Genetic variation and differentiation in Juniperus excelsa M. Bieb. populations in Turkey

Genetic variation within and among six populations of Juniperus excelsa M. Bieb., in a common garden in Lakes District of Turkey, was analyzed using four nuclear microsatellite primer pairs originally developed for J. communis. A total of five loci were observed as Jc037 amplified two distinct size ranges. The number of alleles observed for the species varied from 2 to 13, with an average of 4.5 alleles per locus. The mean expected heterozygosity (H _e) of populations was 0.584, after correction for null alleles. The mean F _IS value (?0.014) was close to zero showing no significant deviation from Hardy–Weinberg equilibrium. A low level of genetic differentiation was observed among populations (F _ST = 0.028; p < 0.001) and Nei’s genetic distance ranged from 0.014 to 0.120 between population pairs. Furthermore, there was no significant correlation between genetic distances on the one hand and geographic distances and trait differentiation on the other hand. However, the eastern populations Bey?ehir and Sorgun showed very similar genotypic structures and were differentiated from all other populations. A continuous monitoring of phenotypic traits and the association between nucleotide variation in functional genes and adaptive traits such as drought and frost tolerance of J. excelsa populations in common gardens will be useful to design effective conservation strategies in the future.     

The Daghestan gene pool: Interethnic and intraethnic differentiation of eight aboriginal ethnic groups: Analysis based on data on the AB0 erythrocyte antigen systems

Analysis of the genetic variation of eight aboriginal Daghestan ethnic groups based on data on the AB0 and Rhesus blood groups has been carried out in a total sample of 18348 subjects. The degree of genetic differentiation (G _ST) and the levels of intraethnic (H _S) and interethnic (H _T) variations of Daghestan ethnic groups have been estimated at two hierarchical levels of the population system. Prevalence of intraethnic diversity over interethnic one has been found in Daghestan populations. The parameters of subdivision of Daghestan populations were compared with those for the populations of all other regions of the Caucasus and the Pamir. The population subdivision of ethnic groups of Daghestan and other regions of the Caucasus is lower than that of Pamir ethnic groups.     

Genetic characterization of Colombian Brahman cattle using microsatellites markers

Genetic structure and diversity of 3789 animals of the Brahman breed from 23 Colombian regions were assessed. Considering the Brahman Zebu cattle as a single population, the multilocus test based on the HW equilibrium, shows significant differences (P < 0.001). Genetic characterization made on the cattle population allowed to examine the genetic variability, calculating a H _o = 0.6621. Brahman population in Colombia was a small subdivision wthin populations (F _it = 0.045), a geographic subdivision almost non-existent or low differentiation (F _st = 0.003) and the F _is calculated (0.042) indicates no detriment to the variability in the population, despite the narrow mating takes place or there is a force that causes the variability is sustained without inbreeding actually affect the cattle population. The outcomes of multivariate analyses, Bayesian inferences and interindividual genetic distances suggested that there is no genetic sub-structure in the population, because of the high rate of animal migration among regions.     

Genetic structure, subdivision, and differentiation in stankewiczii pine (Pinus stankewiczii (Sukacz.) Fomin) populations from mountainous Crimea

In order to analyze the genetic structure, subdivision and differentiation within and between two small isolated populations of the Crimea relict endemic, Pinus stankewiczii (Sukacz.) Fomin, electrophoretic analysis of the isozyme variation at nine enzymatic systems was carried out using 183 oldest trees. It was demonstrated that in populations of P. stankewiczii, 80% of the genes were in polymorphic state. Each tree was heterozygous at 19.1% loci, and at 21.6% loci in artificial 50-year-old plantation. The genetic structure of two populations was less differentiated (D _N = 0.006), compared to their individual localities (D _N = 0.008?0.009). Within-population subdivision of the diffusely dispersed populations was higher (F _ST -G _ST = 1.8–2.0%) than that of the populations themselves (0.8%).     

Genetic variation in populations of Populus davidiana Dode based on microsatellite marker analysis

Populus davidiana Dode, the only aspen in Korea, is useful for restoration because of its fast growth and vigorous reproduction. This study was conducted to estimate the genetic diversity and subdivision in populations of P. davidiana in South Korea using microsatellite markers. DNA from 113 individuals from five populations was amplified using five microsatellite primers. Fifty-three alleles were detected, and the expected heterozygosity was 0.603. The populations of P. davidiana in Korea have high genetic variation despite their peripheral distribution. R _ST (0.213) indicated a significant level of genetic subdivision among populations compared to the differentiation among other aspen populations. The high conservation value of the populations is attributed to its ecological and commercial importance.     

Genetics of Brazil nut (Bertholletia excelsa Humb. & Bonpl.: Lecythidaceae)

Summary We provide an estimate of genetic variation within and between two populations of Bertholletia excelsa (Brazil nut), a large canopy tree found in the rain forests of South America. Average heterozygosity is 0.190, and 54.3% of the sampled loci are polymorphic. The population structure deviates significantly from Hardy-Weinberg expectations for Fest2 and Pgm2 (F =0.405 and 0.443, respectively) in one population, and highly significantly (F=-0.341) for Gdh in the other population. Although allele frequencies of the two populations differ significantly for Aat2, Est5, Mdh1, and Mdh2B, Nei's coefficient of gene differentiation (G_st) indicates that the between-population component (D_st) of genic diversity represents only 3.75% of the size of the within-population component (H_s). The implications of these findings in terms of conservation genetics are that much of the genetic diversity of this species may be preserved within one or a few populations. However, such populations must be very large because it appears that the large amount of genetic variation in Brazil nut populations is maintained by extensive gene flow and bonds of mating over a large area. The genetic architecture of Bertholletia excelsa is similar to that expected for an extensively diploidized paleopolyploid species.     

A Comparative Analysis of Genetic Diversity and Structure in Jaguars (Panthera onca), Pumas (Puma concolor), and Ocelots (Leopardus pardalis) in Fragmented Landscapes of a Critical Mesoamerican Linkage Zone

With increasing anthropogenic impact and landscape change, terrestrial carnivore populations are becoming more fragmented. Thus, it is crucial to genetically monitor wild carnivores and quantify changes in genetic diversity and gene flow in response to these threats. This study combined the use of scat detector dogs and molecular scatology to conduct the first genetic study on wild populations of multiple Neotropical felids coexisting across a fragmented landscape in Belize, Central America. We analyzed data from 14 polymorphic microsatellite loci in 1053 scat samples collected from wild jaguars (Panthera onca), pumas (Puma concolor), and ocelots (Leopardus pardalis). We assessed levels of genetic diversity, defined potential genetic clusters, and examined gene flow for the three target species on a countrywide scale using a combination of individual- and population-based analyses. Wild felids in Belize showed moderate levels of genetic variation, with jaguars having the lowest diversity estimates (H_E = 0.57 ± 0.02; A_R = 3.36 ± 0.09), followed by pumas (H_E = 0.57 ± 0.08; A_R = 4.20 ± 0.16), and ocelots (H_E = 0.63 ± 0.03; A_R = 4.16 ± 0.08). We observed low to moderate levels of genetic differentiation for all three target species, with jaguars showing the lowest degree of genetic subdivision across the country, followed by ocelots and pumas. Although levels of genetic diversity and gene flow were still fairly high, we detected evidence of fine-scale genetic subdivision, indicating that levels of genetic connectivity for wild felids in Belize are likely to decrease if habitat loss and fragmentation continue at the current rate. Our study demonstrates the value of understanding fine-scale patterns of gene flow in multiple co-occurring felid species of conservation concern, which is vital for wildlife movement corridor planning and prioritizing future conservation and management efforts within human-impacted landscapes.     

Genetic structure of populations of Norway spruce (<Emphasis Type="Italic">Picea abies</Emphasis> (L.) Karst. from Ukrainian Carpathians

The genetic diversity, subdivision, and differentiation of nine populations of Norway spruce (Picea abies (L.) Karst.) in Ukrainian Carpathians were studied using electrophoretic analysis of variability of enzyme systems in 346 trees aged from 80 to 150 years. Based on electrophoretic fractionation of enzymes extracted from seed endosperms in vertical slabs of 7.5% polyacrylamide gel, 20 loci of nine enzyme systems (ADH, ACP, DIA, GDH, GOT, MDH, LAP, FDH, SOD) were identified, and 71 allele variant were revealed. Each tree was heterozygous on average in 15.8% of its genes. The populations were characterized by low subdivision (F _ST = 0.017) and differentiation (D _N = 0.005). The main contribution to heterogeneity of population genetic structure was made by loci Dia-3, Lap-1, and Sod-3. Clustering and multivariate analysis revealed no observed trends in geographical or altitudinal position of the populations.     

Genetic diversity of the house mouse <Emphasis Type="Italic">Mus musculus</Emphasis> and geographic distribution of its subspecies-specific RAPD markers on the territory of Russia

Genetic diversity and geographic distribution of taxon-specific RAPD markers was examined in ten local populations of the house mouse Mus musculus (n = 42). The house mice were generally characterized by moderate genetic variation: polymorphism P ₉₉ = 60%, P ₉₅ = 32.57%; heterozygosity H = 0.12; the observed allele number n _a = 1.6; the effective allele number n _e = 1.18; the within-population differentiation ?_s = 0.388; and Shannon index I = 0.19. The degree of genetic isolation of individual local populations was greatly variable. The genetic subdivision index G _st varied from 0.162 to 0.770 at the gene flow of Nm = 2.58?0.149, while the among-population distances D _N varied from 0.026 to 0.178. The largest part of the genetic diversity was found among the populations (H _T = 0.125), while the within-population diversity was twice lower (H _S = 0.06). The samples examined were well discriminated relative to the sets of RAPD markers. The character distribution pattern provided conditional subdivision of the mice into the “western” and the “eastern” groups with the putative boarder along the Baikal Lake. The first group was characterized by the prevalence of the markers typical of M. m. musculus and M. m. domesticus. The second group was characterized by the prevalence of the markers typical of M. m. musculus, M. m. gansuensis, M. m. castaneus, M. m. domesticus, and M. m. wagneri. The genotype of the nominative subspecies M. m. musculus was background for all populations. In the populations examined some of earlier described subspecies-specific molecular markers were found at different frequencies, pointing to the involvement of several subspecies of M. musculus in the process of hybridization.     

Differentiation among populations of the Rhodiola iremelica Boriss. (Grassulaceae) in the Southern Urals

Isoenzyme markers and polyacrylamide gel electrophoresis have been used to study the genetic structure of populations of Rhodiola iremelica Boriss. (Grassulaceae), a southern Ural endemic protected by the state and included in the Red Data Book of Bashkortostan Republic. A relatively large genetic variation at the species level has been found. The subdivision among populations (F _ST = 0.115) is higher than in most cross-pollination angiosperms. No consistent pattern has been observed in the spatial distribution of its genetic variation. The relatively high differentiation among samples of R. iremelica characterized by small effective population sizes, may be accounted for by genetic drift, inbreeding, and a restricted gene flow. To preserve the population gene pool, in situ protection of the species in nature is insufficient. It seems advisable to create synthetic populations ex situ and reintroduce them into nature.     

Population Genetic Structure of a Widespread Bat-Pollinated Columnar Cactus

Bats are the main pollinators and seed dispersers of Stenocereus thurberi, a xenogamous columnar cactus of northwestern Mexico and a good model to illustrate spatial dynamics of gene flow in long-lived species. Previous studies in this cactus showed differences among populations in the type and abundance of pollinators, and in the timing of flowering and fruiting. In this study we analyzed genetic variability and population differentiation among populations. We used three primers of ISSR to analyze within and among populations genetic variation from eight widely separated populations of S. thurberi in Sonora, Mexico. Sixty-six out of 99 of the ISSR bands (P = 66.7%) were polymorphic. Total heterozygosity for all populations sampled revealed high genetic diversity (H_sp = 0.207, H_BT = 0.224). The AMOVA showed that most of the genetic variation was within populations (80.5%). At the species level, estimates of population differentiation, θ = 0.175 and θ^B = 0.194, indicated moderate gene flow among populations. The absence of a significant correlation between genetic and geographic distances indicated little isolation by geographic distance. The large genetic variation and diversity found in S. thurberi is consistent with its open reproductive system and the high mobility of bats, a major pollinator. However, small changes in number or kind of pollinators and seed dispersal agents, in the directionality of migratory routes, and/or in the timing of flowering and fruiting among populations, can critically affect gene flow dynamics.     

Genetic differentiation of Altai-Sayan endemic Hedysarum theinum Krasnob. (Fabaceae) evaluated by inter-simple sequence repeat analysis

The objective of the research described in this paper was to evaluate the level of genetic variability and differentiation between the populations of Hedysarum theinum Krasnob., endemic species of Altai-Sayan Mountains. In this study, six inter-simple sequence repeat (ISSR) primers were used and generated a total of 132 molecular markers, 126 of which were polymorphic (95.5%). The large amount of DNA polymorphism at the intrapopulation level (H _pop/H _sp = 70.5) was evidenced by the analysis of a molecular variance (AMOVA) of 88.2%. The high genetic similarity (I = 0.875) detected between the populations of H. theinum reflects the strongly restricted endemic range of H. theinum, which facilitates the gene flow among populations and outcrossing. Due to the significant genetic diversity revealed among individuals against a background of moderate population differentiation collecting samples for ex situ H. theinum conservation from a small number of populations is acceptable. Finally, selected highly polymorphic ISSR markers produced consistently repeatable patterns are discussed as a powerful tool for genotype identification and the qualification of root feedstock.     

Genetic variation in cultivated Rheum tanguticum populations

To examine whether cultivation reduced genetic variation in the important Chinese medicinal plant Rheum tanguticum, the levels and distribution of genetic variation were investigated using ISSR markers. Fifty-eight R. tanguticum individuals from five cultivated populations were studied. Thirteen primers were used and a total of 320 DNA bands were scored. High levels of genetic diversity were detected in cultivated R. tanguticum (PPB = 82.19, H = 0.2498, H_B = 0.3231, I = 0.3812) and could be explained by the outcrossing system, as well as long-lived and human-mediated seed exchanges. Analysis of molecular variance (AMOVA) showed that more genetic variation was found within populations (76.1%) than among them (23.9%). This was supported by the coefficient of gene differentiation (G_st = 0.2742) and Bayesian analysis (θ_B = 0.1963). The Mantel test revealed no significant correlation between genetic and geographic distances among populations (r = 0.1176, p = 0.3686). UPGMA showed that the five cultivated populations were separated into three clusters, which was in good accordance with the results provided by the Bayesian software STRUCTURE (K = 3). A short domestication history and no artificial selection may be an effective way of maintaining and conserving the gene pools of wild R. tanguticum.     

Genetic consequences of fragmentation in “arbor vitae,” eastern white cedar (Thuja occidentalis L.), toward the northern limit of its distribution range

We tested the hypothesis that marginal fragmented populations of eastern white cedar (EWC) are genetically isolated due to reduced pollen and gene flow. In accordance with the central-marginal model, we predicted a decrease in population genetic diversity and an increase in differentiation along the latitudinal gradient from the boreal mixed-wood to northern coniferous forest. A total of 24 eastern white cedar populations were sampled along the north-south latitudinal gradient for microsatellite genotyping analysis. Positive F_is values and heterozygote deficiency were observed in populations from the marginal (F_is = 0.244; P_HW = 0.0042) and discontinuous zones (F_is = 0.166; P_HW = 0.0042). However, populations from the continuous zone were in HW equilibrium (F_is = −0.007; P_HW = 0.3625). There were no significant latitudinal effects on gene diversity (H_s), allelic richness (AR), or population differentiation (F_st). Bayesian and NJT (neighbor-joining tree) analyses demonstrated the presence of a population structure that was partly consistent with the geographic origins of the populations. The impact of population fragmentation on the genetic structure of EWC is to create a positive inbreeding coefficient, which was two to three times higher on average than that of a population from the continuous zone. This result indicated a higher occurrence of selfing within fragmented EWC populations coupled with a higher degree of gene exchange among near-neighbor relatives, thereby leading to significant inbreeding. Increased population isolation was apparently not correlated with a detectable effect on genetic diversity. Overall, the fragmented populations of EWC appear well-buffered against effects of inbreeding on genetic erosion.     

Analysis of population genetic structure of two closely related tortricid species of economic importance on macadamias and litchis in South Africa

Abstract

• 1 The macadamia nut borer Thaumatotibia (Cryptophlebia) batrachopa and the litchi moth Cryptophlebia peltastica are Afrotropical species causing extensive damage to cultivated macadamias and litchis in the northernmost provinces in South Africa. Cryptophlebia peltastica also occurs as natural populations throughout the country.
• 2 To analyse the population genetic structure of the two species, amplified fragment length polymorphism analysis was conducted. Patterns of genetic diversity in C. peltastica populations in the Mpumalanga province, where the species is controlled, were compared with those in the Western Cape, where populations occur under natural conditions.
• 3 Gene diversity was high within T. batrachopa populations (H = 0.2219) with significant genetic differentiation among populations (G_st = 0.358). Cluster analysis showed that geographical populations were closely related and extensive divergence was found over local scales.
• 4 Similar to that of T. batrachopa, genetic diversity and population differentiation was high within both C. peltastica Mpumalanga and Western Cape populations (H = 0.1906 and 0.1687 and G_st = 0.4124 and 0.3799, respectively).
• 5 It is suggested that the population genetic structure of both species is influenced by their limited ability to disperse. In addition, chemical control of C. peltastica in the Mpumalanga province has not succeeded in reducing the population size, but the C. peltastica population subdivision in the Western Cape may be influenced by the limited distribution of host plants in this region.

     

Genetic variability in five populations of Partamona helleri (Hymenoptera, Apidae) from Minas Gerais State, Brazil

Partamona is a Neotropical genus of stingless bees that comprises 33 species distributed from Mexico to southern Brazil. These bees are well-adapted to anthropic environments and build their nests in several substrates. In this study, 66 colonies of Partamona helleri from five localities in the Brazilian state of Minas Gerais (São Miguel do Anta, Teixeiras, Porto Firme, Viçosa and Rio Vermelho) were analyzed using nine microsatellite loci in order to assess their genetic variability. Low levels of observed (H_o = 0.099-0.137) and expected (H _e = 0.128-0.145) heterozygosity were encountered and revealed discrete genetic differentiation among the populations (F _ST = 0.025). AMOVA further showed that most of the total genetic variation (94.24%) in P. helleri was explained by the variability within local populations.     

Genetic diversity of Sinojackia dolichocarpa (Styracaceae), a species endangered and endemic to China,detected by inter-simple sequence repeat (ISSR)

Sinojackia dolichocarpa, a species endangered and endemic to China, is distributed only in the regional area of Shimen and Sangzhi in Hunan Province. Inter-simple sequence repeat (ISSR) markers were used to investigate the genetic diversity within and among the four natural populations of S. dolichocarpa. Leaf samples were collected from 84 individuals. Thirteen ISSR primers selected from 80 primers gave rise to 137 discernible DNA bands of which 100 (72.99%) were polymorphic. On average each primer gave rise to 10.5 bands including 7.7 bands with polymorphic profile. At the species level, high genetic diversity was detected (PPB: 72.99%; H_E: 0.2255; Ho: 0.3453). However, relatively low genetic diversity existed within populations. Population in Maozhuhe (MZH) exhibits the greatest level of variability (PPB: 40.38%, H_E: 0.1566, Ho: 0.2330), whereas the population in Jingguanmen (JGM) finds its own variability at the lowest level (PPB: 30.66%; H_E: 0.1078; Ho: 0.1601). A high level of genetic differentiation among populations was revealed by Nei's gene diversity statistics (45.30%), Shannon's information measure (45.24%) and analysis of molecular variance (AMOVA) (52.88%). The main factors responsible for the high level of differentiation among populations are probably related to the selfing reproductive system and the isolation of populations. The strong genetic differentiation among populations indicates that the management for the conservation of genetic variability in S. dolichocarpa should aim to preserve every population.     

Genetic diversity and structure in fragmented populations of the endangered species Ranunculus cabrerensis (Ranunculaceae): implications for conservation

Ranunculus cabrerensis is an endemic and endangered species of the Northwestern Iberian Peninsula. The molecular markers AFLP and ISSR were used to investigate the genetic diversity and population structure of four populations across its known distribution. Fifteen selective primer combinations of AFLP and seventeen ISSR primer combinations produced a total of 2830 and 103 unambiguously repeatable fragments respectively, of which 97.57 and 81.38% were polymorphic for both markers. The genetic diversity of R. cabrerensis at species level was high (H _E = 0.294 by ISSR and H _E = 0.191 by AFLP) and differentiation between sampled locations was also relatively high (G _ST = 0.316 and 0.158 by ISSR and AFLP analysis respectively) compared to other studies of endangered and rare species using the same techniques. The analysis of molecular variance (AMOVA) indicated that the main genetic variation was within sampled locations (73% by AFLP; 52% by ISSR), even though the variation among locations was also significant. Principal Coordinates, NeighborNet and Bayesian analyses revealed a weak but significant relationship between the genetic structures of different populations in R. cabrerensis, with gene flow acting as a homogenizing force that prevents stronger differentiation of populations. Finally, suggestions for conservation strategies to preserve the genetic resources of this species are outlined.     

Population genetic structure of the tongue sole (Cynoglossus semilaevis) in Korea based on multiplex PCR assays with 12 polymorphic microsatellite markers

The tongue sole, Cynoglossus semilaevis, is an important fishery resource in Korea. About 100 tongue sole sampled from three major habitats along the western coast of Korea were assessed using multiplex assays with 12 highly polymorphic microsatellite loci to explore the population genetic structure of the species; 151 alleles and similar high levels of gene diversity (mean number of alleles (N_A) = 10.42, mean expected heterozygosity (He) = 0.78) were detected. Three populations showed significant Hardy–Weinberg equilibrium deviations at four loci. Although a significant difference in the number of unique alleles was observed among populations, genetic population subdivision was low by F-statistics (overall F _ST = 0.007, p < 0.05). However, this substructure was not supported by analysis of molecular variance or analyses of isolation by distance. The results suggest a lack of genetic structure among the tongue sole populations in Korean waters and that the populations should be managed as a single unit. The lack of genetic differentiation among samples may be due to high levels of larval dispersal in ocean currents. Alternatively, the populations may have diverged too recently for significant genetic differentiation to have become evident. Given the intensity of tongue sole aquaculture activity in China, which adjoins the western coast of Korea, the possibility that aquaculture may have partially contributed to the population genetic characteristics detected cannot be excluded. This study provides the basic information on nature population structure of C. semilaevis that may help to preserve and manage tongue soles in Korea.     

Genetic structure of the Korean black scraper Thamnaconus modestus inferred from microsatellite marker analysis

The Korean black scraper, Thamnaconus modestus, is one of the most economically important maricultural fish species in Korea. However, the annual catch of this fish has been continuously declining over the past several decades. In this study, the genetic diversity and relationships among four wild populations and two hatchery stocks of Korean black scraper were assessed based on 16 microsatellite (MS) markers. A total of 319 different alleles were detected over all loci with an average of 19.94 alleles per locus. The hatchery stocks [mean number of alleles (N _A) = 12, allelic richness (A _R) = 12, expected heterozygosity (He) = 0.834] showed a slight reduction (P > 0.05) in genetic variability in comparison with wild populations (mean N _A = 13.86, A _R = 12.35, He = 0.844), suggesting a sufficient level of genetic variation in the hatchery populations. Similarly low levels of inbreeding and significant Hardy–Weinberg equilibrium deviations were detected in both wild and hatchery populations. The genetic subdivision among all six populations was low but significant (overall F _ST = 0.008, P < 0.01). Pairwise F _ST, a phylogenetic tree, and multidimensional scaling analysis suggested the existence of three geographically structured populations based on different sea basin origins, although the isolation-by-distance model was rejected. This result was corroborated by an analysis of molecular variance. This genetic differentiation may result from the co-effects of various factors, such as historical dispersal, local environment and ocean currents. These three geographical groups can be considered as independent management units. Our results show that MS markers may be suitable not only for the genetic monitoring of hatchery stocks but also for revealing the population structure of Korean black scraper populations. These results will provide critical information for breeding programs, the management of cultured stocks and the conservation of this species.