Allozyme diversity in Macbridea alba (Lamiaceae), an endemic florida mint

Macbridea alba is a herbaceous perennial mint endemic to the panhandle region of Florida. We used starch gel electrophoresis to describe allozyme diversity and genetic structure in this federally threatened plant. Ten populations were analyzed, with an average sample size of 47 plants (range 41-48 plants) per population. Of the 22 loci analyzed, 11 (50%) were polymorphic, with an average of 36.2% of the loci polymorphic within populations. Gene diversity measures for the species (Hes = 0.121) and for the populations (Hep = 0.099) were slightly higher than means found for other surveyed endemic plants. Compared to nine previously analyzed woody mints, however, M. alba is genetically depauperate. Little genetic structure was evident within the species, with 92% of the total genetic variation found within populations. Genetic identities between population pairs were high (mean I = 0.98). The perennial life habit of M. alba and long-distance pollination by bumblebees may contribute to the maintenance of genetic diversity within this threatened species.     

Comparative Assessment of Genetic Variability in the Populations of Endemic and Endangered Yellow Catfish, Horabagrus brachysoma (Teleostei: Horabagridae), Based on Allozyme, RAPD, and Microsatellite Markers

The comparative assessment of genetic diversity using allozymes, random amplified polymorphic DNA (RAPD), and microsatellite markers was conducted in endemic and endangered yellow catfish (Horabagrus brachysoma) sampled from three locations in Western Ghats river systems of India. Among the three markers, microsatellites show more polymorphism, having 100% polymorphic loci, whereas allozymes show the least (56%). In RAPD, 60.5% of fragments were polymorphic. Observed heterozygosity and F(ST) values were very high in microsatellites, compared with the other markers. Microsatellite and RAPD markers reported a higher degree of genetic differentiation than allozymes among the populations depicted by pairwise F(ST)/G(ST), AMOVA, Nei's genetic distance, and UPGMA dendrogram. The three classes of markers demonstrated striking genetic differentiation between pairs of H. brachysoma populations. The data emphasize the need for fishery management, conservation, and rehabilitation of this species.     

Genetic structure of an endangered plant, Antirrhinum microphyllum (Scrophulariaceae): allozyme and RAPD analysis

Thirteen allozyme loci and 68 random amplified polymorphic DNA (RAPD) markers were analyzed to assess the genetic diversity and population structure of threatened Antirrhinum microphyllum (Scrophulariaceae), a narrow endemic of central Spain known from only four populations. According to allozyme data, species genetic diversity (p = 46.15%, A = 2.61, and H(e) = 0.218), as well as within-population genetic diversity (p = 44.23%, A = 2.10, and H(e) = 0.204), were high when compared to average estimates for other narrowly distributed plant species. Ninety-four percent of species genetic diversity corresponded to within-population genetic diversity. Nevertheless, significant differences were found among populations in allele frequencies of four of the six polymorphic loci, and three private alleles were detected. Inbreeding coefficients (F(IS)) suggest that populations are structured in genetic neighborhoods. The RAPDs also showed high levels of genetic diversity (p = 89.71% and H(e) = 0.188 at the species level, and p = 67.65% and H(e) = 0.171 at the population level). Nei's genetic distances estimated both from allozymes and RAPDs indicated low differentiation among populations. In spite of this, the low frequencies of certain alleles and the presence of private alleles indicate that efforts should be made to conserve all four remaining populations.     

Isolation and characterization of microsatellite loci in Santalum austrocaledonicum,Santalaceae

The forest tree Santalum austrocaledonicum is endemic to the archipelagos of New Caledonia and Vanuatu, and is threatened by the reduction of the populations due to exploitation. In order to investigate the genetic diversity and structure of this species, we developed eight pairs of primers for nuclear microsatellites. These loci were polymorphic in all the populations, with a mean of three to 33 alleles per locus.     

Allozyme diversity in natural populations of Viola palmensis Webb & Berth. (Violaceae) from La Palma (Canary Islands): implications for conservation genetics

Genetic diversity was measured by allozyme electrophoresis in eight natural populations of the threatened Canarian endemic Viola palmensis Webb & Berth. (Violaceae). Nineteen alleles corresponding to 11 gene loci were detected. High levels of genetic diversity were found, ranging from 36.3 to 45.4 % for the percentage of polymorphic loci (P), from 1.45 to 1.60 for the average number of alleles per locus (A) and from 0.128 to 0.200 for the expected heterozygosity (H(e)). Between 85.5 and 96.6 % of genetic variability was apportioned within populations. As a whole, populations were not at Hardy-Weinberg equilibrium, with a deficit of heterozygous individuals attributable to the existence of genetic structuring in the populations analysed. The levels of interpopulation genetic differentiation were low (mean F(ST) = 0.100), while genetic identity pair-wise comparisons were high (mean I = 0.973) suggesting considerable levels of gene flow among populations. No relationship was detected between genetic differentiation and geographical distances between populations. An outcrossing insect-mediated breeding system might contribute to pollen dispersion of this species. For conservation genetics we suggest in situ preservation areas are defined that are free of disturbance and that include populations with the highest genetic diversity.     

Allozyme diversity and morphometrics of Melocactus paucispinus (Cactaceae) and evidence for hybridization with M. concinnus in the Chapada Diamantina, North-eastern Brazil

BACKGROUND AND AIMS: Melocacatus paucispinus (Cactaceae) is endemic to the state of Bahia, Brazil, and due to its rarity and desirability to collectors it has been considered threatened with extinction. This species is usually sympatric and inter-fertile with M. concinnus, and morphological evidence for hybridization between them is present in some populations. Levels of genetic and morphological variation and sub-structuring in populations of these species were assessed and an attempt was made to verify the occurrence of natural hybridization between them. METHODS: Genetic variability was surveyed using allozymes (12 loci) and morphological variability using multivariate morphometric analyses (17 vegetative characters) in ten populations of M. paucispinus and three of M. concinnus occurring in the Chapada Diamantina, Bahia. KEY RESULTS: Genetic variability was low in both species (P = 0.0-33.3, A = 1.0-1.6, H(e) = 0.000-0.123 in M. paucispinus; P = 0.0-25.0, A = 1.0-1.4, H(e) = 0.000-0.104 in M. concinnus). Deficit of heterozygotes within the populations was detected in both species, with high values of F(IS) (0.732 and 0.901 in M. paucispinus and M. concinnus, respectively). Evidence of hybridization was detected by the relative allele frequency in the two diaphorase loci. High levels of genetic (F(ST) = 0.504 in M. paucispinus and 0.349 in M. concinnus) and morphological (A = 0.20 in M. paucispinus and 0.17 in M. concinnus) structuring among populations were found. CONCLUSIONS: The Melocactus spp. displayed levels of genetic variability lower than the values reported for other cactus species. The evidence indicates the occurrence of introgression in both species at two sites. The high F(ST) values cannot be explained by geographical substructuring, but are consistent with hybridization. Conversely, morphological differentiation in M. paucispinus, but not in M. concinnus, is probably due to isolation by distance.     

Levels and patterns of genetic variation in the endangered species Abronia macrocarpa

Genetic variation was evaluated in the federally endangered species Abronia macrocarpa (large-fruited sand-verbena), an herbaceous perennial restricted to deep sandy soils and endemic to three counties of east-central Texas. Seven of the ten known populations were sampled and analyzed using starch gel electrophoresis of eight enzymes coded by 18 interpretable loci. Duplicate gene expression was observed for four loci, suggesting polyploid ancestry for the lineage that includes A. macrocarpa. Values for estimators of genetic polymorphism within populations (ranges: P = 38.9%-61.1%, A = 1.7-2.1, H = 0.122-0.279) exceeded average values for seed plants (P = 34.2%, A = 1.53, H = 0.113). Genotype proportions at most loci in most populations were in Hardy-Weinberg equilibrium, consistent with obligate outcrossing previously documented for this species; exceptions could be attributed to population substructure. Values of F(ST) tended to be high, ranging from 0.021 to 0.481 for individual loci (mean F(ST) = 0.272), indicating substantial divergence and limited gene flow among populations, despite their close geographic proximity. Pairwise values of Nei's genetic identity between populations ranged from 0.799 to 0.975 and tended to be influenced by geographic proximity of population pairs. Collectively, these data suggest a long history of isolation among populations that have not been subjected to bottlenecks. Isolation of A. macrocarpa populations apparently results from the disjunct occurrence of suitable habitat and perhaps has been accentuated by human disturbance.     

Genome scan to detect genetic structure and adaptive genes of natural populations of Cryptomeria japonica

We investigated 29 natural populations of Cryptomeria japonica using 148 cleaved amplified polymorphic sequence markers to elucidate their genetic structure and identify candidate adaptive genes of this species. In accordance with the inferred evolutionary history of the species during and after the last glacial episode, the genetic diversity was higher in western populations than in northern populations. The results of phylogenetic and genetic structure analyses suggest that populations of the two main varieties of the species have clearly diverged from each other and that two of the examined loci are strongly associated with the differentiation between the two varieties. Using a coalescent simulation based on F(ST) and H(e) values, we detected five genes that had higher, and two that had lower, values than the respective 99% confidence intervals (C.I.s) that are theoretically expected intervals under a neutral infinite-island model. We also detected 13 outlier loci using a coalescent simulation based on the assumption that the 2 varieties originated from the splitting of an ancestral population. Four of these loci were detected by both methods, two of which were detected in a genetic structure analysis as loci associated with differentiation between the two varieties of the species, and are strong candidates for genes that have been subject to selection.     

Testing of microsatellite primers with different populations of Eurasian spruces Picea abies (L.) Karst. and Picea obovata Ledeb

From a clone library containing microsatellite DNA fragments of Norwegian spruce, seven pairs of primers were selected. These primers were tested to be the markers in the genetic structure analysis of nine populations of Eurasian spruce species Picea abies (L.) Karst. and Picea obovata Ledeb. Five pairs of these primers identified polymorphic loci with the allele numbers from 6 to 15. In the populations examined, the observed and expected heterozygosity values assessed at five loci varied from 0.1778 to 0.6556 and from 0.7800 to 0.900, respectively. In the populations examined, the values of F(st) index varied from 0.0691 to 0.2551 with the mean value of 0.1318. On the dendrogram based on Nei genetic distances, the populations formed three groups: Pskov-Ciscarpathia, Komi-Tatarstan-Arkhangelsk, Kazakhstan-Karelia(natural)-Karelia(culture)-Krasnoyarsk. Five of the primer pairs tested proved useful for analysis of the population genetic structure in Eurasian spruce species.     

High genetic diversity in the remnant island population of hihi and the genetic consequences of re-introduction

The maintenance of genetic diversity is thought to be fundamental for the conservation of threatened species. It is therefore important to understand how genetic diversity is affected by the re-introduction of threatened species. We use establishment history and genetic data from the remnant and re-introduced populations of a New Zealand endemic bird, the hihi Notiomystis cincta, to understand genetic diversity loss and quantify the genetic effects of re-introduction. Our data do not support any recent bottleneck events in the remnant population. Furthermore, all genetic diversity measures indicate the remnant hihi population has retained high levels of genetic diversity relative to other New Zealand avifauna with similar histories of decline. Genetic diversity (N(A) , alleles per locus, allelic richness, F(IS) and H(S) ) did not significantly decrease in new hihi populations founded through re-introduction when compared to their source populations, except in the Kapiti Island population (allelic richness and H(S) ) which had very slow post-re-introduction population growth. The N(e) /N(c) ratio in the remnant population was high, but decreased in first-level re-introductions, which together with significant genetic differentiation between populations (F(ST) & Fisher's exact tests) suggest that extant populations are diverging as a result of founder effects and drift. Importantly, simulations of future allele loss predict that the number of alleles lost will be higher in populations with a slow population growth, fewer founding individuals and with nonrandom mating. Interestingly, this species has very high levels of extra-pair paternity which may reduce reproductive variance by allowing social and floater males to reproduce a life history trait that together with a large remnant population size may help maintain higher levels of genetic diversity than expected.     

Isolation and characterization of microsatellite loci in Santalum insulare,Santalaceae

The forest tree Santalum insulare is endemic to the archipelagos of eastern Polynesia and is threatened by important anthropic pressures. In order to investigate the genetic diversity and structure of this species, we developed eight pairs of primers for nuclear microsatellites. One hundred and sixty‐two individuals distributed in 10 islands were analysed. These loci were all polymorphic and displayed three to 15 alleles per locus. Significant Hardy–Weinberg deviation was detected and interpreted as a result of Wahlund effect. These markers constitute an efficient tool in investigating the genetic patterns of S. insulare populations.     

Allozyme variation and structure of the Canarian endemic palm tree Phoenix canariensis (Arecaceae): implications for conservation

Electrophoretic analysis of 18 allozyme loci was used to estimate the levels and structuring of genetic variation within and among natural populations of the protected endemic palm species from the Canary Islands (Phoenix canariensis) to evaluate its genetic relationship with the widespread congener P. dactylifera, and to assess comparatively the genetic variation in the populations where the two species coexist with morphologically intermediate plants (mixed populations). Our survey revealed that the within-population component explains roughly 75% of the genetic variation levels detected in P. canariensis (A=1.59; P=41.8; He=0.158), which rank higher than those reported for other species of the Arecaceae. A Principal Component analysis (PCA) based on allele frequencies consistently separates populations of P. canariensis and P. dactylifera, and reveals a close genetic relationship between P. canariensis and the mixed populations. Reduced levels of genetic variation in P. canariensis with respect to P. dactylifera, the fact that the genetic makeup of the Canarian endemic (with no unique alleles) is a subset of that found in P. dactylifera, and the high genetic identity between both species strongly suggest that P. canariensis is recently derived from a common ancestor closely related to P. dactylifera.     

Development of microsatellite markers in Fosterella rusbyi (Bromeliaceae) using 454 pyrosequencing

? Premise of the study: Polymorphic microsatellite markers were developed for Fosterella rusbyi (Bromeliaceae) to evaluate the population genetic structure and genetic diversity of natural populations of F. rusbyi and other Fosterella species in Bolivia. ? Methods and Results: 454 pyrosequencing technology was used to generate 73027 sequence reads from F. rusbyi DNA, which together contained 2796 perfect simple sequence repeats (SSRs). Primer pairs were designed for 30 loci, of which 15 were used to genotype 30 F. rusbyi plants from two geographical areas in Bolivia. All markers were polymorphic, with two to nine alleles in the overall sample. Cross-species amplification was tested in 10 additional Fosterella species. Seven loci showed consistent amplification in six or more species. ? Conclusions: The 15 SSR markers developed for F. rusbyi are promising candidates for population genetic analyses within F. rusbyi and other species of Fosterella.     

巴东木莲等位酶的遗传多样性

采用超薄平板聚丙烯酰胺等电聚焦技术对中国特有濒危植物巴东木莲(Manglietia patungensis Hu)的遗传多样性进行了初步的分析。通过对8个酶系统18个酶位点的检测,结果表明,巴东木莲具有较高的遗传多样性。种水平多态位点的百分数(Ps)为66．7,平均预期杂合度(He)为0．178。高于多年生木本植物的平均水平。居群间分化系数为0．107,说明巴东木莲的遗传变异的89．3％来自于居群内。     

Genetic variation within and among populations of the narrow endemic,delphinium viridescens (Ranunculaceae)

Delphinium viridescens Leiberg (Ranunculaceae) is a narrow endemic, known from only 17 populations in the Wenatchee Mountains of central Washington. Electrophoretic data for ten loci and approximately 50 plants from each of the 17 populations indicate high levels of variability both within and among populations. High levels of heterozygosity, coupled with a general conformance of genotype frequencies to Hardy-Weinberg expectations, suggest that D. viridescens is an outcrossing species, and outcrossing rates range from 0.391 to 1.454. Although all populations share a suite of common alleles, interpopulational differences in allele frequency were detected. Nei's genetic identities range from 0.883 to 1.000, with a mean of 0.964, suggesting only slight differentiation among populations and at least moderate levels of interpopulational gene flow. However, F_ST values indicate greater interpopulational heterogeneity. The data from this study are intended for use in developing a management plan for D. viridescens, to maintain the viability of this species, and to assess the need for its listing as threatened or endangered.     

High levels of allozyme variation within populations and low allozyme divergence within and among species of Hemerocallis (Liliaceae)

Thirty populations from five species of Hemerocallis in Korea were analyzed by starch gel electrophoresis to measure genetic diversity and to determine genetic population structure and the amount of genetic divergence within and between species at 12 isozyme loci. In addition, Moran's I spatial autocorrelation statistics were used to examine the spatial distribution of allozyme polymorphisms in populations of H. thunbergii and H. hakuunensis. Populations of five Korean species maintain high levels of genetic variation and little differentiation among populations and species. Mean expected heterozygosities range from 0.165 in H. hongdoensis, an island endemic, to 0.265 in H. taeanensis, and a total of 81 alleles across the 12 loci were detected in the five species. G(ST) values for each of the five species were low, ranging from 0.051 in H. taeanensis to 0.078 in H. hakuunensis. Mean intraspecific Nei's genetic identities (I) between populations of the five species were all above 0.97. However, a considerable level of heterozygote deficiencies within populations was detected, ranging from 0.242 to 0.411 measured as F(IS) statistics. This deficiencies may be due to inbreeding, limited pollen and seed dispersal, or from the pooling of subpopulations that differ in allele frequencies. A small spatial scale population substructuring (<12 m) was found in H. thunbergii and H. hakuunensis. A group of populations from each of the five previously designated Hemerocallis species (based on their morphology, ecology, and phenology) agrees with our allozyme data, though pairwise comparisons among species had high I values (from 0.862, H. middendorffii vs. H. hongdoensis, to 0.969, H. thunbergii vs. H. taeanensis). This is attributed to the presence of the same high-frequency alleles in different species at seven loci. In addition, no "diagnostic allele" that appears in all populations of one species, but is absent in other species, was detected at the 12 isozyme loci. These all suggest that species of Hemerocallis in Korea may have recently derived from an ancestor or progenitor harboring high levels of genetic diversity.     

Characterization of microsatellite markers in the threatened sand skink (Neoseps reynoldsi)

We characterized microsatellite loci for the sand skink (Neoseps reynoldsi) for future studies of genetic structure in this threatened taxon. We screened a partial genomic library enriched for microsatellites, designed primers for eight loci and assessed these markers for polymorphism across 11 populations in central Florida. Preliminary analyses indicate deviations from Hardy–Weinberg expectations for most loci, suggesting population genetic structure across the sampled populations; therefore, understanding genetic connectivity is critical for maintaining genetic variation in this species.     

Conservation genetics of the endangered Iberian steppe plant Ferula loscosii (Apiaceae)

Ferula loscosii (Lange) Willk (Apiaceae) is a threatened endemic species native to the Iberian Peninsula. The plant has a narrow and disjunct distribution in three regions, NE, C and SE Spain. Genetic variability within and among 11 populations from its natural distribution was assessed using allozymes. Intermediate levels of genetic diversity were detected in F. loscosii (P(99%) = 36.83; H(E) = 0.125; H(T) = 0.152). However, the highest genetic diversity (58%) corresponded to the threatened populations from SE and C Spain (H(T) = 0.169) rather than the more abundant and larger populations from NE Spain (Ebro valley) (H(T) = 0.122). Low to moderate levels of genetic structure were found among regional ranges (G(ST) = 0.134), and several statistical spatial correlation analyses corroborated substantial genetic differentiation among the three main regional ranges. However, no significant genetic differentiation was found among the NE Spain populations, except for a northernmost population that is geographically isolated. Outcrossing mating and other biological traits of the species could account for the maintenance of the present values of genetic diversity within populations. The existence of an ancestral late Tertiary wider distribution of the species in SE and C Spain, followed by the maintenance of different Quaternary refugia in these warmer areas, together with a more recent and rapid post-glacial expansion towards NE Spain, are arguments that could explain the low genetic variability and structure found in the Ebro valley and the higher levels of diversity in the southern Iberian populations.     

Genetic Diversity and Differentiation in Hedychium spicatum, a Valuable Medicinal Plant of Indian Himalaya

Hedychium spicatum, a perennial rhizomatous medicinal plant distributed in subtropical and temperate parts, is considered nearly endemic to the Himalayan region.In this study allozyme markers were utilized to assess genetic variations and relationships among 12 distinct populations of this species from the West Himalaya of India. A high level of genetic diversity was found among the populations. Of the 13 loci generated using eight enzymes, 12 (92%) were polymorphic. F-statistics suggested a prevalence of a high heterozygote excess among populations (F(IS) = -0.51). Gene flow estimates and geographic distances between populations did not correlate significantly (r = -0.0258, P < 0.3550). The excess heterozygosity may be attributed to high pollinator mobility and inbreeding coefficient within the subpopulation, relative to the total F(IS) value. High frequencies of several alleles at different loci probably reflect the breeding pattern, as the species propagates clonally as well as through seeds. We also discuss conservation implications for the target species.     

Population genetic structure of a California endemic branchiopod,Branchinecta sandiegonensis

Branchinecta sandiegonensis (Crustacea: Anostraca) is a narrow range endemic fairy shrimp discontinuously distributed in ephemeral pools on coastal mesas in San Diego County, USA. Ten populations across the range of the species were subjected to allozyme analysis for eleven loci. The species exhibits low variability (P₉₅ =9.1–45.5) and one third of the loci tested did not conform to Hardy-Weinberg equilibrium expectations. The species also exhibited a high degree of genetic differentiation between populations. F _ST values (fixation index) for most pairs of populations were above 0.25 (0.036–0.889).Low genetic variability and high genetic structure may result from low gene flow and founder effects due to habitat fragmentation and the lack of potential vectors for cyst dispersal. The unpredictable rainfall of the region also creates potential for variable population sizes which could affect structure and variability. This revised version was published online in August 2006 with corrections to the Cover Date.