Local genetic structure in a clonal dioecious angiosperm

We used seven microsatellite loci to characterize genetic structure and clonal architecture at three different spatial scales (from meters to centimetres) of a Cymodocea nodosa population. C. nodosa exhibits both sexual reproduction and vegetative propagation by rhizome elongation. Seeds remain buried in the sediment nearby the mother plant in a dormant stage until germination. Seed dispersal potential is therefore expected to be extremely restricted. High clonal diversity (up to 67% of distinct genotypes) and a highly intermingled configuration of genets at different spatial scales were found. No significant differences in genetic structure were found among the three spatial scales, indicating that genetic diversity is evenly distributed along the meadow. Autocorrelation analyses of kinship estimates confirmed the absence of spatial clumping of genets at small spatial scale and the expectations of a very restricted seed dispersal (observed dispersal range 1-21 m) in this species.     

High population differentiation and extensive clonality in a rare mallee eucalypt: Eucalyptus curtisii Conservation genetics of a rare mallee eucalypt

Microsatellite polymorphisms were analysed toassess the extent and pattern of geneticdiversity within and between isolatedpopulations of the rare mallee eucalypt, Eucalyptus curtisii. Twelve populations intotal were sampled throughout the 500 km rangeof the species in South-east Queensland.Results from analysis of 5 loci indicated ahigh degree of clonality within many of thesites, with two populations being comprised ofsingle genets. Estimates of radial growth ratessuggest that these clones may be between 4000and 9000 years old. Low overall levels ofgenetic diversity were recorded for thespecies, H _e = 0.54, however a highlysignificant amount of populationdifferentiation was observed, R _ST =0.22. There was no evidence of isolation bydistance and although there were morphologicaldifferences between some populations, this wasunrelated to molecular variation.The low level of genetic diversity and highproportion of interpopulation variation agreeswith the findings of other studies onregionally distributed eucalypts. The findingsindicate that previous estimates of theeffective population size of the species arelargely overestimated and that the individualpopulations are sufficiently differentiatedthat they should be treated as separatemanagement units. Further study is recommendedto elucidate the full extent of clonality inthe species and to conduct germination trialson seed collected from clonal populations.     

Historical translocations and stocking alter the genetic structure of a Mediterranean lobster fishery

Stocking is often used to supplement wild populations that are overexploited or have collapsed, yet it is unclear how this affects the genetic diversity of marine invertebrate populations. During the 1970s, a lobster stock enhancement program was carried out around the island of Corsica in the Mediterranean using individuals translocated from the Atlantic coast of France. This included the release of thousands of hatchery‐reared postlarval lobsters and several adult individuals, but no monitoring plan was established to assess whether these animals survived and recruited to the population. In this study, we sampled European lobster (Homarus gammarus) individuals caught around Corsica and tested whether they showed Atlantic ancestry. Due to a natural marked phylogeographic break between Atlantic and Mediterranean lobsters, we hypothesized that lobsters with dominant (>0.50) Atlantic ancestry were descended from historical stocking releases. Twenty Corsican lobsters were genotyped at 79 single nucleotide polymorphisms, and assignment analysis showed that the majority (13) had dominant Atlantic ancestry. This suggests that the hatchery stocking program carried out in Corsica during the 1970s, using individuals translocated from the Atlantic coast of France, has likely augmented local recruitment but at a cost of altering the genetic structure of the Corsican lobster population.     

Population genetic structure of Vallisneria americana,a dioecious clonal macrophyte

The population genetic structure and spatial genetic structure of the dioecious aquatic macrophyte Vallisneria americana was examined near Turkey Island in the Detroit River in late summer of 1991. The density and distribution of male, female, and vegetative ramets was determined for three transects parallel, and three transects perpendicular to the island, at mean water depths of 38–306 cm. A strong male-biased sex ratio was observed in shallow water, while sex ratios became increasingly female-biased, and plant density increased, at greater water depths. Cellulose acetate gel electrophoresis was used to characterize the allozyme phenotype of each ramet that had been screened for seven enzyme systems. Overall, 91 allozyme phenotypes were identified. A single allozyme phenotype accounted for 33%–55% of all the ramets (depending on the transect), indicating extensive regional vegetative growth. However, the population as a whole displayed high genetic diversity (H_T = 0.3403), with most of the diversity occurring within transects (H_s = 0.3297) rather than between transects (D_ST = 0.0106). The possible factors accounting for the high small-scale genetic diversity of this clonal aquatic plant species are discussed.     

Admixture as the basis for genetic mapping

Genetic mapping in natural populations is increasing rapidly in feasibility and accessibility. As with many areas in genetics, advances in molecular techniques and statistics are drastically altering how we can investigate inheritance in wild organisms. For ecology and evolution, this is particularly significant and promising, because many of the organisms of interest are not amenable to conventional genetic approaches. Admixture mapping falls within a family of statistical approaches that use natural recombination and linkage disequilibrium between genetic markers and phenotypes as the basis for mapping. Our aim in this review is to provide a snapshot of previous and ongoing research, existing methods and challenges, the nature of questions that can be investigated and prospects for the future of admixture mapping.     

Leaf gas exchange in a clonal eucalypt plantation as related to soil moisture, leaf water potential and microclimate variables

In order to determine how environmental and physiological factors affect leaf gas exchange in a 9-year-old clonal eucalypt plantation (Eucalyptus grandis Hill ex. Maiden hybrids) in the State of Espirito Santo, Brazil, the diurnal patterns of predawn leaf water potential (Ψ_pd), and leaf gas exchange were monitored from November 1995 to August 1996. Soil water content (Θ) and microclimatic variables were also recorded. Most of the rainfall during the experimental period occurred from October to December 1995 and from March to April 1996, causing a significant variation in Θ and Ψ_pd. A high positive correlation (r ²=0.92) was observed between Ψ_pd and Θ measured at 0.3 m depth from the soil surface. During conditions of high soil water availability, the maximum values of stomatal conductance for water vapor (g _s) and net photosynthetic rate (A) were over 0.4 mol m^–2 s^–2 and l5 μmol m^–2 s^–1, respectively. The results showed that Ψ_pd and leaf gas exchange of the examined trees were susceptible to changes in the water content of the upper soil layers, where the major concentration of active roots occur. Multiple linear regression analysis indicated that photosynthetic active radiation (Q), vapor pressure deficit (VPD), atmospheric CO₂ molar fraction (C _a), and Ψ_pd were the most important factors controlling g _s whereas Q and VPD were the main microclimatic variables controlling A. Received: 5 November 1998 / Accepted: 10 November 1999     

野古草种群克隆的遗传变异和遗传结构

用酶电泳法和同工酶分析对东北松嫩草原西北部野古草种群克隆遗传变异性和种群遗传结构做了探讨。讨论了遗传多样性、地理距离和遗传距离之间的关系、大种群和小种群的遗传变异性和种群间的基因流 ;种群间 ,包括大种群和小种群间基因流、遗传和地理距离对遗传多样性的影响、昆虫和风传粉、种群籽苗的补充、遗传多样性的发生和保持 ,自交不亲和性和无性繁殖及体细胞突变     

Using adult groups of red-cockaded woodpeckers for translocations and population augmentation

The red-cockaded woodpecker (Picoides borealis; hereafter RCW) was listed as federally endangered in 1973 after a population decline due primarily to habitat loss. Habitat fragmentation produces isolated populations of RCWs and managers often translocate subadult birds to augment existing populations. Although several studies have examined success of translocating subadults, detailed studies examining translocations of adults have been limited. We evaluated the feasibility and success of using adult RCWs for translocation and augmentation of existing populations in Morehouse Parish, Louisiana, 2006–2009. We translocated 41 primarily adult RCWs, consisting of 12 potential breeding groups (PBGs) and 5 single bird groups to suitable habitat at the Morehouse Parish Conservation Area (MPCA). Fifty-nine percent of translocated RCWs remained on the MPCA and 45% became breeders. Thirty-four percent of translocated RCWs were breeding after being on the MPCA for 2 breeding seasons, suggesting that translocated adult RCWs can augment the breeding population within 2 years of translocation. Fledglings contributed by translocated RCWs ranged from 11% to 30% of the total fledglings on the MPCA. There were 5 PBGs established on the MPCA from translocated RCWs and 20% of the fledglings had at least 1 translocated parent. Success rates for translocation of adults in our study were lower than previous studies where subadults were used. However, previous research suggested that demographically isolated groups have a high risk of abandonment and extirpation, and thus do not contribute to the recovery of the species. The success rates we observed suggest that translocating adult groups may be a useful tool in RCW recovery, and hence should be considered by managers when demographically isolated groups occur. © 2011 The Wildlife Society.     

Whole-genome sequencing as a first-tier diagnostic framework for rare genetic diseases

Rare diseases affect nearly 300 million people globally with most patients aged five or less. Traditional diagnostic approaches have provided much of the diagnosis; however, there are limitations. For instance, simply inadequate and untimely diagnosis adversely affects both the patient and their families. This review advocates the use of whole genome sequencing in clinical settings for diagnosis of rare genetic diseases by showcasing five case studies. These examples specifically describe the utilization of whole genome sequencing, which helped in providing relief to patients via correct diagnosis followed by use of precision medicine.     

Assessing the genetic legacy of a rare,clonal Australian shrub <Emphasis Type="Italic">Grevillea infecunda</Emphasis> (Proteaceae)

Reliance on clonal reproduction is associated with an increased risk of extinction. Grevillea infecunda is a rare, putatively sterile shrub restricted to 11 populations in a localized coastal region of south-eastern Australia. We assessed the genetic diversity, clonal diversity and spatial distribution of clones in all populations of G. infecunda to guide conservation management. Eight chloroplast haplotypes were identified from the trnL – trnF and trnQ – rps16 intergenic spacer regions. All individuals belonged to a single maternal lineage dominated by one haplotype (95/111 samples). Minor haplotypes differed from the common haplotype only by single mutational steps. However, microsatellite markers revealed 89 multilocus genotypes (MLGs) in 38 multilocus lineages (MLLs) of variable size. MLLs were not shared among populations and ramets from different MLLs rarely intermingled physically. New shoots arising after fire were confirmed to belong to previously-existing MLLs, indicating that this species exhibits adaptation to fire. Genetically similar MLGs were more likely to be found in close proximity than less similar MLGs, resulting in significant spatial autocorrelation to ca 350 m. Genetic diversity was moderate but genotypic diversity was low once likely clonality was taken into account. Clonality appears to have arisen several times within the holly-leafed grevilleas and examining G. infecunda is a step towards understanding why and how often clonality occurs, and the long-term evolutionary outcomes of this life history.     

High genetic diversity in a rare and endangered sunflower as compared to a common congener

Determining the genetic structure of isolated or fragmented species is of critical importance when planning a suitable conservation strategy. In this study, we use nuclear and chloroplast SSRs (simple sequence repeats) to investigate the population genetics of an extremely rare sunflower, Helianthus verticillatus Small, which is known from only three locations in North America. We investigated levels of genetic diversity and population structure compared to a more common congener, Helianthus angustifolius L., using both nuclear and chloroplast SSRs. We also investigated its proposed hybrid origin from Helianthus grosseserratus Martens and H. angustifolius. Twenty-two nuclear SSRs originating from the cultivated sunflower (Helianthus annuus L.) expressed sequence tag (EST) database, and known to be transferable to H. verticillatus and its putative parental taxa, were used in this study thereby allowing for statistical control of locus-specific effects in population genetic analyses. Despite its rarity, H. verticillatus possessed significantly higher levels of genetic diversity than H. angustifolius at nuclear loci and equivalent levels of chloroplast diversity. Significant levels of population subdivision were observed in H. verticillatus but of a magnitude comparable to that of H. angustifolius. Inspection of multilocus genotypes also revealed that clonal spread is highly localized. Finally, we conclude that H. verticillatus is not of hybrid origin as it does not exhibit a mixture of parental alleles at nuclear loci, and it does not share a chloroplast DNA haplotype with either of its putative parents.     

Assessing fine-scale genetic structure and relatedness in the micro-endemic Florida bog frog

The Florida bog frog (Rana okaloosae) is restricted to approximately 25 seepage drainages on the Florida Panhandle, southeastern USA. We evaluated fine-scale (<1–10 km) genetic structure among 80 samples from a long-term study area in one portion of its range. We also included co-distributed samples (N = 48) from bronze frogs (R. clamitans). Individual R. okaloosae were significantly more related to one another than expected under panmixia, though significant patterns of isolation-by-distance were detected reflecting limited dispersal. Bayesian clustering failed to identify discrete genetic clusters within species. Subtle, though important differences in genetic structuring between R. okaloosae and R. clamitans suggests that future efforts to predict the impact of landscape changes on Rana okaloosae, should focus on the species itself rather than R. clamitans as a surrogate species.     

Cryptic changes in the genetic structure of a highly clonal coral population and the relationship with ecological performance

Elkhorn coral, Acropora palmata, relies heavily on clonal propagation and often displays low genotypic (clonal) diversity. Populations in the Florida Keys experienced rapid declines in tissue cover between 2004 and 2006, largely due to hurricanes and disease, but remained stable from 2006 to 2010. All elkhorn colonies in 150 m² permanent study plots were genotyped in 2006 (n = 15 plots) and 2010 (n = 24 plots), and plots sampled in both years were examined for changes in allelic and genotypic diversity during this period of stable ecological abundance. Overall, genetic diversity of Florida plots was low and declined further over the 4-yr period; seven of the 36 original genets and two of 67 alleles (among five microsatellite loci) were lost completely from the sampled population, and an additional 15 alleles were lost from individual reefs. In 2010, Florida plots (~19 colonies) contained an average of 2.2 ± 1.38 (mean ± SD) genets with a significant negative correlation between colony abundance and genotypic diversity. When scaled to total tissue abundance, genotypic diversity is even lower, with 43 % of genets below the size of sexual maturity. We examined the hypothesized positive relationship of local genotypic diversity with ecological performance measures. In Florida plots (n = 15), genotypic diversity was not significantly correlated with tissue loss associated with chronic predation, nor with acute disease and storm-fragmentation events, though this relationship may be obscured by the low range of observed diversity and potential confounding with abundance. When more diverse plots in Curaçao (n = 9) were examined, genotypic diversity was not significantly correlated with resistance during an acute storm disturbance or rate of recovery following disturbance. Cryptic loss of genetic diversity occurred in the apparently stable Florida population and confirms that stable or even increasing abundance does not necessarily indicate genetic stability.     

The features of the hippocampal structure as a neuroanatomical basis for differences in behavior

Neuromorphological and behavioural studies have been made on several strains of mice (C57B1, DBA/2, SEC) and on the spiny mouse Acomys cahirinus. It was shown that animals with different genotypes differ by the size of fascia dentata and by the extension of the pyramidal layer in CA3 field of the hippocamp. Animals with a higher learning capacity exhibited smaller layer of granular cells in the fascia dentata, which may be due to a lower density of neurones in this region. Terminals of the mossy fibers--the axons of granular cells--were found mainly on the apical dendrites of the pyramidal cells in CA3 field. On the contrary, in animals with lower capacities to learning, mossy fiber terminals were observed mainly on the basal dendrites of the pyramidal cells, the extent of the granular layer in these animals being significantly larger.     

Pseudomonas syringae lipopolysaccharides: Immunochemical characteristics and structure as a basis for strain classification

Lipopolysaccharide (LPS) preparations of 34 Pseudomonas syringae strains of 19 pathovars were prepared by saline extraction from wet cells and purified by repeated ultracentrifugation. The preparations reacted with homologous O-antisera, obtained by rabbit immunization with heat-killed bacterial cells. Through inhibition of homologous reactions between LPS preparations of heterologous strains (enzyme immunoassay, EIA), it was established for the first time that high serological affinity between strains is observed only if their LPS contains O-specific polysacc haride chains (OPS) comprised of completely identical rather than partially similar units. The central linear part of the OPS was found to be serologically inert when shielded with side groups. Data on immunochemical characteristics of the LPS and OPS structure are analyzed in relation to the design of P. syringae classification scheme.     

Spatial genetic structure within a metallicolous population of Arabidopsis halleri, a clonal, self-incompatible and heavy-metal-tolerant species

Arabidopsis halleri, a close wild relative of A. thaliana, is a clonal, insect-pollinated herb tolerant to heavy metals (Zn, Pd, Cd) and a hyperaccumulator of Zn and Cd. It is of particular interest in the study of evolutionary processes and phytoremediation. However, little is known about its population gene flow patterns and the structure of its genetic diversity. We used five microsatellite loci to investigate the genetic structure at a fine spatial scale (10 cm to 500 m) in a metallicolous population of A. halleri. We also studied the contributions made by clonal propagation and sexual reproduction (seed and pollen dispersal) to the genetic patterns. Clonal diversity was high (D(G) > 0.9). Clonal spread occurs only at short distances (< 1 m). Both clonal spread and limited dispersal, associated with sexual reproduction, contribute to the significant spatial genetic structure revealed by spatial autocorrelation analysis. The shape of the autocorrelogram suggests that seed dispersal is restricted and pollen flow extensive, which may be related to intense activity by insect pollinators. Clonal spread was more extensive in the lowly polluted zone than in the highly polluted zone. This cannot be interpreted as a strategy for promoting the propagation of adapted genotypes under the harshest ecological constraints (highest heavy metal concentrations). The higher fine-scale spatial genetic structure found in the lowly polluted zone can be ascribed to plant densities that were lower than in the highly polluted zone. No evidence of genetic divergence due to spatial heavy metal heterogeneity was found between lowly and highly polluted zones.     

Fine-scale spatial genetic structure and clonal distribution of the cold-water coral Lophelia pertusa

Determining the spatial genetic structure within and among cold-water coral populations is crucial to understanding population dynamics, assessing the resilience of cold-water coral communities and estimating genetic effects of habitat fragmentation for conservation. The spatial distribution of genetic diversity in natural populations depends on the species’ mode of reproduction, and coral species often have a mixed strategy of sexual and asexual reproduction. We describe the clonal architecture of a cold-water coral reef and the fine-scale population genetic structure (<35 km) of five reef localities in the NE Skagerrak. This study represents the first of this type of analysis from deep waters. We used thirteen microsatellite loci to estimate gene flow and genotypic diversity and to describe the fine-scale spatial distribution of clonal individuals of Lophelia pertusa. Within-population genetic diversity was high in four of the five reef localities. These four reefs constitute a genetic cluster with asymmetric gene flow that indicates metapopulation dynamics. One locality, the Säcken reef, was genetically isolated and depauperate. Asexual reproduction was found to be a highly important mode of reproduction for L. pertusa: 35 genetic individuals were found on the largest reef, with the largest clone covering an area of nearly 300 m².     

Within-population spatial genetic structure, neighbourhood size and clonal subrange in the seagrass Cymodocea nodosa

Abstract The extent of clonality within populations strongly influences their spatial genetic structure (SGS), yet this is hardly ever thoroughly analysed. We employed spatial autocorrelation analysis to study effects of sexual and clonal reproduction on dispersal of the dioecious seagrass Cymodocea nodosa. Analyses were performed both at genet level (i.e. excluding clonal repeats) and at ramet level. Clonal structure was characterized by the clonal subrange, a spatial measure of the linear limits where clonality still affects SGS. We show that the clonal subrange is equivalent to the distance where the probability of clonal identity approaches zero. This combined approach was applied to two meadows with different levels of disturbance, Cadiz (stable) and Alfacs (disturbed). Genotypic richness, the proportion of the sample representing distinct genotypes, was moderate (0.38 Cadiz, 0.46 Alfacs) mostly due to dominance of a few clones. Expected heterozygosities were comparable to those found in other clonal plants. SGS analyses at the genet level revealed extremely restricted gene dispersal in Cadiz (Sp = 0.052, a statistic reflecting the decrease of pairwise kinship with distance), the strongest SGS found for seagrass species, comparable only to values for selfing herbaceous land plants. At Cadiz the clonal subrange extended across shorter distances (20-25 m) than in Alfacs (30-35 m). Comparisons of sexual and vegetative components of gene dispersal suggest that, as a dispersal vector within meadows, clonal spread is at least as important as sexual reproduction. The restricted dispersal and SGS pattern in both meadows indicates that the species follows a repeated seedling recruitment strategy.