Genetic Identity Values Research Articles

Allozyme differentiation of two populations of the genus Neoplecostomus Eigenmann & Eigenmann, 1888 (Teleostei, Loricariidae) from the upper Paraná River basin, Brazil

Allozyme electrophoresis was used to examine 12 enzymatic systems in two populations of the genus Neoplecostomus from the Paraná River basin. Samples of Neoplecostomus sp. 1 were collected in Paraitinguinha stream of the Tietê River basin, in the municipality of Salesópolis, São Paulo State, and those of Neoplecostomus sp. 2 from São Domingos stream of the Rio Grande River basin, in the municipality of Muzambinho, Minas Gerais State. The genetic variability of the two populations was estimated by Nei’s expected heterozygosity and was considered lower than average for populations of freshwater fish. The proportion of polymorphic loci was low (only 5.26% for the locus Idh). The low frequency of heterozygosity for both populations revealed a high fixation of alleles for each locus. Homozygote excess was observed in both populations. The values of Nei’s genetic identity and the presence of loci with different allele frequencies in both populations may imply that the two populations belong to different species. The genetic variability between populations was compared to other data for loricariids.

Multiple paternity in the Black Caiman (Melanosuchus niger) population in the Anavilhanas National Park, Brazilian Amazonia

AbstractThe formation of dominance hierarchies in which the female mates with a large dominant male is common among crocodilians. However, there is the possibility of polyandry, in which females mate with multiple partners during a single breeding season and generate offspring with multiple paternity. In the present study, eight pairs of heterologous primers developed for Alligator mississippiensis and Caiman latirostris were used to determine whether multiple paternity exists in the Black Caiman, Melanosuchus niger. For such, we analyzed 34 Black Caiman offspring from the Anavilhanas Archipelago in the Negro River (state of Amazonas, Brazil). The specimens came from six groups, each containing five or six hatchlings. Paternity exclusion and genetic identity indices were calculated to test the robustness of the microsatellite loci. Simple allele counts and maximum likelihood estimation of family clusters were used to determine the likelihood of occurrence of multiple paternity. Among the eight loci tested, five were effective at determining paternity, with paternity exclusion values close to 1.0 (QC = 0.92) and genetic identity values close to zero (IC < 0.01). Using the simple allele count, six cases of multiple paternity were detected and confirmed in three hatchling groups by four different microsatellite loci. However, maximum likelihood analysis indicated multiple paternity in all the groups analyzed, with five family clusters identified in one hatchling group alone. Considering that this species is listed according to IUCN as Lower Risk/Conservation Dependent, our results have direct conservation implications. Multiple paternity increases effective population size by maintaining genetic variation, and thus could be an important mechanism to maintain genetic diversity in isolated local populations.

Allozyme comparison of the species and colour morphs of the nemertean genus Quasitetrastemma Chernyshev, 2004 (Hoplonemertea: Tetrastemmatidae) from the Sea of Japan

Biochemical genetics was applied to clarify the taxonomic status of the colour morphs of Quasitetrastemma nigrifrons and the sibling species Quasitetrastemma stimpsoni. Five colour morphs and two species were compared using 17 and 24 allozyme loci, respectively. The high average genetic identity value obtained for most of the colour morphs of Q. nigrifrons (I = 0.981) suggests that they belong to the same species. Both Q. stimpsoni and Q. nigrifrons have a lower average I-value (I = 0.718 ± 0.089) and are therefore considered to be separate species. According to the allozyme data, Q. nigrifrons var. pallidum is a heterogeneous group; most specimens are more similar to Q. nigrifrons, although some are closer to Q. stimpsoni.

Morphometric and Allozyme Variation inCulex tritaeniorhynchusMosquito Populations from India

Four populations of Culex tritaeniorhynchus (Giles) (Diptera: Culicidae), collected from Bellary, Cuddalore, Pune, and the Microbial Containment Complex laboratory culture in India were analyzed for morphological and allozyme variation. Multivariate analysis based on eight morphological characteristics and three morphometric indices was used to investigate the morphological variations among the four populations. Principal component analysis of the data suggested that siphon, saddle, and anal gills related variables were most important. Discriminant factor analysis of morphological data revealed that the four populations form significantly different clusters which can be differentiated from each other based on siphon, saddle, and pectin teeth related variables. Allozyme electrophoresis of the four populations revealed that the mean heterozygosity per locus value had high variation, ranging from 0.0879 to 1.794. Fst values between 0 and 0.519 suggested genetic differentiation within these populations. Fis values ranged from 0 to 1 with most of the values closer to 1. The allelic frequencies and Nei's genetic identity values showed that genetic differences between populations were small, but significant. Some of the morphological and allozyme variations in the Cx. tritaeniorhynchus populations could be partly attributed to the environmental conditions. The findings suggested that transition of morphological characters and allozyme variations in Cx. tritaeniorhynchus populations seem to be consequences of influence and selection by the environmental conditions. These results indicated that populations of Cx. tritaeniorhynchus in non-endemic areas of Japanese encephalitis (JE) virus infection have higher adaptability as compared to endemic areas of JE infection.

Genetic variation in the endangered Rutaceae species Citrus hongheensis based on ISSR fingerprinting

Citrus hongheensis is a critically endangered species endemic to the Honghe river region in southeastern Yunnan, China. Its genetic diversity and differentiation were investigated using Inter-Simple Sequence Repeat (ISSR) markers. One hundred primers were screened, and a total of 245 loci were amplified from seven natural populations by 13 informative and reliable primers. Of these 245 ISSR loci, 233 were polymorphic and the detected variations revealed a relatively high level of intraspecific genetic diversity. At the population level, the mean percentage of polymorphic loci (PPB) was 36.50%, while the average expected heterozygosity (He) and Shannon diversity index (Ho) were 0.1327 and 0.1972, respectively. At the species level (across all populations), PPB was 95.10%, while He and Ho were 0.3520 and 0.5195, respectively. A high Gst value (0.6247) indicated that there is significant differentiation among populations, which was confirmed by AMOVA analysis (I broken vertical bar st = 0.6420). Pairwise genetic identity (I) values among populations ranged from 0.6341 to 0.7675, with a mean of 0.7008. We propose that the high level of genetic differentiation may be the result of habitat fragmentation and limited gene flow (Nm = 0.1502). For effective in situ conservation and population restoration of C. hongheensis it will be important to maintain historical processes, including high outbreeding rates, sufficient gene flow, and large effective population sizes.

English

Inter-simple sequence repeats markers were used to estimate the genetic diversity of Pogonatherum paniceum (Lam.) Hack. from Sichuan Province, Yunnan Province, Chongqing City and Guangxi Zhuang  Autonomous Region in China. 100 primers were carried out on 22 wild populations, 14 could produce highly reproducible inter-simple sequence repeats markers′ bands. Out of the 239 discernable DNA fragments, 227 were polymorphic. The percentage of polymorphic bands was 94.98% at the species level. Nei’s gene diversity and Shannon information index were 0.312 and 0.471, respectively. This indicated that the genetic diversity of P. paniceum (Lam.) Hack. was low. The values of genetic identity ranged from 0.548 to 0.820 with a mean of 0.673. Nei’s genetic distance between 22 populations ranged from 0.198 to 0.601. Unweighted pair group method with arithmetic mean cluster analysis based on Nei’s genetic distance showed that most populations were positioned into the relevant areas. Significant correlation between genetic and geographic altitude distances among populations was found by Mantel test. The high score of percentage of polymorphic bands might be caused by low frequent polymorphism distributed in different populations.   Key words: P. paniceum (Lam.) Hack., ISSR, genetic diversity, southwest China.

Mitochondrial DNA control region database in Banco Nacional de Datos Genéticos, Argentina

To analyze the distribution of different haplotypes of mitochondrial control region DNA in a large sample of argentine population who assisted to the Banco Nacional de Datos Genéticos (BNDG) looking for their identity in cases of civil state suppression during the dictatorial government (1976–1983). A total of 1168 unrelated argentine individuals who assisted to the BNDG were sampled for the analysis. Mitochondrial DNA Control Region sequences were determined for both hypervariable regions 1 (HV1) and 2 (HV2). Blood samples were used as the DNA source. The amplification for both hypervariable regions was performed in a Perkin Elmer 9700 thermal cycler. The cycle sequencing was performed using the BigDye ® Terminator v 1.1 Cycle Sequencing Kit (Applied Biosystems) and automated sequencing was performed in an ABIPRISM ® 3100 Genetic Analyzer (Applied Biosystems). Analysis of mitochondrial DNA sequencing data was performed by manual method. The hypervariable region 1 (HV1) was analyzed between positions 16023 and 16428 and the hypervariable region 2 (HV2) between 50 and 480 according to the Anderson Sequence. To analyze these results a database was created and statistical parameters were calculated. From 1168 haplotypes analyzed, 794 were unique. Haplotype frequencies were estimated by haplotype counting. Values of Genetic Identity ( P) and Genetic Diversity ( h) were calculated, being 3.3939 × 10 −3 and 0.9974 respectively. This Mitochondrial Control Region DNA database provides useful information for genetic profiles comparison and maternal lineage determination in our lab.

GENETIC AND MORPHOLOGIC DIVERSITY IN CASTANEA MOLLISSIMA IN YANSHAN DISTRICT AND THE DABIE MOUNTAIN DISTRICT, CHINA

Genetic and morphological diversity of Castanea mollissima were surveyed in China including Yanshan district and the Dabie Mountain district in the summers of 2005 and 2006. Nine populations including 82 varieties were sampled at Beijing, Hebei, Shandong, Zhejiang, Shanxi, Hubei, Henan, Jiangsu, and Anhui provinces. Allozyme analysis indicates that genetic subdivision is present in all populations at relatively low levels and variation among population is 4.25%. Significant differences existed in allele frequencies among populations. Genetic identity values range from 0.8766 to 0.9978. Within population variation was greater than that among population. Patterns of morphological variance, estimated through measurements of leaf length, leaf width, index of leaf, nut length, nut width, index of nut, weight of nut, paralleled those displayed by allozyme analysis. Species conservation strategies for Castanea mollissima should concentrated on the maintenance of within-population levels of diversity, such as varieties, and protection of adjacent populations.

Assessment of genetic variation of selected spiderplant (Cleome gynandra L.) morphotypes from western Kenya

In the genetic variation study of the 4 spiderplant morphotypes, 10 out of the 12 primers screened generated 31 polymorphic bands. Nei’s coefficient of gene differentiation showed that the morphotypes were differentiated. Nei’s genetic identity value calculated from the RAPD data ranged from 0.3 to 0.6 indicating the degree of genetic identity between the morphotypes. Dendrograms constructed from a matrix calculated on the basis of UPGMA clustering algorithm revealed that the 4 morphotypes formed 3 groups.

Population Genetics of Astragalus bibullatus (Fabaceae) Using AFLPs

Astragalus bibullatus (Fabaceae) is an endangered plant species endemic to limestone cedar glades in Tennessee. Data from 134 amplified fragment length polymorphism (AFLP) fragments indicate that populations of this species are genetically very similar, with genetic identity values ranging from 0.976 to 0.991. Approximately 10% of the species' total genetic variation is due to differences among populations (F(ST) = 0.102), and a principle coordinate analysis based on genetic distance among individuals revealed considerable overlap between populations. Averaging across populations, 38.4% of the AFLP markers were polymorphic, and the mean expected heterozygosity was 0.120. These estimates are higher than what has previously been reported for this species based on a survey of allozyme variation. Despite the overall similarity of populations of this species, a model-based clustering approach revealed the presence of 2 (possibly 3) genetically distinct subgroups. The results of this study highlight the utility of DNA-based markers for conservation genetic studies in genetically depauperate species and reveal that detectable levels of genetic substructuring may be present even in relatively undifferentiated species.

Genetic variation in the soil phthiracarid mite, Steganacarus (S.) magnus (Nicolet, 1855) (Acarida, Oribatida) (Notulae Oribatologicae XL)

Genetic divergence and variability at 14 enzyme loci were examined in and between Italian populations of two edaphic Oribatid (Acarida, Oribatida) species, Steganacarus (Steganacarus) magnus (8 populations) and S. (S.) hirsutus (1 population). The seven populations belonging to S. (S.) magnus can be divided into two groups according to their phenotype, form anomala (A) (MON, ARG, AST, CDO) and form magna (M) (MAL, MAM, RIF) while another can be considered as hybrid between the two preceding groups (ZOC). Genetic identity (I) values between the S. (S.) magnus populations in spite of their morphological differences ranged from 0.977 to 1.000 showing the great genetic similarity of simple local populations while those of S. (S.) hirsutus indicated two distinct morphological species. The genetic distances between all the populations examined were very low despite the ecological differences and geographical distances between the collecting sites. Genetic variability estimates in all the populations of both species were very low when compared to those reported for most arthropods. Some explanatory considerations are suggested.

Genetic diversity within and among populations of shortleaf pine (Pinus echinata Mill.) and loblolly pine (Pinus taeda L.)

Shortleaf pine (n=93) and loblolly pine (n=112) trees representing 22 seed sources or 16 physiographic populations were sampled from Southwide Southern Pine Seed Source Study plantings located in Oklahoma, Arkansas, and Mississippi. The sampled trees were grown from short- leaf pine and loblolly pine seeds formed in 1951 and 1952, prior to the start of intensive forest management across their native ranges. Amplification fragment length polymorphism (AFLP) markers were developed and used to study genetic diversity and its structure in these pine species. After screening 48 primer pairs, 17 and 21 pairs were selected that produced 794 and 647 AFLPs in shortleaf pine and loblolly pine, respectively. High-AFLP-based genetic diversity exists within shortleaf pine and loblolly pine, and most (84.73% in shortleaf pine; 87.69% in loblolly pine) of this diversity is maintained within physiographic populations. The high value of unbiased measures of genetic identity and low value of genetic distance for all pairwise comparisons indicates that the populations have similar genetic structures. For shortleaf pine, there was no significant correlation between geographic distance and genetic distance (r=0.28), while for loblolly pine there was a weak but significant correlation (r=0.51).

ISSR and RAPD Markers Assessed Genetic Variation of Aerides maculosum — an Epiphytic Orchid from Goa, India

Aerides maculosum Lindl is one of the most important orchids valued for its beautiful inflorescence/flowers. The present study aimed to understand the level of genetic variation among the populations of A. maculosum using RAPD and ISSR markers. Among the 35 primers tested, 13 RAPD and 6 ISSR primers were selected for the analysis. Total of 101 RAPD and 40 ISSR fragments were generated. High level of polymorphism was recorded in RAPD (90.45%) compared to ISSR (72.85 %). Nei’s average genetic identity values for different populations of A. maculosum- ranged from 0.465 to 0.762 (RAPD), while for ISSR it ranged from 0.475 to 0.975. The present study provides important insights about genetic variation in A. masculosum and may facilitates the conservation and management of this species.

Allozyme differentiation and relationships within Hypostomus Lacépède, 1803 (Osteichthyes: Loricariidae) from the upper Paraguay River basin, Brazil

Nine hypostomine populations from Manso Reservoir (Rio Manso and Rio Cuiabá, upper Paraguay River basin, Brazil) were surveyed using allozyme electrophoresis. Three, sampled at the same sites, were not identified to the species level and were designated as Hypostomus sp. 1, Hypostomus sp. 2 and Hypostomus sp. 3. The survey resulted in 25 loci from 14 scored enzyme systems. Allozyme data allowed diagnostic marker recording for all species analyzed, including the undescribed taxa. Mean expected heterozygosity values were quite variable, ranging from 0.029 to 0.079. Hypotheses to explain this variation are discussed. The allelic frequencies and Nei's genetic identity values showed that Hypostomus sp. 1, Hypostomus sp. 2 and Hypostomus sp. 3 should be considered true biological species, and distinct from the other five Hypostomus species and Pterygoplichthys anisitsi.

Population genetics of Matthiola bolleana (Brassicaceae) in the Canary Islands

Genetic variation at 11 isozyme loci was used to explore the levels and apportionment of genetic variation in the eight known populations of Matthiola bolleana, an endemic Brassicaceae to the Eastern Canarian islands of Fuerteventura and Lanzarote. Within islands, ecosystem antiquity and uniformity, lack of evidence for selection or genetic bottlenecks, the high genetic identities between the populations, and the low values of F ST converge to suggest that the high levels of variation detected have been maintained in a context of prolonged environmental stability through an overall predominance of outbreeding and unrestricted gene flow. Despite the geographical closeness between Fuerteventura and Lanzarote and the long range dispersal features of the propagules of M. bolleana, we detected a striking qualitative genetic differentiation between the two islands. We suggest that wind direction has made seed and pollen flow between Fuerteventura and Lanzarote much less likely than expected, and that the lack of inter-island dispersal has far overriden the influence of stochastic forces and of the reproductive attributes of M. bolleana in shaping the patterns of inter-island genetic differentiation. However, genetic similarity in M. bolleana is within the ranges defined by Canarian taxa for which the extent of genetic differentiation has also been assessed using the values of isozyme genetic identity.

Genetic variation and reproductive system among North American species ofNuttallanthus(Plantaginaceae)

We examined the effect of reproductive and life history strategies on the amount and partitioning of genetic variation in three annual species of Nuttallanthus. The North American species N. canadensis, N. floridanus, and N. texanus have regional to widespread ranges that overlap in the southeastern USA, are characterized by homogeneous populations and high fecundity, and possess showy, fragrant flowers seemingly adapted for insect pollination and outbreeding. Field and greenhouse studies on plants from 25 populations indicated that reproductive strategies were similar among species and showed predominant self-fertilization via cleistogamy and self-pollination prior to anthesis in chasmogamous flowers. Species were reproductively isolated and demonstrated complete cross-incompatibility after experimental crosses and no evidence for hybridization in mixed populations. Genetic variation was assessed using starch gel electrophoresis to resolve 15 isozyme loci in 50 populations. Conspecific genetic identity (I) values were high (0.819-0.936), but interspecific comparisons indicated many qualitative allelic differences and correspondingly low I values (0.516-0.623). Low levels of polymorphism and observed heterozygosity within populations and the disproportionate amount of gene diversity distributed among populations were concordant with reproductive data. The pattern of genetic differentiation was most similar to that observed in species with a predominantly inbreeding mating system.

Genetic diversity of Litsea szemaois, an endangered species endemic to China, detected by inter-simple sequence repeat (ISSR)

Litsea szemaois is a critically endangered species endemic to southern Yunnan,China. We assessed the genetic variability within and among eight extant populations of this species using ISSR PCR (10 primers). We expected a low genetic diversity level, but our results revealed an extraordinarily high level of specific genetic diversity (at species level: percentage of polymorphic loci PPB=87.01%, effective number of alleles N_(e)=1.4006, Nei's (1973) gene diversity H=0.2466, and Shannon's Information index H_(sp)=0.3826; at population level: PPB=37.99%, N_(e)=1.2500, Nei's (1973) gene diversity H=0.1418, and Shannon's Information index H_(pop)=0.2088. The diferences among populations in levels of genetic diversity were very obvious, with the highest level (PPB=72.73%) in Mandian population and the lowest level (PPB=18.18%) in Jinghong population. A low level of genetic differentiation among populations was detected based on Nei's genetic diversity analysis (37%), Shannon's diversity index (45%), and AMOVA (27.01%). This may result from out-breeding. Pairwise genetic identity (I) values among populations ranged from 0.8233 to 0.9761. There was no correlation between genetic and geographic distance among the populations studied. The influence of human activity and forest fragmentation may play a prominent role in creating this species's current endangered status.

Genetic diversity of Miyamasukashi‐yuri (Lilium maculatum Thunb. var. bukosanense), an endemic and endangered species at Mount Buko, Saitama, Japan

Abstract Lilium maculatum var. bukosanense, Miyamasukashi‐yuri in Japanese, grows endemically in Saitama Prefecture, Japan, and is listed in the Saitama Prefecture Red Data Book as a critically endangered plant. Articles about its genetic diversity and population genetic structure have not been reported. Before it is lost, population genetic studies can provide information for efficient in situ conservation as well as for possible future use in breeding programs. Therefore, we carried out a population genetic study of natural L. maculatum var. bukosanense using chloroplast DNA (cpDNA) and inter‐simple sequence repeat (ISSR) markers. In this study, fresh leaves of 46 L. maculatum var. bukosanense individuals were collected from two populations in Mount Buko. By polymerase chain reaction (PCR)‐restriction fragment length polymorphism analysis of cpDNA, we estimated the maternal origin of individuals sampled. Sixteen cpDNA primer pairs were tested, and only four of them produced clear bands. Twenty‐four combinations from these PCR fragments combined with six restriction enzymes were assayed; however, only 18 of them could be digested, producing two to four fragments. All individuals of L. maculatum var bukosanense analyzed were virtually identical for all primer–enzyme combinations. These findings suggest that the maternal origin of the 46 individuals analyzed is close. In addition, we analyzed ISSR markers to provide mainly biparental inheritance. PCR products of five anchored simple sequence repeat primers showed polymorphism, indicating that the individuals sampled were not clones, and thus it appears that they could have been reproduced from seeds. The primers yielded a total of 30 polymorphic bands (i.e. an average of six polymorphic bands per primer). The mean genetic distance and genetic identity values between the populations were 0.032 and 0.97, respectively. These findings suggest that all individuals from both populations are genetically similar. The individuals growing at 1000 m have greater genetic variation than those individuals from 650 m and this could possibly be attributed to altitude. A significant correlation between gene diversity and population size is also reported. From the results presented here some strategies for its in situ and ex situ conservation might be considered.

Esterase polymorphism in remanant populations of Aspidosperma polyneuron Müll.Arg. (Apocynaceae)

The population genetic structure of the endangered tree species Aspidosperma polyneuron Mull.Arg. (Apocynaceae) was reported based on analysis of esterase polymorphism in two remanant populations. Allelic variation was detected at three isoesterase loci (Est-3, Est-9, and Est-10). The proportion of polymorphic loci for both populations was 30% and deviation from Hardy-Weinberg equilibrium was observed for the Est-3 locus observed in the northern population. Segregation distortion and the lower level of observed and expected heterozygosity in this population were attributed to founder genotype. The high genetic identity values for northern and northwestern populations are in accordance with the low levels of interpopulation genetic divergence demonstrated by the F(ST) (0.03) value. The F(IS) value (0.23) indicated moderate levels of inbreeding. A. polyneuron can be indicated as an example of endangered species suggesting high genetic variation in contrast to the low genetic variation reported for endangered species. The esterase isozymes may be a good genetic marker for studies of natural A. polyneuron populations.

Comparative Analysis of Genetic Divergence among Sexual Ancestors of Apomictic Complexes Using Isozyme Data

Genetic variation of agamospecies might originate from mutations, facultative sexuality, and from hybridization of genetically divergent sexual taxa. Genetic variation and distance of sexual species of the apomictic Ranunculus auricomus complex are evaluated by means of isozyme markers for each of three populations of three diploid species, which are representatives of the two main morphological collective groups (coll.) in goldilocks (Ranunculus cassubicus coll., R. auricomus coll. s. str.). Low genetic identity values between the species ($$\mathrm{mean}\,=0.760$$) and between the two groups ($$\mathrm{mean}\,=0.721$$) support the hypothesis that the apomictic R. auricomus complex may have originated from hybrids of genetically very divergent ancestors. Since mutations, backcrossing to sexuals, and facultative recombination within agamospermous populations are probably rare in goldilocks, the genetic divergence of ancestors might be the most important factor for genetic and genotypic variation in agamospecies. To evaluate the generality of this feature, genetic diversity measures of agamospecies of other comparable complexes are compiled: the Antennaria rosea complex, the Antennaria neodioica complex, Erigeron compositus s.l., and Taraxacum sect. Ruderalia. All apomicts of these complexes are putatively of allopolyploid, recent origin with few unique alleles, are allopatric to sexual ancestors that inhibit backcrossing, and might have only a moderate facultative sexuality within populations. Genotypic diversity measures and observed heterozygosity (Ho) of apomicts are regressed against genetic diversity measures and mean genetic identity of the putative sexual ancestor taxa. Genetic distance of sexuals is a highly significant predictor of genotypic diversity in apomicts as measured by proportion of distinguishable multilocus genotypes per population ($$F=244.355$$, $$P=0.004$$) and significant for number of genotypes per population ($$F=18.875$$, $$P=0.023$$). Ho of sexuals is a significant predictor for Ho of apomicts ($$F=43.794$$, $$P=0.022$$). I conclude that genetic divergence of sexuals is an important factor for the origin of genotypic variation in agamic groups, although it might be often augmented by other factors, especially backcrossing with sexuals and recombination.