Population genetic structure of the endangered tropical tree species Caryocar brasiliense, based on variability at microsatellite loci

We report the population genetic structure of the endangered tropical tree species Caryocar brasiliense, based on variability at 10 microsatellite loci. Additionally, we compare heterozygosity and inbreeding estimates for continuous and fragmented populations and discuss the consequences for conservation. For a total of 314 individuals over 10 populations, the number of alleles per locus ranged from 20 to 27 and expected and observed heterozygosity varied from 0.129 to 0.924 and 0.067 to 1.000, respectively. Significant values of theta and R(ST) showed important genetic differentiation among populations. theta was much lower than R(ST), suggesting that identity by state and identity by descent have diverged in these populations. Although a significant amount of inbreeding was found under the identity by descent model (f = 0.11), an estimate of inbreeding for microsatellite markers based on a more adequate stepwise mutation model showed no evidence of nonrandom mating (R(IS) = 0.04). Differentiation (pairwise F(ST)) was positively correlated with geographical distance, as expected under the isolation by distance model. No effect of fragmentation on heterozygosity or inbreeding could be detected. This is most likely due to the fact that Cerrado fragmentation is a relatively recent event (approximately 60 years) compared to the species life cycle. Also, the populations surveyed from both fragmented and disturbed areas were composed mainly of adult individuals, already present prior to ecosystem fragmentation. Adequate hypothesis testing of the effect of habitat fragmentation will require the recurrent analysis of juveniles across generations in both fragmented and nonfragmented areas.     

Microsatellite analysis of genetic diversity and population genetic structure of a wild rice (<Emphasis Type="Italic">Oryza rufipogon</Emphasis> Griff.) in China

Genetic diversity and population genetic structure of natural Oryza rufipogon populations in China were studied based on ten microsatellite loci. For a total of 237 individuals of 12 populations collected from four regions, a moderate to high level of genetic diversity was observed at population levels with the number of alleles per locus ( A) ranging from 2 to 18 (average 10.6), and polymorphic loci ( P) from 40.0% to 100% (average 83.3%). The observed heterozygosity ( H(O)) varied from 0.163 to 0.550 with the mean of 0.332, and the expected heterozygosity ( H(E)) from 0.164 to 0.648 with the mean of 0.413. The level of genetic diversity for Guangxi was the highest. These results are in good agreement with previous allozyme and RAPD studies. However, it was unexpected that high genetic differentiation among populations was found ( R(ST) = 0.5199, theta = 0.491), suggesting that about one-half of the genetic variation existed between the populations. Differentiation (pairwise theta) was positively correlated with geographical distance ( r = 0.464), as expected under the isolation by distance model. The habitat destruction and degradation throughout the geographic range of O. rufipogon may be the main factor attributed to high genetic differentiation among populations of O. rufipogon in China.     

Population genetic structure of the lemon shark (Negaprion brevirostris) in the western Atlantic: DNA microsatellite variation

DNA microsatellite markers were used to characterize the population genetic structure of the lemon shark, Negaprion brevirostris, in the western Atlantic. This study demonstrates for the first time the usefulness of microsatellites to study population genetic structure and mating systems in the Chondricthyes. Lemon sharks (mostly juveniles) were sampled non-destructively from four locations, Gullivan Bay and Marquesas Key in Florida, Bimini, Bahamas, and Atol das Rocas, Brazil. At least 545 individuals were genotyped at each of four dinucleotide loci. The number of alleles per locus ranged from 19 to 43, and expected heterozygosities ranged from 0.69 to 0.90. Relatively little genetic structure was found in the western Atlantic, with small but significant values for estimators of F(ST) and R(ST) among populations, theta (0.016) and rho (0.026), respectively. No sharp discontinuities were found between the Caribbean sites and Brazil, and most alleles were found at all four sites, indicating that gene flow occurs throughout the western Atlantic with no evidence for distinct stocks.     

Isolation and characterization of microsatellite loci from the truffle‐like ectomycorrhizal fungi Rhizopogon occidentalis and Rhizopogon vulgaris

We have isolated and characterized five microsatellite loci from Rhizopogon occidentalis and six loci from Rhizopogon vulgaris (Boletales, Basidiomycota). Microsatellite variation was assessed using 32 R. occidentalis and 48 R. vulgaris individuals from four populations in California. The number of alleles across populations ranged from two to 10 for R. occidentalis and three to eight for R. vulgaris. Expected heterozygosity values within populations ranged from 0.00 to 0.85 for R. occidentalis and 0.00 to 0.75 for R. vulgaris. These are the first microsatellite loci isolated for R. occidentalis and R. vulgaris and will be useful in the examination of their population genetic structure.     

Genetic and morphological differentiation in the clam Coelomactra antiquata (Bivalvia: Veneroida) along the coast of China

Coelomactra antiquata is a commercially exploited bivalve, and its populations have been severely declining in the coast of China during the last two decades. In order to provide guidelines for conservation strategies and management programs, four populations of C. antiquata, representing the most important populations in China, were analysed morphologically and genetically to reveal the genetic structure by using 7 polymorphic allozyme loci and 12 morphological variables. The mean allele richness ranged from 2.79 to 3.53, while the mean heterozygosity ranged from 0.326 to 0.519. All genetic distance metrics revealed high level of genetic differentiation between the three northern populations and one southern population. The marked genetic differentiation can be explained by the freshwater outflow of Yangtze River and upwelling of Zhejiang province. The morphological analyses were in accordance with the allozyme data, which also disclosed a high degree of differentiation between the northern and southern populations. The results obtained in this study indicate that the northern and southern populations in C. antiquata should be treated as separate units for conservation management.     

海南岛中华蜜蜂遗传多样性的微卫星DNA分析

为了解海南岛中华蜜蜂Apis cerana cerana的遗传多样性和遗传结构及其与大陆种群的关系, 本研究应用10个微卫星DNA标记对海南岛11个地点627个蜂群的627头工蜂样本和大陆2个地点102个蜂群的102头工蜂样本进行了分析。结果表明： 海南岛中华蜜蜂遗传多样性较高, 单个位点检测到等位基因5～17个; 各种群平均等位基因数为4.5～7.0个, 平均杂合度为0.59～0.65。海南岛中华蜜蜂在10个位点上表现出相似遗传结构, 文昌和屯昌种群在AT101位点的等位基因频率较特殊。岛内 岛外中华蜜蜂的遗传分化系数F_ST范围为0.06～0.13; 文昌、 屯昌种群分别同海南岛内其他9个种群的F_ST（0.06～0.12）大于这9个种群间的FST（0～0.05）。海南岛中华蜜蜂同邻近大陆种群发生了明显的遗传分化; 除文昌、 屯昌种群发生中等程度的分化外, 海南岛内其他种群之间遗传分化较小。本研究结果对海南岛中华蜜蜂资源的保护和合理利用具有重要的指导意义。     

Population genetic structure of mahogany (Swietenia macrophylla King, Meliaceae) across the Brazilian Amazon, based on variation at microsatellite loci: implications for conservation

Mahogany (Swietenia macrophylla, Meliaceae) is the most valuable and intensively exploited Neotropical tree. No information is available regarding the genetic structure of mahogany in South America, yet the region harbours most of the unlogged populations of this prized hardwood. Here we report on the genetic diversity within and the differentiation among seven natural populations separated by up to 2100 km along the southern arc of the Brazilian Amazon basin. We analysed the variation at eight microsatellite loci for 194 adult individuals. All loci were highly variable, with the number of alleles per locus ranging from 13 to 27 (mean = 18.4). High levels of genetic diversity were found for all populations at the eight loci (mean HE = 0.781, range 0.754-0.812). We found moderate but statistically significant genetic differentiation among populations considering both estimators of FST and RST, theta = 0.097 and rho = 0.147, respectively. Estimates of theta and rho were significantly greater than zero for all pairwise population comparisons. Pairwise rho-values were positively and significantly correlated with geographical distance under the isolation-by-distance model. Furthermore, four of the populations exhibited a significant inbreeding coefficient. The finding of local differentiation among Amazonian mahogany populations underscores the need for in situ conservation of multiple populations of S. macrophylla across its distribution in the Brazilian Amazon. In addition, the occurrence of microgeographical genetic differentiation at a local scale indicates the importance of maintaining populations in their diverse habitats, especially in areas with mosaics of topography and soil.     

Genetic and morphological variation in the venus clam Cyclina?sinensis along the coast of China

Six geographic samples of Cyclina sinensis were collected from the coast along China and analyzed to reveal morphological and genetic variation by using nine allozyme loci and 11 morphological variables. The discriminant function analysis (DFA) of morphology suggested a clear separation between the southern and northern populations. Polymorphism was detected at nine loci across all six populations. The mean allele number ranged from 2.44 to 2.78, and the mean observed heterozygosity ranged from 0.218 to 0.296. High level of genetic differentiation was found between three northern populations and three southern populations. The marked genetic differentiation can be explained by the upwelling of the Zhejiang province and the freshwater outflow of Yangtze River. The results obtained in this study indicate that the northern and southern populations of C. sinensis should be treated as separate units for conservation management.     

The genetic structure of red raspberry (<Emphasis Type="Italic">Rubus idaeus</Emphasis> L.) populations in Lithuania

The red raspberry (Rubus idaeus L.) is widely distributed in Lithuania and occupies a range of habitats. The presence of coadapted gene pools in local populations of R. idaeus is a question of interest not only to plant scientists, but also to plant breeders. In this study, we investigated the genetic structure of R. idaeus and the influence of local habitats on the genetic diversity within and among populations. Nineteen populations of R. idaeus were sampled from different habitats in various agroclimatic subregions of Lithuania, and analyzed using RAPD markers. 113 RAPD bands were identified among 315 individuals; 84.31% of these were polymorphic. The mean values of Shannon’s information index for different populations ranged from 0.341 to 0.455. Nei’s gene diversity established within populations averaged 0.266. An AMOVA revealed 74% of genetic variation among individuals within populations of R. idaeus, and 23% among populations. The remaining genetic variation was distributed among populations from different agroclimatic subregions (3%). The results of this study suggest that the genetic structure of R. idaeus populations in Lithuania may be influenced partially by isolation by distance as well as by local environmental conditions.     

Esterase Polymorphism and the Analysis of Genetic Diversity and Structure in Cactus Populations Descended from Cereus peruvianus Plants Regenerated In Vitro

The genetic structure of Cereus peruvianus populations descended from cultivated plants (F(1) populations) and from plants regenerated in vitro (R(1) populations) was analyzed using α- and β-esterase isozymes in native PAGE. The estimated proportion of polymorphic loci was higher (50%) in the R(1) populations than the F(1) populations (42.85%). The mean observed (0.5599) and expected (0.5620) heterozygosity in R(1) descendents was also higher than the rates in F(1) descendents (H (o)?=?0.4142; H (e)?=?0.4977). A low level of population differentiation was detected in R(1) descendents (F (st)?=?0.05). In contrast, population differentiation was high in F(1) descendents (0.2583). Esterase analysis using PAGE showed that artificial selection by silvicultural management provides high genetic diversity and a large genetic basis for C.?peruvianus, whereas in vitro selection from callus tissue culture involves an increase of heterozygosity levels in descendents from somaclones and a low level of interpopulational divergence.     

High survival frequencies at low herbicide use rates in populations of Lolium rigidum result in rapid evolution of herbicide resistance

The frequency of phenotypic resistance to herbicides in previously untreated weed populations and the herbicide dose applied to these populations are key determinants of the dynamics of selection for resistance. In total, 31 Lolium rigidum populations were collected from sites with no previous history of exposure to herbicides and where there was little probability of gene flow from adjacent resistant populations. The mean survival frequency across all 31 populations following two applications of commercial rates (375 g ha(-1)) of the acetyl-coenzyme A carboxylase (ACCase) inhibiting herbicide, diclofop-methyl was 0.43%. Survivors from five of these populations were grown to maturity and seed was collected. Dose-response experiments compared population level resistance to diclofop-methyl in these selected lines with their original parent populations. A single cycle of herbicide selection significantly increased resistance in all populations (LD(50) R:S ratios ranged from 2.8 to 23.2), confirming the inheritance and genetic basis of phenotypic resistance. In vitro assays of ACCase inhibition by diclofop acid indicated that resistance was due to a non-target-site mechanism. Following selection with diclofop-methyl, the five L. rigidum populations exhibited diverse patterns of cross-resistance to ACCase and ALS-inhibiting herbicides, suggesting that different genes or gene combinations were responsible for resistance. The relevance of these results to the management of herbicide resistance are discussed.     

Population structure and genetic diversity of Rana dalmatina in the Iberian Peninsula

The increasing fragmentation of natural habitats may strongly affect patterns of dispersal and gene flow among populations, and thus alter evolutionary dynamics. We examined genetic variation at twelve microsatellite loci in the Agile frog (Rana dalmatina) from 22 breeding ponds in the Iberian Peninsula, the southwest limit of its range, where populations of this species are severely fragmented and are of conservation concern. We investigated genetic diversity, structure and gene flow within and among populations. Diversity as observed heterozygosities ranged from 0.257 to 0.586. The mean number of alleles was 3.6. Just one population showed a significant F _IS value. Four populations show evidence of recent bottlenecks. Strong pattern of structure was observed due to isolation by distance and to landscape structure. The average degree of genetic differentiation among populations was F _ST = 0.185. Three operational conservation units with metapopulation structure were identified. Additionally, there are some other isolated populations. The results reinforce the view that amphibian populations are highly structured even in small geographic areas. The knowledge of genetic structure pattern and gene flow is fundamental information for developing programmes for the preservation of R. dalmatina at the limits of its geographic distribution.     

Microsatellite variability and heterozygote deficiency in the arctic-alpine Alaskan wheatgrass (Elymus alaskanus) complex.

Genetic variation in the allotetraploid grass Elymus alaskanus complex was assessed using microsatellites in seven populations from Canada, Greenland, and the U.S.A. Microsatellite variation was compared with allozyme and RAPD variation. Our results indicated that E. alaskanus was highly homozygous but also highly variable. The polymorphic loci ranged from 50 to 100% with a mean of 78.6%, and the mean number of allele per locus was 3.14. Average expected heterozygosity value (HE, gene diversity) varied across populations and ranged from 0.244 to 0.651 with mean of 0.414. The mean value of HE across Canadian populations (0.517) was significantly higher than that across populations in Greenland (0.367). The correlation between allozyme and microsatellite gene diversity value (HE) showed a high positive correlation (r = 0.68), but between RAPD and microsatellite showed a low positive correlation (r = 0.08). Populations were highly differentiated, with 38% of variation among populations. Interpopulation genetic distance showed no association with geographic distance between the population sites of origin. A Hardy-Weinberg exact test for all loci and all populations reveals a significant heterozygote deficiency. Possible explanations for heterozygote deficiency are discussed.     

Population genetic structure of the blue-fronted Amazon (Amazona aestiva, Psittacidae: Aves) based on nuclear microsatellite loci: implications for conservation

The blue-fronted Amazon (Amazona aestiva) is a widely distributed Neotropical parrot and one of the most captured parrots in nature to supply the illegal trade of wild animals. The objectives of the present study were to analyze the genetic structure of A. aestiva to identify management units and support conservation planning and to verified if A. aestiva populations have undergone a recent bottleneck due to habitat loss and capture for the pet trade. The genetic structure was accessed by analyzing six microsatellite loci in 74 individuals of A. aestiva, including samples from the two subspecies (A. a. aestiva and A. a. xanthopteryx), from five populations: four in Brazil and one in Argentina. A significant genetic differentiation (theta = 0.007, p = 0.005) could be detected only between the most distant populations, Tocantins and Argentina, localized at the northeast and southwest limits of the sample sites, respectively. There was no evidence of inbreeding within or between populations, suggesting random mating among individuals. These results suggest a clinal distribution of genetic variability, as observed for variation in plumage color of the two A. aestiva subspecies. Bottleneck analysis did not show a recent reduction in population size. Thus, for the management and conservation of the species, the populations from Argentina and Tocantins should be considered as different management units, and the other populations from the center of the geographical distribution as another management unit.     

Genetic variation and population structure in central and isolated populations of balsam fir, Abies balsamea (Pinaceae)

Genetic variation and spatial genetic structure in balsam fir (Abies balsamea) were examined in two isolated populations in Iowa and Minnesota thought to be paleorefugia and in two ecologically central populations in old-growth forests of Upper Michigan. Overall levels of genetic variability at 22 allozyme loci were lower than that found in most conifer species (H(o) values ranged from 0.005 in the isolated populations to 0.025 in the central populations). The mean F(IS) value (0.154) was larger than usually found in conifers and suggests moderate levels of inbreeding. The mean F(ST), an estimate of genetic diversity among populations, was 3.7% of the total diversity, a value lower than the mean for conifers. Nm, the number of migrants per generation, was 6.5, suggesting either some gene flow among populations or a lack of genetic differentiation. Spatial autocorrelation analysis revealed a moderately patchy structure, with gene flow distances of 30-70 m in the central populations and at least 10 m in the isolated populations. The future of the ecologically central populations depends on maintenance of an intact forest mosaic. The low genetic variability in the small, isolated populations suggests that habitat fragmentation has led to a reduction in evolutionary potential and that the future viability of these populations will likely require active management in the face of global climate change.     

Development of Microsatellite Markers and Analysis of Genetic Diversity and Population Structure of Colletotrichum gloeosporioides from Ethiopia

Twenty three polymorphic microsatellite markers were developed for citrus plant pathogenic fungus, Colletotrichum gloeosporioides, and were used to analyze genetic diversity and population structure of 163 isolates from four different geographical regions of Ethiopia. These loci produced a total of 118 alleles with an average of 5.13 alleles per microsatellite marker. The polymorphic information content values ranged from 0.104 to 0.597 with an average of 0.371. The average observed heterozygosity across all loci varied from 0.046 to 0.058. The gene diversity among the loci ranged from 0.106 to 0.664. Unweighted Neighbor-joining and population structure analysis grouped these 163 isolates into three major groups. The clusters were not according to the geographic origin of the isolates. Analysis of molecular variance showed 85% of the total variation within populations and only 5% among populations. There was low genetic differentiation in the total populations (F_ST = 0.049) as evidenced by high level of gene flow estimate (N_m = 4.8 per generation) among populations. The results show that Ethiopian C. gloeosporioides populations are generally characterized by a low level of genetic diversity. The newly developed microsatellite markers were useful in analyzing the genetic diversity and population structure of the C. gloeosporioides populations. Information obtained from this study could be useful as a base to design strategies for better management of leaf and fruit spot disease of citrus in Ethiopia.     

Absence of population genetic differentiation in the New Zealand greenshell mussel Perna canaliculus (Gmelin 1791) as assessed by allozyme variation

Genetic variation in the endemic New Zealand greenshell mussel, Perna canaliculus (Gmelin 1791), was examined using starch-gel electrophoresis at seven protein-coding loci (Idh; Acon-1; Acon-2; Gpd; Pgi; Pgm; Pgd) in 35 populations (N=1038 mussels). For all loci and all populations, Fisher's exact tests indicated highly significant departures from Hardy-Weinberg equilibrium (HWE), but this overall result was caused by significant heterozygote deficiencies at only two loci (Pgm and Pgd), and in only three northern populations (Kuaotunu, Te Haumi and Days Bay). Allelic and genotypic differentiation between population pairs at individual loci and across all loci were nonsignificant, and genotypic disequilibrium at each locus pair was also nonsignificant for all populations. Genetic variation in all populations was high (mean heterozygosity, 0.210+/-0.113), while Nei's D among populations was very low (0.002+/-0.002). Low population subdivision (θ=-0.001+/-0.002) and high levels of gene flow (Nm(p)=10.18; Nm(θ)=infinity) also indicated that the single panmictic unit model best explains population genetic homogeneity in P. canaliculus over a north-south distance >2000 km. Lack of genetic subdivision in this species is discussed in light of two previous allozyme studies, with differing results: one suggested that a north-south division exists between greenshell mussel stocks, and the other suggested that population structure in this species can be explained through isolation by distance model modified by local hydrology.     

First microsatellite markers developed and applied for the genetic diversity study and population structure of Didymella pisi associated with ascochyta blight of dry pea in Montana

Didymella pisi is the predominant causal pathogen of ascochyta blight of dry pea causing yield losses in Montana, where 415 000 acres were planted to dry pea in 2018. Thirty-three microsatellite markers were developed for dry pea pathogenic fungus, Didymella pisi, these markers were used to analyze genetic diversity and population structure of 205 isolates from four different geographical regions of Montana. These loci produced a total of 216 alleles with an average of 1.63 alleles per microsatellite marker. The polymorphic information content values ranged from 0.020 to 0.990 with an average of 0.323. The average observed heterozygosity across all loci varied from 0.000 to 0.018. The gene diversity among the loci ranged from 0.003 to 0.461. Unweighted Neighbor-joining and population structure analysis grouped these 205 isolates into two major sub-groups. The clusters did not match the geographic origin of the isolates. Analysis of molecular variance showed 85 % of the total variation within populations and only 15 % among populations. There was moderate genetic variation in the total populations (PhiPT = 0.153). Information obtained from this study could be useful as a base to design strategies for improved management such as breeding for resistance to ascochyta blight of dry pea in Montana.     

Development of microsatellite markers in heterostylous Hedyotis chrysotricha (Rubiaceae)

? Premise of the study: Microsatellite primers were developed for a heterostylous herb, Hedyotis chrysotricha to investigate the effect of habitat fragmentation on its genetic diversity and population structure. ? Methods and Results: Twelve primer sets were developed and their polymorphisms were tested on 47 individuals from two island populations of H. chrysotricha in Thousand Island Lake of China. The number of alleles per locus ranged from five to 10, with an average of seven alleles. Expected heterozygosity per locus ranged from 0.284 to 0.821 and observed heterozygosity ranged from 0.191 to 0.851. ? Conclusions: We showed that all of the 12 microsatellite markers developed for H. chrysotricha are polymorphic within populations, which should provide a powerful tool for assessing population structure and genetic diversity across fragmented and continuous populations, and for studying the genetic effects of habitat fragmentation on this species.     

Population structure of plaice (Pleuronectes platessa L.) in northern Europe: microsatellites revealed large-scale spatial and temporal homogeneity

Philopatry to spawning grounds combined with well-known migratory patterns in the flatfish Pleuronectes platessa (plaice) has led to the hypothesis that regional populations may reflect relatively discrete, genetic stocks. Using six microsatellite loci we genotyped 240 adult individuals collected from locations in Norway, the Faeroe plateau, the Irish Sea, the Femer Baelt, Denmark, and the southern North Sea, and 240 0-class juveniles collected from five nursery-ground locations in Iceland, northwest Scotland, two sites in the Wadden Sea, and the Bay of Vilaine in Southern Brittany. The mean number of alleles/locus ranged from 5.3 to 20.4, with a mean of 13.9. Expected heterozygosity was uniformly high across all locations (multilocus H(exp)= 0.744 +/- 0.02). Pairwise comparisons of theta; among all 11 locations revealed significant differentiation between Iceland and all other locations (theta = 0.0290*** to 0.0456***), which is consistent with the deep-water barrier to dispersal in plaice. In contrast, no significant differentiation was found among any of the remaining continental-shelf sampling locations. This suggests that regional stocks are themselves composed of several genetic stocks under a model of panmixia which persists even to the spawning grounds. The presence of significant heterozygote deficiencies at all locations (not due to null alleles) suggests a temporal Wahlund effect yet the absence of significant population differentiation among continental shelf localities makes this explanation alone, difficult to reconcile. Sampling of eggs at the spawning grounds will be required to resolve this issue. Causes of the mismatch between genetic and geographical stocks is discussed in the context of high gene flow.