the taxonomic validity of many Nesophontes species and their wider evolutionary dynamics remain unclear. Here we use both morphometric and palaeogenomic methods to clarify the status and evolutionary history of Nesophontes species from Hispaniola, the second-largest Caribbean island.ResultsPrincipal component analysis of 65 Nesophontes mandibles from late Quaternary fossil sites across Hispaniola identified three non-overlapping morphometric clusters, providing statistical support for the existence of three size-differentiated Hispaniolan Nesophontes species. We were also able to extract and sequence ancient DNA from a ~ 750-year-old specimen of Nesophontes zamicrus, the smallest non-volant Caribbean mammal, including a whole-mitochondrial genome and partial nuclear genes. Nesophontes paramicrus (39-47 g) and N. zamicrus (~ 10 g) diverged recently during the Middle Pleistocene (mean estimated divergence = 0.699 Ma), comparable to the youngest species splits in Eulipotyphla and other mammal groups. Pairwise genetic distance values for N. paramicrus and N. zamicrus based on mitochondrial and nuclear genes are low, but fall within the range of comparative pairwise data for extant eulipotyphlan species-pairs.ConclusionsOur combined morphometric and palaeogenomic analyses provide evidence for multiple co-occurring species and rapid body size evolution in Hispaniolan Nesophontes, in contrast to patterns of genetic and morphometric differentiation seen in Hispaniola’s extant non-volant land mammals. Different components of Hispaniola’s mammal fauna have therefore exhibited drastically different rates of morphological evolution. Morphological evolution in Nesophontes is also rapid compared to patterns across the Eulipotyphla, and our study provides an important new example of rapid body size change in a small-bodied insular vertebrate lineage. The Caribbean was a hotspot for evolutionary diversification as well as preserving ancient biodiversity, and studying the surviving representatives of its mammal fauna is insufficient to reveal the evolutionary patterns and processes that generated regional diversity.

Application of EST-SSR markers for analysis of polymorphism of lettuce varieties (Lactuca sativa L.) of domestic breeding

Purpose. Determination of molecular genetic polymorphism of lettuce cultivars of Ukrainian breeding by EST-SSR markers. Methods. Molecular genetic analysis, statistical methods. Results. The results of molecular genetic polymorphism study of 7 lettuce cultivars by 7 EST-SSR markers are presented. As a result of the analysis by studied markers, 37 alleles were detected with an average 5.29 alleles per locus. The KSL-92 marker, which identified 7 alleles, proved to be the most polymorphic (PIC – Polymorphism Information Content 0.98). The lowest PIC value (0.57) was noted for the KSL-37 marker by which 3 alleles were identified. For assessing the genetic diversity of lettuce cultivars by EST-SSR markers, genetic distances between cultivars were determined based on Jaccard’s similarity coefficient. It was determined that the most similar cultivars with genetic distances 0.17 were ‘Zorepad’ and ‘Malakhit’, ‘Malakhit’ and ‘Dublianskyi’, ‘Dublianskyi’ and ‘Smuhlianka’, ‘Krutianskyi’ and ‘Smuhlianka’. The most distant cultivar was ‘Skarb’ with a genetic distance 0.00 compared to other studied cultivars. According to the calculated genetic distances, the cultivars ‘Zorepad’ and ‘Malakhit’, ‘Malakhit’ and Dublianskyi’, which belong to the same variety Lactuca sativa L. var. secalina have a strong genetic similarity. The cultivars‘Skarb’ and ‘Pohonych’, which belong to the varieties Lactuca sativa L. var. longifolia and Lactuca sativa L. var. angustana, respectively, were genetically distant, what was confirmed by genetic distances values. It was determined that the Shannon index within the lettuce variety by 7 EST-SSR markers is 0.61, between varieties – 0.96, the average value is 1.57. Conclusions. According to the results of studies of 7 lettuce cultivars, it was found that the highest polymorphism was determined by the KSL-92 marker, the minimum of alleles number (3 alleles) was identified by KSL-37 marker. Based on calculated genetic distances, it was noticed that lettuce cultivars, genetic distances between which are 0.17, were the most similar. The most distant cultivar based on 7 EST-SSR markers was ‘Skarb’ cultivar.

Genetic Characterization of Some Cyanobacterial Species Using by RAPD-PCR Technique

Cyanobacteria are the ecologically important organisms due to they thrive in wide variety of habitats and some with the ability to produce secondary metabolites known as cyanotoxin. Besides classical identification methods, DNA fingerprint and many other PCR based molecular approaches have being adopted and well used in the molecular systematics and genetic characterization of Cyanobacteria. In this study, 7 bacterial isolates were analyzed through the RAPD-PCR technique using 15 different randomly selected primers. All the bacterial isolates were produced 306 completely polymorphic amplification products. A minimum 12 and maximum 35 different PCR fragments were obtained by the OPA-14 and Hip-GC primers respectively. The size of RAPD-PCR fragments were varied between 175-3.000 bp. Two different dendrogrames (UPGMA ve Neighbor Joining) were created using Nei’s genetic distance and similarity values, to identify genetic relationships among analyzed bacterial isolates. According to the results, the Synechococcus elongatus and Pseudoanabaena moniliformis are defined as the most distant species, while the Anabaena affisinis and Arthrospira sp. are determined as the closest organisms. Consequently, randomly selected primers have generated 100% polymorphic fragments, indicating high efficiency and successful utilization of RAPD-PCR technique in the genetic characterizations and molecular systematics of different Cyanobacteria isolates. Keywords: Cyanobacteria, genetic characterization, DNA polymorphism, RAPD-PCR technique. DOI: 10.7176/JSTR/6-09-09

The Spatial-Genetic Population Structure of Eptesicus nilssonii (Chiroptera, Vespertilionidae) on the Southern Border of Its Range within European Russia

The spatial and genetic structure of the Eptesicus nilssonii population was studied. The species is characterized by conservatism of wintering sites. The key territories in the gene flow between colonies are swarming sites. After wintering, most individuals fly to a distance not exceeding 15 km, which is confirmed by the positive values of genetic isolation distance (p ≤ 0.05). Females are characterized by natal philopatry, whereas males are characterized by natal dispersal. High genetic diversity and moderate genetic differentiation were found in wintering areas and summer habitat areas. Most intrapopulation groups are heterogeneous, but some show deviations from the Hardy–Weinberg equilibrium (p < 0.05), and inbreeding is possible.

Genetic characterization of silkworm (Bombyx mori L.) strains (Lepidoptera: Bombicidae) with different geographical origin on the basis of isozyme markers

The aim of the present study was to assess genetics variations within and among strains with different geographical origin, belonging to Bulgarian germplasm bank of mulberry silkworm (Bombyx mori L.) and to establish their relationships using isoenzyme markers. Polyacrilamide gel electrophoresis (PAGE) was used to study the isoenzymes of nonspecific esterases (EST), malate dehydrogenase (MDH) and acid phosphatase (ACP) from haemolymph, phosphoglucomutase (PGM) and hexokinase (HK) from silk glands and alkaline phosphatase (ALP) from midgut of mulberry silkworm (Bombyx mori L.). Variability was evident in all of these enzyme systems among twelve strains from Bulgarian germplasm resources of B. mori. Total of nine loci were detected. All of them (100%) were polymorphic. “Null” alleles in four loci were determined. Intra- and inter-strain polymorphism was obtained. The degree of polymorphism ranged from 0% to 77.80%. Low levels of observed heterozygosity in comparison with the expected one have been calculated in almost all of strains as well as deviations from Hardy-Weinberg equilibrium in almost all analyzed loci, resulting of excess of homozygotes. The value of FST was 0.4903. The dendrogram constructed with the values of genetic distance manifests that Romanian strain Cislau Tokay is formed one main clade while the rest strains studied (from Bulgaria, Japan, China, Vietnam, Spain, Syria and Egypt) are formed the other clade with subclades. The genetic data of the tested strains from different geographical regions, would be used for identifying suitable parents for breeding programs with a view to yield improvement in this species with economic significance.

A new large canopy-dwelling species of Phyllodytes Wagler, 1930 (Anura, Hylidae) from the Atlantic Forest of the state of Bahia, Northeastern Brazil.

The known diversity of treefrogs of the genus Phyllodytes has rapidly increased in recent years, currently comprising 14 species. Recent field work in the Atlantic Rainforest of the state of Bahia lead to the discovery of a new large species of Phyllodytes which is herein described based on multiple evidence including morphological, acoustical and genetic data. Phyllodytes sp. nov. is one of the largest species within the genus and presents immaculate yellowish dorsum and limbs. The advertisement call of the species is composed of 7–31 notes (half pulsed/pulsatile-half harmonic) with frequency-modulated harmonics. Phyllodytes sp. nov. has a karyotype of 2n = 22 chromosomes, as also found in other species of the genus. Genetic distance values of the 16S mitochondrial rRNA among Phyllodytes sp. nov. and its congeners range between 6.4 to 10.2%. The description of another new species for this state reinforces the need for further taxonomic work with Phyllodytes in this region that has been revealed as a priority area for research and conservation of this genus.

Comparison of the mitochondrial phylogeographical structure of a generalist and two specialist frog species reveals contrasting patterns in the Eastern and Western Cape provinces of South Africa

AbstractIn this study, we examined the phylogeographical structure of three frog species (Anhydrophryne rattrayi, Arthroleptis wageri and Cacosternum nanum) in the Eastern and Western Cape provinces of South Africa. The first two species are forest dwelling and exhibit direct development, whereas the last species is a habitat generalist, breeding in open freshwater bodies and exhibiting rapid metamorphosis. Evolutionary relationships were inferred using combined mitochondrial DNA (mtDNA) sequence data [16S rRNA and cytochrome b (Cytb)]. Divergence times were estimated for each species using the combined mtDNA dataset, and population genetic structuring was inferred using haplotype networks and analysis of molecular variance using the rapidly evolving Cytb locus. The two forest-dwelling species (Anhydrophryne rattrayi and Arthroleptis wageri) each revealed two statistically well-supported clades and were characterized by marked genetic differentiation and the general absence of shared maternal haplotypes, indicating no maternal gene flow between conspecific populations; a result corroborated by moderate values of pairwise genetic distance. In contrast, for the generalist species C. nanum, two shallow clades were observed and several haplotypes were shared between localities, indicating moderate maternal gene flow. Diversification in the two forest-dwelling species occurred during the Plio-Pleistocene climatic oscillations and was associated with increased xeric conditions, whereas in C. nanum a recent, Holocene divergence was inferred. Ancient climatic factors thought to be causal in the divergences within each of the three species are discussed. The marked mtDNA differentiation in the two forest specialist species suggests the presence of distinct management units that should be considered in future conservation management decisions.