bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evolutionary implications of allozyme and RAPD variation in diploid populations of dioecious buffalograssBuchloë dactyloides
Authors: PEAKALL R. , SMOUSE P. E. , HUFF D. R. 
Published: April 2008

AbstractBuffalograss,Buchloë dactyloides, is widely distributed throughout the Great Plains of North America, where it is an important species for rangeland forage and soil conservation. The species consists of two widespread polyploid races, with narrowly endemic diploid populations known from two regions: central Mexico and Gulf Coast Texas. We describe and compare the patterns of allozyme and RAPD variation in the two diploid races, using a set of 48 individuals from Texas and Mexico (four population samples of 12 individuals each). Twelve of 22 allozyme loci were polymorphic, exhibiting 35 alleles, while seven 10‐mer RAPD primers revealed 98 polymorphic bands. Strong regional differences were detected in the extent of allozyme polymorphism: Mexican populations exhibited more internal gene diversity (He= 0.20, 0.19) than did the Texan populations (He= 0.08, 0.06), although the number of RAPD bands in Texas (n= 62) was only marginally smaller than in Mexico (n= 68).F‐statistics for the allozyme data, averaged over loci, revealed strong regional differentiation (meanFRT=+ 0.30), as well as some differentiation among populations within regions (meanFPR=+ 0.09). In order to describe and compare the partitioning of genetic variation for multiple allozyme and RAPD loci, we performed an Analysis of Molecular Variance (AMOVA). AMOVA for both allozyme and RAPD data revealed similar qualitative patterns: large regional differences and smaller (but significant) population differences within regions. RAPDs revealed greater variation among regions (58.4% of total variance) than allozymes (45.2%), but less variation among individuals within populations (31.9% for RAPDs vs. 45.2% for allozymes); the proportion of genetic variance among populations within regions was similar (9.7% for RAPDs vs. 9.6% for allozymes). Despite this large‐scale concordance of allozyme and RAPD variation patterns, multiple correlation Mantel techniques revealed that the correlations were low on an individual by individual basis. Our findings of strong regional differences among the diploid races will facilitate further study of polyploid evolution in buffalograss.
Evolution of the Cyprinella lutrensis species group. III. Geographic variation in the mitochondrial DNA of Cyprinella lutrensis— the influence of Pleistocene glaciation on population dispersal and divergence
Authors: RICHARDSON L. R. , GOLD J. R. 
Published: April 2008

AbstractWe employed restriction site variation in mitochondrial (mt)DNA to determine if significant phylogeographic structure occurs in the North American cyprinid fish Cyprinella lutrensis. Digestion patterns from 16 restriction endonucleases identified fifty mtDNA haplotypes among 127 individuals of Cyprinella lutrensis assayed from localities in the Gulf Coastal Plain, the Great Plains, and the Central Lowlands. Nucleotide sequence divergence among haplotypes was highly variable (mean ± SE: 2.87%± 0.08; range: 0.14–9.24%). Maximum‐parsimony analysis and the neighbour joining method of tree construction revealed three major groupings (clades) of haplotypes that differed in geographic distribution. Divergence estimates between the basal clade, comprised of haplotypes primarily from the Brazos River in east Texas, and the remaining two clades, place C. lutrensis in the western Gulf Coastal Plain prior to Pleistocene glaciation. Nucleotide sequence divergence between the second clade, comprised of haplotypes from the Trinity and Calcasieu rivers in east Texas and southwestern Louisiana, respectively, and the third clade (comprised primarily of haplotypes from localities north of Texas and affected directly by Pleistocene glaciation), suggest that C. lutrensis colonized gladated regions to the north during the mid‐ to late Pleistocene. This hypothesis is supported by levels of intrapopulational nucleotide diversity in geographic localities outside of Texas and by geological evidence. Despite marked geographic variation in morphometries, meristics, and nuptial coloration, mtDNA variation in glaciated regions was not geographically structured, and subspecies of C. lutrensis were not identifiable by phylogenetic analysis of mtDNA.
Assessment of the stocked or wild origin of anadromous brown trout (Salmo trutta L.) in a Danish river system, using mitochondrial DNA RFLP analysis
Authors: HANSEN M. M. , HYNES R. A. , LOESCHCKE V. , RASMUSSEN G. 
Published: April 2008

AbstractDeclines in the number of anadromous brown trout in the Karup River in Denmark, due to environmental degradation, led to the stocking of large numbers of hatchery trout during the 1980s. This practice was gradually replaced by stocking with the offspring of electrofished local trout The genetic contribution of the hatchery fish to the current population of anadromous trout in the river was estimated by restriction fragment length polymorphism analysis of mitochondrial DNA, using seven restriction endonucleases. Fish from the hatchery strain as well as from five locations in the river system, and from a further unstocked river were screened. Eight haplotypes were observed. The distribution and frequencies of the observed haplotypes revealed little genetic differentiation among stocked populations. The hatchery strain differed significantly from the stocked populations. One haplotype which was found at a high frequency in the hatchery strain was almost absent from the stocked populations. This suggests that the genetic contribution of the hatchery trout to the current population is much less than would be expected from the number of stocked fish. The possible reasons for the failure of the hatchery trout to contribute to the gene pool, and also the implications for conservation biology, are discussed.
Molecular diversity and derivations of populations of Silene acaulis and Saxifraga oppositifolia from the high Arctic and more southerly latitudes
Authors: ABBOTT R. J. , CHAPMAN H. M. , CRAWFORD R. M. M. , FORBES D. G. 
Published: April 2008

AbstractA survey of allozyme diversity within and between populations of Silene acaulis from Spitsbergen, Norway, Iceland and Scotland, showed that populations from the high Arctic (Spitsbergen, > 76°N) contained high levels of diversity and were genetically similar to populations from more southern locations. Indirect measures of gene flow (Nm), calculated from Wrigh's F indicated that there had been extensive gene flow between Spitsbergen and some Norwegian populations. A restriction site analysis of chloroplast DNA (cpDNA) in S. acaulis revealed that all populations contained a single identical cpDNA haplotype, except one population from Norway which also contained a second haplotype. In contrast, five different cpDNA haplotypes were distinguished in a more limited survey of cpDNA variation in Saxifraga oppositifolia, with all five haplotypes present in one of two Spitsbergen populations surveyed. The contrasting cpDNA results for the two species suggest that whereas high‐Arctic populations of Silene acaulis have most likely been derived from immigrants which arrived from the south after the last glacial period, high‐Arctic populations of Saxifraga oppositifolia may be derived, in part, from ancient northern stocks which survived the last glaciation in high‐Arctic refugia.
Diversity and genetic structure of a natural population of Rhizobium leguminosarum bv. trifolii isolated from Trifolium subterraneum L.
Authors: DEMEZAS D. H. , REARDON T. B. , STRAIN S. R. , WATSON J. M. , GIBSON A. H. 
Published: April 2008

AbstractA collection of 121 isolates of Rhizobium leguminosarum biovar (bv.) trifolii was obtained from root nodules of Trifolium subterraneum L. (subclover) plants growing in an established pasture. The collection consisted of a single isolate from each of 18 plants sampled from seven microplots. The following year, a further 28 and 27 isolates were collected from the first and seventh sampling points, respectively. Analysis of restriction fragment length polymorphisms (RFLPs) of both chromosomal and Sym (symbiotic) plasmid DNA and multilocus enzyme electrophoresis (MLEE) were used to assess the diversity, genetic relationships and structure of this population. Symbiotic effectiveness tests were used to examine the symbiotic phenotype of each isolate collected in the first year. Analysis of RFLPs of the first year isolates revealed 13 chromosomal types and 25 Sym plasmid types. Similar Sym plasmid types were grouped into 14 families containing 1–6 members. No new chromosomal types and six new Sym plasmid types were detected in the second year. The symbiotic effectiveness of the first year isolates of the same Sym plasmid type was similar. Significant differences in symbiotic effectiveness were detected between different Sym plasmid types in the same plasmid family. Representative isolates of each chromosomal type Sym plasmid type identified in the first year were analysed using multilocus enzyme electrophoresis. Mean genetic diversity per locus was high (0.559). Enzyme electrophoresis revealed 17 electrophoretic types (ETs). Ouster analysis of the enzyme data revealed large genetic diversity amongst the ETs. Strong linkage disequilibrium was observed for the population as a whole, i.e. clonal population structure, but significantly less disequilibrium was observed among a cluster of ETs suggesting that recombination occurred between ETs within the cluster. Our results revealed that a population of naturally occurring isolates of Rhizobium leguminosarum bv. trifolii can be genetically diverse and support the possibility that recombination plays a role in generating new genotypes.
Glucose utilization by 6pgd genotypes in Lolium perenne
Authors: RAINEY‐FOREMAN D. , MITTON J. B. 
Published: April 2008

AbstractTo gain a deeper understanding of the mechanisms underlying associations between allozyme genotypes and rates of respiration in Lolium perenne, Vmax Km and rates of glucose flux through glycolysis and the pentose phosphate pathway were estimated for the three genotypes of the 6pgd locus. Km Vmax and Vmax/Km differed significantly among genotypes. Values of Km for the 11, 12, and 22 genotypes were 0.29, 0.25, 0.13, while the values of Vmax/Km for die 11, 12, and 22 genotypes were 3.79, 3.85, 6.70. Flux through the pentose shunt did not differ among genotypes at 20 °C, but at 35 °C the rates of flux for the 11, 12, and 22 genotypes were 0.15, 0.25 and 0.42, respectively. Thus, the 6PGD allozyme genotypes differ markedly in both enzyme kinetic characteristics and in flux through a metabolic pathway. These associations reveal potentially causal relationships between allozyme genotypes and rates of respiration.
Natal dispersal and genetic structure in a population of the European wild rabbit (Oryctolagus cuniculus)
Authors: WEBB N. J. , IBRAHIM K. M. , BELL D. J. , HEWITT G. M. 
Published: April 2008

AbstractA combination of behavioural observation, DNA fingerprinting, and allozyme analysis were used to examine natal dispersal in a wild rabbit population. Rabbits lived in territorial, warren based social groups. Over a 6‐year period, significantly more male than female rabbits moved to a new social group before the start of their first breeding season. This pattern of female philopatry and male dispersal was reflected in the genetic structure of the population. DNA fingerprint band‐sharing coefficients were significantly higher for females within the same group than for females between groups, while this was not the case for males. Wrighfs inbreeding coefficients were calculated from fingerprint band‐sharing values and compared to those obtained from allozyme data. There was little correlation between the relative magnitudes of the F‐statistics calculated using the two techniques for comparisons between different social groups. In contrast, two alternative methods for calculating FST from DNA fingerprints gave reasonably concordant values although those based on band‐sharing were consistently lower than those calculated by an ‘allele’ frequency approach. A negative FIS value was obtained from allozyme data. Such excess heterozygosity within social groups is expected even under random mating given the social structure and sex‐biased dispersal but it is argued that the possibility of behavioural avoidance of inbreeding should not be discounted in this species. Estimates of genetic differentiation obtained from allozyme and DNA fingerprint data agreed closely with reported estimates for the yellow‐bellied marmot, a species with a very similar social structure to the European rabbit.
Nonamplifying alleles at microsatellite loci: a caution for parentage and population studies
Authors: PEMBERTON J. M. , SLATE J. , BANCROFT D. R. , BARRETT J. A. 
Published: April 2008

AbstractWhile genotyping wild red deer (Cervus elaphus) at microsatellite loci for paternity assignment, we found three loci (MAP65, BOVIRBP and CelJP23) with segregating nonamplifying alleles. Nonamplifying alleles were detected through mismatches between known mother‐offspring pairs and by significant deviations from Hardy‐Weinberg equilibria. In a wide range of molecular ecology applications, and especially in parentage assignment, the possible existence of undetectable alleles must be taken into account; this may be particularly important for microsatellite data.
Differentiation of the endemic New Zealand greenheaded and brownheaded leafroller moths by restriction fragment length variation in the ribosomal gene complex
Authors: SIN F. Y. T. , SUCKLING D. M. , MARSHALL J. W. 
Published: April 2008

AbstractThis study identified markers in the ribosomal RNA gene complex (rDNA) and evaluated their utility in the differentiation of four endemic New Zealand species of leafroller moth, Planotortrix excessana (Walker), P. octo (Dugdale), Ctenopseustis herana (Felder and Rogenhofer) and C. obliquana (Walker). Pooled genomic DNA from laboratory‐reared specimens of C. herana and C. obliquana could be distinguished with a single restriction enzyme (e.g. ClaI), while P. excessana and P. octo could be satisfactorily distinguished using double digestions with either ClaI/PvuII or ClaI/BglII. It is concluded mat these markers may be used to identify moths from wild populations.
Transposon signatures: species‐specific molecular markers that utilize a class of multiple‐copy nuclear DNA
Authors: PURUGGANAN M. D. , WESSLER S. R. 
Published: April 2008

AbstractTransposable elements are mobile sequences found in nuclear genomes and can potentially serve as molecular markers in various phylogenetic and population genetic investigations. A PCR‐based method that utilizes restriction site variation of element copies within a genome is developed. These patterns of site variation, referred to as transposon signatures, are useful in differentiating between closely related groups. Signature data using the magellan retrotransposon, for example, is useful in examining relationships within the genus Zea and Tripsacum. This method allows transposable elements, or even other multiple‐copy nuclear DNA sequences, to be generally utilized as molecular markers in discriminating between other closely related species and subspecies.
Colonization history of north European field voles (Microtus agrestis) revealed by mitochondrial DNA
Authors: JAAROLA M. , TEGELSTRÖM H. 
Published: April 2008

AbstractThe genetic structure of field vole (Microtus agrestis) populations from northern Europe was examined by restriction fragment length polymorphisms of mitochondrial DNA (mtDNA) in 150 individuals from 67 localities. A total of 83 haplotypes was observed, most of which were rare and highly localized geographically. Overall nucleotide diversity was high (134%), but showed a tendency to decrease with higher latitude. Two major mtDNA lineages differing by 2% in nucleotide sequence were identified. A southern mtDNA lineage was observed in field voles from Britain, Denmark and southern and central Sweden, whereas voles from Finland and northern Sweden belonged to a northern lineage. The strict phylogeographic pattern suggests that the present population generic structure in field voles reflects glacial history: the two groups are derived from different glacial refugia, and recolonized Fennoscandia from two directions. A 150–200‐km‐wide secondary contact zone between the two mtDNA groups was found in northern Sweden. Distinct phylogeographic substructuring was observed within both major mtDNA groups.
Use of RAPD analysis in devising conservation strategies for the rare and endangered Grevillea scapigera (Proteaceae)
Authors: ROSSETTO M. , WEAVER P. K. , DIXON K. W. 
Published: April 2008

AbstractExtensive human impact in south western Australia has resulted in a high incidence of rarity throughout the highly endemic flora of the region. Grevillea scapigera (Proteaceae) is a typical example, with 27 plants (represented by four extant populations) remaining in the wild. In order to devise an appropriate strategy for the conservation of this species, its population genetics were studied using RAPD analysis, which enabled the discrimination of individual plants and the detection of a relatively high amount of variability (V = 0.32) within G. scapigera. This variability was found to be evenly distributed within the plants analysed despite the clear distinction between most populations (87% of the variability being attributable to single plant difference and 13% to population difference). Finally, RAPD analysis was used to select a small group of plants that captured maximum genetic variability to be used in the recovery program of the species. Because of the low genetic difference between populations, the mixing of these selected plants during the recovery process should not create genetic imbalances. The methods used in this study provide a useful model for future projects involving the recovery of rare flora.
Phylogeographic structure in mitochondrial DNA of a South‐east Asian freshwater fish, Hemibagrus nemurus (Siluroidei; Bagridae) and Pleistocene sea‐level changes on the Sunda shelf
Authors: DODSON J. J. , COLOMBANI F. , NG P. K. L. 
Published: April 2008

AbstractWe postulated that the biogeographical history of South‐east Asia contributed to extensive admixture during Pleistocene low sea levels of genetic groups of an obligate freshwater fish (the river catfish, Hemibagrus nemurus) isolated during periods of high sea levels. During Pleistocene glacial maxima, the sea level was lower than at present and the islands of the Sunda shelf (Sumatra, Borneo and Java) and the Asian mainland were connected by lowlands traversed by rivers. Restriction fragment length polymorphisms in mitochondrial DNA were documented for 140 putative H. nemurus analysed from 13 sampling sites resulting in the definition of 35 haplotypes. The high level of haplotype differentiation (mean P × 100 = 2.22, SD = 1.33) indicates that the subdivision of the ancestral H. netnurus group was extensive and probably occurred early in the Pleistocene. The occurrence of some genetically divergent groups of the H. netnurus complex occurring in sympatry in widely separated locations supports the proposition that low sea levels aided the dispersion and mingling of genetic groups. Based on both genetic and morphological evidence, the main H. nemurus line gave rise to three regional groups: (1) a morphologically distinct ‘Indochinese’ group composed of two mtDNA clades overlapping in east peninsular Malaysia; (2) a ‘Sundaic’ group composed of various lineages of differing morphology and genetic identity; (3) a genetically distinct ‘Sarawak’ group in west Borneo, similar in morphology to the ‘Sundaic’ and ‘Indochinese’ groups, but including a small, golden colour morph as a distinct dade. The morphologically similar Sundaic forms from west Java, Sumatra and west Borneo show some degree of genetic divergence, but their phylogenetic relationships are poorly resolved. The most genetically and morphologically distinct Sundaic dade, assigned to H. hoevenii, colonized the Kapuas river (west Borneo), east Sumatra and south peninsular Malaysia. Contrary to our original hypothesis and present biogeographical theory, little exchange of genetic groups has apparently occurred between the mainland and the Sunda Islands during recent glaciations.
A comparison of mtDNA restriction sites vs. control region sequences in phylogeographic assessment of the musk turtle (Sternotherus minor)
Authors: WALKER D. , BURKE V. J. , BARÁK I. , AVISE J. C. 
Published: April 2008

AbstractA total of nearly 800 base pairs of mitochondrial DNA sequence was assayed in each of 52 musk turtles (Sternotherus minor) collected across the species' range in the south‐eastern USA. About one‐half of the sequence information in effect was accessed by conventional recognition‐site assays of the entire mtDNA molecule; the remainder came from direct sequence assays of a normally hypervariable 5′ section of the noncoding control region. The two assay methods produced essentially nonoverlapping sets of variable character states that were compared with respect to magnitudes and phylogeographic patterns of mtDNA variation. The two assay procedures yielded nearly identical outcomes with regard to: (a) total levels of species‐wide mtDNA genetic variation; (b) mean levels of within‐locale variation; (c) extremely high population genetic structure; (d) a phylogenetcally significant separation of samples from the north‐western half of the species' range vs. those in the south‐eastern segment; and (e) considerably lower genetic variability within the north‐western clade. The micro‐ and macro‐phylogeographic mtDNA patterns in the musk turtle are consistent with a low‐dispersal natural history, and with a suspected longer‐term biogeographic history of the species, respectively.
Mitochondrial DNA variation among populations of Oedura reticulata (Gekkonidae) in remnant vegetation: implications for metapopulation structure and population decline
Authors: SARRE S. 
Published: April 2008

AbstractRestriction fragment length polymorphism (RFLP) analysis of mitochondrial DNA was used to examine the regional population structure of a species of gecko (Oedura reticulata) in vegetation remnants within the Western Australian wheatbelt. The species exhibited considerable polymorphism within and between populations with 22 haplotypes recognized among 12 populations. Phylogenetic analysis of haplotypes and clustering of nucleotide divergence among populations demonstrated little regional structure within the species with several haplotypes present in all three regions surveyed. This contrasted markedly with variation in haplotype frequency among populations which showed a high degree of independence between populations indicating that current levels of maternal gene flow are low and that the populations are too small to prevent genetic drift. This conclusion is supported by generally lower numbers of haplotypes in remnant populations than in nearby nature reserves. These findings, combined with demographic data from a previous study, suggest that post‐fragmentation populations of O. reticulata are unable to form a metapopulation structure in the habitat that remains and that stochastic extinction forces alone will be sufficient to severely reduce the regional distribution of this species. This study demonstrates that mtDNA is a useful tool for detecting contemporary population phenomena and can provide qualitative information of practical importance to wildlife managers.