bluuebunny/crossref_metadata_2025_split huggingface dataset:
Complex social organization reflects genetic structure and relatedness in the cooperatively breeding bell miner,Manorina melanophrys
Authors: Painter J. N. , Crozier R. H. , Poiani A. , Robertson R. J. , Clarke M. F. 
Published: March 2003

AbstractThe cooperatively breeding bell miner,Manorina melanophrys, differs from most other cooperative breeding species in the complexity of its social system, where discrete social organization occurs on at least three levels. Microsatellite markers were used to investigate the degree of genetic structure underlying the social organization ofM. melanophrysby comparing colonies, coteries and nest contingents. The genetic data confirmed behavioural observations ofM. melanophrysliving in male kin‐based groups between which females disperse short distances to breed. Estimates ofFSTrevealed restricted gene flow between eight colonies located within 30 km that was significantly associated with geographical distance when the two most distant colonies were included. Within a high density colony significant differences were found between coteries; analysis of the degree of relatedness between coterie members showed that this is due to related individuals associating preferentially with each other. Similarly, the contingent of individuals attending a nest were generally close relatives of the young they were aiding, supporting models invoking kin selection as the selective agency mediating helping.
Chloroplast DNA polymorphism reveals little geographical structure in Castanea sativa Mill. (Fagaceae) throughout southern European countries
Authors: Fineschi S. , Taurchini D. , Villani F. , Vendramin G. G. 
Published: March 2003

AbstractThe distribution of haplotypic diversity of 38 European chestnut (Castanea sativa Mill.) populations was investigated by PCR/RFLP analysis of regions of the chloroplast and mitochondrial genomes in order to shed light on the history of this heavily managed species. The rapid expansion of chestnut starting from 3000 years ago is strongly related to human activities such as agricultural practice. This demonstrates the importance of human impact, which lasted some thousands of years, on the present‐day distribution of the species. No polymorphism was detected for the single mitochondrial analysed region, while a total of 11 different chloroplast (cp) haplotypes were scored. The distribution of the cpDNA haplotypes revealed low geographical structure of the genetic diversity. The value of population subdivision, as measured by GSTc, is strikingly lower than in the other species of the family Fagaceae investigated. The actual distribution of haplotypic diversity may be explained by the strong human impact on this species, particularly during the Roman civilization of the continent, and to the long period of cultivation experienced during the last thousand years.
A universal molecular method for identifying underground plant parts to species
Authors: Linder C. R. , Moore L. A. , Jackson R. B. 
Published: March 2003

AbstractAs part of a large project to determine rooting depth and resource uptake on the Edwards Plateau of central Texas, we developed a DNA‐based technique that allows the below‐ground parts of all plants to be identified to the level of genus and usually to species. Identification is achieved by comparing DNA sequences of the internal transcribed spacer (ITS) region of the 18S–26S nuclear ribosomal DNA repeat, derived from below‐ground plant material, with a reference ITS region database for plants at a site. The method works throughout plants because the plant ITS region can be PCR amplified using a set of universal primers. Congeneric species can usually be identified because the ITS region evolves relatively rapidly. In our study, all roots were easily identified to the level of genus; most congeneric species were identified solely by ITS sequence differences but some required a combination of ITS sequence data and above‐ground surveys of species at a site. In addition to showing the feasibility and efficacy of our technique, we compare it with another DNA‐based technique used to identify below‐ground plant parts. Finally, we also describe a DNA extraction and purification technique that reliably provides high‐quality DNA of sufficient quantity from roots so that PCR can be readily accomplished. Our technique should allow the below‐ground parts of plants in any system to be identified and thereby open new possibilities for the study of below‐ground plant communities.
Ericoid mycorrhizal fungi are common root associates of a Mediterranean ectomycorrhizal plant (Quercus ilex)
Authors: Bergero R. , Perotto S. , Girlanda M. , Vidano G. , Luppi A. M. 
Published: March 2003

AbstractMycorrhiza samples of neighbouring Quercus ilex and Erica arborea plants collected in a postcutting habitat were processed to see whether plants differing in mycorrhizal status harbour the same root endophytes. Three experiments were performed in parallel: (i) isolation, identification and molecular characterization of fungi from surface‐sterilized roots of both plant species; (ii) re‐inoculation of fungal isolates on axenic E. arborea and Q. ilex seedlings; (iii) direct inoculation of field‐collected Q. ilex ectomycorrhizas onto E. arborea seedlings. About 70 and 150 fungal isolates were obtained from roots of Q. ilex and E. arborea, respectively. Among them, Oidiodendron species and five cultural morphotypes of sterile isolates formed typical ericoid mycorrhizas on E. arborea in vitro. Fungi with such mycorrhizal ability were derived from both host plants. Isolates belonging to one of these morphotypes (sd9) also exhibited an unusual pattern of colonization, with an additional extracellular hyphal net. Ericoid mycorrhizas were also readily obtained by direct inoculation of E. arborea seedlings with Q. ilex ectomycorrhizal tips. Polymerase chain–restriction fragment length polymorphism and random amplified polymorphic DNA analyses of the shared sterile morphotypes demonstrate, in the case of sd9, the occurrence of the same genet on the two host plants. These results indicate that ericoid mycorrhizal fungi associate with ectomycorrhizal roots, and the ecological significance of this finding is discussed.
Multi‐locus genetic evidence for rapid ecologically based speciation in Daphnia
Authors: Pfrender M. E. , Spitze K. , Lehman N. 
Published: March 2003

AbstractThe process of speciation involves the divergence of two or more subpopulations of a parent species into independent evolutionary trajectories. To study this process in natural populations requires a detailed knowledge of the genetic and ecological characteristics of the parent species and an understanding of how its populations can lose evolutionary cohesion. The cosmopolitan and speciose genus Daphnia provides many of these features by existing in multiple freshwater habitat types, particularly permanent lakes and temporary ponds, each of which presents distinct ecological challenges. We assayed the genetic composition of 20 temporary pond populations of members of the Daphnia pulex species complex in north‐western Oregon and compared them to published data on related lake and pond populations. We collected molecular genetic data from 13 allozyme loci, from six microsatellite loci, and from the control region of the mitochondrial DNA. By assaying over 400 individual Daphnia for these data, we were able to compile composite genotypes not only of individual Daphnia but of each pond population as a whole. In these ponds, we discovered two distinct genotypic constellations, one which bears resemblance to the lake‐dwelling taxon D. pulicaria, and one which bears resemblance to the pond‐dwelling taxon, D. pulex. Using published genetic data from these and other species as a frame of reference, we characterized 13 of these ponds as being ‘pond‐like’, three as being ‘lake‐like’, and four as being ‘mixed’. Unlike studies performed elsewhere, however, these ponds do not exhibit high probabilities of interspecific hybridization. Over 95% of all individuals have either a lake‐like or a pond‐like genotype at all three genetic systems, suggesting the two forms do not represent hybridized vs. nonhybridized genotypes. Because both types can be found in the same ponds at the same time in gametic disequilibrium, we also discount the possibility that they are two extremes of a single species that is highly genetically subdivided. With these genetic data, and with supporting life‐history and ecological data previously gathered on these pond populations, we conclude that the most likely description of this system is of a taxon caught in the act of speciating, with new pond‐adapted populations periodically stemming from lake‐adapted sources during river flooding events.
SSCP is not so difficult: the application and utility of single‐stranded conformation polymorphism in evolutionary biology and molecular ecology
Authors: Sunnucks P. , Wilson A. C. C. , Beheregaray L. B. , Zenger K. , French J. , Taylor A. C. 
Published: March 2003

AbstractAll genetic markers are estimators of DNA nucleotide sequence variation. Rather than obtaining DNA sequence data, it is cheaper and faster to use techniques that estimate sequence variation, although this usually results in the loss of some information. SSCP (single‐stranded conformation polymorphism) offers a sensitive but inexpensive, rapid, and convenient method for determining which DNA samples in a set differ in sequence, so that only an informative subset need be sequenced. In short, most DNA sequence variation can be detected with relatively little sequencing. SSCP has been widely applied in medical diagnosis, yet few studies have been published in population genetics. The utility and convenience of SSCP is far from fully appreciated by molecular population biologists. We hope to help redress this by illustrating the application of a single simple SSCP protocol to mitochondrial genes, nuclear introns, microsatellites, and anonymous nuclear sequences, in a range of vertebrates and invertebrates.
Geographic pattern of genetic variation in Pinus resinosa: area of greatest diversity is not the origin of postglacial populations
Authors: Walter R. , Epperson B. K. 
Published: March 2003

AbstractGenetic diversity is low in natural populations of red pine, Pinus resinosa, a species that has a vast range across north‐eastern North America. In this study, we examined 10 chloroplast microsatellite or simple sequence repeats (cpSSR) loci in 136 individuals from 10 widespread populations. Substantial variation for the cpSSR loci was observed in the study populations. The contrast with red pine’s lack of variation for other types of loci is likely to be due to the higher mutation rates typical of SSR loci. The amount of variation is lower than that generally found for cpSSR loci in other pine species. In addition, the variation exhibits a striking geographical pattern. Most of the genetic diversity is among populations, with little within populations, indicating substantial isolation of and genetic drift within many populations in the southern half of the species distribution. The greatest diversity now occurs in the north‐eastern part of New England, which is especially intriguing because this entire area was glaciated. Thus the centre of diversity cannot be the origin of postglacial populations, rather it is likely caused by admixture, most probably because of influences from two separate refugia. Furthermore, the pattern indicates that the spread of red pine since the last glaciation is rather more complex than usually described, and it likely includes more than one refugia, complex migration routes, and postglacial‐retreat isolation and genetic drift among shrinking populations in regions of the present southern range.
Speciation, introgressive hybridization and nonlinear rate of molecular evolution in flycatchers
Authors: Sætre Glenn‐Peter , Borge Thomas , Lindell Johan , Moum Truls , Primmer Craig R. , Sheldon Ben C. , Haavie Jon , Johnsen Arild , Ellegren Hans 
Published: March 2003

AbstractEvolutionary history of Muscicapidae flycatchers is inferred from nuclear and mitochondrial DNA (mtDNA) sequence comparisons and population genetic analysis of nuclear and mtDNA markers. Phylogenetic reconstruction based on sequences from the two genomes yielded similar trees with respect to the order at which the species split off. However, the genetic distances fitted a nonlinear, polynomial model reflecting diminishing divergence rate of the mtDNA sequences compared to the nuclear DNA sequences. This could be explained by Haldane’s rule because genetic isolation might evolve more rapidly on the mitochondrial rather than the nuclear genome in birds. This is because hybrid sterility of the heterogametic sex (females) would predate that of the homogametic sex (males), leading to sex biased introgression of nuclear genes. Analyses of present hybrid zones of pied (Ficedula hypoleuca) and collared flycatchers (F. albicollis) may indicate a slight sexual bias in rate of introgression, but the introgression rates were too low to allow proper statistical analyses. It is suggested, however, that the observed deviation from linearity can be explained by a more rapid mutational saturation of the mtDNA sequences than of the nuclear DNA sequences, as supported by analyses of third codon position transversions at two protein coding mtDNA genes. A phylogeographic scenario for the black and white flycatcher species is suggested based on interpretation of the genetic data obtained. Four species appear to have diverged from a common ancestor relatively simultaneously during the Pleistocene. After the last glaciation period, pied and collared flycatchers expanded their breeding ranges and eventually came into secondary contact in Central and Eastern Europe and on the Baltic Isles.
Population genetic structure of the endangered tropical tree species Caryocar brasiliense, based on variability at microsatellite loci
Authors: Collevatti Rosane G. , Grattapaglia Dario , Hay John D. 
Published: March 2003

AbstractWe report the population genetic structure of the endangered tropical tree species Caryocar brasiliense, based on variability at 10 microsatellite loci. Additionally, we compare heterozygosity and inbreeding estimates for continuous and fragmented populations and discuss the consequences for conservation. For a total of 314 individuals over 10 populations, the number of alleles per locus ranged from 20 to 27 and expected and observed heterozygosity varied from 0.129 to 0.924 and 0.067 to 1.000, respectively. Significant values of θ and RST showed important genetic differentiation among populations. θ was much lower than RST, suggesting that identity by state and identity by descent have diverged in these populations. Although a significant amount of inbreeding was found under the identity by descent model (f = 0.11), an estimate of inbreeding for microsatellite markers based on a more adequate stepwise mutation model showed no evidence of nonrandom mating (RIS = 0.04). Differentiation (pairwise FST) was positively correlated with geographical distance, as expected under the isolation by distance model. No effect of fragmentation on heterozygosity or inbreeding could be detected. This is most likely due to the fact that Cerrado fragmentation is a relatively recent event (~60 years) compared to the species life cycle. Also, the populations surveyed from both fragmented and disturbed areas were composed mainly of adult individuals, already present prior to ecosystem fragmentation. Adequate hypothesis testing of the effect of habitat fragmentation will require the recurrent analysis of juveniles across generations in both fragmented and nonfragmented areas.
Mitochondrial DNA phylogeography of lake cisco (Coregonus artedi): evidence supporting extensive secondary contacts between two glacial races
Authors: Turgeon J. , Bernatchez L. 
Published: March 2003

AbstractThe comparative molecular phylogeography of regional fish fauna has revealed the wide distribution of young clades in freshwater fishes of formerly glaciated areas as well as interspecific incongruences in their refugial origins and recolonization routes. In this study, we employed single‐strand conformation polymorphism (SSCP) and sequence analyses to describe mitochondrial DNA (mtDNA) polymorphism among 27 populations of the lake cisco (Coregonus artedi) from its entire range of distribution in order to evaluate the hypothesis of dual glacial refuges proposed by Bernatchez & Dodson against the traditional view that this species is solely of Mississippian origin. Results indicate that this taxon is composed of two closely related groups that are widely distributed and intermixed over most of the sampled range. The estimated level of divergence (0.48%), the contrast in the geographical distribution of each group, as well as the general distribution of C. artedi in North America together support the hypothesis that one group dispersed from a Mississippian refuge via the proglacial lakes, while the other is of Atlantic origin and also took advantages of earlier dispersal routes towards eastern Hudson Bay drainages. However, the signal of past range fragmentation revealed by a nested clade analysis was weak, and did not allow to formally exclude the hypothesis of a single Mississippian origin for both lineages. Comparisons with the phylogeographic patterns of other Nearctic freshwater fishes suggest that the salinity tolerance and thermal sensitivity of lake cisco may have been determinant for its extensive postglacial dispersal. The presence or co‐occurrence of sympatric or allopatric eco/morphotypes were not found to be necessarily associated with the presence of both haplotype groups.
The ‘rare allele phenomenon’ in a ribosomal spacer
Authors: Schilthuizen Menno , Hoekstra Rolf F. , Gittenberger Edmund 
Published: March 2003

AbstractWe describe the increased frequency of a particular length variant of the internal transcribed spacer 1 (ITS‐1) of the ribosomal DNA in a hybrid zone of the land snail Albinaria hippolyti. The phenomenon that normally rare alleles or other markers can increase in frequency in the centre of hybrid zones is not new. Under the term ‘hybrizyme’ or ‘rare allele’ phenomenon it has been recorded in many organisms and different genetic markers. However, this is the first time that it has been found in a multicopy locus. On the one hand, the pattern fits well with the view that purifying selection in hybrid populations works on many loci across the genome and should thus have its effect on many independent molecular markers. On the other hand, the results are puzzling, given that the multiple copies of rDNA are not expected to respond in unison. We suggest two possible explanations for these conflicting observations.
Phylogeography and conservation genetics of the Columbia spotted frog (Rana luteiventris; Amphibia, Ranidae)
Authors: Bos David H. , Sites Jack W. 
Published: March 2003

AbstractThe Columbia spotted frog (Rana luteiventris) has a widespread distribution in western Canada and the western US, although the southern reach of its range is highly fragmented into several isolated populations. Threats from various factors have raised concerns regarding the long‐term survival of many small, isolated populations. Here, we report a study designed to determine the phylogeographic and conservation genetic parameters of R. luteiventris in the western US. Mitochondrial DNA (mtDNA) sequences were examined for phylogeographic structuring using phylogenetic reconstruction methods, coupled with networking and nested clade analyses. These methods permitted a distinction to be made between historic and demographic forces acting to generate geographical patterning of genetic variation. Phylogenetic analysis revealed four geographically correlated monophyletic clades. Three of these clades correspond to well‐defined, nonoverlapping geographical locations in the fragmented portion of the range. The other is comprised of all samples collected from the contiguous range and includes one isolate from northern Wyoming. Networking and nested clade analyses confirmed these results and revealed that historical processes, such as range expansion and vicariance, rather than recurrent gene flow are likely responsible for observed patterns of genetic variation. A measure of genetic variation (θ = 4Neµ) revealed that R. luteiventris populations in Utah have a relatively low amount of genetic variation compared with populations in the continuous portion of the range.
Assessment of genetic structure within and among Bulgarian populations of the common ash (Fraxinus excelsior L.)
Authors: Heuertz Myriam , Hausman Jean‐François , Tsvetkov Ivaylo , Frascaria‐Lacoste Nathalie , Vekemans Xavier 
Published: March 2003

AbstractWe analysed genetic variation within and between populations of the common ash from Bulgaria in order to extract biological information useful in the context of conservation management of eastern European genetic resources of noble hardwood species. A total of 321 trees from three regions of Bulgaria were typed at six highly polymorphic microsatellite loci. Analysis of within‐population inbreeding suggests an upper boundary value of 2.7% for the selfing rate. Significant spatial genetic structure consistent with models of isolation by distance was detected within four out of 10 populations as well as among populations. Estimates of neighbourhood size in the range 38–126 individual trees were obtained based on spatial genetic structure analyses at either the intrapopulation or interpopulation level. Differentiation among populations explained only about 8.7% of total genetic diversity. These results are discussed in comparison with data from social broad‐leaved species such as oak and beech.
Temporal change in genetic structure and effective population size in steelhead trout (Oncorhynchus mykiss)
Authors: Heath Daniel D. , Busch Christopher , Kelly Joanne , Atagi Dana Y. 
Published: March 2003

AbstractThere is a wealth of published molecular population genetic studies, however, most do not include historic samples and thus implicitly assume temporal genetic stability. We tested for changes in genetic diversity and structure in three populations of steelhead trout (Oncorhynchus mykiss) from a northern British Columbia watershed using seven microsatellite loci over 40 years. We found little change in genetic diversity (mean allele numbers and observed and expected heterozygosity), despite large variation in the estimated numbers of steelhead returning to the watershed over the same time period. However, the temporal stability in genetic diversity is not reflected in population structure, which appears to be high among populations, yet significantly variable over time. The neighbour‐joining tree showed that, overall, two of the populations (Zymoetz and Kispiox) clustered separately from the third (Babine); a finding which was not consistent with their geographical separation. The clustering pattern was also not temporally consistent. We used the temporal method to estimate the effective number of breeders (Nb) for the three populations; our values (Nb = 17–102) were low for the large and presumed vigorous populations of steelhead trout sampled. The low Nb values were also not consistent with the generally high genetic diversity estimates, suggesting the possibility of intermittent gene flow among the three populations. The use of temporal analyses in population genetic samples should be a priority; first, to verify observed patterns in contemporary data, and second, to build a dataset of temporal analyses to allow generalizations to be made concerning temporal genetic stability and effective population size in natural populations.