Informative characteristics of 12 divergent domains in complete large subunit rDNA sequences from the harmful dinoflagellate genus, Alexandrium (Dinophyceae)

The genus Alexandrium includes organisms of interest, both for the study of dinoflagellate evolution and for their impacts as toxic algae affecting human health and fisheries. Only partial large subunit (LSU) rDNA sequences of Alexandrium and other dinoflagellates are available, although they contain much genetic information. Here, we report complete LSU rDNA sequences from 11 strains of Alexandrium, including Alexandrium affine, Alexandrium catenella, Alexandrium fundyense, Alexandrium minutum, and Alexandrium tamarense, and discuss their segmented domains and structure. Putative LSU rRNA coding regions were recorded to be around 3,400 bp long. Their GC content (about 43.7%) is among the lowest when compared with other organisms. Furthermore, no AT-rich regions were found in Alexandrium LSU rDNA, although a low GC content was recorded within the LSU rDNA. No intron-like sequences were found. The secondary structure of the LSU rDNA and parsimony analyses showed that most variation in LSU rDNA is found in the divergent (D) domains with the D2 region being the most informative. This high D domain variability can allow members of the diverse Alexandrium genus to be categorized at the species level. In addition, phylogenetic analysis of the alveolate group using the complete LSU sequences strongly supported previous findings that the dinoflagellates and apicomplexans form a clade.     

Pseudomonas viridiflava, a multi host plant pathogen with significant genetic variation at the molecular level

The pectinolytic species Pseudomonas viridiflava has a wide host range among plants, causing foliar and stem necrotic lesions and basal stem and root rots. However, little is known about the molecular evolution of this species. In this study we investigated the intraspecies genetic variation of P. viridiflava amongst local (Cretan), as well as international isolates of the pathogen. The genetic and phenotypic variability were investigated by molecular fingerprinting (rep-PCR) and partial sequencing of three housekeeping genes (gyrB, rpoD and rpoB), and by biochemical and pathogenicity profiling. The biochemical tests and pathogenicity profiling did not reveal any variability among the isolates studied. However, the molecular fingerprinting patterns and housekeeping gene sequences clearly differentiated them. In a broader phylogenetic comparison of housekeeping gene sequences deposited in GenBank, significant genetic variability at the molecular level was found between isolates of P. viridiflava originated from different host species as well as among isolates from the same host. Our results provide a basis for more comprehensive understanding of the biology, sources and shifts in genetic diversity and evolution of P. viridiflava populations and should support the development of molecular identification tools and epidemiological studies in diseases caused by this species.     

Duplication and divergence of the amino-terminal coding region of the complement receptor 1 (CR1) gene. An example of concerted (horizontal) evolution within a gene

Human C3b/C4b receptor or complement receptor type one (CR1) is one of a family of receptor and regulatory glycoproteins that are encoded at a single genetic region (1q32) and are composed largely of a tandemly repeated motif (short consensus repeat or SCR) of approximately 60 amino acids. In addition, CR1 features an internal homology of seven SCRs in length, known as a long homologous repeat, that is reiterated four times, in the major polymorphic size variant, from SCR-1 to SCR-28, and may be reiterated three, five, and six times in other polymorphic forms. In the course of studying CR1, we detected sequences closely related to CR1 on several overlapping genomic clones. We have characterized a 40-kilobase CR1-like genomic region containing 10 potential exons that are 95% homologous to the amino-terminal coding portion of CR1. This region appears to be a partial duplication of CR1 and may encode a related gene. A comparison of CR1 and CR1-like sequences suggests that unequal crossing-over and concerted evolution have occurred within the most precisely reiterated subregion of CR1. Similar mechanisms have been important in the evolution of tandemly repeated genes and could provide the means for generation of the CR1 polymorphic size variants.     

Low courtship song variation in south and southeastern Brazilian populations of Drosophila meridionalis (Diptera, Drosophilidae)

Drosophila meridionalis is a cactus-breeding species with a wide distribution in South America. Most populations of this species are geographically isolated, what provides a promising scenario for studying evolution. Former studies of this species revealed a remarkable karyotypic variation among its populations. Up to six distinct metaphase chromosomes were described, showing that this species is polymorphic at least at the chromosomal level. In order to elucidate the taxonomic status of populations showing different metaphase chromosomes, we analyzed the courtship song of five populations of D. meridionalis in South and Southeastern Brazil. In addition, we analyzed the metaphase chromosomes of each population. Our results show that, despite the two karyotype observed, most courtship song parameters did not vary among the populations. Altogether, our results suggest that D. meridionalis from South and Southeastern Brazil represents one species with an inter-population chromosomal variability.     

Genetic variability in geographic populations of the natterjack toad (Bufo calamita)

Across altitudinal and latitudinal gradients, the proportion of suitable habitats varies, influencing the individual dispersal that ultimately can produce differentiation among populations. The natterjack toad (Bufo calamita) is distributed across a wide geographic range that qualifies the species as interesting for a geographic analysis of its genetic variability. Five populations of B. calamita in the Sierra de Gredos (Spain) were studied in an altitudinal gradient ranging from 750 to 2270 m using microsatellite markers. In addition, we analyzed the latitudinal genetic variation in B. calamita within a global European distribution using genetic diversity parameters (mean number of alleles per locus [M(a)] and expected heterozygosity [H(E)]) obtained from our results and those published in the literature. The low level of genetic differentiation found between populations of B. calamita (F(st) ranging from 0.0115 to 0.1018) and the decreases in genetic diversity with altitude (M(a) from 13.6 to 8.3, H(E) from 0.82 to 0.74) can be interpreted by the combined effects of discontinuous habitat, produced mainly by the high slopes barriers and geographic distance. In the latitudinal gradient, genetic diversity decreases from south to north as a consequence of the colonization of the species from the Pleistocene refugium. We conclude that the genetic variability in B. calamita along its wide altitudinal and latitudinal geographic distribution mainly reflects the colonization history of the species after the last glacial period.     

Molecular characterization of Fagaceae species using inter-primer binding site (iPBS) markers

Retrotransposons (RTNs) contribute for genome evolution, influencing its size and structure. We investigated the utility of the RTN-based markers inter-primer binding site (iPBS) for the molecular characterization of 25 Fagaceae species from genera Castanea, Fagus and Quercus. The assessment of genetic diversity, relationships and structure, as well as taxonomic classification of Fagaceae based on molecular data is important for definition of conservation, forestry management strategies and discrimination among natural hybrids and their parents since natural hybridization may increase with the climate changes. Here, iPBS primers designed by other authors were tested alone and combined. Some of them were discriminative, revealed polymorphism within and among taxa allowing the production of a total of 150 iPBS markers. In addition, several monomorphic iPBS markers were also amplified in each taxon. The UPGMA dendrogram based on the pooled iPBS data revealed 27% of genetic similarity among species. The individuals were clustered per genus and most of the oaks per infrageneric group corroborating the adopted taxonomy. Globally, the iPBS markers demonstrated suitability for DNA fingerprinting, determination of phylogenies and taxonomic discrimination in Fagaceae, and could constitute a useful and alternative tool for germplasm characterization, and for definition of conservation strategies and forestry management. Moreover, these markers would be useful for fingerprinting natural hybrids that share morphological similarities with their parents. Since iPBS markers could also enable insights about RTNs evolution, an eventual correlation among iPBS polymorphism, variability of RTN insertions and/or genome size in Fagaceae is discussed.     

Ribosomal DNA sequence variation among sympatric strains of the Cyclotella meneghiniana complex (Bacillariophyceae) reveals cryptic diversity

Cyclotella meneghiniana Kützing is one of the most commonly found and intensively studied freshwater diatom species. However, it is considered taxonomically problematic because of its unusually wide ecological range and large frustule ultrastructural variation. As part of a study of morphological and genetic variation in this morphospecies, we surveyed nucleotide variation in the hypervariable D1/D2 regions of the 28S rDNA, in the ribosomal internal transcribed spacer region (containing ITS1, the 5.8S rDNA and ITS2) and in the 18S rDNA in a collection of 20 sympatric strains. High genetic variability and strong indications of genetic structure among the Cyclotella meneghiniana strains were found. Representatives of four genetically distinct--apparently reproductively isolated--groups were revealed among them. The random distribution of ITS variation within these four groups indicated that the genetic structure in Cyclotella meneghiniana can probably be explained by the presence of cryptic sexual species rather than by the lack of allogamous sexual reproduction. The morphological features traditionally used for species identification in this group cannot distinguish these putative cryptic species.     

Allozyme diversity within and divergence among species ofTolpis(Asteraceae-Lactuceae) in the Canary Islands: systematic, evolutionary, and biogeographical implications

Plants endemic to oceanic islands represent some of the most unusual and rare taxa in the world. Enzyme electrophoresis was used to assess genetic diversity within and divergence among all endemic species of a small genus of plants on the Canary Islands. Our results show that the genus Tolpis is similar to many other island groups in having generally low allozyme divergence among species, with the highest divergence found among four groups of endemics. The two rare and highly localized species T. glabrescens and T. crassiuscula are each divergent from all other species in the Canaries. Tolpis coronopifolia is also divergent at allozyme loci; this is the only endemic species that is a self-compatible annual (or weak biennial). A large, morphologically variable species complex consisting of T. laciniata and T. lagopoda together with several named and unnamed morphological variants shows low allozyme divergence among its elements. The evolution of polyploidy from diploid ancestors in situ in oceanic archipelagos is uncommon, but the tetraploid T. glabrescens is an exception. Allozyme data do not implicate any extant diploid Tolpis species as parents of the polyploid. It is possible that T. glabrescens originated early in the evolution of Tolpis in the Canary Islands and that its parents are now extinct. The nonendemic T. barbata shows no greater divergence from the Canary Island endemics than some endemics exhibit among themselves. Both changes in allele frequencies and unique alleles are responsible for genetic divergence among species of Tolpis.     

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.     

突尼斯非洲跳鼠（Jaculus jaculus）和埃及跳鼠J.orientalis）群体的等位酶多态及遗传分化

运用16种酶蛋白编码的23个遗传座位对突尼斯非洲跳鼠(Jaculus jaculus)和埃及跳鼠(J.orientalis)自然群体的遗传变异和分化进行了电泳分析.结果表明,与其他啮齿动物等哺乳动物的相关数据比较,发现这两个种群体的遗传变异水平较低.非洲跳鼠群体的观测杂合度(Hobs)为0.08-0.19,多态座位百分比(P)为26.2%-45.2%,每个座何的平均等位基因数(A)为1.1-1.4;埃及跳鼠的Hobs为0.10-0.15,P为29.3%-44.1%,A为1.1-1.7.两个种群体各自的遗传分化程度较低(非洲跳鼠和埃及跳鼠的Fst分别为0.0017和0.0019).而两个种群体间的Fst为0.607(P＜0.05),表明两个种之间高度的遗传分化.本研究支持这两个种分类地位的合法性,并强调了地理因素(环境类犁和生物气候阶段)对两个种遗传结构的影响.     

七筋菇自然居群的遗传结构分析

采用ISSR分子标记,对七筋菇(Clintonia udensis)17个居群的遗传多样性与遗传结构进行了研究。结果表明:七筋菇不同居群的多态位点百分率PPB为11.90%~59.52%,总的多态位点百分率PPB为98.8%,具有高的遗传多样性。Shannon多样性指数(0.6903)和基因分化系数(GST=0.6944)均揭示出七筋菇居群间存在明显的遗传差异,AMOVA分析结果也显示遗传变异主要发生在居群之间(81.47%),而居群内部的遗传变异仅为18.53%。七筋菇居群间的遗传距离从0.1871~0.6632,平均为0.3838,大于同一物种居群间的平均遗传距离值(0.05),同样表明七筋菇居群间的遗传多样性存在较大差异。七筋菇居群间的基因流Nm=0.2200,远远低于一般广布种植物的基因流(Nm=1.881)。Mantel检测显示居群间的遗传距离与地理距离之间没有显著相关性(r=0.029,P=0.3196)。七筋菇分布范围广以及其进化历史是其具有高遗传多样性的原因;居群间存在较高遗传变异可能是由于七筋菇本身的生物学特性、有限的基因流以及遗传漂变等原因造成的。     

Geographic and evolutionary diversification of glucosinolates among near relatives of Arabidopsis thaliana (Brassicaceae)

Glucosinolates are biologically active secondary metabolites that display both intra- and interspecific variation in the order Brassicales. Glucosinolate profiles have not been interpreted within a phylogenic framework and little is known regarding the processes that influence the evolution of glucosinolate diversity at a macroevolutionary scale. We have analyzed leaf glucosinolate profiles from members of the Brassicaceae that have diverged from Arabidopsis thaliana within the last 15 million years and interpreted our findings relative to the phylogeny of this group. We identified several interspecific polymorphisms in glucosinolate composition. A majority of these polymorphisms are lineage-specific secondary losses of glucosinolate characters, but a gain-of-character polymorphism was also detected. The genetic basis of most observed polymorphisms appears to be regulatory. In the case of A. lyrata, geographic distribution is also shown to contribute to glucosinolate metabolic diversity. Further, we observed evidence of gene-flow between sympatric species, parallel evolution, and the existence of genetic constraints on the evolution of glucosinolates within the Brassicaceae.     

Ancestral and recently recruited global control of the Hox genes in development

Genes from the Hox family are involved in the common task of providing nascent embryonic tissues with their positional identity. They are organised in clusters in most species. Mouse Hox genes are regulated in part by gene-proximal regulatory elements, but owe several of their essential properties to the use of global regulatory elements located outside the complexes. The clustered Hox genes in that sense behave as a single large locus. Genomic and sequence data from different animal species suggest that a concerted regulation of the Hox clusters, inherently coupled to their patterning properties, originated early during evolution and pre-figured the temporal colinearity of expression of vertebrate Hox genes. In addition, vertebrates have recruited novel global mechanisms to control the expression of linear subsets of Hox genes in specific embryonic structures. Several of such novel global regulatory circuits have recently been characterised at the molecular genetic level in the mouse.     

Structure and evolution of the mitochondrial control region of the pollen beetle Meligethes thalassophilus (Coleoptera: Nitidulidae).

The organization of the mitochondrial DNA (mtDNA) control region (CR) of the pollen beetle Meligethes thalassophilus is described. This mtDNA CR represents the longest sequenced for beetles so far, since the entire nucleotide sequence ranges from approximately 5000 to approximately 5500 bp. The CR of M. thalassophilus is organized in three distinct domains: a conserved domain near the tRNAIle gene, a variable domain flanking the 12S rRNA gene, and a relatively large central tandem array made up of a variable number of approximately 170 bp repeats that is responsible for the intraspecific length variation observed. Like other CRs found in insects, the M. thalassophilus CR contains two long homopolymeric runs that may be involved in mtDNA replication. Furthermore, conserved stem-and-loop structures in the repetitive domain were identified and their possible role in generating length variation is examined. Intraspecific comparison of the tandem repeat elements of M. thalassophilus suggests mechanisms of concerted evolution leading to homogenization of the repetitive region. The utility of such an array of tandem repeats as a genetic marker for assessing population-level variability and evolutionary relationships among populations is discussed. Finally, the technical difficulties found in isolating the mtDNA CR in beetles are remarked upon.     

Genetic variability in two West Indian anoles (Reptilia, Iguanidae): relation to field thermal biology

Meristic and electrophoretic characters were used as independent estimators of genetic variability within populations of two West Indian Anolis lizard species. The species which uses flexible regulatory behaviours to maintain thermal homeostasis, A. roquet on Martinique, exhibited much less within-population electrophoretic variability than did the species which is behaviourally passive to changes in the thermal environment, A. gundlachi on Puerto Rico. The data suggest that the high genetic variability in A. gundlachi may be an adaptation to its coarse-grained perception of seasonal variation in the thermal environment, whereas A. roquet's low genetic variability may be adaptive because its flexible regulatory behaviours provide a temporally fine-grained perception of the thermal environment. Meristic characters did not demonstrate any interspecific difference in the amount of within-population genetic variability. Discordance in the results of the meristic and electrophoretic analyses suggest either that the two character sets sample dramatically different genetic phenomena or that environmental effects on the development of meristic characters render them unreliable as indicators of the genetic variability within geographically proximate populations.     

Genetic variability in mitochondrial and nuclear genes of Larus dominicanus (Charadriiformes,Laridae) from the Brazilian coast

Several phylogeographic studies of seabirds have documented low genetic diversity that has been attributed to bottleneck events or individual capacity for dispersal. Few studies have been done in seabirds on the Brazilian coast and all have shown low genetic differentiation on a wide geographic scale. The Kelp Gull is a common species with a wide distribution in the Southern Hemisphere. In this study, we used mitochondrial and nuclear markers to examine the genetic variability of Kelp Gull populations on the Brazilian coast and compared this variability with that of sub-Antarctic island populations of this species. Kelp Gulls showed extremely low genetic variability for mitochondrial markers (cytb and ATPase) and high diversity for a nuclear locus (intron 7 of the β-fibrinogen). The intraspecific evolutionary history of Kelp Gulls showed that the variability found in intron 7 of the β-fibrinogen gene was compatible with the variability expected under neutral evolution but suggested an increase in population size during the last 10,000 years. However, none of the markers revealed evidence of a bottleneck population. These findings indicate that the recent origin of Kelp Gulls is the main explanation for their nuclear diversity, although selective pressure on the mtDNA of this species cannot be discarded.     

Phylogeography and population structure of the Yunnan snub-nosed monkey (Rhinopithecus bieti) inferred from mitochondrial control region DNA sequence analysis

Rhinopithecus bieti, the Yunnan snub-nosed monkey, is the nonhuman primate with the highest altitudinal distribution and is also one of the 25 most globally endangered primate species. Currently, R. bieti is found in forests between 3000 and 4500 m above sea level, within a narrow area on the Tibetan Plateau between the Yangtze and Mekong rivers, where it is suffering from loss of habitat and shrinking population size (approximately 1500). To assess the genetic diversity within this species, its population structure and to infer its evolutionary history, we sequenced 401 bp of the hypervariable I (HVI) segment from the mitochondrial DNA control region (CR) for 157 individuals from 11 remnant patches throughout the fragmented distribution area. Fifty-two variable sites were observed and 30 haplotypes were defined. Compared with other primate species, R. bieti cannot be regarded as a taxon with low genetic diversity. Phylogenetic analysis partitioned haplotypes into two divergent haplogroups (A and B). Haplotypes from the two mitochondrial clades were found to be mixed in some patches although the distribution of haplotypes displayed local homogeneity, implying a strong population structure within R. bieti. Analysis of molecular variance detected significant differences among the different geographical regions, suggesting that R. bieti should be separated into three management units (MUs) for conservation. Based on our results, it can be hypothesized that the genetic history of R. bieti includes an initial, presumably allopatric divergence between clades A and B 1.0-0.7 million years ago (Ma), which might have been caused by the Late Cenozoic uplift of the Tibetan Plateau, secondary contact after this divergence as a result of a population expansion 0.16-0.05 Ma, and population reduction and habitat fragmentation in the very recent past.     

Phylogeography and population structure of the golden monkeys (Rhinopithecus roxellana): inferred from mitochondrial DNA sequences

The golden monkey (Rhinopithecus roxellana) is one of the most endangered primate species due to its dramatically shrinking distribution during the past 400 years. Its populations are restricted to three isolated regions, Qinglin (QL), Sichuan/Gansu (SG), and Shennongjia (SNJ) in China. As with other snub-nosed monkeys in China and Vietnam, the biology and evolution of this species is still poorly known. To assess genetic differentiation and explore the relationships among populations of golden monkeys from different geographic locations, 379 bp of mitochondrial DNA control region (CR) hypervariable segment I (HVI) was studied from 60 individuals. Twelve haplotypes were identified from seven populations within the three regions. Haplotype diversity was high (0.845), whereas nucleotide diversity among all haplotypes was low (0.0331). The most recent common ancestor (TMRCA) among mtDNA haplotypes was estimated to have lived approximately 0.48-0.32 million years ago. None of the haplotypes is shared among any of the three regions. Phylogenetic analysis and AMOVA revealed clear and significant phylogeographic structure between the three regions. However, only SG contained haplotypes of the two main clades, indicating either incomplete random sorting of haplotypes or a complex history with phases of population subdivisions and merging of populations. The phylogeographic structure implies that R. roxellana should be regarded as separate management units (MUs) for each of the three regions. It is likely that recent phylogeographic history has shaped the pattern of genetic differentiation observed in the golden monkey and that its populations have suffered significant demographic fluctuation.     

Allozyme diversity in the tetraploid endemic Thymus loscosii (Lamiaceae)

BACKGROUND AND AIMS: Thymus loscosii (Lamiaceae) is a tetraploid perennial species endemic to the Ebro river basin (north-eastern Spain), which is included in the National Catalogue of Endangered Species. It is a tetraploid species (2n = 54), presumably an autotetraploid originated by the duplication of a 2n = 28 genome and the subsequent loss of two chromosomes. Allozyme electrophoresis was conducted to survey the levels and distribution of genetic diversity and to test the previous autopolyploid hypothesis for its origin. In addition, both in situ and ex situ conservation measures are proposed. METHODS: Eight populations were sampled for analysis by standard methods of starch gel electrophoresis, and six putative enzymatic loci were resolved (five consistently and one only partially). KEY RESULTS: Banding patterns exhibited no evidence of fixed heterozygosity and showed both balanced and unbalanced heterozygotes. In addition, most individuals showed a pattern consistent with the presence of three or four alleles at a single locus. High levels of genetic variability were found at population level (P = 85 %, A = 3.0, He = 0.422), in addition to a trend of an excess of heterozygotes. CONCLUSIONS: Allozyme data support the hypothesis that T. loscosii is an autotetraploid, and the high number of alleles at some loci may be due to repeated polyploidization events. The high values of genetic variation found in this species agree with those expected for tetraploids. The excess of heterozygotes may be due to some barriers to inbreeding (e.g. occurrence of gynodioecy) and/or selection for heterozygosity.