Small mammal populations of an agroecosystem in the Atlantic Forest domain, southeastern Brazil.

This study reports 2 years of the population dynamics and reproduction of a small mammal community using the removal method. The study was conducted in a rural area of the Atlantic Forest, in Sumidouro, Rio de Janeiro State, Brazil. The population sizes, age structure and reproduction were studied for the four most common species in the study area. The overall diversity was 1.67 and ranged between 0.8 to 1.67. The species richness was 13 considering the whole study. The most abundant species were the rodents Nectomys squamipes (n = 133), Akodon cursor (n = 74), Oligoryzomys nigripes (n = 25) and the marsupials Didelphis aurita (n = 58) and Philander frenatus (n = 50). Seven other rodents were captured once: Necromys lasiurus, Akodon montensis, Sooretamys angouya, Oecomys catherine, Oxymycterus judex, Euryzygomatomys spinosus and Trinomys iheringi. There were higher peaks for diversity and species richness during the winter (dry) months, probably due to higher food availability. The marsupials had a seasonal reproduction with highest population sizes at the end of the rainy seasons. Nectomys squamipes reproduced mostly during rainy periods. Akodon cursor reproduced predominantly in the winter with the highest population peaks occurring during this season. The analysis of the population dynamics of the rodent species indicated that no species behaved as an agricultural pest, probably due to the heterogeneous landscape of high rotativity of vegetable cultivation. Rodent populations were more susceptible to the removal procedure than marsupial ones.     

Morphological and RAPD analysis of hybridization between Quercus affinis and Q. laurina (fagaceae), two Mexican red oaks

Quercus affinis and Q. laurina are two closely related Mexican red oaks with partially overlapping distributions. Within the area of overlap, there are localities where morphological intergradation occurs. A previous hypothesis explained this pattern as a result of secondary contact between the two species, followed by hybridization and introgression. This possibility was analyzed here by examining foliar and genetic variation in 16 localities situated along a macrogeographic gradient, which included morphologically representative populations of both species and populations from within the area of overlap. Maximum-likelihood hybrid index scores calculated from nine semi-diagnostic RAPD markers indicated a shift in the genetic composition of populations from one species to the other along the macrogeographic gradient, with genetically intermediate populations situated in the area of overlap. Foliar variation followed a partially congruent pattern, but Q. laurina-like morphology predominated in some of the genetically intermediate populations. There were several instances of correlated frequency changeovers of single RAPD markers and morphological characters along the macrogeographic gradient and a few cases of markedly parallel patterns between markers. The results were interpreted as consistent with a hypothesis of secondary contact between the two oak species that has resulted in some differential introgression among markers.     

Detection of the first incidence of Akodon paranaensis naturally infected with the Jabora virus strain (Hantavirus) in Brazil

We characterised hantaviruses circulating in different Akodon rodent species collected in midwestern Santa Catarina (SC), southern Brazil, where the Jabora hantavirus (JABV) strain was first identified in Akodon montensis. Genetic and phylogenetic analyses based on a partial S segment indicated that, in SC, Akodon paranaensis and A. montensis carried the same type of hantavirus. Additionally, we conducted the first genomic characterisation of the complete S segment from the Brazilian JABV strain. This is the first report of A. paranaensis infected with the JABV.     

Random amplified polymorphic DNA markers reveal genetic variation in the symbiotic fungus of leaf-cutting ants

RAPD markers were used to examine the degree of genetic variation within the putatively asexual basidiomycete fungus (Lepiotaceae: provisionally named Leucoagaricus gongylophorus) associated with the leaf-cutting ant species Atta cephalotes. We analyzed fungal isolates from ant nests in two geographically distant sites, two isolates from Panama and five isolates from Trinidad. Ten decamer primers were used to amplify total DNA from these seven fungal isolates, and RAPD banding patterns were compared. Genetic similarity among isolates was determined by pair-wise comparisons of the shared number of DNA bands on an agarose gel. There was considerable genetic variation among isolates of the symbiotic fungus even within sites. Pairs of fungal isolates from the two different sites shared an average of only 36% of the bands in their RAPD profiles, while pairs from the within sites shared an average of 72% of the bands. RAPD markers may be useful for further investigation of the genetic structure of the fungal symbiont within species of leaf-cutting ants.     

A population genetic study of the endangered plant species Limonium dufourii (Plumbaginaceae) based on amplified fragment length polymorphism (AFLP)

Limonium dufourii ( Plumbaginaceae ) is a triploid species with obligate apomictic reproduction and is endemic to the East Mediterranean coast of Spain, where it is present in only six populations, most of which have a very low number of individuals. Genetic variation and population structure in this species was studied using amplified fragment length polymorphisms (AFLPs) as markers, using the same individuals as in a previous study with random amplified polymorphic DNA (RAPD). Three different primers provided 252 bands of which 51 were polymorphic among the 152 individuals analysed. Those polymorphic bands were able to define 65 different phenotypes, of which all but two were present in only one population. The comparative analyses of data from AFLPs with those from RAPDs show a high degree of concordance. Additionally, and given the nature of these markers, we propose the estimation of nucleotide divergences from AFLP patterns. Relationships among the different AFLP patterns and the estimates of population genetic parameters obtained with this evolutionary distance are in good agreement with previous results. These analyses show that substantial genetic variability and differentiation exist within and among populations of L. dufourii . Their higher reproducibility and the possibility of obtaining estimates of nucleotide divergence make AFLPs a much better DNA fingerprinting technique.     

Life history variation between species of the relictual genus Borderea (Dioscoreaceae): phylogeography, genetic diversity, and population genetic structure assessed by RAPD markers

The genus Borderea consists of two species, B. pyrenaica and B. chouardii, taxa which have been previously considered as conspecific due to their overall close morphology. These two sole species of the rare genus of Dioscoreaceae are endemic to the Pyrenees (Spain, France). This mountain range likely operated as a refugium for these plants during the last glaciations. B. chouardii is only known from a single population in the Spanish Prepyrenees and has been classified as at risk of extinction in the Red List of Endangered Species (IUCN); B. pyrenaica shows a narrow distribution range in the central Pyrenees and Prepyrenees. We analysed genetic variation, population structure and differentiation in these two taxa using RAPD markers. Our study was conducted on the same seven populations for which very low levels of genetic differentiation were detected previously through allozyme analysis. By contrast, high levels of genetic variability were detected through the RAPD hypervariable markers. Twelve RAPD primers produced 112 distinct bands in the 397 surveyed individuals, totalling 395 different RAPD phenotypes. Only four bands were monomorphic across all samples of Borderea, whereas 21 of the polymorphic bands were species‐specific (20 for B. chouardii, and one for B. pyrenaica). The largest genetic distances were those between the B. chouardii and the B. pyrenaica phenotypes. An analysis of molecular variance showed greater variance between groups (B. chouardii vs. B. pyrenaica, 76.08%) than within groups (3.60%). RAPD band specificity, phenotypic distances, and the partitioning of variance all support the taxonomic separation of the two species. Statistical evaluation of within‐ and among‐population RAPD genetic variability in B. pyrenaica showed that genetic variability was higher within populations (>80%) than among them. No clear pattern of RAPD differentiation could be observed among the six studied populations of this taxon though slight differences in genetic diversity could be observed in the more isolated Prepyrenean populations compared with the more widespread Pyrenean ones. These results suggest a recent postglacial origin of the present B. pyrenaica populations. © 2003 The Linnean Society of London, Biological Journal of the Linnean Society, 2003, 80 , 483–498.     

RAPD Profiling in Detecting Genetic Variation in Endemic Coelonema (Brassicaceae) of Qinghai-Tibet Plateau of China

Random amplified polymorphic DNA (RAPD) markers were used to measure genetic diversity of Coelonema draboides (Brassicaceae), a genus endemic to the Qilian Mountains of the Qinghai-Tibet Plateau. We sampled 90 individuals in 30 populations of Coelonema draboides from Datong and Huzhu counties of Qinghai Province in P.R. China. A total of 186 amplified bands were scored from the 14 RAPD primers, with a mean of 13.3 amplified bands per primer, and 87% (161 bands) polymorphic bands (PPB) was found. Analysis of molecular variance (AMOVA) shows that a large proportion of genetic variation (84.2%) resides among individuals within populations, while only 15.8% resides among populations. The species shows higher genetic diversity between individuals than other endemic and endangered plants. The RAPDs provide a useful tool for assessing genetic diversity of rare, endemic species and for resolving relationships among populations. The results show that the genetic diversity of this species is high, possibly allowing it to adapt more easily to environmental variations. The main factor responsible for the high level of differentiation within populations and the low level of diversity among populations is probably the outcrossing and long-lived nature of this species. Some long-distance dispersal, even among far separated populations, is also a crucial determinant for the pattern of genetic variation in the species. This distributive pattern of genetic variation of C. draboides populations provides important baseline data for conservation and collection strategies for the species. It is suggested that only populations in different habitats should be studied and protected, not all populations, so as to retain as much genetic diversity as possible.     

Population genetic diversity in the polyploid complex of wheatgrasses using isoenzyme and RAPD data

Thirty five bands (alleles) from six enzyme systems and fifty seven random amplified polymorphic DNA (RAPD) fragments were selected to analyse the genetic diversity of 33 polyploid wheatgrasses (Triticeae) populations of species Thinopyrum junceiforme and Elytrigia pycnantha, and two hybrids, one pentaploid and one novel 9-ploid. Dice’s similarity coefficient, the UPGMA-derived phenograms from RAPD, and allozymes markers showed that the clustering of wheatgrass populations was based on ploidy level. These markers had similar levels of diversity between populations, with high genetic similarity within the same ploidy-level and within population’s individuals. The tetraploid Th. junceiforme populations are closely related, with a large similarity distances varied from 0.8 to 1. Based on the isozyme and RAPD analyses, diploid taxa are related to polyploids with similarity coefficients 0.4.     

Genetic variation within and among populations of a wild rice Oryza granulata from China detected by RAPD and ISSR markers

Genetic variation within and between five populations of Oryza granulata from two regions of China was investigated using RAPD (random amplified polymorphic DNA) and ISSR (inter-simple sequence repeat amplification) markers. Twenty RAPD primers used in this study amplified 199 reproducible bands with 61 (30.65%) polymorphic; and 12 ISSR primers amplified 113 bands with 52 (46.02%) polymorphic. Both RAPD and ISSR analyses revealed a low level of genetic diversity in wild populations of O. granulata. Furthermore, analysis of molecular variance (AMOVA) was used to apportion the variation within and between populations both within and between regions. As the RAPD markers revealed, 73.85% of the total genetic diversity resided between the two regions, whereas only 19.45% and 6.70% were present between populations within regions and within a population respectively. Similarly, it was shown by ISSR markers that a great amount of variation (49.26%) occurred between the two regions, with only 38.07% and 12.66% between populations within regions and within a population respectively. Both the results of a UPGMA cluster, based on Jaccard coefficients, and pairwise distance analysis agree with that of the AMOVA partition. This is the first report of the partitioning of genetic variability within and among populations of O. granulata at the DNA level, which is in general agreement with a recent study on the same species in China using allozyme analysis. Our results also indicated that the percentage of polymorphic bands (PPB) detected by ISSR is higher than that detected by RAPD. It seems that ISSR is superior to RAPD in terms of the polymorphism detected and the amplification reproducibility. Received: 29 March 2000 / Accepted: 15 May 2000     

Genetic distance detected with RAPD markers among selected Australian commercial varieties and boron-tolerant exotic germplasm of pea (Pisum sativum L.)

The optimisation of polymerase chain reaction (PCR) for random amplified polymorphic DNA (RAPD) analysis in pea was investigated and the results were applied to an analysis of five representative Australian varieties and five selected boron-tolerant accessions derived from different geographical regions. Genotypes were compared using 34 random primers (Operon Technologies, Alameda, CA) which generated 180 polymorphic bands. Genetic similarity among genotypes was estimated on the basis of the percentage of common bands between genotypes and a dendrogram was constructed by the unweighted pair grouping method. A pattern of RAPD reaction corresponding to two main groups was discerned. The genetic divergence between Australian varieties and the boron-tolerant accessions suggests an intensive back-crossing programme would be required to transfer boron tolerance to a locally adapted genetic background. Our results show RAPD to be useful for clarifying phylogenic relationships within a species and also to provide useful genetic markers for varietal identification in pea.     

Fast discrimination (RAPD-PCR) of the species forming the pest complex Aleurodicus dispersus–Lecanoideus floccissimus (Hom: Aleyrodidae)

Abstract:  The Aleurodicus dispersus–Lecanoideus floccissimus complex has become a very important agricultural pest in the Canaries. These species are not easily differentiated by their morphological characteristics. The aim of the present study was to obtain genetic markers to unambiguously distinguish both species of this complex. Thus, six random primers were employed to generate RAPD markers. Different RAPD profiles were observed for the different species. The analysis successfully identified 39 reproducible and specific markers for L. floccissimus and 51 for A. dispersus , i.e. bands present in all individuals of one species but never in the other. RAPD markers resulted a useful tool for discriminate both species. Early identification of species and also of biotypes is crucial when designing control strategies to avoid the spread of the pest and consequently the considerable economic losses it causes in tropical crops.     

用RAPD和AFLP的方法对中国卤虫(Artemia)种及亲缘关系的研究

利用ＲＡＰＤ（随机扩增多态ＤＮＡ）和ＡＦＬＰ（扩增片段长度多态性）技术对不同种及种群卤虫的关系进行分析。 １０１个随机引物对４种卤虫Ａｆｒａｎｃｉｓｃａｎａ、Ａ ｕｒｍｉａｎａ、Ａ ｓｉｎｉｃａ和Ａ．ｐａｒｔｈｅｎｏｇｅｎｅｌｉｃａ基因组ＤＮＡ进行扩增,平均每个种获得７５１条带,其中４５８条带为多态性标记,每个引物提供平均７４个标记信息,聚类结果表明Ａ．ｓｉｎｉｃａ是不同于其他旧大陆两性生殖卤虫的一个独立的种。对来自 １５个种及品系的卤虫的 ＡＦＬＰ分析显示了非常好的遗传多态性,采用 １２对引物检测到 ５９４条带,其中 ４８０个为多态性标记。聚类结果表明来自西藏的两性生殖卤虫为不同于中国内陆两性生殖卤虫的新种。而孤雌生殖卤虫在进化过程中可能是多源的,中国内陆和沿海的孤雌生殖卤虫是沿着不同的途径进化的,内陆和沿海的孤雌生殖卤虫可能为不同的种。     

Applicability of RAPD markers on silver-stained polyacrylamide gels to ascertain genetic diversity in Peripatus acacioi (Peripatidae; Onychophora)

RAPD (random amplification of polymorphic DNA) molecular markers can be utilized for analyzing genetic variability in populations for which only a few or no molecular markers are available. They were used in a study of an endangered species, Peripatus acacioi, found in the Tripuí Ecological Station, in Ouro Preto, MG, Brazil. The ecological station was specifically created to protect this velvet worm species, the first of this group found in Brazil. For an initial evaluation of the genetic diversity of this species, DNA samples from the lobopods of four individuals, collected at random, were analyzed using RAPD. Each reaction was run with a different primer (Operon RAPD 10-mer Kits), totaling 13 primers (OPC2, OPC3, OPC4, OPC6, OPC8, OPC10, OPC11, OPL2, OPL7, OPL11, OPL13, OPL18, and OPL19). Due to the low amplification yield, RAPD fragments were separated in polyacrylamide gels and stained with silver nitrate. Numerous bands were observed. Fifty-five of the amplified bands proved to be reproducible, both in terms of presence and intensity. Among these, 27 were variable and 28 were constant. The average number of bands per gel was 4.2. Nine of the 13 primers tested allowed the identification of constant and variable bands among these four individuals. RAPD analysis of genetic variation using silver-stained polyacrylamide gel electrophoresis provided measures of band sharing among the individuals, and therefore could be used in population genetics studies of P. acacioi.     

The clonal and population structure of a rare endemic plant, Wyethia reticulata (Asteraceae): allozyme and RAPD analysis

Genetic structure arises when limited gene flow between populations favours the development of distinct arrays of genetic characters within each population. Determining the spatial scale at which this differentiation occurs is critical to our understanding of population biology and microevolution of species. The genetic structure and spatial pattern of genetic variation in an endemic, clonal perennial, Wyethia reticulata E. Greene, was investigated using random amplified polymorphic DNA (RAPD) markers and allozyme alleles. Large stands (250–360 m²) were found to contain few genetic individuals. Despite the small population sizes and endemism of the species, W. reticulata was highly diverse genetically, with most of the variation (75–81%) distributed within populations. A population structure in full agreement with spatially defined populations was achieved only by combining RAPD and allozyme markers. Analysis using both types of markers appeared to provide estimates of genetic similarity between individuals that were most consistent with empirical data on plant distributions. We postulated that large, long-lived clones dominated genetic relationships within populations but also provided opportunities for gene flow between populations on a longer time scale. The two marker types yielded different estimates of between-individual similarity and revealed disparate patterns of population structure. This result will arise because allozymes and random DNA segments have dissimilar evolutionary dynamics with respect to mutation and selection.     

Identification and genetic variation among Hibiscus species (Malvaceae) using RAPD markers

Germplasm identification and characterization is an important link between the conservation and utilization of plant genetic resources. Traditionally, species or cultivars identification has relied on morphological characters like growth habit or floral morphology like flower colour and other characteristics of the plant. Studies were undertaken for identification and determination of genetic variation within the two species of Hibiscus and 16 varieties of Hibiscus rosa-sinensis L. through random amplified polymorphic (RAPD) markers. Primer screening was made by using the DNA of variety "Prolific". Genetic analysis was made by using ten selected decamer primers. A total of 79 distinct DNA fragments ranging from 0.3 to 2.5 kb were amplified by using ten selected random decamer primers. The genetic similarity was evaluated on the basis of presence or absence of bands. The cluster analysis indicated that the 16 varieties and two species formed one cluster. The first major cluster consisted of three varieties and a second major cluster consisted of two species and 13 varieties. The genetic distance was very close within the varieties and also among the species. Thus, these RAPD markers have the potential for identification of species/varieties and characterization of genetic variation within the varieties. This is also helpful in Hibiscus breeding programs and provides a major input into conservation biology.     

B chromosomes in Brazilian rodents

B chromosomes are now known in eight Brazilian rodent species: Akodon montensis, Holochilus brasiliensis, Nectomys rattus, N. squamipes, Oligoryzomys flavescens, Oryzomys angouya, Proechimys sp. 2 and Trinomys iheringi. Typically these chromosomes are heterogeneous relative to size, morphology, banding patterns, presence/absence of NORs, and presence/absence of interstitial telomeric signals after FISH. In most cases, Bs are heterochromatic and late replicating. Active NORs were detected in two species: Akodon montensis and Oryzomys angouya. As a rule, Bs behave as uni or bivalents in meiosis, there is no pairing between Bs and autosomes or sex chromosomes and also their synaptonemal complexes are isopycnotic with those in A chromosomes.     

RAPD variation within and among natural populations of outcrossing buffalograss [Buchloë dactyloides (Nutt.) Engelm.]

RAPD markers provide a powerful tool for the investigation of genetic variation in natural and domesticated populations. Recent studies of strain/cultivar identification have shown extensive RAPD divergence among, but little variation within, inbred species or cultivars. In contrast, little is known about the pattern and extent of RAPD variation in heterogeneous, outcrossing species. We describe the population genetic variation of RAPD markers in natural, diploid sources of dioecious buffalograss [Buchloë dactyloides (Nutt.) Engelm.]. Buffalograss is native to the semi-arid regions of the Great Plains of North America, where it is important for rangeland forage, soil conservation, and as turfgrass. Most sources of buffalograss germplasm are polyploid; diploid populations are previously known only from semi-arid Central Mexico. This is the first report of diploids from humid Gulf Coastal Texas. These two diploid sources represent divergent adaptive ecotypes. Seven 10-mer primers produced 98 polymorphic banding sites. Based on the presence/ absence of bands, a genetic distance matrix was calculated. The new Analysis of Molecular Variance (AMOVA) technique was used to apportion the variation among individuals within populations, among populations within adaptive regions, and among regions. There was considerable variation within each of the four populations, and every individual was genetically distinct. Even so, genetic divergence was found among local populations. Within-population variation was larger and among-population variation smaller in Mexico than in Texas. The largest observed genetic differences were those between the two regional ecotypes. These patterns of genetic variation were very different from those reported for inbred species and provide important baseline data for cultivar identification and continuing studies of the evolution of polyploid races in this species.     

Genetic Diversity and Population Structure of Yellow Camellia (Camellia nitidissima) in China as Revealed by RAPD and AFLP Markers

Camellia nitidissima, a rare plant but a useful genetic resource for commercial cultivation of ornamental camellias, is distributed in a narrow region of South China and North Vietnam. In this study, RAPD and AFLP markers were used to assess the genetic diversity and population structure of six natural populations of C. nitidissima from Guangxi in South China. Twenty RAPD primers amplified 183 bands, of which 143 bands were polymorphic, and 8 AFLP primer pairs produced 502 bands, of which 364 were polymorphic. Independent as well as combined analyses of the cluster analyses of the RAPD and AFLP fragments showed that the six populations could be classified into two major genetic groups corresponding to the Nanning and Fangcheng areas. The Mantel test revealed significant correlation between the genetic and geographic distances of C. nitidissima populations (r = 0.953, p = 0.036). AMOVA analysis allowed the partitioning of the genetic variation between groups (36.09%), among populations within groups (25.78%), and within populations (38.14%). An understanding of both the genetic diversity and the population structure of C. nitidissima in China can also provide insight into the conservation and management of this endangered species.     

Genetic diversity of the natural populations of Arabidopsis thaliana in China

Although extensive studies have been conducted on the genetic structure of Arabidopsis thaliana (A. thaliana) populations worldwide, the populations from China have never been studied. In this study, we collected 560 individuals from 19 natural populations of A. thaliana distributed in East China along the lower reaches of the Yangtze River, and two populations from northwest China (Xinjiang Province). We adopted two kinds of molecular marker, inter-simple sequence repeats (ISSRs) and random amplified polymorphic DNA (RAPDs) to investigate the genetic diversity within and among populations, and the correlation between the genetic and geographic distances. Thirteen ISSR primers produced 165 polymorphic bands (PPB) (96%) and 11 RAPD primers produced 162 polymorphic bands (98%) in about 560 individuals. The two marker systems generated similar patterns of genetic diversity in these natural populations. The AMOVA analysis indicated about 42-45% of the total genetic variation existed within populations, and found possible geographic structure. The Mantel test revealed a significant correlation between the geographic distance and the genetic distance of these populations in general. A close genetic relationship was found among four populations in the Jiangxi Province, and these always appeared clustered together as a monophyletic group in unweighted pair-group method with arithmetic averages dendrograms based on both ISSR and RAPD data sets. Based on the observation of recolonization and extinction of naturally distributed populations of A. thaliana, and the pattern of their genetic differentiation, the distribution of this species in China might be a result of natural dispersal under the strong influence of human activity.     

内蒙古地区亚洲小车蝗不同地理种群的RAPD分析

采用随机扩增多态性DNA(RAPD)技术对内蒙古地区亚洲小车蝗Oedaleus asiaticus(B.-bienko)9个不同地理种群90个个体进行扩增,8条随机引物扩增共产生了78条带,多态性片段为62条。对Nei′s基因多样性指数和遗传距离进行分析,结果表明:种群间的遗传分化系数为0.2343,即23.43%的遗传变异存在于种群间,种群内的遗传分化系数为0.7657,即76.57%的遗传多样性存在于种群内,群体内遗传多样性大于群体间遗传多样性。用NJ法对这3个种群的Nei′s遗传距离作聚类分析,结果表明亚洲小车蝗不同种群的遗传分化程度与地理距离具有正相关关系。