bluuebunny/crossref_metadata_2025 huggingface dataset:
Genetic variation of geminiviruses: comparison between sexual and asexual host plant populations
Authors: Ooi K. , Yahara T.
Published: March 2003

One of the most promising hypotheses for the evolution of sex is that sexual reproduction is advantageous because it increases the rate of adaptive evolution in response to parasites. To investigate this advantage of sex, we compared genetic variation of geminiviruses infecting sexual and asexual populations of Eupatorium (Asteraceae). The infection frequency was 37.5% in the sexual population and 87.8% in the asexual population. The lower infection frequency in the sexual population might be the result of higher genetic diversity of host plants. If geminiviruses have diverged to counter defence systems of genetically variable hosts, genetic diversity of viruses is expected to be higher in sexual host populations than in asexual host populations. To test this expectation, we used single‐strand conformation polymorphism (SSCP) analysis to examine genetic diversity of the geminiviruses in a DNA region containing the open‐reading frame (ORF) C4 gene, which is known to function as a host range determinant. As predicted, higher genetic diversity of viruses was observed in the sexual population: three SSCP types were found in the asexual population while six types were found in the sexual population. Sequencing of the polymerase chain reaction (PCR) products revealed further genetic diversity. Phylogenetic analysis of the sequences showed that the SSCP types belonged to four different clades. Several SSCP types from the same clade were found in the sexual population, whereas the asexual population included only one SSCP type from each clade. Amino acid replacements of ORF C4 are suggested to be accelerated in the sexual population. This evidence supports the hypothesis that sexual reproduction is advantageous as a defence against epidemic disease.
The effects of regeneration by fragmentation upon clonal diversity in the tropical forest shrub Poikilacanthus macranthus: random amplified polymorphic DNA (RAPD) results
Authors: Bush  , Mulcahy
Published: March 2003

Poikilacanthus macranthus (Acanthaceae), like many shrubs in the neotropical cloud forest of Monteverde, Costa Rica, is capable of regeneration through stem and twig fragments. Our field sampling indicated that reproduction in P. macranthus is primarily through fragmentation in the Monteverde region. Random amplified polymorphic DNAs (RAPDs) were employed to examine clonal diversity in four populations of P. macranthus, and two primers yielded 11 variable markers that were used to identify genets. Sixty‐eight multilocus genotypes were identified out of 277 plants sampled. Clonal diversity values were higher than the average for clonal plant species, as the number of genets per ramet was 0.25, while the mean D value was 0.87 and the mean E value was 0.84.
Chloroplast DNA variation in Dactylis glomerata L. taxa endemic to the Macaronesian islands
Authors: Sahuquillo E. , Lumaret R.
Published: March 2003

In the Dactylis glomerata infraspecific polyploid grass complex, restriction fragment length polymorphisms (RFLPs) of chloroplast DNA (cpDNA) were studied in diploid and tetraploid populations of several taxa endemic to Macaronesia (Madeira and the Canary islands) and in populations from the African and European continental areas closest to Macaronesia. Two chlorotypes, which differed by a single 290‐bp length mutation, were observed in the Macaronesian and the continental populations. Chlorotype I, which is predominant in the whole D. glomerata complex, was found in the majority of continental populations. It was also observed in the most western Macaronesian islands, in the two diploid taxa endemic to the lowland scrub and the high elevation heath of Tenerife, respectively, and in tetraploids endemic to Madeira and La Palma. These island populations were growing under the influence of humid trade winds. Chlorotype II was found in the eastern part of the Archipelago (closer to Africa), which experienced subarid Mediterranean climate conditions, and in very few diploid and tetraploid Mediterranean populations growing at high elevation on the continent. This geographical and climatic distribution of chlorotype variation in Macaronesia is consistent with that reported previously for morphological, allozyme and phenolic variation in the same plant material. Chlorotype II was, however, also observed in tetraploid populations from La Gomera island and in one of the seven tetraploid populations analysed from Madeira, which all showed clearly subtropical characters for morphology, allozymes and phenolic compounds. This result suggests that cpDNA introgression has occurred more than once from the Mediterranean material into the subtropical one and may indicate that colonization between the mainland and islands, or among the islands, probably played a major role in the geographical pattern observed for that marker.
A phylogenetic analysis of body size evolution in theAnolis roquetgroup (Sauria: Iguanidae): character displacement or size assortment?
Authors: Giannasi N. , Thorpe R. S. , Malhotra A.
Published: March 2003

The important role that competition plays in structuring communities is well documented; however, the role of competition in an evolutionary context remains unclear. Evolutionary investigations into the role of competition have often focused on the process of character displacement, and a good example of this is the evolution of body size in theAnolislizards of the Caribbean islands. Previous work on theA. roquetspecies group has taken a phylogenetic approach and concluded that patterns of body size differences are not caused by character displacement but are a result of size assortment. Using a phylogenetic reconstruction based on the sequence of the cytochromebgene (cyt‐b) and ancestral character‐state reconstruction methods, we investigated the roles of character displacement and size assortment. Our results indicated that size assortment alone was insufficient to explain the observed patterns of body size differences. Furthermore, we found that change in body size was associated with a change in allopatry/sympatry, thus supporting the character‐displacement hypothesis. We conclude that patterns of body size differences in theA. roquetspecies group appear to be the result of a combination of character displacement and size assortment because character displacement was only found to be possible on three occasions.
Random amplified polymorphic DNA analysis of southern brown bandicoot (Isoodon obesulus) populations in Western Australia reveals genetic differentiation related to environmental variables
Authors: Cooper M. L.
Published: March 2003

Random amplified polymorphic DNA (RAPD) markers were used to analyse genetic variation within and between populations of Isoodon obesulus in Western Australia. Genetically controlled geographical variation in body size associated with habitat type and rainfall exists in this species, raising the question of whether local conditions may influence gene flow in I. obesulus. The RAPD markers displayed substantial genetic variation, with all animals possessing unique RAPD phenotypes over 39 polymorphic bands produced by three primers. Significant geographical subdivision was apparent (ΦST = 0.208) with southwest locations being divergent from all others, despite there being no physical barriers to gene flow. The pattern of subdivision was unrelated to physical distance between the locations, but was related to both annual rainfall and habitat type. Therefore, the most reasonable explanation for this pattern of subdivision appears to be that gene flow is restricted by selection against migrants between local populations with substantially different habitat type or rainfall. Restriction of gene flow through selection against migrants is rarely investigated, and the results of this study suggest that the importance of this process in the formation of population structure may be underestimated.
Genetic analysis of a documented population bottleneck: introduced Bennett’s wallabies (Macropus rufogriseus rufogriseus) in New Zealand
Authors: Le Page S. L. , Livermore R. A. , Cooper D. W. , Taylor A. C.
Published: March 2003

Few bottlenecks of wild populations are sufficiently well‐documented to constitute models for testing theories about the impact of bottlenecks on genetic variation, and subsequent population persistence. Relevant details of the Bennett’s wallaby (Macropus rufogriseus rufogriseus) introduction into New Zealand were recorded (founder number, source and approximate bottleneck duration) and suggest this may provide a rare opportunity to examine the efficacy of tests designed to detect recent bottlenecks in wild populations. We first assessed the accuracy of historic accounts of the introduction using genetic diversity detected in mitochondrial DNA (mtDNA) and at five microsatellite loci. Phylogenetic analyses of mtDNA
D‐loop sequence haplotypes were consistent with the reported origin of the founders as Tasmania, rather than one of the Bass Strait islands in which Bennett’s wallabies are also found. Microsatellite allele frequencies from the Tasmanian source population were then used to seed bottleneck simulations encompassing varying sizes and numbers of generations, in order to assess the severity of bottleneck consistent with diversity observed in the New Zealand population. The results suggested that the founder number was unlikely to have been as small as the three animals suggested by the account of the introduction. Nonetheless, the bottleneck was probably severe; in the range of three to five pairs of wallabies for one to three generations. It resulted in significantly reduced levels of allelic diversity and heterozygosity relative to the source population. This bottleneck is only detectable under the infinite allele model (IAM) and not under the stepwise mutation model (SMM) or the two‐phase model (TPM), and possible explanations for this are discussed.
Mitochondrial DNA evolution and population history of the Tenerife skink Chalcides viridanus
Authors: Brown R. P. , Campos‐Delgado R. , Pestano J.
Published: March 2003

Recent studies of island lizards have suggested that historical vicariance as a result of volcanism may have played an important role in shaping patterns of within‐island genetic diversity. The skink, Chalcides viridanus, shows variation in morphology within the volcanic island of Tenerife. Two mitochondrial DNA (mtDNA) fragments (from the 12S and 16S rRNA regions) were sequenced in individuals from 17 sites to evaluate the relationship between current phylogeography and the geological history of the island. Three main clades were detected. The two most basal clades were restricted to areas representing the ancient precursor islands of Teno and Anaga in the northwest and northeast of Tenerife, respectively. The third clade showed a widespread geographical distribution and provided evidence of a recent rapid expansion after a bottleneck. Within‐island cladogenesis appears to have taken place during a recent period of volcanic activity and long after the ancient islands had been united by the eruptions that led to the formation of the Cañadas edifice. Evidence of similar biogeographical histories are found in other species in the Canary archipelago, supporting the volcanism scenario as a potentially widespread cause of within‐island differentiation in reptiles.
Mitochondrial DNA control region diversity in the endangered blue chaffinch, Fringilla teydea
Authors: Pestano J. , Brown R. P. , Rodriguez F. , Moreno A.
Published: March 2003

The blue chaffinch (Fringilla teydea) is found only on the two central Canary Islands of Gran Canaria and Tenerife, where it is restricted to pine forest habitat. It is reasonably abundant on the latter island but endangered on the former. Here, sequence variation was studied in a fragment spanning domains I and II of the mitochondrial DNA (mtDNA) control region. Phylogenetic analysis of all haplotypes with a F. coelebs outgroup indicated the two island populations were reciprocally monophyletic, supporting their individual conservation. Unlike in other species, most within‐island haplotype diversity was due to mutations in the domain II region. Surprisingly, genetic diversity was greater in the smaller Gran Canarian population. We suggest that this is unlikely to be maintained under current population sizes although it may be mitigated by incorporating genetic information into the captive breeding programme.
Population structure and mating biology of the polygynous ponerine antGnamptogenys striatulain Brazil
Authors: Giraud T. , Blatrix R. , Poteaux C. , Solignac M. , Jaisson P.
Published: March 2003

Gnamptogenys striatulais a polygynous ponerine ant, whose colonies contain either several differentiated queens or several gamergates. Population structure, queen mating frequency and deviation from random mating were investigated in a north‐eastern Brazilian population. Eight workers from each of 33 queenright colonies and 17 queens and their progeny (20–40 offspring) were genotyped using eight variable microsatellite markers. Population differentiation tests indicated limited gene flow at the scale of several kilometres, and tests of isolation by distance revealed population viscosity at the scale of a few metres. This population structure, together with the frequent colony migrations and fissions observed in the field, suggest that new nests are founded by budding inG. striatula. Genetic data showed that 13 of our 17 queens were single‐mated and four were double‐mated. The estimation of the range of maximal frequency of double‐mated queens in the population was 0.232–0.259, demonstrating that mating frequency is low inG. striatula. The low estimated mean relatedness between the 17 queens and their mates (−0.04 ± 0.49) indicated no evidence of inbreeding inG. striatula.
Molecular evidence of natural hybridization between Abies veitchii and A. homolepis (Pinaceae) revealed by chloroplast, mitochondrial and nuclear DNA markers
Authors: Isoda K. , Shiraishi S. , Watanabe S. , Kitamura K.
Published: March 2003

Sub‐alpine Abies veitchii and A. homolepis are distributed in the central part of Honshu Island, Japan, and their habitats are segregated vertically. These species sometimes form a mixed forest in the overlapping area of the two species, that is, in the upper limit of the A. homolepis habitat and the lower limit of A. veitchii. These species have been considered to be distantly related because they were classified into different sections by most conventional classifications. No natural hybridization has been reported between the two species. The aim of this study was to demonstrate, through the use of molecular markers, whether natural hybridization takes place between these two species at two experimental sites on Mt. Fuji, where the species occur naturally. DNA markers from paternally inherited chloroplast DNA (cpDNA), maternally inherited mitochondrial DNA (mtDNA) and biparentally inherited nuclear DNA (nDNA), were used for this study. As organelle DNA markers, polymerase chain reaction–single strand conformation polymorphism (PCR–SSCP) markers were developed to determine the maternal and paternal species for each individual. Two of 334 individuals possessed a cpDNA haplotype derived from A. homolepis and a mtDNA haplotype from A. veitchii. Furthermore, the nDNA of these two individuals was analysed using the random amplified polymorphic DNA (RAPD) assay to investigate their genomic composition. RAPD analysis indicated that the nuclear genomes of the two individuals were derived from both species. We conclude that A. veitchii and A. homolepis produce natural hybrids, and that their systematic relationship should be re‐evaluated.
Do Wolbachia infections play a role in unidirectional incompatibilities in a field cricket hybrid zone?
Authors: Mandel Mark J. , Ross Charles L. , Harrison Richard G.
Published: March 2003

Two closely related field crickets, Gryllus firmus and G. pennsylvanicus, hybridize along an extensive north–south zone in the eastern United States. Crosses between G. firmus males and G. pennsylvanicus females produce viable and fertile F1, but the reciprocal cross consistently fails to produce offspring. Wolbachia, a bacterial parasite of arthropods that causes unidirectional incompatibilities in a variety of insect species, has been suggested as the cause of the observed incompatibility between G. pennsylvanicus and G. firmus. We examine the presence/absence of Wolbachia strains, defined by sequencing the ftsZ gene, in four cricket populations from the north‐eastern United States. Most G. firmus individuals are infected (100% in Guilford, Connecticut; 65% in Seaside Park, New Jersey) and > 95% of those infected harbour a single strain of Wolbachia. All individuals in G. pennsylvanicus populations (Ithaca, New York; Sharon, Connecticut) are infected; the majority of individuals carry a second strain of Wolbachia, but a significant fraction carry the same strain found commonly in G. firmus. The presence of an apparently identical Wolbachia strain in crickets of both species means that some crosses between G. pennsylvanicus males and G. firmus females should be compatible. We have no evidence of such compatibility. Furthermore, if Wolbachia infections are responsible for the observed incompatibility between species, then incompatibilities must also exist within G. pennsylvanicus, because this species harbours both Wolbachia strains. Although some single pair crosses within G. pennsylvanicus do fail to produce offspring, the proportion is lower than expected if Wolbachia were responsible. Therefore, Wolbachia is unlikely to be involved in reproductive isolation between the two cricket species.
Genetic polymorphism in Gymnodinium galatheanum chloroplast DNA sequences and development of a molecular detection assay
Authors: Tengs Torstein , Bowers Holly A. , Ziman Andrew P. , Stoecker Diane K. , Oldach David W.
Published: March 2003

Nuclear and chloroplast‐encoded small subunit ribosomal DNA sequences were obtained from several strains of the toxic dinoflagellate Gymnodinium galatheanum. Phylogenetic analyses and comparison of sequences indicate that the chloroplast sequences show a higher degree of sequence divergence than the nuclear homologue. The chloroplast sequences were chosen as targets for the development of a 5′–3′ exonuclease assay for detection of the organism. The assay has a very high degree of specificity and has been used to screen environmental water samples from a fish farm where the presence of this dinoflagellate species has previously been associated with fish kills. Various hypotheses for the derived nature of the chloroplast sequences are discussed, as well as what is known about the toxicity of the species.
Spatial population structure in a patchily distributed beetle
Authors: Roslin Tomas
Published: March 2003

The dynamics and evolution of populations will critically depend on their spatial structure. Hence, a recent emphasis on one particular type of structure — the metapopulation concept of Levins — can only be justified by empirical assessment of spatial population structures in a wide range of organisms. This paper focuses onAphodius fossor, a dung beetle specialized on cattle pastures. An agricultural database was used to locate nearly 50 000 local populations ofA. fossorin Finland. Several independent methods were then used to quantify key processes in this vast population system. Allozyme markers and mitochondrial DNA (mtDNA) sequences were applied to examine genetic differentiation of local populations and to derive indirect estimates of gene flow. These estimates were compared to values expected on the basis of direct observations of dispersing individuals and assessments of local effective population size. Molecular markers revealed striking genetic homogeneity inA. fossor.Differentiation was only evident in mtDNA haplotype frequencies between the isolated Åland islands and the Finnish mainland. Thus, indirect estimates of gene flow agreed with direct observations that local effective population size inA. fossoris large (hundreds of individuals), and that in each generation, a substantial fraction (approximately one‐fifth) of the individuals move between populations. Large local population size, extreme haplotype diversity and a high regional incidence ofA. fossorall testify against recurrent population turnover. Taken together, these results provide strong evidence that the whole mainland population ofA. fossoris better described as one large ‘patchy population’, with substantial movement between relatively persistent local populations, than as a classical metapopulation.
A microbial population–species interface: nested cladistic and coalescent inference with multilocus data
Authors: Carbone I. , Kohn L. M.
Published: March 2003

Using sequence data from seven nuclear loci in 385 isolates of the haploid, plant parasitic, ascomycete fungus, Sclerotinia, divergence times of populations and of species were distinguished. The evolutionary history of haplotypes on both population and species scales was reconstructed using a combination of parsimony, maximum likelihood and coalescent methods, implemented in a specific order. Analysis of site compatibility revealed recombination blocks from which alternative (marginal) networks were inferred, reducing uncertainty in the network due to recombination. Our own modifications of Templeton and co‐workers’ cladistic inference method and a coalescent approach detected the same phylogeographic processes. Assuming neutrality and a molecular clock, the boundary between divergent populations and species is an interval of time between coalescence (to a common ancestor) of populations and coalescence of species.
Lack of molluscan host diversity and the transmission of an emerging parasitic disease in Bolivia
Authors: Meunier C. , Tirard, C. , Hurtrez‐Boussès S. , Durand P. , Bargues M. D. , Mas‐Coma S. , Pointier J. P. , Jourdane J. , Renaud F.
Published: March 2003

Fasciolosis is a re‐emerging parasitic disease that affects an increasing number of people in developing countries. The most severe endemic affects the Bolivian Altiplano, where the liver fluke (Fasciola hepatica) and its hermaphroditic snail host,Lymnaea truncatula,have been introduced from Europe. To achieve a better understanding of the epidemiological situation and the consequences of the colonization event of this invasive species, genetic analysis of Bolivian snail populations was needed. Here we compare the genetic diversity and population structure of snail samples from the Bolivian Altiplano with samples from the Old World at six polymorphic microsatellite loci. Whereas some variability exists in the snail populations from the Old World, we observe only a single genotype ofL. truncatulain the Bolivian Altiplano. We discuss the possible explanations for such a reduction in genetic variability, and, given the high natural parasitism pressures exerted on the snail populations, we discuss the relevance of this result for host–parasite interactions.
Microsatellite variation in the yellowhammer Emberiza citrinella: population structure of a declining farmland bird
Authors: Lee Patricia L. M. , Bradbury Richard B. , Wilson Jeremy D. , Flanagan Nicola S. , Richardson Lynne , Perkins Allan J. , Krebs John R.
Published: March 2003

In recent years, there has been much concern in the UK about population declines of widespread species in agricultural habitats. Conservation‐orientated research on declining birds has focused on vital rates of survival and productivity. However, the environmental factors which may influence movements between populations of widespread species is poorly understood. Population genetic structure is an indirect description of dispersal between groups of individuals. To attempt to develop an understanding of genetic structuring in a widespread, but declining, farmland bird, we therefore investigated the yellowhammer, Emberiza citrinella, population in England and Wales using microsatellite data. Our first aim was to investigate whether there was genetic substructuring in the population. A second aim was to investigate if there was a relationship between genetic distances and various environmental variables. Finally, we analysed the microsatellite data for evidence of loss of genetic variation due to population decline. Our data showed a slight but significant structure within the yellowhammer population. This therefore cannot be considered a panmictic population. Our example from South Cumbria implies that high‐altitude barriers may have a slight influence on population structure. However, on the whole, genetic distances between sample sites were not significantly correlated with geographical distances, degrees of population connectivity, high altitudes, or differences in precipitation between sites. Finally, we detected departures from mutation‐drift equilibrium (excess heterozygosity), which is indicative of a loss of genetic variation through recent decline.
Distribution of individual inbreeding coefficients, relatedness and influence of stocking on native anadromous brown trout (Salmo trutta) population structure
Authors: Ruzzante D. E. , Hansen M. M. , Meldrup D.
Published: March 2003

We examined polymorphism at seven microsatellite loci in 4023 brown trout (Salmo trutta) collected from 32 tributaries to the Limfjord, Denmark (~200 km) and from two hatcheries used for stocking. Populations differ in their estimated sizes and stocking histories. Mean individual inbreeding coefficients do not differ among locations within rivers. Relatedness varies between sites within rivers indicating varied local dynamics at a very small geographical scale. Relatedness is sometimes lower than expected among an equal number of simulated individuals with randomized genotypes, suggesting structure within locations. Five per cent of the genetic variance is distributed among rivers (FST = 0.049), but in the western, less heavily stocked, area of the Limfjord a higher proportion of the genetic variance is distributed among rivers than among locations within rivers. The reverse is true of the eastern, more heavily stocked, area of the Limfjord. Here, a higher proportion of the genetic variance is distributed among locations within rivers than among rivers. Assignment tests reveal that the majority of trout (mean 77% of all fish) are more probably of local origin than hatchery origin but this proportion varies regionally, with rivers in the western area of the Limfjord showing a relatively high (mean 88%) and those in the eastern area showing a relatively low (mean 72%) proportion of locally assigned trout. These results can be interpreted as reflecting stocking impact. Also, the proportion of locally assigned trout correlates with the populations’ stocking histories, with rivers presently subjected to stocking (hatchery trout) showing low (mean ~0.73), and rivers where stocking was discontinued showing high (mean ~0.84) proportions of local fish, probably reflecting lower survival of hatchery than of wild trout. There is evidence for isolation by distance at a large geographical scale when individual river populations are pooled into nine geographical regions but not at a small geographical scale when populations are considered individually. We reject the null hypothesis that stocking has had no impact on population structure but the relatively high proportion of locally assigned trout in populations where stocking with domestic fish no longer takes place suggests limited long‐term success of stocking.
Detection of genetically divergent clone mates in apomictic dandelions
Authors: Mes Ted H. M. , Kuperus P. , Kirschner J. , Štepánek J. , Štorchová H. , Oosterveld P. , Den Nijs J. C. M.
Published: March 2003

This study aims to identify genetically diverged clone mates in apomictic dandelions. Clone mates are defined as individuals that may have diverged as a result of mutation accumulation and that have undergone only clonal reproduction since their most recent common ancestor. Based on distinctive morphology and an aberrant and rare chloroplast haplotype, northwest European individuals of Taraxacum section Naevosa are well suited for the detection of clonal lineages in which mutation has occurred. In the case of strictly clonal reproduction, nuclear genetic variability was expected to be hierarchically organized. Nucleotide polymorphisms in internal transcribed spacer (ITS) sequences, however, were incompatible with a clonal structure of the Norwegian individuals, probably due to persistent ancestral polymorphisms that pre‐date the origin of the Naevosa clone. This interpretation is supported by the presence of ITS variants in section Naevosa that were also found in distantly related dandelions. In contrast to the ITS sequence data, amplified fragment length polymorphisms (AFLPs), isozymes and microsatellites strongly supported the contention of prolonged clonal reproduction and mutation accumulation in Norwegian Naevosa. Because these markers are generally considered to be more variable and more rapidly evolving than ITS sequences, mutations in these markers probably evolved after the origin of the clone. Within the Norwegian clone, a surprising number of markers distinguished the clone mates. As a consequence, incorporation of mutation in the detection of clone mates is anticipated to have a big impact on estimates of size, geographical range and age of clones as well as on experimental designs of studies of clonal plants.
Genetic variation in original and colonizing Drosophila buzzatii populations analysed by microsatellite loci isolated with a new PCR screening method
Authors: Frydenberg J. , Pertoldi C. , Dahlgaard J. , Loeschcke V.
Published: March 2003

A new polymerase chain reaction‐based screening method for microsatellites is presented. Using this method, we isolated 12 microsatellite loci from Drosophila buzzatii, two of which were X‐linked. We applied the other 10 microsatellite loci to the analysis of genetic variation in five natural populations of D. buzzatii. Two populations were from the species’ original distribution in Argentina, whereas the other three were from Europe (two) and Australia that were colonized 200 and 65 years ago, respectively. Allelic variation was much larger in the original populations than in the colonizing ones and there was a tendency to decreased heterozygosity in the colonizing populations. We used three different statistical procedures for detecting population bottlenecks. All procedures suggested that the low variability in the populations in the Old World was not the result of the recent population decline, but was due to a founder effect followed by a population expansion. In fact, one procedure which detects population expansions and declines based on the genealogical history of microsatellite data suggested that an expansion had taken place in all the colonized populations.
Spatial autocorrelation and linkage of Mendelian RAPD markers in a population of Picea abies Karst
Authors: Bucci Gabriele , Menozzi Paolo
Published: March 2003

The spatial clustering of single‐ and di‐locus genotypes in a natural, continuous population of Norway spruce was investigated using 69 Mendelian Random Amplified Polymorphic DNA (RAPD) markers that covered about 15% of the species’ genome, and whose linkage relationships were known. Spatial autocorrelation techniques and randomization tests, applied to both single‐ and di‐locus genotypes, revealed a weak, though significant, spatial structure at the scale 0–200 m (5% of single‐locus and 7% of di‐locus genotypes). To assess the relative importance of isolation by distance and linkage between markers on their spatial genetic structuring, we grouped joins between sampled trees into ‘equivalence categories’ expected to show similar, specific patterns of spatial distribution under isolation by distance. Results from both single‐ and di‐locus analyses were consistent with the existence of patches of like homozygotes (about 8% and 11% of loci at the single‐ and di‐locus level, respectively) surrounded by a mix of like heterozygotes. Similar structuring has been predicted by simulation models under isolation by distance and selective neutrality. Overall, linkage between markers accounted for an increase of spatial clumping of di‐locus genotypes involving tightly linked loci with recombination fractions up to 0.1, a consequence of limited, stochastic spread of single‐locus genotypes in space. Our results support the hypothesis that isolation by distance and linkage have a small, though significant, effect even within continuous forest tree populations. In general, the spatial distribution of multilocus genotypes within populations should be interpreted with caution when linkage relationships among the markers used are unknown.
Molecular analysis of a 11 700‐year‐old rodent midden from the Atacama Desert, Chile
Authors: Kuch Melanie , Rohland Nadin , Betancourt Julio L. , Latorre Claudio , Steppan Scott , Poinar Hendrik N.
Published: March 2003

DNA was extracted from an 11 700‐year‐old rodent midden from the Atacama Desert, Chile and the chloroplast and animal mitochondrial DNA (mtDNA) gene sequences were analysed to investigate the floral environment surrounding the midden, and the identity of the midden agent. The plant sequences, together with the macroscopic identifications, suggest the presence of 13 plant families and three orders that no longer exist today at the midden locality, and thus point to a much more diverse and humid climate 11 700 years ago. The mtDNA sequences suggest the presence of at least four different vertebrates, which have been putatively identified as a camelid (vicuna), two rodents (Phyllotis and Abrocoma), and a cardinal bird (Passeriformes). To identify the midden agent, DNA was extracted from pooled faecal pellets, three small overlapping fragments of the mitochondrial cytochrome b gene were ampli‐fied and multiple clones were sequenced. These results were analysed along with com‐plete cytochrome b sequences for several modern Phyllotis species to place the midden sequence phylogenetically. The results identified the midden agent as belonging to an ancestral P. limatus. Today, P. limatus is not found at the midden locality but it can be found 100 km to the north, indicating at least a small range shift. The more extensive sampling of modern Phyllotis reinforces the suggestion that P. limatus is recently derived from a peripheral isolate.
Complex patterns of mating revealed in a Eucalyptus regnans seed orchard using allozyme markers and the neighbourhood model
Authors: Burczyk J. , Adams W. T. , Moran G. F. , Griffin A. R.
Published: March 2003

The neighbourhood model apportions offspring of individual mother plants to self‐fertilization, outcrossing to males within a circumscribed area around the mother plant (the neighbourhood), and outcrossing to males outside the neighbourhood. Formerly the model was applied only to haploid pollen gametes in the offspring of conifers, but is extended so that it can be used with genotypic data from diploid offspring of both angiosperms and gymnosperms. In addition, it is shown that the mating parameters can be estimated without independent estimates of allele frequencies in the pollen pools outside the neighbourhood; thus the model might be applied effectively to natural populations exposed to unknown external pollen sources. Parameters of the neighbourhood mating model were estimated for a 10‐year‐old seed orchard population of the insect‐pollinated tree, Eucalyptus regnans, in southeast Australia, which contained a mixture of two geographical provenances (Victoria and Tasmania). The mating patterns revealed were complex. Crosses between trees of the same provenance occurred three times more often than crosses between trees of different provenances. Levels of self‐fertilization and patterns of mating within neighbourhoods were influenced by provenance origin, crop fecundity and orchard position (central vs. edge) of mother trees. Gene dispersal, however, was extensive, with approximately 50% of effective pollen gametes coming from males more than 40 m away from mother trees (average distance between neighbouring trees was 7.4 m). Thus, insect pollinators are efficient promoters of cross‐fertilization in this orchard, with the result that the effective number of males mating with each female is large.
Microsatellite analysis of genetic divergence among populations of giant Galápagos tortoises
Authors: Ciofi Claudio , Milinkovitch Michel C. , Gibbs James P. , Caccone Adalgisa , Powell Jeffrey R.
Published: March 2003

Giant Galápagos tortoises represent an interesting model for the study of patterns of genetic divergence and adaptive differentiation related to island colonization events. Recent mitochondrial DNA work elucidated the evolutionary history of the species and helped to clarify aspects of nomenclature. We used 10 microsatellite loci to assess levels of genetic divergence among and within island populations. In particular, we described the genetic structure of tortoises on the island of Isabela, where discrimination of different taxa is still subject of debate. Individual island populations were all genetically distinct. The island of Santa Cruz harboured two distinct populations. On Isabela, populations of Volcan Wolf, Darwin and Alcedo were significantly different from each other. On the other hand, Volcan Wolf showed allelic similarity with the island of Santiago. On Southern Isabela, lower genetic divergence was found between Northeast Sierra Negra and Volcan Alcedo, while patterns of gene flow were recorded among tortoises of Cerro Azul and Southeast Sierra Negra. These tortoises have endured heavy exploitation during the last three centuries and recently attracted much concern due to the current number of stochastic and deterministic threats to extant populations. Our study complements previous investigation based on mtDNA diversity and provides further information that may help devising tortoise management plans.
First synthesize new viruses then regulate their release? The case of the wild rabbit
Authors: Angulo E. , Cooke B.
Published: March 2003

European wild rabbits originated in southwestern Europe but have been introduced into many other countries world‐wide, becoming serious pests in many instances. As a consequence of rabbits being regarded so differently, applied research for their management often has opposing goals, namely their conservation or their control. Furthermore, modern gene technology has led to the concept of using genetically modified myxoma viruses for rabbit management, again with quite contrary aims in mind. In this paper we explain the possible ecological and economic consequences of using these genetically modified viruses inappropriately and we consider whether national and international regulations are sufficient to prevent improper use. If international regulations are inadequate, molecular biologists and ecologists must consider the consequences of their research and advice beyond their own country to avoid unwanted impacts.
Genetic structure and reproduction dynamics of Salix reinii during primary succession on Mount Fuji, as revealed by nuclear and chloroplast microsatellite analysis
Authors: Lian Chunlan , Oishi Ryuya , Miyashita Naoya , Nara Kazuhide , Nakaya Hironobu , Wu Bingyun , Zhou Zhihua , Hogetsu Taizo
Published: March 2003

The early stage of volcanic desert succession is underway on the southeastern slope of Mount Fuji. We used markers of nuclear microsatellites (simple sequence repeats; SSR) and chloroplast microsatellites (cpSSR) to investigate the population genetic structure and reproduction dynamics of Salix reinii, one of the dominant pioneer shrubs in this area. The number of S. reinii genets in a patch and the area of the largest genet within the patch increased with patch area, suggesting that both clonal growth and seedling recruitment are involved in the reproduction dynamics of S. reinii. Five polymorphic cpSSR markers were developed for S. reinii by sequencing the noncoding regions between universal sequences in the chloroplast genome. Nineteen different cpSSR haplotypes were identified, indicating that S. reinii pioneer genets were created by the long‐distance dispersal of seeds originating from different mother genets around the study site, where all vegetation was destroyed during the last eruption. Furthermore, the clustered distributions of different haplotypes within each patch or plot suggested that newly colonized genets tended to be generated from seeds dispersed near the initially established mother genets. These results revealed that the establishment of the S. reinii population on the southeastern slope of Mount Fuji involved two sequential modes of seed dispersal: long‐distance dispersal followed by short‐distance dispersal.
Bayesian inferences on the recent island colonization history by the bird Zosterops lateralis lateralis
Authors: Estoup A. , Clegg S. M.
Published: March 2003

The founding of new populations by small numbers of colonists has been considered a potentially important mechanism promoting evolutionary change in island populations. Colonizing species, such as members of the avian species complex Zosterops lateralis, have been used to support this idea. A large amount of background information on recent colonization history is available for one Zosterops subspecies, Z. lateralis lateralis, providing the opportunity to reconstruct the population dynamics of its colonization sequence. We used a Bayesian approach to combine historical and demographic information available on Z. l. lateralis with genotypic data from six microsatellite loci, and a rejection algorithm to make simultaneous inferences on the demographic parameters describing the recent colonization history of this subspecies in four southwest Pacific islands. Demographic models assuming mutation–drift equilibrium or a large number of founders were better supported than models assuming founder events for three of four recently colonized island populations. Posterior distributions of demographic parameters supported (i) a large stable effective population size of several thousands individuals with point estimates around 4000–5000; (ii) a founder event of very low intensity with a large effective number of founders around 150–200 individuals for each island in three of four islands, suggesting the colonization of those islands by one flock of large size or several flocks of average size; and (iii) a founder event of higher intensity on Norfolk Island with an effective number of founders around 20 individuals, suggesting colonization by a single flock of moderate size. Our inferences on demographic parameters, especially those on the number of founders, were relatively insensitive to the precise choice of prior distributions for microsatellite mutation processes and demographic parameters, suggesting that our analysis provides a robust description of the recent colonization history of the subspecies.
Mitochondrial markers in the antLeptothorax rugatulusreveal the population genetic consequences of female philopatry at different hierarchical levels
Authors: Rüppell Olav , Strätz Michaela , Baier Bernd , Heinze Jürgen
Published: March 2003

Leptothorax rugatulus, an abundant North American ant, displays a conspicuous queen size polymorphism that is related to alternative reproductive tactics. Large queens participate mainly in mating flights and found new colonies independent of their mother colony. In contrast, small queens do not found new colonies independently, but seek readoption into their natal nest which results in multiple‐queen colonies (polygyny). Populations differ strongly in the ratio of small to large queens, the prevalent reproductive tactic and colony social structure, according to ecological parameters such as nest site stability and population density. This study compares the genetic structure of two strongly differing populations within the same mountain range. Data from microsatellites and mitochondrial DNA give no evidence for alien reproductives in polygynous colonies. The incidence of alien workers in colonies (as determined by mitochondrial haplotype) was low and did not differ between monogynous and polygynous colonies. We found significant population viscosity (isolation‐by‐distance) at the mitochondrial level in only the predominantly polygynous population, which supports the theoretical prediction that female philopatry leads to mtDNA‐specific population structure. Nuclear and mitochondrial genetic diversity was similar in both populations. The genetic differentiation between the two investigated populations was moderate at the mitochondrial level, but not significantly different from zero when measured with microsatellites, which corroborates limited dispersal of females (but not males) at a larger scale.
Biochemical basis of hyper‐recombinogenic activity of Pseudomonas aeruginosa RecA protein in Escherichia coli cells
Authors: Namsaraev Eugene A. , Baitin Dmitry , Bakhlanova Irina V. , Alexseyev Andrey A. , Ogawa Hideyuki , Lanzov Vladislav A.
Published: March 2003

The replacement of Escherichia coli recA gene (recAEc) with the Pseudomonas aeruginosa recAPa gene in Escherichia coli cells results in constitutive hyper‐recombination (high frequency of recombination exchanges per unit length of DNA) in the absence of constitutive SOS response. To understand the biochemical basis of this unusual in vivo phenotype, we compared in vitro the recombination properties of RecAPa protein with those of RecAEc protein. Consistent with hyper‐recombination activity, RecAPa protein appeared to be more proficient both in joint molecule formation, producing extensive DNA networks in strand exchange reaction, and in competition with single‐stranded DNA binding (SSB) protein for single‐stranded DNA (ssDNA) binding sites. The RecAPa protein showed in vitro a normal ability for cleavage of the E. coli LexA repressor (a basic step in SOS regulon derepression) both in the absence and in the presence (i.e. even under suboptimal conditions for RecAEc protein) of SSB protein. However, unlike other hyper‐recombinogenic proteins, such as RecA441 and RecA730, RecAPa protein displaced insufficient SSB protein from ssDNA at low magnesium concentration to induce the SOS response constitutively. In searching for particular characteristics of RecAPa in comparison with RecAEc, RecA441 and RecA803 proteins, RecAPa showed unusually high abilities: to be resistant to the displacement by SSB protein from poly(dT); to stabilize a ternary complex RecA::ATP::ssDNA to high salt concentrations; and to be much more rapid in both the nucleation of double‐stranded DNA (dsDNA) and the steady‐state rate of dsDNA‐dependent ATP hydrolysis at pH 7.5. We hypothesized that the high affinity of RecAPa protein for ssDNA, and especially dsDNA, is the factor that directs the ternary complex to bind secondary DNA to initiate additional acts of recombination instead of to bind LexA repressor to induce constitutive SOS response.