bluuebunny/crossref_metadata_2025_split huggingface dataset:
Microsatellite diversity and genetic structure of fragmented populations of the rare, fire‐dependent shrubGrevillea macleayana
Authors: England Phillip R. , Usher Annette V. , Whelan Robert J. , Ayre David J. 
Published: March 2003

AbstractRecent habitat loss and fragmentation superimposed upon ancient patterns of population subdivision are likely to have produced low levels of neutral genetic diversity and marked genetic structure in many plant species. The genetic effects of habitat fragmentation may be most pronounced in species that form small populations, are fully self‐compatible and have limited seed dispersal. However, long‐lived seed banks, mobile pollinators and long adult lifespans may prevent or delay the accumulation of genetic effects. We studied a rare Australian shrub species,Grevillea macleayana(Proteaceae), that occurs in many small populations, is self‐compatible and has restricted seed dispersal. However, it has a relatively long adult lifespan (c. 30 years), a long‐lived seed bank that germinates after fire and is pollinated by birds that are numerous and highly mobile. These latter characteristics raise the possibility that populations in the past may have been effectively large and genetically homogeneous. Using six microsatellites, we found thatG. macleayanamay have relatively low within‐population diversity (3.2–4.2 alleles/locus;Hexp= 0.420–0.530), significant population differentiation and moderate genetic structure (FST = 0.218) showing isolation by distance, consistent with historically low gene flow. The frequency distribution of allele sizes suggest that this geographical differentiation is being driven by mutation. We found a lack mutation‐drift equilibrium in some populations that is indicative of population bottlenecks. Combined with evidence for large spatiotemporal variation of selfing rates, this suggests that fluctuating population sizes characterize the demography in this species, promoting genetic drift. We argue that natural patterns of pollen and seed dispersal, coupled with the patchy, fire‐shaped distribution, may have restricted long‐distance gene flow in the past.
Genetic structure and phylogeography of European catfish (Silurus glanis) populations
Authors: Triantafyllidis A. , Krieg F. , Cottin C. , Abatzopoulos T. J. , Triantaphyllidis C. , Guyomard R. 
Published: March 2003

AbstractThe genetic structure of Silurus glanis (Europe’s largest freshwater fish species) across most of its natural distribution was investigated using 10 microsatellite loci. The revealed levels of genetic diversity were much higher than previous allozyme and restriction fragment length polymorphism mitochondrial DNA analyses had shown; relative levels of variability among populations were however, in good agreement with the previous studies. Populations from large basins (Volga and Danube rivers) were the most polymorphic, while samples from the smaller Greek rivers, which are more prone to genetic bottleneck, exhibited the lowest levels of genetic diversity. Microsatellite multilocus genotyping permitted the assignment of individual fish to their population of origin with a score as high as 98.3%. Despite the great genetic differentiation of S. glanis populations, no consistent pattern of geographical structuring was revealed, in contrast to previous studies of European freshwater fish species. A model of isolation by distance seems more probable and a hypothesis of recent dispersion from only one glacial refugium is proposed. The discovery of the highest levels of microsatellite and mitochondrial diversity in the Volga sample and the presence of river connections, during the Pleistocene, between this area and all major areas of the present catfish distribution, place this refugium around the Ponto‐Caspian region. Combining these data with those from previous studies, a number of markers are now available to monitor wild and hatchery populations even at the individual level.
Land barriers and open oceans: effects on gene diversity and population structure in Avicennia germinans L. (Avicenniaceae)
Authors: Dodd R. S. , Afzal‐Rafii Z. , Kashani N. , Budrick J. 
Published: March 2003

Abstract Avicennia germinans L. is a widespread mangrove species occupying the west coast of Africa and the Atlantic and Pacific coasts of the Americas from the Bahamas to Brazil and Baja California to Peru. An amplified fragment length polymorphism (AFLP) molecular analysis was carried out to assess genetic architecture within this species and to evaluate the effects of the Atlantic Ocean and the Central American Isthmus (CAI) on population and regional genetic diversity and differentiation. In total, 349 polymorphic AFLP fragments were identified among 144 individuals from 14 populations from the east Atlantic, west Atlantic and east Pacific. Levels of genetic diversity varied considerably among populations, but were generally higher in populations from the east Atlantic. Regional differentiation between the Pacific coast and Atlantic populations was greater than between east and west Atlantic populations, suggesting that the CAI has had an important influence on population genetic structure in this species. The lower level of divergence of east Atlantic from west Atlantic populations suggests some dispersal across the Atlantic Ocean, although migration rates are probably low; Nm from GST equal to 0.41 and accumulation of private and rare alleles in the east Atlantic. Population differentiation did not appear to follow an isolation by distance model and has probably resulted from complex patterns of population bottlenecks, and founder events due to landscape changes during the Pleistocene, particularly in the west Atlantic. The molecular data provide no support for the treatment of east Atlantic populations as a separate species A. africana.
Locating the sources of an invasive pest, grape phylloxera, using a mitochondrial DNA gene genealogy
Authors: Downie D. A. 
Published: March 2003

AbstractRange expansions through human introductions have increased with global commerce and have led to the extinction of native species, alterations in community structure and pest status of the invasive species. Inferring the evolutionary history of invasive species can help to build a firmer footing for management tactics. This study used mitochondrial DNA (mtDNA) sequence comparisons of samples collected from the native and introduced ranges of a pest herbivore of cultivated grapes, grape phylloxera (Daktulosphaira vitifoliae Fitch, Phylloxeridae) to infer the sources and pattern of introductions into worldwide viticulture. Introductions into viticulture from its native North American range first occurred in the mid‐19th century. The pattern of spread has suggested a focus of introduction into France, but independent introductions may have occurred elsewhere. The results show that the introduced population represents a limited subsample of the native genetic diversity. The data suggest that most grape phylloxera in viticulture, including all European, have originated in the northeastern USA where the grape species Vitis riparia dominates. There was evidence for independent introductions into South Africa and California. Most California haplotypes were most closely related to native grape phylloxera from the Atlantic Coast on V. vulpina. It is likely that subsequent spread from California into Australia, New Zealand and Peru has occurred.
Trans‐specific evolution of opsin alleles and the maintenance of trichromatic colour vision in Callitrichine primates
Authors: Surridge Alison K. , Mundy Nicholas I. 
Published: March 2003

AbstractMany New World (NW) primates possess a remarkable polymorphism in an X‐linked locus, which encodes for the visual pigments (opsins) used for colour vision. Females that are heterozygous for opsin alleles of different spectral sensitivity at this locus have trichromatic colour vision, whereas homozygous females and males are dichromatic, with poor colour discrimination in the red–green range. Here we describe an extensive survey of allelic variation in both exons and introns at this locus within and among species of the Callitrichines (marmosets and tamarins). All five genera of Callitrichines have the X‐linked polymorphism, and only the three functional allelic classes described previously (with maximum wavelength sensitivities at about 543 nm, 556 nm and 563 nm) were found among the 16 species and 233 or more X‐chromosomes sampled. In spite of the homogenizing effects of gene conversion, phylogenetic analyses provide direct evidence for trans‐specific evolution of alleles over time periods of at least 5–6 million years, and up to 14 million years (estimated from independent phylogenies). These conclusions are supported by the distribution of insertions and deletions in introns. The maintenance of polymorphism over these time periods requires an adaptive explanation, which must involve a heterozygote advantage for trichromats. The lack of detection of alleles that are recombinant for spectral sensitivity suggests that such alleles are suboptimal. The two main hypotheses for the selective advantage of trichromacy in primates are frugivory for ripe fruits and folivory for young leaves. The latter can be discounted in Callitrichines, as they are not folivorous.
Microsatellite analysis reveals remating by wild Mediterranean fruit fly females, Ceratitis capitata
Authors: Bonizzoni M. , Katsoyannos B. I. , Marguerie R. , Guglielmino C. R. , Gasperi G. , Malacrida A. , Chapman T. 
Published: March 2003

AbstractAccurate estimates of remating in wild female insects are required for an understanding of the causes of variation in remating between individuals, populations and species. Such estimates are also of profound importance for major economic fruit pests such as the Mediterranean fruit fly (Ceratitis capitata). A major method for the suppression of this pest is the sterile insect technique (SIT), which relies on matings between mass‐reared, sterilized males and wild females. Remating by wild females will thus impact negatively on the success of SIT. We used microsatellite markers to determine the level of remating in wild (field‐collected) Mediterranean fruit fly females from the Greek Island of Chios. We compared the four locus microsatellite genotypes of these females and their offspring. Our data showed 7.1% of wild females remated. Skewed paternity among progeny arrays provided further evidence for double matings. Our lowest estimate of remating was 3.8% and the highest was 21%.
Evidences for multiple maternal lineages of Caryocar brasiliense populations in the Brazilian Cerrado based on the analysis of chloroplast DNA sequences and microsatellite haplotype variation
Authors: Collevatti Rosane G. , Grattapaglia Dario , Hay JOHN. D. 
Published: March 2003

AbstractIn this work we report on the phylogeography of the endangered tree species Caryocar brasiliense based on variability in two classes of maternally inherited chloroplast DNA sequences with different rates of molecular evolution. Eleven sequence haplotypes of a noncoding region between the genes trnT and trnF and 21 distinct 10‐locus microsatellite haplotypes could be identified in a total of 160 individuals, collected in 10 widespread populations of C. brasiliense. An amova indicated that most of the variation can be attributed to differences among populations, both for DNA sequence (87.51%) and microsatellites (84.38%). Phylogeography based on a median‐joining network analysis of the noncoding region showed a sharp difference from the analysis of microsatellite haplotypes. Nevertheless, both analyses indicated that multiple lineages may have contributed to the origin of C. brasiliense populations in Brazilian Cerrado. Incongruences in the microsatellite haplotypes network suggest that homoplasy, which emerged from recurrent and independent mutations, greatly influenced the evolution of the C. brasiliense chloroplast genome. We hypothesize that our results may show the outcome of the restriction of ancient relic populations to moist refugias during extended droughts coinciding with glaciation in the northern hemisphere. The subsequent spread to favourable areas throughout Central Brazil may have caused contact between different lineages during the interglacial periods. The extinction of megafauna dispersers in the last glaciation may have caused a restriction in seed movement and currently, gene flow has been occurring mainly by pollen movement.
Divergent selection maintains adaptive differentiation despite high gene flow between sympatric rainbow smelt ecotypes (Osmerus mordaxMitchill)
Authors: Saint‐Laurent Robert , Legault Michel , Bernatchez Louis 
Published: March 2003

AbstractIn this study, we investigate the relative role of historical factors and evolutionary forces in promoting population differentiation in a new case of sympatric dwarf and normal ecotypes of the rainbow smelt (Osmerus mordaxMitchill) in Lac Saint‐Jean (Québec, Canada). Our first objective was to test the hypothesis that the evolution of sympatric smelt ecotypes in Lac Saint‐Jean has been contingent upon the secondary contact between two evolutionary lineages in postglacial times. Secondly, theQSTmethod was applied to test the null hypothesis that the extent of phenotypic differences relative to that of neutral marker variation would be similar in comparisons involving populations within and among ecotypes. Thirdly, we applied a quantitative‐genetic method as an exploratory assessment as to whether the amount of gene flow observed between populations could affect divergence in adaptive traits under specific conditions. This study revealed a unique situation of dwarf and normal smelt ecotypes that are, respectively, characterized by selmiparous and iteroparous life histories and the occurrence in each of two genetically distinct populations that synchronously use the same spawning habitat in two tributaries. Historical contingency has apparently played little role in the origin of these populations. In contrast, an important role of divergent natural selection in driving their phenotypic divergence was suggested. While divergent selection has apparently been strong enough to maintain phenotypic differentiation in the face of migration, this study suggests that gene flow has been sufficiently important to modulate the extent of adaptive differentiation being achieved between ecotypes, unless the extent of stabilizing selection acting on smelt ecotypes is much more pronounced than usually reported in natural populations.
Fine‐scale genetic structure in a free‐living ungulate population
Authors: Coltman D. W. , Pilkington J. G. , Pemberton J. M. 
Published: March 2003

AbstractThe fine‐scale genetic structure of wild animal populations has rarely been analysed, yet is potentially important as a confounding factor in quantitative genetic and allelic association studies, as well as having implications for population dynamics, inbreeding and kin selection. In this study, we examined the extent to which the three spatial subunits, or hefts, of the Village Bay population of Soay sheep (Ovis aries) on St Kilda, Scotland, are genetically structured using data from 20 microsatellite and protein loci. Allele frequencies differed significantly among three hefts in all the study years we considered (1987–2000 inclusive). Small but significantly positive FST and negative FIS values were observed in most years, indicating that the hefts are genetically differentiated, and that within each heft there is more observed heterozygosity than would be expected if each were an isolated breeding population. Males showed less fidelity to their natal heft, and as a consequence higher levels of relatedness within hefts were observed among females than among males. There was a significant negative relationship between geographical proximity and relatedness in pairwise comparisons involving females, and on average pairs of females located within 50 m of each other were related at the equivalent level of second cousins. Structure is therefore largely driven by incomplete postnatal dispersal by females. Mating appears to be random with respect to the spatial‐genetic substructure of the hefts, and therefore genetic structure does not contribute to the overall rate of inbreeding in the population. However, genetic substructure can lead to allelic associations and generate environmental effects within lineages that have the potential to confound heritability analyses and allelic association studies.
Patterns of linkage disequilibrium in mitochondrial DNA of 16 ruminant populations
Authors: Slate J. , Phua S. H. 
Published: March 2003

AbstractMitochondrial DNA (mtDNA) is a widely employed molecular tool in phylogeography, in the inference of human evolutionary history, in dating the domestication of livestock and in forensic science. In humans and other vertebrates the popularity of mtDNA can be partially attributed to an assumption of strict maternal inheritance, such that there is no recombination between mitochondrial lineages. The recent demonstration that linkage disequilibrium (LD) declines as a function of distance between polymorphic sites in hominid mitochondrial genomes has been interpreted as evidence of recombination between mtDNA haplotypes, and hence nonclonal inheritance. However, critics of mtDNA recombination have suggested that this association is an artefact of an inappropriate measure of LD or of sequencing error, and subsequent studies of other populations have failed to replicate the initial finding. Here we report the analysis of 16 ruminant populations and present evidence that LD significantly declines with distance in five of them. A meta‐analysis of the data indicates a nonsignificant trend of LD declining with distance. Most of the earlier criticisms of patterns between LD and distance in hominid mtDNA are not applicable to this data set. Our results suggest that either ruminant mtDNA is not strictly clonal or that compensatory selection has influenced patterns of variation at closely linked sites within the mitochondrial control region. The potential impact of these processes should be considered when using mtDNA as a tool in vertebrate population genetic, phylogenetic and forensic studies.
Historical demography and genetic structure of sister species: deermice (Peromyscus) in the North American temperate rain forest
Authors: Zheng Xiaoguang , Arbogast Brian S. , Kenagy G. J. 
Published: March 2003

AbstractTo investigate the evolutionary and biogeographical history ofPeromyscus keeniandP. maniculatuswithin the coastal forest ecosystem of the Pacific Northwest of North America, we sampled 128 individuals from 43 localities from southeastern Alaska through Oregon. We analysed mitochondrial DNA variation using DNA sequence data from the mitochondrial cytochrome‐b(cyt‐b) gene and control region, and we found two distinct clades consistent with the morphological designation of the two species. The sequence divergence between the two clades was 0.0484 substitutions per site for cyt‐band 0.0396 for the control region, suggesting that divergence of the two clades occurred during the middle to late Pleistocene. We also examined the historical demography of the two clades using stepwise and exponential expansion models, both of which indicated recent rapid population growth. Furthermore, using the programmigratewe found evidence of migration from populations north of the Fraser River (British Columbia) to the south in both clades. This study demonstrates the utility of these model‐based demographic methods in illuminating the evolutionary and biogegographic history of natural systems.
A new approach to study dispersal: immigration of novel alleles reveals female‐biased dispersal in great reed warblers
Authors: Hansson Bengt , Bensch Staffan , Hasselquist Dennis 
Published: March 2003

AbstractWe use the assignment technique and a new approach, the ‘novel allele technique’, to detect sex‐biased dispersal in great reed warblersAcrocephalus arundinaceus. The data set consisted of immigrants and philopatric birds in a semi‐isolated population in Sweden scored at 21 microsatellite loci. Fourteen cohorts were represented of which the four earliest were used to define a reference population. Female immigrants had lower assignment probability than males (i.e. were less likely to have been sampled in the reference population), and carried the majority of ‘novel alleles’ (i.e. alleles observed in the population for the first time). The difference in number of novel alleles between sexes was caused by a strong over‐representation of females among the few individuals that carried several novel alleles, and there was a tendency for a corresponding female bias among individuals with low assignment probabilities. Immigrant males had similar or lower reproductive success than females. These results lead us to conclude that important interregional gene flow in great reed warblers depends on relatively few dispersing females, and that the novel allele technique may be a useful complement to the assignment technique when evaluating dispersal patterns from temporally structured data.
Mid‐cell Z ring assembly in the absence of entry into the elongation phase of the round of replication in bacteria: co‐ordinating chromosome replication with cell division
Authors: Regamey A. , Harry E. J. , Wake R. G. 
Published: March 2003

We have shown previously that, when spores of a thymine‐requiring strain of Bacillus subtilis were grown out in the absence of thymine, mid‐cell Z rings formed over the nucleoid and much earlier than might be expected with respect to progression into the round of replication. It is now shown that such conditions allow no replication of oriC. Rather than replication, partial degradation of the oriC region occurs, suggesting that the status of this region is connected with the ‘premature’ mid‐cell Z ring assembly. A correlation was observed between entry into the replication elongation phase and a block to mid‐cell Z rings. The conformation of the nucleoid under various conditions of DNA replication inhibition or limitation suggests that relief of nucleoid occlusion is not primarily responsible for mid‐cell Z ring formation in the absence of thymine. We propose the existence of a specific structure at mid‐cell that defines the Z ring nucleation site (NS). It is suggested that this NS is normally masked by the replisome upon initiation of replication or soon after entry into the elongation phase, and subsequently unmasked relatively late in the round. During spore outgrowth in the absence of thymine, this checkpoint control over mid‐cell Z ring assembly breaks down prematurely.
Two independent transcriptional units control the complex and simultaneous expression of the bmp paralogous chromosomal gene family in Borrelia burgdorferi
Authors: Dobrikova Elena Yu , Bugrysheva Julia , Cabello Felipe C. 
Published: March 2003

The chromosomal paralogous gene family 36 encodes for four lipoproteins with high amino acid homology that are expressed in vivo in humans and animals and are immunogenic. Transcriptional analysis of the bmp gene cluster indicated that all four genes of this cluster are expressed in vitro and constitute two transcriptional units with a complex pattern of transcription, including alternative monocistronic and polycistronic messages. One unit consists of bmpD, whose transcription is coupled to the transcription of the ribosomal protein genes, rpsG and rpsL. The second unit includes bmpC, bmpA and bmpB. The simultaneous expression of the four bmp genes in Borrelia burgdorferi suggests that their gene products may have either different or complementary functions. Primer extension experiments identified promoters for bmpD, bmpC and bmpA, but not for bmpB. The concentration of gene‐specific mRNA paralleled its promoter homology to the Escherichia coliσ70 promoter. The linkage of bmpD expression to rpsL and rpsG suggests that the expression of this gene may be controlled by growth‐related global regulation mechanisms in B. burgdorferi. These results indicate that the bmp family constitutes a good model for the investigation of complex regulation of chromosomal gene expression in this bacteria.