bluuebunny/crossref_metadata_2025 huggingface dataset:
Typing of artiodactyl MHC‐DRB genes with the help of intronic simple repeated DNA sequences
Authors: SCHWAIGER F.W. , BUITKAMP J. , WEYERS E. , EPPLEN J.T.
Published: April 2008

An efficient oligonucleotide typing method for the highly polymorphic MHC‐DRB genes is described for artiodactyls like cattle, sheep and goat. By means of the polymerase chain reaction, the second exon of MHC‐DRB is amplified as well as part of the adjacent intron containing a mixed simple repeat sequence. Using this primer combination we were able to amplify the MHC‐DRB exons 2 and adjacent introns from all of the investigated 10 species of the family of Bovidae and giraffes. Therefore, the DRB genes of novel artiodactyl species can also be readily studied. Oligonucleotide probes specific for the polymorphisms of ungulate DRB genes are used with which sequences differing in at least one single base can be distinguished. Exonic polymorphism was found to be correlated with the allele lengths and the patterns of the repeat structures. Hence oligonucleotide probes specific for different simple repeats and polymorphic positions serve also for typing across species barriers. The strict correlation of sequence length and exonic polymorphism permits a preselection of specific oligonucleotides for hybridization. Thus more than 20 alleles can already be differentiated from each of the three species.
Detection of highly polymorphic microsatellite loci in a species with little allozyme polymorphism
Authors: HUGHES C. R. , QUELLER D. C.
Published: April 2008

Microsatellite loci are regions of DNA containing tandem repeats of a short sequence motif; they occur abundantly in all eukaryotic genomes and have been shown to be a rich source of highly polymorphic genetic markers in humans and other mammals. These loci are particularly suitable for population studies because they can be relatively easily scored using a combination of polymerase chain reaction (PCR) amplification of each locus followed by electrophoresis to separate alleles. This paper details a method for finding these loci in any species. This method demonstrates that trinucleotide microsatellite loci are abundant and highly polymorphic in the social wasp Polistes annularis, whereas allozyme electrophoresis reveals very little polymorphism. The first six loci examined were all polymorphic with a mean observed heterozygosity of 0.62; in comparison average heterozygosity of 33 allozymes was 0.035. We suggest that this method can be used to detect variation where other methods have failed, making it an ideal tool for population and conservation geneticists who must deal with populations lacking other types of genetic variability.
Scientific principles for ecologically based risk assessment of transgenic organisms
Authors: REGAL P. J.
Published: April 2008

It is critical to base scientific risk assessment of genetically engineered organisms (GEOs) on appropriate scientific concepts. A variety of ‘generic safety’ models has now largely been recognized to have been based on outdated scientific thinking. One broad safety argument that is still used is that genetic engineering categorically is nothing but an extension of selective breeding. It is explained here, though, that the mechanisms and potentials of the two can be profoundly different. This does not mean that every GEO is ecologically dangerous; but some types of GEOs may be considerably more risky than what could be produced with selective breeding, especially when an ecologically competent host is supplemented with novel features that may increase its competitiveness. In addition, genetic ‘side effects’ raise food‐safety issues; and the possibility that they may sometimes increase ecological competitiveness cannot be ruled out, though this would be quite rare. Field plots have a proper use: to gather particular data that could be used in analysing the risks of commercial releases. But it is not scientific to call a small, confined, field population, isolated from potential competitors, a ‘test or release’ and then conclude that because ‘nothing happened’ the GEO will be safe when commercialized, or indeed that all GEOs will be safe.
Studying and managing the risk of cross‐fertilization between transgenic crops and wild relatives
Authors: KAREIVA P. , MORRIS W. , JACOBI C. M.
Published: April 2008

Drawing on field studies of pollen dispersal, we identify features of the hybridization process that need quantification. Our emphasis is on standardized measures, as opposed to the idiosyncratic and often anecdotal methods with which gene flow or out‐crossing data are currently reported. In addition to proposing specific maximum likelihood approaches, we summarize some results to date from small‐scale field trials that bear on the risks anticipated for large‐scale commercialization. We conclude that absolute containment of recombinant pollen or genes is unlikely if physical isolation is the only containment strategy. Because we conclude that the escape of transgenic pollen is inevitable, we argue that the focus of risk analysis should be shifted towards the ‘invasiveness’ of transgenic plants and ‘mitigation’ of their impact on natural, as well as agricultural systems.
The impact of hybrids between genetically modified crop plants and their related species: introgression and weediness
Authors: DARMENCY H.
Published: April 2008

Assessing the impact of hybrids between transgenic plants and nontarget wild species involves answering several questions such as: (i) what are the hybridization and introgression rates; (ii) what is the behaviour of a transgene in a wild population; and (iii) what will be the consequences of the expression of a transgene in a wild population? These issues are discussed using results from experiments on oilseed rape and wild related Brassiceae. Evidence is given of large variations in the estimates of cross‐fertilization probabilities. The first stage of introgression into wild populations is demonstrated to occur spontaneously through back‐crossing. Population analysis may also be valuable to detect traces of past introgression. Data from the literature on weed biology, and especially herbicide resistance, are used to illustrate the behaviour of a new gene in weed populations. The need for computer models simulating the introgression process is stressed.
The impact of hybrids between genetically modified crop plants and their related species: biological models and theoretical perspectives
Authors: GLIDDON C.
Published: April 2008

Forces affecting the rate of spread and increase of hybrids between genetically modified crop plants and their related species remain qualitatively similar, irrespective of whether genetic modification was achieved using traditional methods, those of biotechnology or as a result of the natural evolutionary process. However, the precise magnitude of the forces and, consequently, the likely environmental impact of such hybrids, may depend strongly on the nature of the gene or genes introduced into the native species. While many classes of transgenes are similar to those manipulated by conventional breeding techniques or evolution, biotechnology offers the potential to introduce genes into crops which are novel both from the point of view of function and origin. The qualitative similarity between transgenes and the products of conventional or evolutionary modification suggests that a historical view of the environmental impact of hybrids between traditionally produced crops or exotic species and their relatives would be of use in estimating the probable fate of hybrids containing transgenes in the environment. However, with certain classes of transgenes for which there are no existing analogues, there will need to be greater care in assessing the possible risks associated with release into the environment.
Differentiation of aphid clones by arbitrarily primed polymerase chain reaction (AP‐PCR) DNA fingerprinting
Authors: FUKATSU T. , ISHIKAWA H.
Published: April 2008

Differentiation of aphid clones was attempted using AP‐PCR which is a simple and rapid method to obtain DNA fingerprints of complex genomes. To establish optimal reaction conditions and examine reproducibility of the method, a laboratory‐maintained clone of the pea aphid, Acyrthosiphon pisum, was used as test material. Under the reaction conditions employed, identical fingerprint patterns were obtained throughout a wide range of template DNA amount, from 5 to 800 ng, and irrespective of aphid instar. No changes in the patterns were seen throughout five parthenogenetic generations. When this method was applied to a wild population of the gall‐forming aphid, Ceratovacuna nekoashi, five groups of insects originating from different galls formed on the same twig were successfully differentiated from one another by means of polymorphic fingerprint bands. In contrast, the fingerprints of the insects derived from the subgalls of the same gall were identical. These results indicated that in C. nekoashi: (i) members of a gall constitute a clonal population; (ii) a gall is founded by a single fundatrix; and (iii) intergall migration is absent or at least not frequent.
Population genetic structure of Yushania niitakayamensis (Bambusoideae, Poaceae) in Taiwan
Authors: HSIAO J.‐Y. , RIESEBERG L. H.
Published: April 2008

Yushania niitakayamensis is distributed in Taiwan, south‐west China and northern Philippines. In Taiwan, the species occurs in the central mountain ranges from 1500 to 3500 m in altitude. Morphological variation, especially in terms of plant height, is large, with plants ranging from 10 cm to 5 m in height. The species appears to spread mainly by rhizomes and flowers rarely, leading to the prediction that most populations are comprised of a single or a few clonal genotypes and that the observed morphological variation is primarily due to phenotypic plasticity. The purpose of the present study was to investigate the genetic structure of this species on Mt Hohuan in central Taiwan. Ten plants from a single clone and ten plants of unknown genetic background were surveyed at one site in order to select RAPD primers useful for clone identification. Plants at a second site were collected at 1‐m intervals across a 50‐m transect through the population. Plants at one extreme (exposed portion) of the transect were approximately 15–30 cm in height, whereas plants up to 410 cm in height were found at the other shaded end of the transect. Comparison of amplification profiles for 12 primers revealed that in contrast to our predictions of genetic uniformity, many samples had reproducibly different RAPD amplification profiles, with the 51 samples representing 31 clones. These data imply that the clone size is relatively small, and the population is actually highly diverse genetically. The genetic variation in this population may be due to a higher frequency of sexual reproduction during the evolutionary history of the species and/or a high somatic mutation rate for RAPD loci in clones of Yushania.
A molecular analysis of relationships and biogeography within a species complex of Holarctic fish (genus Osmerus)
Authors: TAYLOR E. B. , DODSON J. J.
Published: April 2008

Episodes of trans‐Arctic faunal exchange and isolation between the north Pacific and Atlantic ocean basins have been implicated as important historic geological events contributing to extant patterns of genetic diversity and structure in Holarctic faunas. We made a further test of the significance of such biogeographic events by examining mitochondrial DNA (mtDNA) restriction fragment length and cytochrome b sequence polymorphism among north Pacific and Arctic, north‐western Atlantic (north‐eastern North American), and north‐eastern Atlantic (European) regional forms of the boreal smelt, genus Osmerus. Our analyses also assessed whether the regional forms within this ‘species complex’: (i) represent a single widely distributed and polytypic species, or is composed of three geographically distinct species, and (ii) resulted from a single split from north Pacific ancestral Osmerus or two independent Pacific‐Atlantic divergences. MtDNA sequence divergence estimates among forms ranged from 5.6–8.9% and from 6.1–8.5% based on restriction fragment and 300 base pairs of cytochrome b sequencing, respectively. Divergence within forms averaged less than 0.5% for fragment analysis and no differences were detected from sequence analysis. Provisional dating of lineage separations in Osmerus based on our sequence divergence estimates suggested a mid‐Pliocene to early Pleistocene time frame for diversification among the forms. These estimated lineage separation dates support the idea that geological events in ‘Beringia’ and the surrounding trans‐Arctic area (e.g. opening of the Bering Seaway, Pleistocene glacial advances), occurring over a similar time frame, have influenced radiation in Osmerus. Phenetic and parsimony analyses of the sequence divergence estimates and of sequence polymorphisms suggested that the north Pacific/Arctic form and the northwestern Atlantic form shared a common ancestor more recently than either has with the north‐eastern Atlantic form, thus supporting the hypothesis that the species complex has arisen from two independent Pacific‐Atlantic divergences probably beginning during the mid‐Pliocene.
Differential expression of genes of Pseudomonas syringae on leaves and in culture evaluated with random genomic lux fusions
Authors: CIRVILLERI G. , LINDOW S. E.
Published: April 2008

Differential expression of genes of Pseudomonas syringae strain B728a on plants and in culture was assessed by measuring light production by a large collection of mutant strains containing random genomic insertions of a promoterless lux operon. Reporter gene fusions were made using Tn4431 containing luxCDABE from Vibrio fisheri. Light production reproducibly increased seven‐fold when n‐decanal was added to cells harvested from plant surfaces, to over 800‐fold when added to cells cultured on a solidified culture medium, thus increasing the sensitivity of this reporter gene system. One of the 173 mutants tested exhibited significantly higher light production on plants than on solidified culture media compared to other mutants, while one lux fusion‐containing strain produced significantly more light on culture media than on plants relative to the other mutants. The plant‐inducible genes identified were not required for pathogenicity of this strain. Approximately 2% of the genes of P. syringae are apparently transcribed more actively in cells growing epiphytically on plants than in common culture media indicating that bacterial cells on plants may have substantially different behaviours than that of cultured cells.
Mate fidelity and parentage in Cory's shearwater Calonectris diomedea ‐ field studies and DNA fingerprinting
Authors: SWATSCHEK I. , RISTOW D. , WINK M.
Published: April 2008

Field studies on Cory's shearwater Calonectris diomedea, which were carried out in a breeding colony in the Aegean Sea between 1989 and 1993, revealed that almost all breeding mates stay together over many consecutive years. Mates usually changed when one partner disappeared (e.g. through death), whereas ‘divorce’ occurred at a rate of 2.7%. Since birds are nesting at very close quarters, the potential for extrapair copulation (EPC) and subsequent extrapair fertilization (EPF) seems to be high. Multilocus DNA fingerprints were used to determine the true parentage of 46 offspring (broods contain a single chick only) from 29 pairs (few pairs were studied in two and three successive years). There were no cases of extrapair paternity.
Multilocus DNA fingerprinting detects population differentiation in the outbred and abundant fish species Poecilia latipinna
Authors: LAUGHLIN T. F. , TURNER B. J.
Published: April 2008

Several workers have suggested that multilocus multilocus variable number of tandem repeat (VNTR) based ‘DNA fingerprints’ are not useful in detecting differentiation among outbred populations. They suggest that the extremely high mutation rates and complexity associated with multilocus VNTR fragments make detection of interpopulation differences against a background of extremely high intrapopulation variation unlikely. This paper shows that DNA fingerprinting with the multilocus VNTR probes (GACA)4 and (CT)9 reveal significant population differences in VNTR frequencies between Florida and Georgia populations of the outbred, abundant and vagile fish species Poecilia latipinna. Differences in mutation rates among some VNTR loci may account for the ability to detect interpopulation differentiation with these probes. These results suggest that appropriate species/probe combinations would allow investigations of population structure on a microgeographical scale even in outbred species with multilocus VNTR probes where less‐sensitive techniques have failed.
Genetic variation of microsatellite loci in a bottlenecked species: the northern hairy‐nosed wombat Lasiorhinus krefftii
Authors: TAYLOR A. C. , SHERWIN W. B. , WAYNE R. K.
Published: April 2008

We investigate the utility of hypervariable microsatellite loci to measure genetic variability remaining in the northern hairy‐nosed wombat, one of Australia's rarest mammals. This species suffered a dramatic range and population reduction over the past 120 years and now exists as a single colony of about 70 individuals at Epping Forest National Park, central Queensland. Because our preliminary research on mitochondrial DNA and multilocus DNA fingerprints did not reveal informative variation in this population, we chose to examine variation in microsatellite repeats, a class of loci known to be highly polymorphic in mammals. To assess the suitability of various wombat populations as a reference for comparisons of genetic variability and subdivision we further analysed mitochondrial DNA cytochrome b sequence, using phylogenetic methods. Our results show that appreciable levels of variation still exist in the Epping Forest colony although it has only 41% of the heterozygosity shown in a population of a closely‐related species. From museum specimens collected in 1884, we also assessed microsatellite variation in an extinct population of the northern hairy‐nosed wombat, from Deniliquin, New South Wales, 2000 km to the south of the extant population. The apparent loss of variation in the Epping Forest colony is consistent with an extremely small effective population size throughout its 120‐year decline.
Hierarchical structure of mitochondrial DNA gene flow among humpback whales Megaptera novaeangliae, world‐wide
Authors: BAKER C. S. , SLADE R. W. , BANNISTER J. L. , ABERNETHY R. B. , WEINRICH M. T. , LIEN J. , URBAN J. , CORKERON P. , CALMABOKIDIS J. , VASQUEZ O. , PALUMBI S. R.
Published: April 2008

The genetic structure of humpback whale populations and subpopulation divisions is described by restriction fragment length analysis of the mitochondrial (mt) DNA from samples of 230 whales collected by biopsy darting in 11 seasonal habitats representing six subpopulations, or ‘stocks’, world‐wide. The hierarchical structure of mtDNA haplotype diversity among population subdivisions is described using the analysis of molecular variance (AMOVA) procedure, the analysis of gene identity, and the genealogical relationship of haplotypes as constructed by parsimony analysis and distance clustering. These analyses revealed: (i) significant partitioning of world‐wide genetic variation among oceanic populations, among subpopulations or ‘stocks’ within oceanic populations and among seasonal habitats within stocks; (ii) fixed categorical segregation of haplotypes on the south‐eastern Alaska and central California feeding grounds of the North Pacific; (iii) support for the division of the North Pacific population into a central stock which feeds in Alaska and winters in Hawaii, and an eastern or ‘American’ stock which feeds along the coast of California and winters near Mexico; (iv) evidence of genetic heterogeneity within the Gulf of Maine feeding grounds and among the sampled feeding and breeding grounds of the western North Atlantic; and (v) support for the historical division between the Group IV (Western Australia) and Group V (eastern Australia, New Zealand and Tonga) stocks in the Southern Oceans. Overall, our results demonstrate a striking degree of genetic structure both within and between oceanic populations of humpback whales, despite the nearly unlimited migratory potential of this species. We suggest that the humpback whale is a suitable demographic and genetic model for the management of less tractable species of baleen whales and for the general study of gene flow among long‐lived, mobile vertebrates in the marine ecosystem.
Species status and population genetic structure of the flightless chafer beetles Prodontria modesta and P. bicolorata (Coleoptera; Scarabaeidae) from South Island, New Zealand
Authors: EMERSON B. C. , WALLIS G. P.
Published: April 2008

This study uses isozyme electrophoresis to investigate the systematic status of two rare flightless chafer beetle species, Prodontria modesta and P. bicolorata, currently distinguished solely on the basis of colour. Seven polymorphic loci were analysed for the species in sympatry and allopatry. In sympatry, gene frequencies imply no genetic barrier between the two colour forms. Wright's hierarchical F‐statistics were calculated to determine how the genetic variation is partitioned across the geographic range of the two species. Strong geographic structuring occurs at the population level but there is little genetic differentiation attributable to species. Comparisons of morphological measurements are in support of the electrophoretic results. The systematic significance of the two distinct colour forms is thus questionable. Under the biological, recognition or phylogenetic species concepts, the genetic data suggest that there is only one species, polytypic for a colour pattern. Most of the genetic diversity of this group of beetles lies within and among populations, which differ quite markedly over their geographic range, rather than between the two named species.
DNA fingerprinting in Speke's gazelle: a test for genetic distinctness, and the correlation between relatedness and similarity
Authors: BUTLER M. A. , TEMPLETON A. R. , READ B.
Published: April 2008

In the absence of pedigree information, the determination of genetic distinctness of populations can only be made by genetic methods. Using DNA fingerprinting on the North American captive herd of Speke's gazelle Gazella spekei, we were able to address two hypotheses. First, two new individuals were found to have come from a genetically distinct population (P= 0.008, permutation test), and represent potential new founders to be added to the population. Secondly, genetic similarity was not significantly correlated with relatedness under extreme inbreeding and very close relationship (coefficient of relationship range 0.304‐0.717).
Genetic structure and mating system in the palila, an endangered Hawaiian honeycreeper, as assessed by DNA fingerprinting
Authors: FLEISCHER R. C. , TARR C. L. , PRATT T. K.
Published: April 2008

We conducted DNA fingerprinting analyses to ascertain the mating system and population genetic structure of the palila, an endangered Hawaiian honeycreeper, which occupies a fragmented range on the Mauna Kea volcano of the island of Hawai'i. DNA fingerprinting of twelve complete families from the Pu'u La'au population revealed no evidence of extrapair fertilization or intraspecific brood parasitism. Band‐sharing coefficients from fingerprints produced with two probes revealed that the large Pu'u La'au population on the southwest slope of Mauna Kea, and a smaller, geographically separate population on the east slope (at Kanakaleonui) had relatively high and virtually identical levels of minisatellite variability (mean S of 0.27 for each population based on combined data of M13 and Jeffreys 33.15 probes). The two populations also had nearly identical allele frequencies based on their mean corrected similarity, Sij, of 0.98. These data suggest that the two populations have not been fragmented long and/or have sufficient current gene flow to ameliorate any affects of genetic drift. We conclude that present levels of inbreeding are low within both populations, and that proposed translocations of individuals from Pu'u La'au to Kanakaleonui appear appropriate from a genetic standpoint.
Modelling problems in conservation genetics using Drosophila: consequences of fluctuating population sizes
Authors: WOODWORTH L. M. , MONTGOMERY M. E. , NURTHEN R. K. , BRISCOE D. A. , FRANKHAM R.
Published: April 2008

Many natural populations fluctuate widely in population size. This is predicted to reduce effective population size, genetic variation, and reproductive fitness, and to increase inbreeding. The effects of fluctuating population size were examined in small populations of Drosophila melanogaster of the same average size, but maintained using either fluctuating (FPS) or equal (EPS) population sizes.FPS lines were maintained using seven pairs and one pair in alternate generations, and EPS lines with four pairs per generation. Ten replicates of each treatment were maintained. After eight generations, FPS had a higher inbreeding coefficient than EPS (0.60 vs. 0.38), a lower average allozyme heterozygosity (0.068 vs. 0.131), and a much lower relative fitness (0.03 vs. 0.25). Estimates of effective population sizes for FPS and EPS were 3.8 and 7.9 from pedigree inbreeding, and 4.9 vs. 7.1 from changes in average heterozygosities, as compared to theoretical expectations of 3.3 vs. 8.0. Results were generally in accordance with theoretical predictions. Management strategies for populations of rare and endangered species should aim to minimize population fluctuations over generations.
Applications of mitochondrial DNA analysis in conservation: a critical review
Authors: MORITZ C.
Published: April 2008

Patterns of variation in mitochondrial DNA (mtDNA) increasingly are being investigated in threatened or managed species, but not always with clearly defined goals for conservation. In this review I identify uses of mtDNA analysis which fall into two different areas: (i) ‘gene conservation’ ‐ the identification and management of genetic diversity, and (ii) ‘molecular ecology’ ‐ the use of mtDNA variation to guide and assist demographic studies of populations. These two classes of application have different conceptual bases, conservation goals and time‐frames. Gene conservation makes extensive use of phylogenetic information and is, in general, most relevant to long‐term planning. Appropriate uses here include identification of Evolutionarily Significant Units and assessment of conservation priority of taxa or areas from an evolutionary perspective. Less appropriate are inferences about fitness from within‐population diversity and about species boundaries. Molecular ecology makes more use of allele frequencies and provides information useful for short‐term management of populations. Powerful applications are to identify Management Units and to define and use naturally occurring genetic tags. Estimating demographic parameters, e.g migration rate and population size, from patterns of mtDNA diversity is fraught with difficulty, particularly where populations are fluctuating, and is unlikely to produce quantitative estimates sufficiently accurate to be useful for practical management of contemporary populations. However, through comparative studies, mtDNA analysis can provide qualitative signals of population changes, allowing efficient targeting of resource‐intensive ecological studies. Thus, there are some relatively straightforward uses of mtDNA, preferably in conjunction with assays of nuclear variation, that can make a significant contribution to the long‐term planning and short‐term execution of species recovery plans.
Development of RAPD markers in two introduced fire ants,Solenopsis invictaandS. richteri, and their application to the study of a hybrid zone
Authors: SHOEMAKER D. DEWAYNE , ROSS K. G. , ARNOLD M. L.
Published: April 2008

We developed RAPD DNA markers useful in distinguishing the fire antsSolenopsis invictaandS. richteri.An initial survey of 200 primers revealed seven informative markers; family studies allowed us to determine expression patterns and to confirm Mendelian inheritance of these markers. The seven RAPD markers, one of which is inherited as a codominant marker, were employed along with three allozyme markers to describe the structure of a hybrid zone that has formed between the two species in the USA, where they have been introduced. The data suggest minor introgression of alleles from one parental species (S. richteri) into the other (S. invicta), which most likely reflects the documented recent movement of this hybrid zone. This pattern is interpreted as interspecific introgression rather than shared intraspecific polymorphism on the basis of comparisons with samples from native, non‐hybridizing populations in South America that lack such polymorphism. The data further reveal that the structure of the hybrid zone in the USA varies geographically. One parental species (S. invicta) and the hybrids exhibit a mosaic distribution in the east; a gradual transition between the parental species occurs in the centre, with a large intervening area of hybrid genotypes only; and there is apparent contact between parental populations with a small or no intervening zone of hybridization in the west. These differing patterns in the structure of the hybrid zone presumably reflect the unique histories of colonization in different parts of the range of introduced fire ants.
Phylogeny of mitochondrial DNA clones in tassel‐eared squirrels Sciurus aberti
Authors: WETTSTEIN P. J. , LAGER P. , JIN L. , STATES J. , LAMB T. , CHAKRABORTY R.
Published: April 2008

The tassel‐eared squirrel, Sciurus aberti, includes six subspecies which occupy restrictive and apparently identical habitats in Ponderosa pine forests in the south‐western United States and Mexico; the strict habitat requirement of this species is based on dietary requirements which are only fulfilled in these forests. To examine evolutionary relationships among certain subspecies of S. aberti, we obtained estimates of nucleotide diversity within subspecies as well as nucleotide divergence between subspecies using mitochondrial DNA (mtDNA) analysis. Restriction site polymorphisms were identified in samples of the four US subspecies: S. a. aberti (Abert), S. a. kaibabensis (Kaibab), S. a. ferreus (Ferreus), and S. a. chuscensis (Chuska) Fourteen mtDNA clones were resolved that were, with one exception, uniquely subspecific. Dendrograms constructed by neighbour‐joining and maximum parsimony methods revealed two major assemblages: (1) an Abert/Kaibab group; and (2) a Ferreus/Chuska group. The Abert vs. Ferreus clones exhibited the greatest net nucleotide divergence, with a lineage separation estimate approximating 572 000 years ago assuming a nucleotide substitution rate of 7.15 × 10‐9/year/site. Five out of ten Chuska squirrels shared a clone with one Abert sample; the relative sizes of these two populations and their respective ranges as well as their close proximity support the proposal for relatively recent intermixing of Abert and Chuska populations resulting in what appears to be Abert → Chuska migration. Nucleotide diversity within subspecies ranked as Kaibab < Ferreus < Abert < Chuska; the relatively high diversity for the Chuska sample is based on the apparent introgression of Abert mtDNA. The relative diversity exhibited by Kaibab, Ferreus and Aberti samples corresponds to the range size of the respective subspecies.
The establishment of a hybrid zone between red and sika deer (genusCervus)
Authors: ABERNETHY K.
Published: April 2008

Japanese sika deer (Cervus nippon nippon) were introduced to Scotland around 80 years (20 generations) ago. The sika phenotype is expanding its range and hybridizing extensively with native red deer (Cervus elaphus) leading to the establishment of a hybrid zone. This zone is currently moving and cannot be considered to be at equilibrium. Cervid genotypes and mitochondrial haplotypes were mapped across the sika phenotype range, using diagnostic protein isozymes, microsatellite nuclear DNA markers and RFLPs in mtDNA. These were analysed to estimate heterozygote deficits and nuclear linkage disequilibria and cytonuclear disequilibria in relation to gene frequencies and time since contact. Introgression was found in both taxa and strong linkage disequilibria and heterozygote deficits characterize the populations longest exposed to hybridization. Populations further from the introduction site, where hybridization is facilitated by the dispersal of sika‐like stags, show low values for linkage disequilibria and heterozygote deficit. The observed patterns in genotype are explained in terms of assortative mating and a selective advantage of the sika genotype. The genetic integrity of the Scottish mainland red deer is shown to be at risk from the invasion of sika.
Analysis of population genetic structure with RAPD markers
Authors: LYNCH M. , MILLIGAN B. G.
Published: April 2008

Recent advances in the application of the polymerase chain reaction make it possible to score individuals at a large number of loci. The RAPD (random amplified polymorphic DNA) method is one such technique that has attracted widespread interest. The analysis of population structure with RAPD data is hampered by the lack of complete genotypic information resulting from dominance, since this enhances the sampling variance associated with single loci as well as induces bias in parameter estimation. We present estimators for several population‐genetic parameters (gene and genotype frequencies, within‐ and between‐population heterozygosities, degree of inbreeding and population subdivision, and degree of individual relatedness) along with expressions for their sampling variances. Although completely unbiased estimators do not appear to be possible with RAPDs, several steps are suggested that will insure that the bias in parameter estimates is negligible. To achieve the same degree of statistical power, on the order of 2 to 10 times more individuals need to be sampled per locus when dominant markers are relied upon, as compared to codominant (RFLP, isozyme) markers. Moreover, to avoid bias in parameter estimation, the marker alleles for most of these loci should be in relatively low frequency. Due to the need for pruning loci with low‐frequency null alleles, more loci also need to be sampled with RAPDs than with more conventional markers, and some problems of bias cannot be completely eliminated.
Paternity exclusion by DNA fingerprinting, and mate guarding in the hooded seal Cystophora cristata
Authors: McRAE S. B. , KOVACS K. M.
Published: April 2008

Hooded seal Cystophora cristata trios consist of an adult female, her pup, and an attending adult male. Using DNA fingerprinting, we excluded the possibility that the attending males within hooded seal trios were the fathers of the pups, proving that these hooded seals did not remain paired from one breeding season to the next. Behavioural observations of the trios after capture and release revealed that male hooded seals displace one another in attending nursing females. Mate guarding appears to be the preferred mating strategy available to male hooded seals given intense competition for females, a very brief nursing period, and oestrus occuring soon after weaning, but its effectiveness remains unclear.
Identification of kin structure among Guam rail founders: a comparison of pedigrees and DNA profiles
Authors: HAIG S. M. , BALLOU J. D. , CASNA N. J.
Published: April 2008

Kin structure among founders can have a significant effect on subsequent population structure. Here we use the correlation between DNA profile similarity and relatedness calculated from pedigrees to test hypotheses regarding kin structure among founders to the captive Guam rail (Rallus owstoni) population. Five different pedigrees were generated under the following hypotheses: (i) founders are unrelated; (ii) founders are unrelated except for same‐nest chicks; (iii) founders from the same major site are siblings; (iv) founders from the same local site are siblings; and (v) founders are related as defined by a UPGMA cluster analysis of DNA similarity data. Relatedness values from pedigrees 1, 2 and 5 had the highest correlation with DNA similarity but the correlation between relatedness and similarity were not significantly different among pedigrees. Pedigree 5 resulted in the highest correlation overall when using only relatedness values that changed as a result of different founder hypotheses. Thus, founders were assigned relatedness based on pedigree 5 because it had the highest correlations with DNA similarity, was the most conservative approach, and incorporated all field data. The analyses indicated that estimating relatedness using DNA profiles remains problematic, therefore we compared mean kinship, a measure of genetic importance, with mean DNA profile similarity to determine if genetic importance among individuals could be determined via use of DNA profiles alone. The significant correlation suggests this method may provide more information about population structure than was previously thought. Thus, DNA profiles can provide a reasonable explanation for founder relatedness and mean DNA profile similarity may be helpful in determining relative genetic importance of individuals when detailed pedigrees are absent.
DNA fingerprinting reveals significant amounts of genetic variation in a wild raspberry Rubus idaeus population
Authors: ANTONIUS K. , NYBOM H.
Published: April 2008

Establishing the genotypic distribution in natural plant populations is an important part of ecological studies concerning plant growth, reproduction and turn‐over. Restriction enzyme‐digested DNA samples, isolated from 24 plants of a natural Rubus idaeus population, were analysed with DNA fingerprinting using the M13 repeat sequence as well as a synthetic (AC)/(TG) polydinucleotide as hybridization probes. All the examined samples exhibit unique DNA fingerprint patterns, suggesting that vegetative reproduction may be considerably more restricted in wild R. idaeus populations than previously assumed. By comparison, all samples of the apomictic blackberry species Rubus nessensis, collected on the same location, were completely identical.
The local distribution of highly divergent mitochondrial DNA haplotypes in toque macaques Macaca sinica at Polonnaruwa, Sri Lanka
Authors: HOELZER G. A. , DITTUS W. P. J. , ASHLEY M. V. , MELNICK D. J.
Published: April 2008

Surveys of mitochondrial DNA (mtDNA) variation in macaque monkeys have revealed extremely high levels of intraspecific divergence among haplotypes. One consistent pattern that has emerged from these studies is that divergent haplotypes are geographically segregated so that sampling a few matrilines from a given region shows them to be identical, or a closely related subset of haplotypes. Geographically structured mtDNA variation has also been commonly observed in other taxa. In this study, haplotype variation and distribution are studied in detail within a local population of toque macaques. The results show that highly divergent haplotypes, differing by 3.1% in their nucleotide sequences, coexist in this population and that they may be spatially segregated even on this micro‐geographic scale. Furthermore, these differences are maintained between social groups that exchange male migrants, and thus nuclear genes, frequently.
Fluorescent Pseudomonas species categorized by using polymerase chain reaction (PCR)/restriction fragment analysis of 16S rDNA
Authors: LAGUERRE G. , RIGOTTIER‐GOIS L. , LEMANCEAU P.
Published: April 2008

A rapid procedure for the identification of fluorescent pseudomonads, based on the polymerase chain reaction (PCR) and restriction fragment analysis of 16S rDNA genes is described. Thirty‐one strains belonging to 10 different Pseudomonas species of the Pseudomonas fluorescens rRNA branch were characterized. Amplified rDNA was digested with 13 different restriction endonucleases. The combined data from restriction analysis enabled the definition of 17 different 16S rDNA genotypes. All type strains belonging to different species were differentiated. The good correlation between grouping obtained using restriction analysis with other molecular classification criteria demonstrates the value of the described method to characterize rapidly fluorescent Pseudomonas strains at the species level.
Molecular biogeography of clonal lineages in a high‐Arctic apomictic Daphnia complex
Authors: WEIDER L. J. , HOBAEK A.
Published: April 2008

An electrophoretic survey of 81 populations of arctic Daphnia pulex from around the Svalbard archipelago revealed the presence of 49 unique allozyme clones (N= 3357). Two closely related clones accounted for 66% of the total sample, and were widespread across the archipelago. Restriction fragment length polymorphisms (RFLPs) of a 2.1‐kb fragment of mtDNA (NADH‐4 and NADH‐5 subunits), amplified using the polymerase chain reaction (PCR), revealed the presence of eight mtDNA haplotypes. One haplotype was particularly widespread, and the two most abundant allozyme clones shared this haplotype. Nonrandom distribution patterns of clones were observed, and are most likely the result of historical events (i.e. founder effects) related to the past glacial history of the archipelago. The data are discussed with reference to past glaciation events, and attempts are made to discern the colonization history of this apomictic complex.
Genetic differentiation inHippocrepis emerus(Leguminosae): allozyme and DNA fingerprint variation in disjunct Scandinavian populations
Authors: Lönn M. , Prentice H. C. , Tegelström H.
Published: April 2008

The structure of genetic variation in disjunct Scandinavian populations ofHippocrepis emeruswas studied using allozymes and DNA fingerprinting. Variation in the three native regional populations in Scandinavia was compared with that in a recently introduced population in Sweden. In contrast to the recently introduced population, the native Scandinavian isolates ofH. emerusshowed high levels of allozyme fixation and low levels of DNA diversity. Variation in allozymes and at DNA fingerprint loci showed closely congruent patterns of geographic variation, with pronounced differentiation between the native Norwegian and Swedish isolates of the species. The structure of genetic variation in native ScandinavianH. emerusis interpreted in terms of historical population bottlenecks and founder events during the species' postglacial immigration into Scandinavia.
Postglacial expansion and genome subdivision in the European grasshopper Chorthippus parallelus
Authors: Cooper S. J. B. , Ibrahim K. M. , Hewitt G. M.
Published: April 2008

A noncoding nuclear DNA marker sequence (Cpnl‐1) was used to investigate subdivision in the grasshopper Chorthippus parallelus and deduce postglacial expansion patterns across its species range in Europe. Investigation of the spatial distribution of 71 Cpnl‐1 haplotypes and estimation of levels of genetic differentiation (KST values) between populations and geographic regions provided evidence for subdivision of C. parallelus into at least five major geographic regions and indicated that the French form of C. parallelus originated after range expansion from a Balkan refugium, Further evidence for subdivision of C. parallelus between Italy and northern Europe suggests that the Alps may have formed a significant barrier to gene flow in this grasshopper.
Generation of RAPD‐PCR primers for the identification of isolates of Glomus mosseae, an arbuscular mycorrhizal fungus
Authors: Lanfranco L. , Wyss P. , Marzachi C. , Bonfante P.
Published: April 2008

Mycorrhizal fungi are usually identified on the basis of the morphological characters shown by fruit bodies, spores, vegetative mycelia or symbiotic structures. The development of molecular techniques provides a valuable and alternative approach to identify mycorrhizal fungi, especially when it is difficult to gather a sufficient number of data on morphological features. Short arbitrary oligonucleotides were used as primers for the amplification of genomic DNA extracted from spores of arbuscular fungi. The RAPD fingerprints showed banding patterns which allowed us to distinguish between species and even isolates within Glomales. In order to identify mycorrhizal fungi during their symbiotic phase, a nonpolymorphic RAPD band identified as marker for some isolates of Glomus mosseae was purified from agarose gels and cloned in a bluescript vector. The fragment was sequenced and specific primers (PO‐M3) were designed for the mycorrhizal fungus. They specifically and successfully amplified the DNA not only from G. mosseae spores, but also from roots of pea, clover, leek and onion plants when they were colonized by G. mosseae isolates.
Monoandry and polyandry in bumble bees (Hymenoptera; Bombinae) as evidenced by highly variable microsatellites
Authors: Estoup A. , Scholl A. , Pouvreau A. , Solignac M.
Published: April 2008

Highly variable microsatellites enabled a precise assessment of the number of queen matings in the colonies of five bumble bee species. Fifteen of the sixteen microsatellites initially cloned from B. terrestris had flanking regions similar enough to allow PCR amplification on the other Bombus species analysed. The microsatellites selected for intracolony study (four per species) were characterized by a high heterozygosity (0.58–0.93) and a large number of alleles (3–18) in the local populations from which the colonies originated. A single male appeared to have inseminated the queens in the colonies of four species, B. terrestris, B. lucorum, B. lapidarius and B. pratorum, which belong to three subgenera, whereas two of the three analysed colonies of B. hypnorum were polyandrous (minimum number of two and four patrilines, respectively).
Parentage analysis within a semi‐free‐ranging group of Barbary macaques Macaca sylvanus
Authors: von SEGESSER F. , SCHEFFRAHN W. , MARTIN R. D.
Published: April 2008

This study of a group of semi‐free‐ranging Barbary macaques Macaca sylvanus aimed to determine paternity, to establish whether any individual male achieved prominent mating success and to assess genetic variability. Analyses involved electrophoresis of 15 blood protein systems and multilocus DNA fingerprinting (isotopic and nonisotopic). Genetic variability was low; only two blood protein systems were polymorphic. Although all DNA‐fingerprints were individual‐specific, they showed a high average band‐sharing index value (0.67). Nevertheless, a combination of all methods permitted inference of paternity in 11 out of 15 (73%) cases tested. Several males from different age classes fathered infants.