Extremely high molecular diversity within the East Asian nematode Caenorhabditis sp. 5

Most relatives of the self-fertilizing hermaphroditic nematode model organism Caenorhabditis elegans reproduce via obligate outbreeding between males and females, which also represents the ancestral mode of reproduction within the genus. However, little is known about the scope of genetic diversity and differentiation within such gonochoristic species, especially those found outside of temperate Europe and North America. It is critical to understand the evolutionary processes operating in these species to provide a framework for deciphering the evolution of hermaphroditism and a baseline for the application of outcrossing Caenorhabditis to problems in evolutionary genetics. Here, we investigate for the first time molecular sequence variation for Caenorhabditis sp. 5, a species found commonly in eastern Asia. We identify enormous levels of standing genetic variation that approach the levels observed in the marine broadcast-spawning sea squirt, Ciona savignyi. Although we document significant isolation by distance, we demonstrate that the high polymorphism within C. sp. 5 is not because of strong differentiation among populations or to the presence of cryptic species. These findings illustrate that molecular population genetic approaches to studying obligately outbreeding species of Caenorhabditis will prove powerful in identifying and characterizing functionally and evolutionarily important features of the genome.     

Minos transposon causes germline transgenesis of the ascidian Ciona savignyi

An ascidian, Ciona savignyi, is regarded as a good experimental animal for genetics because of its small and compact genome for which a draft sequence is available, its short generation time and its interesting phylogenic position. ENU-based mutagenesis has been carried out using this animal. However, insertional mutagenesis using transposable elements (transposons) has not yet been introduced. Recently, one of the Tc1/mariner superfamily transposons, Minos, was demonstrated to cause germline transgenesis in the related species Ciona intestinalis. In this report, we show that Minos has the ability to transpose from DNA to DNA in Ciona savignyi in transposition assays. Although the activity was slightly weaker than in Ciona intestinalis, Minos still caused germline transgenesis in Ciona savignyi. In addition, one insertion seemed to have caused an enhancer trapping. These results indicate that Minos provides a potential tool for transgenic techniques such as insertional mutagenesis in Ciona savignyi.     

Identification and population genetic comparison of three ascidian species based on mtDNA sequences

Ascidians are sessile marine chordate invertebrates found along seashores worldwide and are typically regarded as invasive organisms. Knowledge concerning their global genetic structure and subsequent invasive potential is limited. Here, we identified three ascidians—Ciona robusta, Ciona savignyi, and Styela clava from the northeast region of China using morphological characteristics and mitochondrial cytochrome c oxidase subunit I (cox1) as genetic marker. We additionally used phylogenetics to aid in the identification of these three species. The results of a population genetic analysis showed that among the three species, the level of haplotype diversity was particularly high within C. savignyi, and nucleotide diversity varied moderately. We divided the three species separately into native and invasive populations using 170 cox1 sequences from global resources to explore population genetic structure and invasive potential. Although in the network analysis Ciona spp. formed haplogroups of native and invasive populations, some haplotypes were still shared. We found that the haplotypes did not cluster within the network of S. clava. Our AMOVA results also showed that Ciona spp. had a weak genetic structure, and less genetic differentiation was present in S. clava. These data suggest that there are extensive incursions of these three ascidians into different geographical regions. Global comparisons of ascidian populations will help in the understanding of their population genetic structure and invasive potential, hence providing important insights regarding conservation as well as management.     

Population genetics of the potentially invasive African fruit fly species, Ceratitis rosa and Ceratitis fasciventris (Diptera: Tephritidae)

A set of 10 microsatellite markers was used to survey the levels of genetic variability and to analyse the genetic aspects of the population dynamics of two potentially invasive pest fruit fly species, Ceratitis rosa and C. fasciventris, in Africa. The loci were derived from the closely related species, C. capitata. The degree of microsatellite polymorphism in C. rosa and C. fasciventris was extensive and comparable to that of C. capitata. In C. rosa, the evolution of microsatellite polymorphism in its distribution area reflects the colonization history of this species. The mainland populations are more polymorphic than the island populations. Low levels of differentiation were found within the Africa mainland area, while greater levels of differentiation affect the islands. Ceratitis fasciventris is a central-east African species. The microsatellite data over the Uganda/Kenya spatial scale suggest a recent expansion and possibly continuing gene flow within this area. The microsatellite variability data from C. rosa and C. fasciventris, together with those of C. capitata, support the hypothesis of an east African origin of the Ceratitis spp.     

Self- and cross-fertilization in the solitary ascidian Ciona savignyi

Solitary ascidians are hermaphrodites that release sperm and eggs simultaneously. However, many species are self-sterile, owing to a self/non-self recognition system operating at the outer surface of the chorion during sperm-egg interaction. In Ciona intestinalis, self-incompatibility is thought to have a genetic basis. Here, we report a survey of the self-fertilization potential of a Santa Barbara, California, population of Ciona savignyi, a close relative of C. intestinalis. We found that, in contrast to reports on C. intestinalis, C. savignyi is highly self-fertile. However, using two nonlethal recessive mutant strains, aimless (aim) and immaculate (imc), and a stable transgenic strain that expresses green fluorescent protein (GFP) in the notochord to follow offspring genotype, we demonstrate that non-self sperm outcompete self-sperm in fertilization competition assays. When the chorion was removed, both self- and non-self sperm performed equally well in the competition assay. Thus the non-self/self gamete recognition in C. savignyi is not absolute but relative, and is mediated by one or more components in the chorion. We discuss the significance of this finding in the context of natural populations in the wild, where individuals of C. savignyi are typically found growing in large groups that spawn in unison and where self-fertilization would be expected to be very rare.     

Ascidians as a vertebrate-like model organism for physiological studies of Rho GTPase signaling

GTPases of the Rho family are evolutionarily conserved proteins that control cell shape dynamics during physiological processes as diverse as cell migration and polarity, axon outgrowth and guidance, apoptosis and phagocytosis. In mammals, 18 Rho proteins are distributed in 7 subfamilies. Rho, Rac and Cdc42 are the best-characterized ones, benefiting from the use of worm and drosophila, which only express these 3 subfamilies. An additional model would therefore help understand the physiological role of other mammalian subfamilies. We identified in genome databases the complete Rho family of two ascidians, Ciona intestinalis and Ciona savignyi, and showed that these families contain single ancestors of most mammalian Rho subfamilies. In Ciona intestinalis, all Rho genes are expressed and display specific developmental variations of mRNA expression during tadpole formation. Although C. intestinalis expresses five additional Rac compared to the closely related Ciona savignyi, only two appeared fully active in functional assays. Last, we identified in Ciona intestinalis database more than 50 Rho regulators (RhoGEFs and RhoGAPs) and 20 effector targets, whose analysis further supports the notion that Rho signaling components are of comparable complexity in mammals and ascidians. Since the tadpole of ascidians combines vertebrate-like developmental features with reduced cell number, particularly adapted to evolutionary and developmental biology studies, our data advocate this model for physiological studies of Rho signaling pathways.     

Mating system and population structure of Acacia aroma and A. macracantha (Fabaceae)

Acacia aroma and A. macracantha are closely related species that inhabit northern and central Argentina. The reproductive barriers between them seem to be weak. They exhibit low genetic differentiation, high levels of interspecific gene flow, and extensive areas of sympatry. Isoenzymatic approaches were used to evaluate the population structure and mating system parameters in natural Argentine populations of A. aroma and A. macracantha and to provide new tools for the analysis of relationships between these two species. All studied populations had high levels of genetic variability and no significant departures from Hardy-Weinberg expectations, but the two species did not differ from each other. Most variability occured within populations. Mating system analysis showed high levels of outcrossing, no biparental inbreeding, and a high probability that individuals within progeny arrays are full rather than half sibs. In all A. aroma and A. macracantha populations, polymorphic loci had the same allelic variants, and no geographic or genetic isolation between species was found. The results favor the hypothesis that these two entities represent a single polymorphic species rather than two distinct species.     

Genetic variation in flowering phenology and avoidance of seed predation in native populations of Ulex europaeus

The genetic variation in flowering phenology may be an important component of a species’ capacity to colonize new environments. In native populations of the invasive species Ulex europaeus, flowering phenology has been shown to be bimodal and related to seed predation. The aim of the present study was to determine if this bimodality has a genetic basis, and to investigate whether the polymorphism in flowering phenology is genetically linked to seed predation, pod production and growth patterns. We set up an experiment raising maternal families in a common garden. Based on mixed analyses of variance and correlations among maternal family means, we found genetic differences between the two main flowering types and confirmed that they reduced seed predation in two different ways: escape in time or predator satiation. We suggest that this polymorphism in strategy may facilitate maintain high genetic diversity for flowering phenology and related life‐history traits in native populations of this species, hence providing high evolutionary potential for these traits in invaded areas.     

中华猕猴桃和美味猕猴桃自然居群遗传结构及其种间杂交渐渗

 利用9对SSR引物对中华猕猴桃（Actinidia chinensis）和美味猕猴桃（A. deliciosa）两近缘种的5个同域分布复合体和各自1个非同域分布居群进行了遗传多样性、居群遗传结构的分析以及种间杂交渐渗的探讨。结果表明：1）两物种共有等位基因比例高达81.13%,物种特有等位基因较少（中华猕猴桃：13.27%,美味猕猴桃：5.61%）,但共享等位基因表型频率在两近缘种间存在差异,而且与各同域复合体中两物种样本的交错程度或间距存在关联;2）两种猕猴桃均具有极高遗传多样性,美味猕猴桃的遗传多样性（H_o＝0 .749, PIC＝0.818）都略高于中华猕猴桃（H_o＝0.686,PIC＝0.799）;3）两猕 猴桃物种均具有较低的Nei’s居群遗传分化度,但AMOVA分析结果揭示种内异域居群间（F_ST=0.091 5）和同域复合体种间（F_ST=0.111 5）均存在一定程度的遗传分化;中华猕猴桃居群遗传分化（G_ST=0.086; F_ST=0.212 1）高于美味猕猴桃（G_ST= 0.080;F_ST=0.142 0）;4）同域分布复合体两物种间的遗传分化（G_ST=0.020）低于物种内异域居群间的遗传分化（中华猕猴桃：G_ST=0.086; 美味猕猴桃：G_ST=0.080）,同域复合体物种间的基因流（N_m＝7.89 -29.75）远远高于 同种异域居群间（中华猕猴桃：N_m =2.663; 美味猕猴桃：N_m=2.880）; 5）居群UPGMA聚类揭示在同一地域的居群优先聚类,个体聚类结果显示多数个体聚在各自居群组内,但各地理居群并不按地理距离的远近聚类,这与Mantel相关性检测所揭示的居群间遗传距离与地理距离没有显著性相关的结果一致。进一步分析表明两种猕猴桃的遗传多样性和居群遗传结构不仅受其广域分布、远交、晚期分化等生活史特性的影响,同时还与猕猴桃的染色体基数高 (x=29)、倍性复杂和种间杂交等因素密切相关,其中两种猕猴桃的共享祖先多态性和同域分布种间杂交基因渗透对两猕猴桃的居群遗传结构产生了重要影响。     

Computational analysis of Ciona intestinalis operons

Operons are clusters of genes that are co-regulated from a common promoter. Operons are typically associated with prokaryotes, although a small number of eukaryotes have been shown to possess them. Among metazoans, operons have been extensively characterized in the nematode Caenorhabditis elegans in which ～15% of the total genes are organized into operons. The most recent genome assembly for the ascidian Ciona intestinalis placed ～20% of the genes (2909 total) into 1310 operons. The majority of these operons are composed of two genes, while the largest are composed of six. Here is reported a computational analysis of the genes that comprise the Ciona operons. Gene ontology (GO) terms were identified for about two-thirds of the operon-encoded genes. Using the extensive collection of public EST libraries, estimates of temporal patterns of gene expression were generated for the operon-encoded genes. Lastly, conservation of operons was analyzed by determining how many operon-encoded genes were present in the ascidian Ciona savignyi and whether these genes were organized in orthologous operons. Over 68% of the operon-encoded genes could be assigned one or more GO terms and 697 of the 1310 operons contained genes in which all genes had at least one GO term. Of these 697 operons, GO terms were shared by all of the genes within 146 individual operons, suggesting that most operons encode genes with unrelated functions. An analysis of operon gene expression from nine different EST libraries indicated that for 587 operons, all of the genes that comprise an individual operon were expressed together in at least one EST library, suggesting that these genes may be co-regulated. About 50% (74/146) of the operons with shared GO terms also showed evidence of gene co-regulation. Comparisons with the C. savignyi genome identified orthologs for 1907 of 2909 operon genes. About 38% (504/1310) of the operons are conserved between the two Ciona species. These results suggest that like C. elegans, operons in Ciona are comprised of a variety of genes that are not necessarily related in function. The genes in only 50% of the operons appear to be co-regulated, suggesting that more complex gene regulatory mechanisms are likely operating.     

Evaluation of genetic diversity in Piper spp using RAPD and SRAP markers

Random amplified polymorphic DNA (RAPD) and sequence-related amplified polymorphism (SRAP) analysis were applied to 74 individual plants of Piper spp in Hainan Island. The results showed that the SRAP technique may be more informative and more efficient and effective for studying genetic diversity of Piper spp than the RAPD technique. The overall level of genetic diversity among Piper spp in Hainan was relatively high, with the mean Shannon diversity index being 0.2822 and 0.2909, and the mean Nei's genetic diversity being 0.1880 and 0.1947, calculated with RAPD and SRAP data, respectively. The ranges of the genetic similarity coefficient were 0.486-0.991 and 0.520-1.000 for 74 individual plants of Piper spp (the mean genetic distance was 0.505 and 0.480) and the within-species genetic distance ranged from 0.063 to 0.291 and from 0.096 to 0.234, estimated with RAPD and SRAP data, respectively. These genetic indices indicated that these species are closely related genetically. The dendrogram generated with the RAPD markers was topologically different from the dendrogram based on SRAP markers, but the SRAP technique clearly distinguished all Piper spp from each other. Evaluation of genetic variation levels of six populations showed that the effective number of alleles, Nei's gene diversity and the Shannon information index within Jianfengling and Diaoluoshan populations are higher than those elsewhere; consequently conservation of wild resources of Piper in these two regions should have priority.     

Genetic Variation Within and Among Populations of Rhodiola alsia (Crassulaceae) Native to the Tibetan Plateau as Detected by ISSR Markers

Genetic variation of 10 Rhodiola alsia (Crassulaceae) populations from the Qinghai–Tibet Plateau of China was investigated using intersimple sequence repeat (ISSR) markers. R. alsia is an endemic species of the Qinghai–Tibet Plateau. Of the 100 primers screened, 13 were highly polymorphic. Using these primers, 140 discernible DNA fragments were generated with 112 (80%) being polymorphic, indicating pronounced genetic variation at the species level. Also there were high levels of polymorphism at the population level with the percentage of polymorphic bands (PPB) ranging from 63.4 to 88.6%. Analysis of molecular variance (AMOVA) showed that the genetic variation was mainly found among populations (70.3%) and variance within populations was 29.7%. The main factors responsible for the high level of differentiation among populations are probably the isolation from other populations and clonal propagation of this species. Occasional sexual reproduction might occur in order to maintain high levels of variation within populations. Environmental conditions could also influence population genetic structure as they occur in severe habitats. The strong genetic differentiation among populations in our study indicates that the conservation of genetic variability in R. alsia requires maintenance of as many populations as possible.     

Genetic diversity and phylogenetic relatedness among six endemic Pterostylis species (Orchidaceae; series Grandiflorae) of Western Australia, as revealed by allozyme polymorphisms

Starch gel electrophoresis was employed to survey the allozyme polymorphism and phylogenetic relationships among 35 populations covering six closely related Western Australian endemic Pterostylis species (series Grandiflorae); viz P. rogersii, P. aspera, P. angusta, P. hamiltonii, P. scabra and P. aff. alata. The aim of this study was to determine intraspecific and interspecific genetic diversity and species relationships based on allozyme analysis. The frequencies of 56 alleles at 12 enzyme systems coded by 15 loci were determined along with a mean intraspecific genetic identity value. Allozyme markers clearly discriminated populations belonging to different species. Nei's genetic distance/identity co-efficient was used to measure the level of genetic differentiation among populations and species. Based on these values, a dendrogram was constructed which revealed that all the populations clustered into groups corresponding to the respective species. Gene diversity analysis among all the species revealed total genetic diversity H(t) of 0.23 with co-efficient of gene differentiation 10% (G(st)=0.10). Mean genetic variability (H(e)=0.136, P=40%) was also higher than for other outbreeding plant species. Mean genetic identity coefficient of populations of all species was 0.859 which increased to 0.877 upon exclusion of P. aff. alata, indicating a high degree of similarity among all species except P. aff. alata which segregated distinctively from the rest. Overall, the investigation provided independent support for the morphological segregation of these taxa.     

POPULATION GENETICS AND COLONY STRUCTURE OF THE ARGENTINE ANT (LINEPITHEMA HUMILE) IN ITS NATIVE AND INTRODUCED RANGES

Abstract.— Introduced species often possess low levels of genetic diversity relative to source populations as a consequence of the small population sizes associated with founder events. Additionally, native and introduced populations of the same species can possess divergent genetic structuring at both large and small geographic scales. Thus, genetic systems that have evolved in the context of high diversity may function quite differently in genetically homogeneous introduced populations. Here we conduct a genetic analysis of native and introduced populations of the Argentine ant (Linepithema humile) in which we show that the population‐level changes that have occurred during introduction have produced marked changes in the social structure of this species. Native populations of the Argentine ant are characterized by a pattern of genetic isolation by distance, whereas this pattern is absent in introduced populations. These differences appear to arise both from the effects of recent range expansion in the introduced range as well as from differences in gene flow within each range. Relatedness within nests and colonies is lower in the introduced range than in the native range as a consequence of the widespread genetic similarity that typifies introduced populations. In contrast, nestmates and colony‐mates in the native range are more closely related, and local genetic differentiation is evident. Our results shed light on the problem posed for kin selection theory by the low levels of relatedness that are characteristic of many unicolonial species and suggest that the loss of genetic variation may be a common mechanism for the transition to a unicolonial colony structure.     

Genetic Structure and Gene Flow in Elymus glaucus (blue wildrye): Implications for Native Grassland Restoration

Interest in using native grass species for restoration is increasing, yet little is known about the ecology and genetics of native grass populations or the spatial scales over which seed can be transferred and successfully grown. The purpose of this study was to investigate the genetic structure within and among populations of Elymus glaucus in order to make some preliminary recommendations for the transfer and use of this species in revegetation and restoration projects. Twenty populations from California, Oregon, and Washington were analyzed for allozyme genotype at 20 loci, and patterns of variation within and among populations were determined. Allozyme variation at the species level was high, with 80% of the loci polymorphic and an average expected heterozygosity (an index of genetic diversity) of 0.194. All but two of the populations showed some level of polymorphism. A high degree of population differentiation was found, with 54.9% of the variation at allozyme loci partitioned among populations (F_st= 0.549). A lesser degree of genetic differentiation among closely spaced subpopulations within one of the populations was also demonstrated (F_st= 0.124). Self-pollination and the patchy natural distribution of the species both likely contribute to the low level of gene flow (N_m= 0.205) that was estimated. Zones developed for the transfer of seed of commercial conifer species may be inappropriate for transfer of E. glaucus germplasm because conifer species are characterized by high levels of gene flow. Limited gene flow in E. glaucus can facilitate the divergence of populations over relatively small spatial scales. This genetic differentiation can be due to random genetic drift, localized selective pressures, or both. In order to minimize the chances of planting poorly adapted germplasm, seed of E. glaucus may need to be collected in close proximity to the proposed restoration site.     

Genetic diversity of bacterial strains isolated from soils, contaminated with polycyclic aromatic hydrocarbons, by 16S rRNA gene sequencing and amplified fragment length polymorphism fingerprinting

In order to study microbial diversity in a polycyclic aromatic hydrocarbon-impacted soil, 14 bacterial strains were analyzed by 16S rRNA gene sequencing and amplified fragment length polymorphism (AFLP) analysis. Bacterial strains isolated from two different hydrocarbon-polluted sites were identified to the species level by 16S rRNA full-gene sequencing using MicroSeq 16S rRNA gene sequencing. Their genome was subsequently analyzed by high-resolution genotyping with AFLP analysis, in order to monitor species variability and to differentiate closely related strains. Cluster analysis based on AFLP fingerprinting showed intra-specific polymorphism, even among strains with 100% 16S rRNA gene sequence identity. The results show that AFLP is a powerful, highly reproducible and discriminatory tool for revealing genetic relationships in bacterial populations. The ability to differentiate and track related closely microbes is fundamental for studying structure and dynamics of microbial communities in contaminated ecosystems.     

Measures of divergence between populations and the effect of forces that reduce variability

Wright's FST and related statistics are often used to measure the extent of divergence among populations of the same species relative to the net genetic diversity within the species. This paper compares several definitions of FST which are relevant to DNA sequence data, and shows that these must be used with care when estimating migration parameters. It is also pointed out that FST is strongly influenced by the level of within-population diversity. In situations where factors such as selection on closely linked sites are expected to have stronger effects on within-population diversity at some loci than at others, differences among loci can result entirely from differences in within- population diversities. It is shown that several published cases of differences in FST among regions of high and low recombination in Drosophila may be caused in this way. For the purpose of comparisons of levels of between-population differences among loci or species which are subject to different intensities of forces that reduce variability within local populations, absolute measures of divergence between populations should be used in preference to relative measures such as FST.