bluuebunny/crossref_metadata_2025_split huggingface dataset:
Molecular investigations in populations of Spartina anglica C.E. Hubbard (Poaceae) invading coastal Brittany (France)
Authors: Baumel A. , Ainouche M. L. , Levasseur J. E. 
Published: March 2003

Abstract Spartina anglica is a classical example of recent alloploid speciation. It arose during the end of the nineteenth century in England by hybridization between the indigenous Spartina maritima and the introduced East‐American Spartina alterniflora. Duplication of the hybrid genome (Spartina × townsendii) gave rise to a vigorous allopolyploid involved in natural and artificial invasions on different continents. Spartina anglica was first recorded in France in 1906, and since then, it has spread all along the western French coast. Earlier studies revealed that native British populations display consistent morphological plasticity and lack of isozyme variation. In this paper, we use different molecular markers (randomly amplified polymorphic DNA, intersimple sequence repeats and restriction patterns from nuclear and chloroplast DNA sequences) to analyse the genetic patterns of the French populations of S. anglica. Our results show that French populations are mainly composed of one ‘major’ multilocus genotype. This genotype is identical to the first‐generation hybrid S. × townsendii from England. Losses of few markers from this genotype are observed but are restricted to a few populations from Brittany; it is likely that they appeared independently, subsequent to their introduction. In southern Brittany, no hybrids between S. anglica and S. maritima have been found where the two species co‐occur. All French populations of S. anglica display the same chloroplast DNA sequences as S. alterniflora, the maternal genome donor. These findings are consistent with a severe genetic bottleneck at the time of the species formation, as a consequence of a unique origin of the species. Both parental nuclear sequences are present in the allopolyploid populations, revealing that for the markers investigated, no extensive changes have occurred in this young species.
Glacial biogeography of North American coho salmon (Oncorhynchus kisutch)
Authors: Smith Christian T. , Nelson R. John , Wood Chris C. , Koop Ben F. 
Published: March 2003

AbstractTo study the glacial biogeography of coho we examined 20 microsatellite loci and mitochondrial DNA D‐loop sequence in samples from Alaska to California. Microsatellite data divided our samples among five biogeographic regions: (1) Alaska and northern coastal British Columbia; (2) the Queen Charlotte Islands; (3) the mainland coast of British Columbia and northern Washington State; (4) the Thompson River; and (5) Oregon and California. The D‐loop sequence data suggested three geographical regions: (1) Oregon and California; (2) the Thompson River; and (3) all the other sites north of the southern ice margin. Microsatellite data revealed no difference in the number of alleles in different regions, but mitochondrial DNA data revealed a cline of decreasing diversity from south to north. We suggest that the two signals presented by these different marker types illuminate two time frames in the history of this species. Endemic microsatellite diversity in Alaska and on the Queen Charlotte Islands provides evidence in favour of Fraser Glaciation refugia in these regions. The loss of mitochondrial variation from south to north suggests that one of the earlier, more extensive, Pleistocene glaciations eliminated coho from its northern range.
Statistical properties of population differentiation estimators under stepwise mutation in a finite island model
Authors: Balloux F. , Goudet J. 
Published: March 2003

AbstractMicrosatellite loci mutate at an extremely high rate and are generally thought to evolve through a stepwise mutation model. Several differentiation statistics taking into account the particular mutation scheme of the microsatellite have been proposed. The most commonly used is , which is independent of the mutation rate under a generalized stepwise mutation model.

and

are commonly reported in the literature, but often differ widely. Here we compare their statistical performances using individual‐based simulations of a finite island model. The simulations were run under different levels of gene flow, mutation rates, population number and sizes. In addition to the per locus statistical properties, we compare two ways of combining

over loci. Our simulations show that even under a strict stepwise mutation model, no statistic is best overall. All estimators suffer to different extents from large bias and variance. While

better reflects population differentiation in populations characterized by very low gene‐exchange,

gives better estimates in cases of high levels of gene flow. The number of loci sampled (12, 24, or 96) has only a minor effect on the relative performance of the estimators under study. For all estimators there is a striking effect of the number of samples, with the differentiation estimates showing very odd distributions for two samples.
Patterns of genetic diversity and biogeographical history of the tropical wetland tree, Pterocarpus officinalis (Jacq.), in the Caribbean basin
Authors: Rivera‐Ocasio E. , Aide T. M. , McMillan W. O. 
Published: March 2003

AbstractStudies examining intraspecific variation in plant species with widespread distributions and disjunct populations have mainly concentrated on temperate species. Here, we determined the genetic structure of a broadly distributed wetland tropical tree, Pterocarpus officinalis (Jacq.), from eight Neotropical populations using amplified length fragment polymorphisms (AFLP). AFLPs proved highly variable with almost half (48%) of the genetic variation at these loci occurring among individuals within populations. Nonetheless, there was a strong geographical pattern in the distribution of AFLP variation within P. officinalis. Caribbean and continental populations fell into two well‐defined genetic clusters supported by the presence of a number of unique AFLP bands. Within these two regions, there were also strong genetic differences among populations, caused mainly by frequency differences in AFLP bands, making it difficult to determine the evolutionary relationships among populations. In addition, our analysis of P. officinalis revealed striking differences in the levels of AFLP variation among the eight populations sampled. In general, Caribbean populations had lower genetic diversity than continental populations. Moreover, there was a clear loss in AFLP diversity with distance from the continent among Caribbean populations. The overall genetic pattern within P. officinalis suggests that past colonization history, coupled with genetic drift within local populations, rather than contemporary gene flow are the major forces shaping variation within this species.
Comparison of genetic diversity estimates within and among populations of maritime pine using chloroplast simple‐sequence repeat and amplified fragment length polymorphism data
Authors: Ribeiro M. M. , Mariette S. , Vendramin G. G. , Szmidt A. E. , Plomion C. , Kremer A. 
Published: March 2003

AbstractWe compared the genetic variation of Pinus pinaster populations using amplified fragment length polymorphism (AFLP) and chloroplast simple‐sequence repeat (cpSSR) loci. Populations’ levels of diversity within groups were found to be similar with AFLPs, but not with cpSSRs. The high interlocus variance associated with the AFLP loci could account for the lack of differences in the former. Although AFLPs revealed much lower genetic diversity than cpSSRs, the levels of among‐population differentiation found with the two types of marker were similar, provided that loci showing fewer than four null‐homozygotes, in any population, were pruned from the AFLP data. Moreover, the French and Portuguese populations were clearly differentiated from each other, with both markers. The Mantel test showed that the genetic distance matrix calculated using the AFLP data was correlated with the matrix derived from the cpSSRs. Because of the concordance found between markers we conclude that gene flow was indeed the predominant force shaping nuclear and chloroplastic genetic variation of the populations within regions, at the geographical scale studied.
Spawning times, reproductive compatibilities and genetic structuring in theAcropora asperagroup: evidence for natural hybridization and semi‐permeable species boundaries in corals
Authors: Van Oppen Madeleine J. H. , Willis Bette L. , Van Rheede Teun , Miller David J. 
Published: March 2003

AbstractSpecies boundaries among five sympatric coral species of the Indo‐PacificAcropora asperagroup were examined by a combination ofin vitrobreeding trials, comparisons of spawning times and DNA sequence analysis of ribosomal DNA internal transcribed spacer (rDNA ITS) and 5.8S regions. The breeding trials showed that reproductive compatibility exists between at least some colonies of all the species pairs tested, suggesting a large potential for natural hybridization and introgression. TheAcroporaITS regions exhibited extremely high levels of variability (up to ∼62% for ITS1, ∼11% for 5.8S and ∼43% for ITS2), but most of the variation was shared among four of the five species,A. millepora,A. papillare,A. pulchraandA. spathulata,consistent with extensive introgression. Phylogenetic analyses did not resolve these four species as distinct clusters across a wide biogeographic region stretching from the southern Great Barrier Reef to Papua New Guinea. However, most colonies of the fifth species,A. aspera, constituted a distinct clade in phylogenetic analyses. This is consistent with our observations of a semi‐permeable temporal barrier involving differences in spawning times between this and the other four species. Although the majority of colonies of all five species generally spawned within 90 min of each other, in two out of four years, gametes were absent prior to mass spawning episodes from at least someA. asperacolonies. Hence, our data suggest that transient reproductive barriers may be the result of year‐to‐year variation in the date of spawning and that this difference in spawning time contributes to the genetic structure detected amongAcroporaspecies in this group. Occasional leakage through the reproductive barrier was confirmed by the observation ofA. aspera ×A. pulchraF1hybrids, identified based on additivity of ITS sequences.
Offspring sexual dimorphism and sex‐allocation in relation to parental age and paternal ornamentation in the barn swallow
Authors: Saino N. , Ambrosini R. , Martinelli R. , Calza S. , Møller A. P. , Pilastro A. 
Published: March 2003

AbstractWe analysed the morphology of nestling barn swallows (Hirundo rustica) in relation to their sex, and laying and hatching order. In addition, we studied sex‐allocation in relation to parentage, parental age and expression of a secondary sexual character of fathers. Molecular sexing was conducted using the sex chromosome‐linked avian CHD1 gene. Sex of the offspring was not associated with laying or hatching order. None of nine morphological, serological and immunological variables varied in relation to offspring sex. Sexual dimorphism did not vary in relation to parental age and expression of a paternal secondary sexual character. The proportion of sons declined with brood size. Individual males and females had a similar proportion of sons during consecutive breeding years. The proportion of sons of individual females declined with age, but increased with the expression of a secondary sexual character of their current mate. The generalized lack of variation in sexual dimorphism among nestlings may suggest that barn swallows do not differentially invest in sons vs. daughters. Alternatively, male offspring may require different parental effort compared to their female siblings in order to attain the same morphological state. The lack of variation in offspring sexual dimorphism with paternal ornamentation suggests no adjustment of overall parental effort in relation to reproductive value of the two sexes. However, male‐biased sex ratio among offspring of highly ornamented males may represent an adaptive sex‐allocation strategy because the expression of male ornaments is heritable and highly ornamented males are at a sexual selection advantage.
Microsatellite variation in the reintroduced Pennsylvania elk herd
Authors: Lenney Williams Christen , Serfass Thomas L. , Cogan Rawland , Rhodes Olin E. 
Published: March 2003

AbstractRelocation programs have restored elk (Cervus elaphus) to portions of its vast historical range. We examine the consequences of these relocation programs by assessing variation at 10 microsatellite loci in three elk herds, a source herd (Yellowstone National Park), a large herd reintroduced from Yellowstone (Custer State Park) and a bottlenecked herd reintroduced from both Yellowstone and Custer (the Pennsylvania herd). Observed single locus heterozygosities ranged from 0.000 to 0.739. Multi‐locus heterozygosities ranged from 0.222 to 0.589. Although significant differences were detected among all three herds, the Yellowstone National Park and Custer State Park herds possessed similar levels of variation and heterozygosity, and the genetic distance between these two herds was small. The Pennsylvania herd, on the other hand, experienced a 61.5% decrease in heterozygosity relative to its source herds, possessed no unique and few rare alleles, and the genetic distances between the Pennsylvania herd and its sources were large. Simulations were performed to identify bottleneck scenarios in agreement with levels of variation in the Pennsylvania herd. Our data confirm that the rate of population growth post‐relocation may have important genetic consequences and indicate that theoretical predictions regarding the maintenance of genetic variation during relocation events must be viewed with caution when small numbers of a polygynous species are released.
Population differentiation and nuclear gene flow in the Dominican anole (Anolis oculatus)
Authors: Stenson Andrew G. , Malhotra Anita , Thorpe Roger S. 
Published: March 2003

AbstractAllele frequency data from nuclear microsatellite loci were used to investigate patterns of nuclear gene flow and population structure in the morphologically variable Dominican anole (Anolis oculatus). All six loci used proved to be highly polymorphic, with an average of 18.8 alleles per locus. Test for Hardy–Weinberg equilibrium revealed small numbers of heterozygote deficiencies at single loci in single populations and consistent patterns of increasingly significant heterozygote deficiency in global tests across populations and loci. No significant relationship between FST and patristic distances estimated from mitochondrial DNA sequences was detected and estimates of FIS were significantly higher in females than in males, indicating that gene flow may be sex‐biased and mediated mainly by male migration. A highly significant correlation between linearized FST and loge (geographical distance) indicates that geographical proximity is a significant factor in the genetic structure of A. oculatus populations. However, levels of gene flow between morphologically differentiated parapatric populations are frequently seen to be relatively high. This supports the hypothesis of natural selection being the driving force behind the development and maintenance of morphological variation and shows that adaptive differentiation may be maintained despite the homogenizing influence of gene flow. Generally, the morphologically variable populations of A. oculatus are seen to be poor candidates for in situ speciation, but an exceptional case on the west coast of Dominica indicates that isolation resulting from vicariant events may lead to rapid differentiation at both mitochondrial and nuclear loci. This provides a possible mechanism for anole speciation on other Caribbean islands.
Major histocompatibility complex variation in red wolves: evidence for common ancestry with coyotes and balancing selection
Authors: Hedrick P. W. , Lee R. N. , Garrigan D. 
Published: March 2003

AbstractWe examined variation at a class II major histocompatibility complex (MHC) gene (DRB1) in the captive red wolf population and samples of coyotes from Texas and North Carolina. We found 4 alleles in the 48 red wolves, 8 alleles in the 10 coyotes from Texas and 15 alleles in the 29 coyotes from North Carolina. Two of the four alleles found in red wolves, Caru‐2 and Caru‐4, were found in both the Texas and North Carolina coyote samples. Allele Caru‐1, previously found in gray wolves, was also found in the North Carolina sample. The most frequent red wolf allele, Caru‐3, was not found in any of the coyote samples. However, an allele found in both the Texas and North Carolina coyote samples is only one nucleotide (one amino acid) different from this red wolf allele. Overall, it appears from examination of this MHC gene that red wolves are more closely related to coyotes than to gray wolves. There were a number of different types of evidence supporting the action of balancing selection in red wolves. Namely, there was: (i) an excess of heterozygotes compared with expectations; (ii) a higher rate of nonsynonymous than synonymous substitution for the functionally important antigen‐binding site positions; (iii) an eight times higher average heterozygosity of individual amino acids at the positions identified as part of the antigen‐binding site than those not associated with it; (iv) the amino acid divergence of four red wolf alleles was greater than that expected from a simulation of genetic drift; and (v) the distribution of alleles, and the distributions of amino acids at many positions were more even than expected from neutrality. Examination of the level and pattern of linkage disequilibria between pairs of sites suggest that the heterozygosity, substitution and frequencies at individual amino acids are not highly dependent upon each other.
Wolbachiainfections and superinfections in cytoplasmically incompatible populations of the European cherry fruit flyRhagoletis cerasi(Diptera, Tephritidae)
Authors: Riegler Markus , Stauffer Christian 
Published: March 2003

AbstractWolbachiais an obligately intracellular, maternally inherited bacterium which has been detected in many arthropods.Wolbachiainfections disperse in host populations by mechanisms such as cytoplasmic incompatibility (CI). CI leads to embryonic mortality which occurs when infected males mate with uninfected females or females with a differentWolbachiastrain. Populations of the European cherry fruit flyRhagoletis cerasi(Diptera, Tephritidae) were found to be infected by two differentWolbachiastrains,wCer1 andwCer2. Superinfections with both strains occurred throughout southern and central Europe and infections withwCer1 were found in northern, western and eastern Europe. Strong unidirectional CI between European populations ofR. cerasiwere first reported in the 1970s. From the conformity in the recent geographical distribution of theWolbachiainfections and the CI expression patterns found 25 years ago it was deduced thatwCer2 potentially causes CI inR. cerasi. The comparison of the geographical distributions indicated thatwCer1 + 2 must have spread intowCer1‐infected populations in some areas. In other regions, a spread ofwCer1 + 2 was probably prevented by dispersal barriers. There, a sharp transition from infected to superinfected populations suggested regional isolation betweenwCer1 andwCer1 + 2‐infected populations.
Slow mitochondrial DNA sequence evolution in the Anthozoa (Cnidaria)
Authors: Shearer T. L. , van Oppen M. J. H. , Romano S. L. , Wörheide G. 
Published: March 2003

AbstractMitochondrial genes have been used extensively in population genetic and phylogeographical analyses, in part due to a high rate of nucleotide substitution in animal mitochondrial DNA (mtDNA). Nucleotide sequences of anthozoan mitochondrial genes, however, are virtually invariant among conspecifics, even at third codon positions of protein‐coding sequences. Hence, mtDNA markers are of limited use for population‐level studies in these organisms. Mitochondrial gene sequence divergence among anthozoan species is also low relative to that exhibited in other animals, although higher level relationships can be resolved with these markers. Substitution rates in anthozoan nuclear genes are much higher than in mitochondrial genes, whereas nuclear genes in other metazoans usually evolve more slowly than, or similar to, mitochondrial genes. Although several mechanisms accounting for a slow rate of sequence evolution have been proposed, there is not yet a definitive explanation for this observation. Slow evolution and unique characteristics may be common in primitive metazoans, suggesting that patterns of mtDNA evolution in these organisms differ from that in other animal systems.
Similar estimates of population genetic composition and sex ratio derived from carcasses and faeces of Eurasian otter Lutra lutra
Authors: Dallas John F. , Coxon Karen E. , Sykes Tim , Chanin Paul R. F. , Marshall Freda , Carss David N. , Bacon Philip J. , Piertney Stuart B. , Racey Paul A. 
Published: March 2003

AbstractCollecting faeces is viewed as a potentially efficient way to sample elusive animals. Nonetheless, any biases in estimates of population composition associated with such sampling remain uncharacterized. The goal of this study was to compare estimates of genetic composition and sex ratio derived from Eurasian otter Lutra lutra spraints (faeces) with estimates derived from carcasses. Twenty per cent of 426 wild‐collected spraints from SW England yielded composite genotypes for 7–9 microsatellites and the SRY gene. The expected number of incorrect spraint genotypes was negligible, given the proportions of allele dropout and false allele detection estimated using paired blood and spraint samples of three captive otters. Fifty‐two different spraint genotypes were detected and compared with genotypes of 70 otter carcasses from the same area. Carcass and spraint genotypes did not differ significantly in mean number of alleles, mean unbiased heterozygosity or sex ratio, although statistical power to detect all but large differences in sex ratio was low. The genetic compositions of carcass and spraint genotypes were very similar according to confidence intervals of θ and two methods for assigning composite genotypes to groups. A distinct group of approximately 11 carcass and spraint genotypes was detected using the latter methods. The results suggest that spraints can yield unbiased estimates of population genetic composition and sex ratio.