bluuebunny/crossref_metadata_2025 huggingface dataset:
Simple sequence repeats provide a direct estimate of pollen‐mediated gene dispersal in the tropical tree Gliricidia sepium
Authors: Dawson I. K. , Waugh R. , Simons A. J. , Powell W.
Published: November 2003

An understanding of the processes that determine the observed patterns of genetic variation in natural plant populations is an important factor in the management of biodiversity. Pollen‐mediated gene dispersal is recognized as a major determinant of population genetic structure. Here, the utility of simple sequence repeat (SSR) analysis was investigated for the measurement of pollen‐mediated gene transfer by paternity exclusion in a restricted, fragmented and endangered population of the insect‐pollinated tropical leguminous tree Gliricidia sepium located in Guatemala. Data at a single SSR locus, which revealed six allelic variants, were employed to generate minimum distance curves of pollen dispersal. Combined data from all six alleles indicated that a minimum of 1.8% of transfer events occurred over a distance of greater than 75 m. However, this value represents an underestimate because of the exclusion approach employed for analysis. Considering the four rarest alleles in the population only (combined frequency = 0.196), which provides a less biased indicator of gene transfer, a minimum of 6.1% of pollen movements could be attributed to greater than 75 m. One extreme example of gene transfer of over 275 m was recorded. Estimates of pollen transfer suggest a homogenizing effect on genetic structure over the spatial scale of the study population and provide an important indicator for the genetic management of natural and exotic stands of G. sepium. This study provides the first example of SSR analysis being employed to estimate directly pollen movement in a natural stand of any tree species.
Patterns of differentiation among wild rabbit populations Oryctolagus cuniculus L. in arid and semiarid ecosystems of north‐eastern Australia
Authors: Fuller S. J. , Wilson J. C. , Mather P. B.
Published: November 2003

Feral rabbit populations in Australia have generally been managed using localized control procedures. While these procedures may result in local extinctions, persistence of populations will depend on the probability of recolonization. Genetic markers developed using temperature gradient gel electrophoresis (TGGE) combined with heteroduplex analysis (HA) of mitochondrial DNA (mtDNA) were used to characterize the degree of subdivision and extent of gene flow within and among rabbit populations distributed over large distances (up to 1000 km) in southern Queensland (QLD) and north‐west New South Wales (NSW), Australia. TGGE analyses revealed significant heterogeneity in mtDNA control region haplotype frequencies. From heterogeneity χ2 tests, it was evident that the differentiation observed was largely attributable to five sites which were located in the semiarid eastern region, whereas haplotype frequencies were homogeneous throughout the arid western region. These results suggest that there are independent population systems within the study area. The extent of gene flow among local populations within each system is related to the spatial configuration of acceptable habitat patches and the persistence of the populations is determined by the probability of recolonization following local extinction. These data suggest that to provide better overall control of rabbit populations, different management strategies may be necessary in arid and semiarid ecosystems. In arid south‐west QLD and north‐west NSW, where extensive gene flow occurs over large distances, rabbit populations should be managed at a regional level. In semiarid eastern QLD, where gene flow is restricted and populations are more isolated, localized control procedures may provide effective short‐term relief. These results indicate that in nonequilibrium systems with patchy distribution of individuals, the interpretation of migration rate from estimates of gene flow obtained using existing genetic models must include an understanding of the spatial and temporal scales over which population processes operate.
Genetic analysis of brown‐headed cowbirds Molothrus ater raised by different hosts: data from mtDNA and microsatellite DNA markers
Authors: Gibbs H. L. , Miller P. , Alderson G. , Sealy S. G.
Published: November 2003

Ecological and behavioural data suggest that female brood parasitic brown‐headed cowbirds Molothrus ater are host generalists; this predicts that there should be no genetically differentiated host races within cowbird populations. We tested this hypothesis by comparing differentiation in two rapidly evolving DNA markers (mtDNA control region sequence and nuclear DNA microsatellite loci) among unrelated cowbird chicks raised by two ecologically distinct hosts. No differentiation was observed in either marker supporting the absence of host race hypothesis.
Population substructure in Alkanna orientalis (Boraginaceae) in the Sinai Desert, in relation to its pollinator behaviour
Authors: Wolff K. , El‐Akkad S. , Abbott R. J.
Published: November 2003

Subpopulation genetic structure was studied in a population of the short‐lived perennial plant Alkanna orientalis from the Sinai Desert, Egypt. The population investigated was subdivided for sampling into four subpopulations, which were located within three steep‐sided wadis and a central plain area. Results from previous studies suggested that bee pollinator behaviour was likely to cause limited gene dispersal within the population and that subpopulations might have diverged from each other genetically. Seven RAPD primers were used to detect polymorphisms in the population. Differences between sub‐populations in fragment frequency were found for several of the 45 polymorphic RAPD fragments scored. Population subdivision was evident from cluster analysis, and an analysis of genetic distances showed that there was significant genetic differentiation between all subpopulations. Nevertheless, more extensive gene flow appears to take place within the population than was expected, as demonstrated by a higher level of genetic similarity between subpopulations from two of the narrow wadis and the interconnecting plain. It is suggested that seed transport mediated by periodic flash floods is responsible for this pattern.
Analysis of microsatellite DNA from old scale samples of Atlantic salmon Salmo salar: a comparison of genetic composition over 60 years
Authors: Nielsen E. E. , Hansen M. M. , Loeschcke V.
Published: November 2003

Microsatellite analysis was applied to scale samples of Atlantic salmon collected up to 60 years ago. Samples from the 1930s, from a now endangered Danish population, were compared with recent samples (1989), to test if the present population consists of descendants from the original one. Allele frequencies had changed over time, but individuals from the two samples caught about 60 years apart clustered together when compared with the closest neighbouring population and another reference population. However, fewer alleles were detected in the recent sample from the endangered population, most likely due to a population bottleneck or sampling artefacts.
The microevolution of the Galápagos marine iguana Amblyrhynchus cristatus assessed by nuclear and mitochondrial genetic analyses
Authors: Rassmann K. , Tautz D. , Trillmich F. , Gliddon C.
Published: November 2003

Marine iguanas may have inhabited the Galápagos archipelago and its former, now sunken islands for more than 10 million years (Myr). It is therefore surprising that morphological and immunological data indicate little evolutionary divergence within the genus. We utilized mitochondrial DNA (mtDNA) sequence analyses and nuclear DNA fingerprinting to re‐evaluate the level and pattern of genetic differentiation among 22 marine iguana populations from throughout the archipelago. Both genetic marker systems detect a low level of within‐genus divergence, but they show contrasting levels of geographical subdivision among the populations. The mitochondrial gene pools of populations from different regions of the archipelago are isolated, and the mtDNA pattern appears to follow the sequence in which the islands were colonized by marine iguanas. Conversely, the nuclear DNA study indicates substantial interpopulational gene exchange, and the geographical distribution of the nuclear markers seems to be determined by isolation by distance among the populations. The natural history of marine iguanas suggests that the contrasting nuclear and mitochondrial DNA patterns result from an asymmetric migration behaviour of the two sexes, with higher (active and passive) interisland dispersal for males than females. Separate genetic analyses for the sexes appear to support this hypophesis. Based on these findings, a scenario is proposed that explains the marine iguanas' low genetic divergence, notwithstanding their long evolutionary history in the Galápagos archipelago.
Phylogenetic evidence of mitochondrial DNA introgression among pocket gophers in New Mexico (family Geomyidae)
Authors: Ruedi M. , Smith M. F. , Patton J. L.
Published: November 2003

Mitochondrial DNA (mtDNA) variation in the cytochrome b gene was determined for two divergent taxa of pocket gophers, Thomomys bottae actuosus and T. b. ruidosae. These two taxa hybridize in a narrow contact zone, but introgression of nuclear markers such as allozymes or chromosomes does not extend much beyond the hybrid zone (Patton et al. 1979). We found that despite their distinctness, the two subspecies shared very similar mtDNA haplotypes. By a comparison of phylogenetic histories derived from nuclear markers (allozymes) and from mtDNA haplotypes sampled in different populations of T. bottae from New Mexico, we show that apparent similarity is due to an introgression of T. b. ruidosae mtDNA into T. b. actuosus nuclear background. Evidence of introgression is not limited to the present‐day contact zone between these two taxa, but extends at least 75 km away from it. The actuosus haplotype coexists along with the ruidosae mtDNA in the Gallinas Mts., which are inhabited by otherwise pure T. b. actuosus, while further north only typical actuosus haplotypes were detected. Of several potential mechanisms which could lead to such a geographical pattern of variation, we argue that a combination of range shifts due to climatic fluctuations, and genetic drift are most likely. Horizontal gene transfers due to hybridization are historical events which seem rather common among pocket gophers. Although they can be identified with careful phylogenetic study using independent data sets, the potential for misinterpreting a gene tree as an organismal tree is great in this and other groups of animals.
Genetic variation at allozyme and RAPD loci in sessile oak Quercus petraea (Matt.) Liebl.: the role of history and geography
Authors: Le Corre V. , Dumolin‐Lapègue S. , Kremer A.
Published: November 2003

The nuclear genetic variation within and among 21 populations of sessile oak was estimated at 31 RAPD loci in conjunction with previous estimates of variation at eight allozyme loci. The aim of the study was to assess the relative role of isolation‐by‐distance and postglacial history on patterns of nuclear variation. Because of its small effective population size and maternal transmission, the chloroplast genome is a good marker of population history. Both kinds of nuclear variation (RAPD and allozyme) were therefore compared, first, to the geographical distances among populations and, secondly, to chloroplast DNA restriction polymorphism in the same populations. Multiple Mantel tests were used for this purpose. Although RAPDs revealed less genetic diversity than allozymes, levels of genetic differentiation (GST) were identical. The standard genetic distance calculated at all RAPD loci was correlated with geographical distances but not with the genetic distance calculated from chloroplast DNA data. Conversely, allozyme variation was correlated with chloroplast DNA variation, but not with geography. Possibly, divergent selection at two allozyme loci during the glacial period could explain this pattern. Because of its greater number of loci assayed, RAPDs probably provided a less biased picture of the relative role of geography and history.
Analysis of genetic diversity in common loon Gavia immer using RAPD and mitochondrial RFLP techniques
Authors: Dhar A. K. , Pokras M. A. , Garcia D. K. , Evers D. C. , Gordon Z. J. , Alcivar‐Warren A.
Published: November 2003

We used random amplified polymorphic DNA (RAPD) and restriction fragment length polymorphisms (RFLP) of mitochondrial cytochrome b (cyt b) gene to evaluate the genetic diversity in common loon Gavia immer populations from two regions in the United States: New England (NE) and Michigan (MI). RAPD analysis with 18 primers showed 74% polymorphism in NE and 50% in MI loons (similarity coefficient F= 0.92). Although no population‐specific markers were found, the frequencies of some RAPD bands varied between the two populations suggesting geographical differences. RFLP analyses with BamHI enzyme and a 307‐bp mitochondrial cyt b gene showed four haplotypes in the NE loon samples and two in the MI samples. The mtDNA haplotype diversity was 0.74 for NE and 0.51 for MI loons, supporting the RAPD data that NE loons have greater genetic diversity than MI loons.
Multilocus DNA fingerprints in the plant Cynoglossum officinale L. and their use in the estimation of selfing
Authors: Vrieling K. , Saumitou‐Laprade P. , Meelis E. , Epplen J. T.
Published: November 2003

We have developed a nonradioactive oligonucleotide multilocus DNA fingerprinting method for Cynoglossum officinale. Of the 19 probes tested, six probes yielded banding patterns for all restriction enzymes used. All but one of the informative probes are repeats with a four‐base motif. Approximately 60% of the loci appeared to be polymorphic. The sensitivity of the nonradioactive method was equal to that of the radioactive method. In addition, a new simple calculation method is presented to estimate selfing rates and approximate 95% confidence limits from the DNA fingerprint profiles avoiding ‘between‐gel’ comparisons. The selfing rates differed significantly (as determined from 95% confidence intervals) between naturally pollinated individuals of C. officinale within the experimental population. The estimates ranged from 0 to 70% selfing.
Indo‐West Pacific patterns of genetic differentiation in the high‐dispersal starfish Linckia laevigata
Authors: Williams S. T. , Benzie J. A. H.
Published: November 2003

Genetic variation in four natural populations of the starfish Linckia laevigata from the Indo‐West Pacific was examined using restriction fragment analysis of a portion of the mtDNA including the control region. Digestion with seven restriction enzymes identified 47 haplotypes in a sample of 326 individuals. Samples collected from reef sites within each location were not significantly differentiated based on ΦST or spatial distribution of haplotypes, indicating that dispersal is high over short to moderate distances. Evidence of gene flow is further supported by the low divergence among haplotypes and the lack of any clear geographical structuring among different haplotypes in the gene phylogeny. However, analysis of molecular variance (AMOVA), ΦST and contingency χ2 analyses of the spatial distribution of haplotypes demonstrate the presence of significant broad scale population genetic structure among the four widespread locations examined. RFLP data are consistent with high gene flow between the Philippines and Western Australia and moderate gene flow between the Great Barrier Reef (GBR) and Fiji, but only limited gene flow between either the Philippines or Western Australia and either the GBR or Fiji. The presence of mtDNA structure contrasts with previous allozyme data which suggest that dispersal among widely separated locations is equivalent to dispersal among populations within the highly connected GBR studies. This discordance between patterns of gene flow inferred from these two markers cannot be fully accounted for by differences in effective population size for mtDNA. This might suggest that while mtDNA variation may represent contemporary patterns of gene flow, allozyme variation among populations is yet to reach equilibrium between drift and migration over the range surveyed.
Molecular evidence for an extinct parent of the tetraploid species Microseris acuminata and M. campestris (Asteraceae, Lactuceae)
Authors: Roelofs D. , Van Velzen J. , Kuperus P. , Bachmann K.
Published: November 2003

To determine the origin of the tetraploid annuals Microseris campestris and M. acuminata, chloroplast RFLP, RAPD and ITS sequence variability among nine populations of the two polyploids and 14 populations of the diploid annuals M. elegans and M. douglasii have been surveyed. Previously described variable chloroplast restriction sites infer M. douglasii as the possible maternal parent of both tetraploid species. However, the chloroplast genome typical for M. douglasii has now also been found in some plants of M. elegans. RAPD analysis revealed 172 polymorphic DNA markers that defined all four species as genetically distinct groups, but demonstrated closer associations between M. douglasii and M. acuminata, and between M. elegans and M. campestris. Sequencing of the ITS‐1 and ITS‐2 region yielded 73 phylogenetically informative sites. Thirty base‐pair mutations separated the annual Microseris species from the outgroup, Uropappus lindleyi. The putative interspecific allotetraploid M. campestris contained only one type ITS sequence that, on the basis of eight synapomorphic substitutions was derived from M. elegans. The single ITS of M. acuminata shares six common sites with M. douglasii. Surprisingly, six sites were synapomorphic for the two tetraploids, M. campestris and M. acuminata, suggesting recombination within the ITS of both species with that of a common, now extinct, parental taxon, possibly the donor of the M. douglasii type chloroplasts found in both tetraploids. These results confirm the interpretation of M. campestris as derived from M. douglasii (extinct population) and M. elegans, and resolve the unknown origin of M. acuminata as an intraspecific hybrid between two very distinct populations of M. douglasii, one of them the same extinct M. douglasii form that contributes to M. campestris.
Micro‐ and macrogeographical genetic structure of colonies of naked mole‐rats Heterocephalus glaber
Authors: Faulkes C. G. , Abbott D. H. , O'Brien H. P. , Lau L. , Roy M. R. , Wayne R. K. , Bruford M. W.
Published: November 2003

Patterns of genetic structure in eusocial naked mole‐rat populations were quantified within and among geographically distant populations using multilocus DNA fingerprinting and mitochondrial DNA (mtDNA) sequence analysis. Individuals within colonies were genetically almost monomorphic, sharing the same mtDNA control region haplotype and having coefficients of band sharing estimated from DNA fingerprints ranging from 0.93 to 0.99. Family analysis of a hybrid captive colony of naked mole‐rats with increased levels of genetic variability using multilocus DNA fingerprinting gave results consistent with Mendelian inheritance, and has revealed for the first time that multiple paternity can occur. In a survey of wild colonies from Ethiopia, Somalia and locations in northern and southern Kenya, we have examined mtDNA control region sequence variation in 42 individuals from 15 colonies, and together with multilocus DNA fingerprinting and mtDNA cytochrome‐b sequence analysis in selected individuals have shown that these populations show considerable genetic divergence. Most of the variance in sequence divergence was found to be between geographical locations (Φct= 0.68) and there was a significant correlation between sequence divergence and geographical separation of haplotypes. Six colonies from Mtito Andei in southern Kenya shared the same control region haplotype, suggesting a recent common maternal ancestor. In contrast, out of four colonies at Lerata in north Kenya, three haplotypes were identified, and phylogenetic analysis suggests that this area may be a zone where two distinct lineages are in close proximity. Genetic distances were maximal between Ethiopian and southern Kenyan populations at 5.8% for cytochrome‐b, and are approaching interspecific values seen between other Bathyergids.
Inheritance of RAPD molecular makers in lake trout Salvelinus namaycush
Authors: Stott W. , Ihssen P. E. , White B. N.
Published: November 2003

Inheritance patterns of randomly amplified polymorphic DNA (RAPD) phenotypes were tested in 13 full‐sib families of lake trout Salvelinus namaycush. Single‐pair matings of parents with known phenotypes were made, and up to 20 progeny of each mating were used to test inheritance patterns. Seven RAPD primers amplified 13 polymorphic bands. With the exception of one family, expected segregation ratios for dominant Mendelian genetic traits were observed. Our results support previously reported findings that RAPD markers can be considered Mendelian traits and therefore could be used for analysis of genetic population structure.
Interspecific microsatellite markers for the study of pinniped populations
Authors: Gemmell N. J. , Allen P. J. , Goodman S. J. , Reed J. Z.
Published: November 2003

Microsatellites have rapidly become the marker of choice for a wide variety of population genetic studies. Here we describe 20 pinniped microsatellite markers which have been tested across 18 pinniped species. The majority of these markers have broad utility in all pinnipeds and provide a strong base for detailed population genetic studies in the Pinnipedia.
General vs. local differentiation between two closely related white oak species
Authors: Bodénès C. , Labbé T. , Pradère S. , Kremer A.
Published: November 2003

The geographical distribution of species differentiation throughout the natural range of two sympatric, closely related species of oaks, Quercus petraea (Matt) Liebl. and Quercus robur L., was investigated. By sampling species in pairs in different European regions, from Spain to Poland and Romania, the differentiation between the two species could be subdivided into general and local differentiation. Nine sequence characterized amplified region (SCAR) markers corresponding to genomic regions which discriminate the two species were analysed using single‐strand conformation polymorphism (SSCP) or classical electrophoresis (double‐stranded DNA on agarose gel) on PCR products providing, respectively, codominant and dominant markers. Similar levels of gene diversity (HE) within the two species were observed, varying generally from 0.3 to 0.5 for dominant markers and from 0.5 to 0.86 for codominant markers. SSCP loci exhibited numerous alleles that were differently involved in species differentiation. The geographical distribution of species differentiation is heterogeneous between the regions, the north‐east populations exhibiting higher differentiation than the others. For most loci, general differentiation was higher than local differentiation and was interpreted as the result of historical causes, selection pressures, and intra‐ and interspecific gene flow.
The clonal and population structure of a rare endemic plant, Wyethia reticulata (Asteraceae): allozyme and RAPD analysis
Authors: Ayres D. R. , Ryan F. J.
Published: November 2003

Genetic structure arises when limited gene flow between populations favours the development of distinct arrays of genetic characters within each population. Determining the spatial scale at which this differentiation occurs is critical to our understanding of population biology and microevolution of species. The genetic structure and spatial pattern of genetic variation in an endemic, clonal perennial, Wyethia reticulata E. Greene, was investigated using random amplified polymorphic DNA (RAPD) markers and allozyme alleles. Large stands (250–360 m2) were found to contain few genetic individuals. Despite the small population sizes and endemism of the species, W. reticulata was highly diverse genetically, with most of the variation (75–81%) distributed within populations. A population structure in full agreement with spatially defined populations was achieved only by combining RAPD and allozyme markers. Analysis using both types of markers appeared to provide estimates of genetic similarity between individuals that were most consistent with empirical data on plant distributions. We postulated that large, long‐lived clones dominated genetic relationships within populations but also provided opportunities for gene flow between populations on a longer time scale. The two marker types yielded different estimates of between‐individual similarity and revealed disparate patterns of population structure. This result will arise because allozymes and random DNA segments have dissimilar evolutionary dynamics with respect to mutation and selection.
Conservation genetics of the plain pigeon Columba inornata in Puerto Rico and the Dominican Republic
Authors: Young D. L. , Allard M. W.
Published: November 2003

Genetic sequence variation in the mitochondrial D‐loop was assessed for 42 individuals of the plain pigeon Columba inornata from Puerto Rico and the Dominican Republic. While overall genetic diversity was low in these populations, five haplotypes were observed, with one unique to Puerto Rico and three haplotypes unique to the Dominican Republic sample (with haplotype diversity of hPR= 0.479 and hDR= 0.591, and nucleotide diversity of πPR= 0.2% and πDR= 0.4% where the subscripts correspond to Puerto Rico and the Dominican Republic, respectively). A G‐test of haplotype frequencies between these two populations suggest that these two subspecies (C. i. wetmorei and C. i. inornata) are genetically distinct and should be managed separately. With little apparent gene flow between these two islands (estimates of migration Nm= 1.18) it would appear that the endangered species C. i. wetmorei is endemic to the island of Puerto Rico and that these current populations were not founded by a recent extinction and recolonization event from the Dominican Republic.
Cryptic invasions of the crab Carcinus detected by molecular phylogeography
Authors: Geller J. B. , Walton E. D. , Grosholz E. D. , Ruiz G. M.
Published: November 2003

Coastal marine ecosystems world‐wide are threatened by invasions of nonindigenous species. The ubiquity of marine sibling species identifiable only by genetic analysis suggests that many invasions are cryptic and therefore undetected, causing an underestimation of the actual number and impacts of invading species. We test this hypothesis with European crabs in the genus Carcinus that have invaded five regions globally. Partial 16S ribosomal RNA gene sequences confirm sibling species status of morphologically similar Atlantic C. maenas and Mediterranean C. aestuarii. Based on 16S rRNA haplotypes, crabs from California, New England and Tasmania were all C. maenas. However, we report the cryptic multiple invasion of both species in Japan and South Africa, where only C. aestuarii and C. maenas, respectively, were previously recognized.
RST Calc: a collection of computer programs for calculating estimates of genetic differentiation from microsatellite data and determining their significance
Authors: Goodman S. J.
Published: November 2003

R
ST, an analogue of FST, provides a convenient approach for estimating levels of genetic differentiation from microsatellite data. This paper examines current approaches for calculating estimates of RST and suggests a weighting scheme based on the transformation of allele sizes at loci across data sets. Combined within an analysis of variance framework this scheme yields an estimator of RST analogous to the θ estimator of FST. Software for the IBM‐PC is described which carries out such calculations and assesses the significance of RST or Nm estimates using bootstrap and permutation tests.
Endophytic fungal DNA, the source of contamination in spruce needle DNA
Authors: Camacho F. J. , Gernandt D. S. , Liston A. , Stone J. K. , Klein A. S.
Published: November 2003

DNA isolated and amplified from higher plants may originate from symbiotic microbes occupying plant tissues. A recent report on the phylogeny of Picea contained sequence data that upon later analysis proved to originate from filamentous ascomycetes. Isolates of endophytic fungi from Picea foliage collected from the same location as the original samples were examined to identify the source of the contaminating DNA. The ITS region of isolates was screened by Southern blotting using an oligonucleotide probe homologous to a unique portion of the reported ‘spruce’ sequences. This study identifies a DNA sequence originally attributed to Picea engelmannii (Engelmann spruce) as Hormonema dematioides, a ubiquitous foliar endophyte of conifers. Infections of plants by endophytic fungi are common and their presence is not revealed by external symptoms. Plant molecular researchers should be aware of the potential for this type of DNA contamination.
Molecular evolution at Mhc genes in two populations of chinook salmon Oncorhynchus tshawytscha
Authors: Miller K. M. , Withler R. E. , Beacham T. D.
Published: November 2003

The DNA sequences of four exons of the MHC (major histocompatibilty complex) were examined in chinook salmon (Oncorhynchus tshawytscha) from an interior (Nechako River) and a coastal (Harrison River) population in the Fraser River drainage of British Columbia. Mhc class I A1, A2 and A3 sequences and a class II B1 sequence were obtained by PCR from each of 16–20 salmon from each population. The class I A1 and a pair of linked A2–A3 exons were derived from two different classical salmonid class I genes, Sasa‐A and Onmy‐UA, respectively. Allelic variation for B1, A1 and A2 was characterized by the high levels of nonsynonymous substitution indicative of the effects of natural selection on Mhc domains that contain peptide binding regions. The number of alleles detected at each of the four exons ranged from three (B1) to 22 (A1), but levels of nucleotide sequence divergence at all four exons were low relative to classical mammalian Mhc genes. The nucleotide similarity among alleles ranged between 89 and 99% over all exons, and all four domains possessed only two major sequence motifs. Allelic distributions at B1, A1 and A3 confirmed the genetic distinctiveness of the Harrison and Nechako chinook salmon populations revealed in previous studies. The two major allelic motifs of B1 and A1 segregated strongly between the populations. In spite of evidence that allelic diversity at these chinook salmon Mhc exons has been generated by selection, the level and distribution of diversity in the two salmon populations strongly reflected the demographic history of the species, which has been characterized by repeated bottlenecks and isolation‐by‐distance in glacial refugia.
A genomic polymorphism located downstream of the gcvP gene of Escherichia coli that correlates with ecological niche
Authors: Turner S. J. , Lewis G. D. , Bellamy A. R.
Published: November 2003

Current evolutionary theory proposes that niche‐adapted microbial populations might evolve through selection for favoured genotypes followed by clonal expansion (Maynard‐Smith, 1991). Possible correlations between genomic variation and ecological niche in Escherichia coli isolates derived from human and animal sources were investigated by randomly amplified polymorphic DNA (RAPD) analysis. A 1.6‐kb polymorphic marker was identified which was present in 60% of isolates from human clinical specimens but was present in less than 5% of isolates derived from ovine and bovine faeces. The marker maps to a region of the chromosome located immediately downstream from the gene encoding the glycine decarboxylase P‐protein (gcvP). DNA sequences from marker‐positive and marker‐negative isolates exhibit an abrupt loss of homology immediately downstream from the transcription termination point of the gene which extends for at least 130‐base pairs beyond the gcvP transcription terminator. Sequences spanning this region in marker‐negative isolates exhibit similarity to the cognate sequence from E. coli K‐12, while the corresponding region in marker‐positive isolates bears no similarity to any other published sequence. The utility of the marker for investigating the occurrence of human‐derived E. coli in the environment was studied in a rural stream. Although the stream carried a high background of animal‐derived E. coli, the marker could only be detected in isolates obtained downstream of the human faecal input. The polymorphism therefore shows promise for identification of human‐derived E. coli within environments containing isolates from multiple and diverse sources. The methods described here could be used to generate further markers suitable for investigating microbial population ecology.
Genetic structure of an aphid studied using microsatellites: cyclic parthenogenesis, differentiated lineages and host specialization
Authors: Sunnucks P. , De Barro P. J. , Lushai G. , MacLean N. , Hales D.
Published: November 2003

In a previous study, samples of the grain aphid Sitobion avenae (F.) were collected from wheat and adjacent cocksfoot hosts in a population thought to be primarily parthenogenetic, and DNA from individual aphids was analysed with a multilocus technique. Here we have applied single‐locus microsatellites and a mitochondrial DNA marker to a subset of the same DNA extracts, and have made several additional inferences about important genetic and population processes in S. avenae. Microsatellite analysis indicated very high levels of genic and genotypic variation. S. avenae fell into three genotypic groups inferred to be almost noninterbreeding, while analysis of linkage and Hardy‐Weinberg equilibria suggested high levels of sexual recombination within each genotypic group. Host specialization was evident: one lineage was found only on wheat, and one (bearing many alleles inferred to be introgressed from the blackberry‐grass aphid S. fragariae (Walker)) was found only on cocksfoot. The third group of interrelated genotypes was found commonly on both hosts. Although most genotypes were found only once, some were much more numerous in the sample than expected from the frequency of the alleles they contained. This, and rapid temporal changes in genotypic composition of samples, indicates strong selective differences between genotypes and lineages. In the major genotypic group, the commonest genotypes were significantly more homozygous than were rare ones: thus these data may help to explain the frequent observation of homozygous excess in aphid allozymes. The genotype group showing S. avenae‐like as well as S. fragariae‐like alleles also carried S. fragariae‐like mitochondrial DNA in at least 25/31 cases, indicating gender‐asymmetrical hybridization.
Techniques for application of faecal DNA methods to field studies of Ursids
Authors: Wasser S. K. , Houston C. S. , Koehler G. M. , Cadd G. G. , Fain S. R.
Published: November 2003

We describe methods for the preservation, extraction and amplification of DNA from faeces that facilitate field applications of faecal DNA technology. Mitochondrial, protein encoding and microsatellite nuclear DNA extracted and amplified from faeces of Malayan sun bears and North American black bears is shown to be identical to that extracted and amplified from the same individual's tissue or blood. A simple drying agent, silica beads, is shown to be a particularly effective preservative, allowing easy and safe transport of samples from the field. Methods are also developed to eliminate the risk of faecal DNA contamination from hair present in faeces.
Genetic variation in Costa Rican populations of the tropical timber species Cedrela odorata L., assessed using RAPDs
Authors: Gillies A. C. M. , Cornelius J. P. , Newton A. C. , Navarro C. , Hernández M. , Wilson J.
Published: November 2003

Cedrela odorata L. (Spanish cedar), an economically important timber species native to the American tropics, is the focus of increasing conservation concern due to high rates of deforestation within its native range. To assess the extent of the genetic diversity within and between populations of this species, samples were obtained from 10 widely dispersed populations within Costa Rica and analysed for random amplified polymorphic DNA (RAPD) variation. Fourteen 10‐mer primers were used to generate 97 polymorphic RAPD bands. Presence/absence data for all bands were subjected to a pairwise genetic distance analysis, according to Jaccard's coefficient, then neighbour‐joining cluster analysis was performed on these distances, as was an analysis of molecular variance (AMOVA), to assess levels of differentiation between populations and regions, and Shannon's Diversity Index was used to quantify levels of diversity within and between populations. Results indicated highly significant genetic differentiation (P < 0.004, AMOVA) between populations originating from the North Pacific and Atlantic/South Pacific regions of Costa Rica, with 35.3% of the total variation attributable to a difference between these areas. Little differentiation was recorded between populations from within the same region (P= 0.757, AMOVA), and 65.1% of the total variance was attributable to variation within populations. Estimated values for within‐population diversity, calculated as Hpop/Hsp by means of Shannon's Diversity Index, were found to vary greatly between primers, but the overall within‐population component of genetic diversity was 0.45. Possible reasons for the high degree of intraspecific genetic variation within this species are discussed and the implications of these results for the conservation and use of its genetic resources are described.
Exclusion probabilities for single‐locus paternity analysis when related males compete for matings
Authors: Double M. C. , Cockburn A. , Barry S. C. , Smouse P. E.
Published: November 2003

The statistical power of single‐locus paternity analyses has previously been assessed by calculating an expected exclusion probability (E), the probability of excluding a randomly chosen nonfather. This E‐statistic assumes that putative sires are a random selection of individuals from a panmictic study population. In species that display male natal philopatry, closely related individuals may be the principal competitors for paternity. In such structured populations, the E statistic will overestimate exclusion probability because males competing for paternity are more closely related than males chosen randomly from the population. A suite of loci thought to be sufficient for a panmictic population may frequently incorrectly assign paternity to close relatives of true sires. This study provides equations for calculating the expected probability of excluding a close male relative of the genetic sire (Erel) for any genotyping system that uses codominant markers. We also describe the use of Monte Carlo modelling to estimate exclusion probabilities when multiple male relatives compete for paternity. We show that the utility of a set of codominant markers will depend on the breeding behaviour and social system of the species in question.
Antagonistic natural selection revealed by molecular sex identification of nestling collared flycatchers
Authors: Merilä J. , Sheldon B. C. , Ellegren H.
Published: November 2003

Natural selection may act in different directions during different life‐history stages, or in different directions on different classes of individuals. Antagonistic selection of this kind may be an important mechanism by which additive genetic variation for quantitative traits is maintained, and can prevent populations or species reaching local adaptive peaks. This paper reports the results of a study of viability selection on morphological traits of nestling collared flycatchers Ficedula albicollis. Analyses performed without knowledge of the sex of nestlings suggested that no selection was occurring on these traits. However, using molecular sex identification with the avian CHD gene, it is shown that selection acts in different directions on male and female body size from fledging to breeding, apparently favouring relatively small males and large females. The results suggest that differential selection on male and female nestlings may contribute to purely phenotypic sexual size dimorphism in this species. These findings highlight the potential of newly developed molecular sexing techniques to reveal the consequences of an individual's gender for many aspects of its life history in taxa where gender cannot be determined on the basis of external appearance.
Glacial survival does not matter: RAPD phylogeography of Nordic Saxifraga oppositifolia
Authors: GABRIELSEN T. M. , BACHMANN K. , JAKOBSEN K. S. , BROCHMANN C.
Published: November 2003

The arctic‐alpine Saxifraga oppositifolia has recently been suggested to have survived the last glaciation in high‐arctic refugia, based on a finding of more genetic (RFLP) variation in Svalbard compared with more southern areas. To elucidate the migration history of this allogamous species, we analysed 18 populations from Norway, Svalbard and Novaya Zemlya using random amplified polymorphic DNAs (RAPDs). There was no more RAPD variation in the high Arctic than further south. In an analysis of molecular variance (AMOV A), most of the RAPD variation was found within populations (64%). There was less intrapopulational variation in Svalbard (65%) than in northern Norway (78%) and southern Norway (86%), suggesting that there is more inbreeding towards the north, probably because of lower pollinator activity. Twenty‐eight per cent of the RAPD variation was found among populations within these geographical regions, and only 9% was found among the regions. In PCO and UPGMA analyses, plants and populations of different geographical origins were to a large extent intermingled. There was, however, a distinct, south‐north clinal geographical structuring of the RAPD variation both in the PCO analysis and in a spatial autocorrelation (Mantel) analysis. These results suggest that there has been extensive gene flow among more or less continuously distributed populations of S. oppositifolia during the Weichselian, and that the extant Nordic populations were established after massive, centripetal immigration from these genetically variable, periglacial populations. The postglacial period may not have been sufficiently long for the subsequently isolated populations of this long‐lived, allogamous perennial to diverge. Given the high levels of migration inferred from this study, genetic differentiation of glacial survivor populations, if any existed, would most likely have been swamped in the postglacial period. Thus, our molecular data support recent conclusions based on palaeobotanical and biogeographical data that the glacial survival hypothesis is superfluous.
Species‐specific primers discriminate schistosome intermediate hosts: unambiguous PCR diagnosis of Bulinus forskalii group taxa (Gastropoda: Planorbidae)
Authors: JONES C. S. , NOBLE L. R. , LOCKyER A. E. , BROWN D. S. , ROLLINSON D.
Published: November 2003

The morphological definition of taxa has proved difficult within the Bulinus forskalii group, which includes intermediate hosts of medically important Schistosoma species in West Africa. Although B. forskalii and B. senegalensis transmit different schistosome species they are conchologically similar and their distributions overlap. Randomly amplified polymorphic DNA (RAPD) allows differentiation of sibling species in the genus Bulinus, but RAPDs are difficult to standardize, impairing their value as a taxonomic tool. Hence, RAPD products diagnostic for either B. senegalensis or B. forskalii from West Africa were cloned, sequenced and a panel of species‐specific primers designed. Sequencing of RAPD products identified a homology in two apparently independent RAPD loci, a problem where RAPDs are indiscriminately scored for phylogenetic analyses. Specificity of primers was confirmed by widespread sampling throughout each species' range. This approach produced a simple, robust, unambiguous PCR‐based species identification strategy for this difficult group.
Lack of concordance between mtDNA gene flow and population density fluctuations in the bank vole
Authors: Stacy J. E. , Jorde P. E. , Steen H. , Ims R. A. , Purvis A. , Jakobsen K. S.
Published: November 2003

The genetic structure of bank voles Clethrionomys glareolus was determined from analyses of mitochondrial DNA (mtDNA) sequences, and compared with previous data on geographical synchrony in population density fluctuations. From 31 sample sites evenly spaced out along a 256‐km transect in SE Norway a total of 39 distinct mtDNA haplotypes were found. The geographical distribution of the haplotypes was significantly nonrandom, and a cladistic analysis of the evolutionary relationship among haplotypes shows that descendant types were typically limited to a single site, whereas the ancestral types were more widely distributed geographically. This geographical distribution pattern of mtDNA haplotypes strongly indicates that the range and amount of female dispersal is severely restricted and insufficient to account for the previously observed synchrony in population density fluctuations. We conclude that geographical synchrony in this species must be caused by factors that are external to the local population, such as e.g. mobile predators.
The occurrence of mountain hare mitochondrial DNA in wild brown hares
Authors: Thulin C.‐G. , Jaarola M. , Tegelström H.
Published: November 2003

If interspecific hybrids are fertile and backcross to either parental species, transmission of mitochondrial DNA over the species barrier can occur. To investigate if such transmission has occurred between the brown hare Lepus europeus Pall and the mountain hare L. timidus L. in Scandinavia, an analysis of genetic variation in mitochondrial DNA from 36 hares, collected from 15 localities, was performed. Sequence divergence of mtDNA between species was estimated at 8 ± 1% (SD). Intraspecific mtDNA sequence divergence varied between 0.09 and 0.38% in brown hares and 0.10 and 1.44% in mountain hares. In six out of 18 brown hares examined, two different haplotypes of mountain hare origin were detected, demonstrating a transmission of mtDNA haplotypes from mountain hares to brown hares. The results indicate that interspecific hybridization between the two species occurs in wild populations.
The problem of sampling families rather than populations: relatedness among individuals in samples of juvenile brown trout Salmo trutta L.
Authors: Hansen M. M. , Nielsen E. E. , Mensberg K.‐L. D.
Published: November 2003

In species exhibiting a nonrandom distribution of closely related individuals, sampling of a few families may lead to biased estimates of allele frequencies in populations. This problem was studied in two brown trout populations, based on analysis of mtDNA and microsatellites. In both samples mtDNA haplotype frequencies differed significantly between age classes, and in one sample 17 out of 18 individuals less than 1 year of age shared one particular mtDNA haplotype. Estimates of relatedness showed that these individuals most likely represented only three full‐sib families. Older trout exhibiting the same haplotypes generally were not closely related.