Genetic and epigenetic insight into morphospecies in a reef coral

Incongruence between conventional and molecular systematics has left the delineation of many species unresolved. Reef‐building corals are no exception, with phenotypic plasticity among the most plausible explanations for alternative morphospecies. As potential molecular signatures of phenotypic plasticity, epigenetic processes may contribute to our understanding of morphospecies. We compared genetic and epigenetic variation in Caribbean branching Porites spp., testing the hypothesis that epigenetics—specifically, differential patterns of DNA methylation—play a role in alternative morphotypes of a group whose taxonomic status has been questioned. We used reduced representation genome sequencing to analyse over 1,000 single nucleotide polymorphisms and CpG sites in 27 samples of Porites spp. exhibiting a range of morphotypes from a variety of habitats in Belize. We found stronger evidence for genetic rather than epigenetic structuring, identifying three well‐defined genetic groups. One of these groups exhibited significantly thicker branches, and branch thickness was a better predictor of genetic groups than depth, habitat or symbiont type. In contrast, no clear epigenetic patterns emerged with respect to phenotypic or habitat variables. While there was a weak positive correlation between pairwise genetic and epigenetic distance, two pairs of putative clones exhibited substantial epigenetic differences, suggesting a strong environmental effect. We speculate that epigenetic patterns are a complex mosaic reflecting diverse environmental histories superimposed over a relatively small heritable component. Given the role of genetics in branching Porites spp. morphospecies we were able to detect with genomewide sequencing, use of such techniques throughout the geographic range of these corals may help settle their phylogeny.     

Which adaptations of some invasive Ludwigia spp. (Rosidae,Onagraceae) populations occur in contrasting hydrological conditions in Western France?

Biological invasions in wetlands by Water Primroses (Ludwigia grandiflora ssp. hexapetala and L. peploides ssp. montevidensis) are an increasing problem especially in wet meadows. The aim of this paper is to quantify differences between species and the adaptation of these amphibious plants in order to establish the consequences for site managers. The hypotheses were: (i) that these species differ in biomass and morphology, and (ii) that terrestrial habitats determine particular adaptations such as reduced biomass, more roots and a bushy form. Biomasses from five sites were collected, following seasonal changes and biological traits were measured on selected plants. Comparing species in aquatic habitats, L. peploides produced less biomass than L. grandiflora. Comparing habitats for L. grandiflora, the biomass in meadows was almost twice that in dykes, particularly due to old stems, the converse of the hypothesis. Terrestrial forms were characterized by a bushy morphology, with shorter internodes and stems, as well as more secondary ramifications, while in aquatic habitats the plant architecture was simpler. Models were built linking morphology to species, sites and water conditions. Adaptations to terrestrial habitats of a particularly resistant form with a significant potential biomass are practical constraints for farmers and managers.     

A new subspecies ofArenaria grandiflora (Caryophyllaceae) from the Rif mountains (Northern Morocco)

A new subspecies,A. grandiflora subsp.gomarica (Caryophyllaceae), is described from the mountains of northern Morocco. The new taxon is tetraploid and has been confused in the past either with the Balearic endemicA. grandiflora subsp.glabrescens or with the widespreadA. grandiflora subsp.grandiflora, which is also present in the African continent. Detailed morphological analysis showed that plants from the Rif mountains are closely related toA. grandiflora subsp.glabrescens, but differ from it in having a longer calyx, smaller seed size, and a glandular indument on pedicels, leaves and calyx.Arenaria grandiflora subsp.gomarica can be distinguished from all infraspecific taxa of theA. grandiflora complex by the combined presence of a heterotrichous (simple and pluricellular eglandular hairs, glandular hairs) indument on the inflorescences and glandular hairs on the calyx.     

Molecular genetic examination of the polymorphic Arctic charr Salvelinus alpinus of Thingvallavatn, Iceland

Thingvallavatn, Iceland contains two sympatric morphotypes (benthic and limnetic) of Arctic charr Salvelinus alpinus. Each morphotype is composed of two morphs and these differ markedly in ecology, behaviour and life history. We used molecular genetic approaches to test whether (i) genetic heterogeneity exists among morphs and (ii) if morphs arose in allopatry and came into secondary contact or arose sympatrically within the lake through genetic segregation and/or phenotypic plasticity. Direct sequencing of 275 bp of the mitochondrial DNA (mtDNA) control region, mtDNA restriction fragment length polymorphisms and single locus minisatellite analyses detected insufficient variation to test our hypotheses. Analysis of multilocus minisatellite band sharing detected no significant differences between morphs within the same morphotype. However, significant differences among morphs belonging to different morphotypes suggest some genetic heterogeneity in Thingvallavatn charr. Limnetic charr from Thingvallavatn were more similar to sympatric benthic charr than to allopatric limnetics from two other Icelandic lakes. This suggests that the Thingvallavatn morphs arose sympatrically within the lake rather than in allopatry followed by secondary contact.     

Genome‐wide DNA methylation alterations of Alternanthera philoxeroides in natural and manipulated habitats: implications for epigenetic regulation of rapid responses to environmental fluctuation and phenotypic variation

Alternanthera philoxeroides (alligator weed) is an invasive weed that can colonize both aquatic and terrestrial habitats. Individuals growing in different habitats exhibit extensive phenotypic variation but little genetic differentiation in its introduced range. The mechanisms underpinning the wide range of phenotypic variation and rapid adaptation to novel and changing environments remain uncharacterized. In this study, we examined the epigenetic variation and its correlation with phenotypic variation in plants exposed to natural and manipulated environmental variability. Genome‐wide methylation profiling using methylation‐sensitive amplified fragment length polymorphism (MSAP) revealed considerable DNA methylation polymorphisms within and between natural populations. Plants of different source populations not only underwent significant morphological changes in common garden environments, but also underwent a genome‐wide epigenetic reprogramming in response to different treatments. Methylation alterations associated with response to different water availability were detected in 78.2% (169/216) of common garden induced polymorphic sites, demonstrating the environmental sensitivity and flexibility of the epigenetic regulatory system. These data provide evidence of the correlation between epigenetic reprogramming and the reversible phenotypic response of alligator weed to particular environmental factors.     

Clonal spread of invasive Ludwigia hexapetala and L. grandiflora in freshwater wetlands of California

Ludwigia hexapetala and L. grandiflora are recent, aggressive invaders of freshwater wetlands in California. To assess the relative role of sexual versus clonal reproduction in invasive spread, we used AFLP markers to genotype 794 ramets of L. hexapetala sampled from 27 populations in three watersheds of California, and 150 ramets of L. grandiflora from five populations in a fourth watershed. We then used two analytical methods, similarity thresholds and character incompatibilities, to distinguish genotypic variation within genets (clones) from variation between genets. Our analyses revealed extremely limited genotypic and genet variation in invasive L. hexapetala and L. grandiflora within California. Within L. hexapetala, 95% of the ramets analyzed represented a single genet. The genet was the only one detected in 20 populations. The remaining seven populations contained two to nine genets. Within L. grandiflora, all ramets were of only one genotype. Thus, invasive spread within and between populations, and across watersheds, appears to be almost exclusively clonal and brought about by the dispersal of vegetative propagules. The extremely low seedling recruitment indicates that management should target vegetative dispersal and growth.     

Epigenetic patterns newly established after interspecific hybridization in natural populations of Solanum

Interspecific hybridization is known for triggering genetic and epigenetic changes, such as modifications on DNA methylation patterns and impact on phenotypic plasticity and ecological adaptation. Wild potatoes (Solanum, section Petota) are adapted to multiple habitats along the Andes, and natural hybridizations have proven to be a common feature among species of this group. Solanum × rechei, a recently formed hybrid that grows sympatrically with the parental species S. kurtzianum and S. microdontum, represents an ideal model for studying the ecologically and evolutionary importance of hybridization in generating of epigenetic variability. Genetic and epigenetic variability and their correlation with morphological variation were investigated in wild and ex situ conserved populations of these three wild potato species using amplified fragment length polymorphism (AFLP) and methylation‐sensitive amplified polymorphism (MSAP) techniques. We observed that novel methylation patterns doubled the number of novel genetic patterns in the hybrid and that the morphological variability measured on 30 characters had a higher correlation with the epigenetic than with the genetic variability. Statistical comparison of methylation levels suggested that the interspecific hybridization induces genome demethylation in the hybrids. A Bayesian analysis of the genetic data reveled the hybrid nature of S. × rechei, with genotypes displaying high levels of admixture with the parental species, while the epigenetic information assigned S. × rechei to its own cluster with low admixture. These findings suggested that after the hybridization event, a novel epigenetic pattern was rapidly established, which might influence the phenotypic plasticity and adaptation of the hybrid to new environments.     

Sexual reproduction of two alien invasive Ludwigia (Onagraceae) on the middle Loire River,France

Ludwigia peploides (Kunth) Raven ssp. montevidensis (Spreng.) Raven and Ludwigia grandiflora (Michaux) Greuter and Burdet ssp. hexapetala (Hooker and Arn.) Nesom and Kartesz, are expanding their geographic range due to clonal reproduction; these taxa are considered the most important nuisance aquatic plants in French river habitats. During 1970s, these two species have colonized former channels and river banks of the middle Loire River, previously scarcely covered by aquatic vegetation. Now, the exotic Ludwigia build up dense and continuous stands with potentially high impact on biodiversity and sedimentation rates.     

Jack of all nectars, master of most: DNA methylation and the epigenetic basis of niche width in a flower-living yeast

In addition to genetic differences between individuals as a result of nucleotide sequence variation, epigenetic changes that occur as a result of DNA methylation may also contribute to population niche width by enhancing phenotypic plasticity, although this intriguing possibility remains essentially untested. Using the nectar‐living yeast Metschnikowia reukaufii as study subject, we examine the hypothesis that changes in genome‐wide DNA methylation patterns underlie the ability of this fugitive species to exploit a broad resource range in its heterogeneous and patchy environment. Data on floral nectar characteristics and their use by M. reukaufii in the wild were combined with laboratory experiments and methylation‐sensitive amplified polymorphism (MSAP) analyses designed to detect epigenetic responses of single genotypes to variations in sugar environment that mimicked those occurring naturally in nectar. M. reukaufii exploited a broad range of resources, occurring in nectar of 48% of species and 52% of families surveyed, and its host plants exhibited broad intra‐ and interspecific variation in sugar‐related nectar features. Under experimental conditions, sugar composition, sugar concentration and their interaction significantly influenced the mean probability of MSAP markers experiencing a transition from unmethylated to methylated state. Alterations in methylation status were not random but predictably associated with certain markers. The methylation inhibitor 5‐azacytidine (5‐AzaC) had strong inhibitory effects on M. reukaufii proliferation in sugar‐containing media, and a direct relationship existed across sugar × concentration experimental levels linking inhibitory effect of 5‐AzaC and mean per‐marker probability of genome‐wide methylation. Environmentally induced DNA methylation polymorphisms allowed genotypes to grow successfully in extreme sugar environments, and the broad population niche width of M. reukaufii was largely made possible by epigenetic changes enabling genotype plasticity in resource use.     

Variable maternal methylation overlapping the nc886/vtRNA2-1 locus is locked between hypermethylated repeats and is frequently altered in cancer

Cancer is as much an epigenetic disease as a genetic one; however, the interplay between these two processes is unclear. Recently, it has been shown that a large proportion of DNA methylation variability can be explained by allele-specific methylation (ASM), either at classical imprinted loci or those regulated by underlying genetic variants. During a recent screen for imprinted differentially methylated regions, we identified the genomic interval overlapping the non-coding nc886 RNA (previously known as vtRNA2-1) as an atypical ASM that shows variable levels of methylation, predominantly on the maternal allele in many tissues. Here we show that the nc886 interval is the first example of a polymorphic imprinted DMR in humans. Further analysis of the region suggests that the interval subjected to ASM is approximately 2 kb in size and somatically acquired. An in depth analysis of this region in primary cancer samples with matching normal adjacent tissue from the Cancer Genome Atlas revealed that aberrant methylation in bladder, breast, colon and lung tumors occurred in approximately 27% of cases. Hypermethylation occurred more frequently than hypomethylation. Using additional normal-tumor paired samples we show that on rare occasions the aberrant methylation profile is due to loss-of-heterozygosity. This work therefore suggests that the nc886 locus is subject to variable allelic methylation that undergoes cancer-associated epigenetic changes in solid tumors.     

Chromosome study of hybrid and gynogenetic offspring of artificial crosses between members of the catfish families Clariidae and Pangasiidae

Synopsis Artificial hybridization between species of the catfish families Clariidae (Clarias macrocephalus) and Pangasiidae (Pangasius sutchi) resulted in first generation offspring comprising two intermediate morphotypes and one morphotype indistinguishable from its clariid parent. The two intermediate morphotypes apparently correspond to hybrid morphotypes 2 and 4 resulting from earlier hybridization experiments between the same parent species (Tarnchalanukit 1986). We did not obtain morphotypes 1 and 3. Chromosome spreads of the relatively pangasiid-like morphotype 2 reveal a diploid number of 57, presumably comprising one set of Clarias (n=27) and one of Pangasius (n=30) chromosomes. The relatively clariid-like morphotype 4 is a triploid with 84 chromosomes, presumably comprising two sets from Clarias (2n=54) and one from Pangasius (n=30). Finally, the morphotype indistinguishable from Clarias, is a diploid with 54 chromosomes, apparently arising from gynogenesis.     

DNA Hypomethylation Affects Cancer-Related Biological Functions and Genes Relevant in Neuroblastoma Pathogenesis

Neuroblastoma (NB) pathogenesis has been reported to be closely associated with numerous genetic alterations. However, underlying DNA methylation patterns have not been extensively studied in this developmental malignancy. Here, we generated microarray-based DNA methylation profiles of primary neuroblastic tumors. Stringent supervised differential methylation analyses allowed us to identify epigenetic changes characteristic for NB tumors as well as for clinical and biological subtypes of NB. We observed that gene-specific loss of DNA methylation is more prevalent than promoter hypermethylation. Remarkably, such hypomethylation affected cancer-related biological functions and genes relevant to NB pathogenesis such as CCND1, SPRR3, BTC, EGF and FGF6. In particular, differential methylation in CCND1 affected mostly an evolutionary conserved functionally relevant 3′ untranslated region, suggesting that hypomethylation outside promoter regions may play a role in NB pathogenesis. Hypermethylation targeted genes involved in cell development and proliferation such as RASSF1A, POU2F2 or HOXD3, among others. The results derived from this study provide new candidate epigenetic biomarkers associated with NB as well as insights into the molecular pathogenesis of this tumor, which involves a marked gene-specific hypomethylation.     

前列腺癌的DNA甲基化及其临床应用

目前认为恶性肿瘤的形成是遗传和表观遗传机制共同作用的结果。表观遗传机制包括DNA甲基化、组蛋白修饰和miRNA。DNA异常甲基化(高甲基化和低甲基化)是前列腺癌最具特征的表观遗传改变, 它能够导致基因组不稳定, 调控基因的异常表达, 在前列腺癌的形成和发展中起到重要作用。同时, DNA甲基化作为前列腺癌表观遗传研究的一个热点, 为临床前列腺癌的早期诊断、预后评估及药物治疗提供新的方法和途径。文章根据前列腺癌的DNA高甲基化和低甲基化的最新研究成果阐述了前列腺癌形成的表观遗传学机制, 并且讨论了它们在前列腺癌临床转化方面的最新研究进展。     

RAPD analysis of genome variability of planted ginseng,Panax ginseng

Genome variability of 23 ginseng plants (Panax ginseng) grown in culture in Primorskii Krai was studied by RAPD method. Eleven arbitrary chosen primers were used to analyze 138 loci of DNA samples, 17 of which appeared to be polymorphic. The OPD-11-1000 fragment was found to be a RAPD marker allowing plants to be differentiated according to their morphotype. Using five primers, it was demonstrated that the genetic polymorphism of the cultivated plants is lower than that in nature (7.6% and 10.6%, respectively). Dendrograms of genetic relatedness are in accord with genetic differences between individuals of plantedP. ginseng belonging to different morphotypes, and demonstrate close relatedness of one of the morphotypes to wild plants. This morphotype could be recommended for reintroduction into natural habitats.     

Ongoing speciation within the Anastrepha fraterculus cryptic species complex: the case of the Andean morphotype

The Anastrepha fraterculus (Wiedemann) (Diptera: Tephritidae) cryptic species complex is currently composed of seven taxonomically recognized morphotypes. Both, pre‐ and post‐zygotic isolation has been documented among four of these morphotypes, revealing that in fact they appear to be distinct biological entities. In order to progress in the full delimitation of species within the complex, we examined reproductive isolation between a Colombian population of the Andean morphotype and populations belonging to four other morphotypes spanning from Mexico to Argentina. Flies from the Andean morphotype exhibited strong pre‐zygotic mating isolation through temporal partitioning of mating activity. Post‐zygotic isolation was observed for crosses of males of all morphotypes and Andean morphotype females, yet most of the F1 hybrid ♂ × F1 hybrid ♀ self‐crosses showed normal levels of fertility, a finding suggesting a nuclear–cytoplasmic interaction according to previous studies. Overall, the Andean morphotype within the complex also appears to be a distinct biological entity. We discuss the implications of these findings for the understanding of speciation mechanisms in the Neotropical genus Anastrepha.     

Genetic divergence between and within two color morphotypes of <Emphasis Type="Italic">Parapercis sexfasciata</Emphasis> (Perciformes: Pinguipedidae) from Tosa Bay,southern Japan

The anterior half of the mitochondrial DNA control region (mtCR) sequence (ca. 400 base pairs) was compared between two color morphotypes (A, B) of Parapercis sexfasciata from Tosa Bay, southern Japan, using 16 and 21 specimens, respectively. Intramorphotypic mtCR divergences were only 0.0–0.5% and 1.0–2.5% for morphotypes A and B, respectively. In contrast, intermorphotypic mtCR divergence was much greater, 12.7–14.0%. Furthermore, phylogenetic analysis using a neighbor-joining algorithm, with P. multifasciata as an outgroup, showed that each morphotype was reciprocally monophyletic. These results and the distinct coloration and overlapping distribution indicate that the two color morphotypes of P. sexfasciata represent two distinct species. Mismatch distribution analysis suggested that both morphotypes had undergone population expansion; however, estimates of initial population sizes and mutational timescales suggested that morphotype B comprises historically larger and older populations than morphotype A.     

Genetic diversity in Taro (Colocasia esculenta Schott, Araceae) in China: An ethnobotanical and genetic approach

Taro,Colocasia esculenta (Araceae), is a widely distributed and important food crop in the humid tropics and subtropics. Relatively neglected by science, much knowledge of genetic diversity in taro is with farmers. Taro genetic resources managed by five ethnic communities and Han farming villages in diverse ecosystems were sampled and characterized in Yunnan Province, southwest China. This study documented a new type of flowering taro selected by farmers which is widely and intensively cultivated for its edible flower. Samples representing 20 traditional cultivars were grouped into five major morphotypes according to ethnobotanical, agro-morphological, and preliminary genetic characterization. Folk taxonomy and uses tended to confirm the five morphotypes recognized by peoples of Yunnan for their distinctive properties and uses. These major taro morphotypes are key units for assessing how patterns of use maintain genetic diversity and to monitor potential genetic erosion. The morphotype groups also suggest possible evolutionary relationships in cultivated taros.     

Antibiotic-induced DNA methylation changes in calluses of Arabidopsis thaliana

This study was carried out to determine the involvement of the antibiotic kanamycin, commonly used as a selective agent in transformation protocols, in the phenomenon of somaclonal variation. Both genetic and epigenetic events were looked for. Two complementary approaches were used to evaluate global methylation changes in the genome of callus derived from the leaves of Arabidopsis thaliana L.; immunolabelling using monoclonal-antibodies raised against 5-methylcytosine in order to define the relative abundance of methylated cytosine; the analysis of methylation-sensitive polymorphism technique (MSAP) to assess methylation changes at CCGG sequences. In addition, the same samples were analysed using AFLPs in order to determine the extent of genomic change with respect to callus grown in the absence of kanamycin and plants grown from seed. The use of kanamycin as a selective agent caused extensive methylation changes in the genome with both hyper- and hypomethylation events seen. However, the net result was genome-wide hypomethylation: this effect was dosage dependent; the higher the dose, the greater the effect. At the same time, sequence mutation was detected.     

Leaf morphological responses to variation in water availability for plants in the <Emphasis Type="Italic">Piriqueta caroliniana</Emphasis> complex

Distribution of plants and the expression of traits associated with environmental variation can be affected by both average conditions and the variance in conditions including extreme climatic events. We expect that these same factors should affect the distribution of plants in hybrid zones between ecologically distinct species where the hybrids should occupy ecotones or intermediate habitats. We evaluated water availability and leaf morphological differences among parental and hybrid populations of herbaceous perennial plants in the Piriqueta caroliniana complex along environmental gradients in Southeastern North America. We focus on two taxa in this group; the viridis morphotype, which occurs in southern Florida, and the caroliniana morphotype, which is distributed from northern Florida to southern Georgia. Advanced-generation hybrid derivatives of these morphotypes occupy a broad geographic region that extends across much of central Florida. Overall, we found that hybrid populations occurred in significantly drier locations, indicating that their habitat requirements are transgressive (i.e., exceeding parental values) rather than intermediate to the parental morphotypes. Water availability differed between the two sampling years, and plants displayed morphological changes in response to these changes in moisture. During the drier year, leaves were narrower and more hirsute, corroborating experimental results that these leaf traits are plastic, and confirming that plasticity occurs in natural habitats. Hybrids exhibited intermediate leaf traits (shape and size) across both years, and displayed transgressive (hair density) leaf traits during the drier year. The apparent canalization of the hybrids’ leaf morphological traits may contribute to their tolerance of variable environmental conditions and may partially explain why they have displaced the caroliniana morphotype in central Florida.