bluuebunny/crossref_metadata_2025_split huggingface dataset:
Microsatellite analysis of North American wapiti (Cervus elaphus) populations
Authors: Polziehn Renee O. , Hamr Joe , Mallory Frank F. , Strobeck Curtis 
Published: March 2003

AbstractEleven populations of wapiti (Cervus elaphus) were analysed for genetic diversity using 12 microsatellite loci. Samples were taken from Vancouver Island, British Columbia; Burwash and French River herds in Ontario; Ya Ha Tinda Ranch, Alberta; and Banff, Elk Island, Jasper, Kootenay, Riding Mountain, Yellowstone and Yoho National Parks. Overall, wapiti populations have on average three to four alleles per locus and an average expected heterozygosity that ranged from 25.75 to 52.85%. The greatest genetic distances were observed between the Vancouver population and all other populations. Using the assignment test, Roosevelt wapiti (C. e. rooseveltiMerriam 1897) assigned only to the Vancouver Island population. The distance and assignment values suggest a divergence of the Roosevelt wapiti from other populations and support the subspecific status for the Vancouver Island population. No evidence was found for the existence of unique Eastern wapiti (C. e. canadensisErxleben 1777) in the Burwash or French River herds in Ontario. The overlapping distribution of genotypes from indigenous populations from Riding Mountain, Elk Island and Yellowstone National Parks suggests that wapiti were once a continuous population before settlers decimated their numbers. The lack of differentiation between these populations raises questions about the status of Manitoban (C. e.manitobensisMillais 1915) and Rocky Mountain (C. e.nelsoniBailey 1935) subspecies.
Genetic diversity in an endangered alpine plant,Eryngium alpinumL. (Apiaceae), inferred from amplified fragment length polymorphism markers
Authors: Gaudeul M. , Taberlet P. , Till‐Bottraud I. 
Published: March 2003

AbstractEryngium alpinumL. is an endangered species found across the European Alps. In order to obtain base‐line data for the conservation of this species, we investigated levels of genetic diversity within and among 14 populations from the French Alps. We used the amplified fragment length polymorphism (AFLP) technique with three primer pairs and scored a total of 62 unambiguous, polymorphic markers in 327 individuals. Because AFLP markers are dominant, within‐population genetic structure (e.g.FIS) could not be assessed. Analyses based either on the assumption of random‐mating or on complete selfing lead to very similar results. Diversity levels within populations were relatively high (mean Nei’s expected heterozygosity = 0.198; mean Shannon index = 0.283), and a positive correlation was detected between both genetic diversity measurements and population size (Spearman rank correlation:P = 0.005 andP = 0.002, respectively). Moreover,FSTvalues and exact tests of differentiation revealed high differentiation among populations (mean pairwiseFST = 0.40), which appeared to be independent of geographical distance (nonsignificant Mantel test). Founder events during postglacial colonizations and/or bottlenecks are proposed to explain this high but random genetic differentiation. By contrast, we detected a pattern of isolation by distance within populations and valleys. Predominant local gene flow by pollen or seed is probably responsible for this pattern. Concerning the management ofE. alpinum, the high genetic differentiation leads us to recommend the conservation of a maximum number of populations. This study demonstrates that AFLP markers enable a quick and reliable assessment of intraspecific genetic variability in conservation genetics.
Historical biogeography in a linear system: genetic variation of Sea Rocket (Cakile maritima) and Sea Holly (Eryngium maritimum) along European coasts
Authors: Clausing G. , Vickers K. , Kadereit J. W. 
Published: March 2003

AbstractThe exclusively coastal Cakile maritima and Eryngium maritimum represent a linear biogeographical system. Genetic variation among 25 individuals of C. maritima and 16 individuals of E. maritimum, from the coasts of Europe, North Africa and the Canary Islands, was analysed using random amplified polymorphic DNAs (RAPDs) and intersimple sequence repeats (ISSRs). Genetic distances (Dice) were calculated and used to investigate the correlation between genetic and geographical distances, to construct Neighbour Joining (NJ) trees, and to compare mean genetic distances between areas within and across species. Genetic distances and geographical distances measured along the coast are well correlated in Cakile and Eryngium. This implies that dispersal in both species is largely along the coast. The NJ analyses resulted in the recognition of Atlantic and Mediterranean clusters in both Cakile and Eryngium. The genetic distance between these two clusters is much larger in Eryngium (0.285) than in Cakile (0.037). Mean genetic distances are substantially higher in the Mediterranean than in the Atlantic clusters in both species, and higher in Cakile than in Eryngium particularly in the Atlantic cluster. It is argued that all similarities and differences between the two species can be explained with the presumed distribution of the two species in the Würm glacial as reconstructed from their extant temperature requirements, the distribution of ice cover, permafrost, and sea surface temperatures in that period, and indirect fossil evidence.
Microsatellite analysis of a population crash and bottleneck in the Mauna Kea silversword,Argyroxiphium sandwicensessp.sandwicense(Asteraceae), and its implications for reintroduction
Authors: Friar E. A. , Ladoux T. , Roalson E. H. , Robichaux R. H. 
Published: March 2003

AbstractThe Mauna Kea silversword,Argyroxiphium sandwicensessp.sandwicense, has experienced both a severe population crash associated with an increase in alien ungulate populations on Mauna Kea, and a population bottleneck associated with reintroduction. In this paper, we address the genetic consequences of both demographic events using eight microsatellite loci. The population crash was not accompanied by a significant reduction in number of alleles or heterozygosity. However, the population bottleneck was accompanied by significant reductions in observed number of alleles, effective number of alleles, and expected heterozygosity, though not in observed heterozygosity. The effective size of the population bottleneck was calculated using both observed heterozygosities and allele frequency variances. Both methods corroborated the historical census size of the population bottleneck of at most three individuals. The results suggest that: (i) small populations, even those that result from severe reductions in historical population size and extent, are not necessarily genetically depauperate; and (ii) species reintroduction plans need to be conceived and implemented carefully, with due consideration to the genetic impact of sampling for reintroduction.
Genetic isolation by distance in Arabidopsis thaliana: biogeography and postglacial colonization of Europe
Authors: Sharbel Timothy F. , Haubold Bernhard , Mitchell‐Olds Thomas 
Published: March 2003

Abstract Arabidopsis thaliana provides a useful model system for functional, evolutionary and ecological studies in plant biology. We have analysed natural genetic variation in A. thaliana in order to infer its biogeographical and historical distribution across Eurasia. We analysed 79 amplified fragment length polymorphism (AFLP) markers in 142 accessions from the species’ native range, and found highly significant genetic isolation by distance among A. thaliana accessions from Eurasia and southern Europe. These spatial patterns of genetic variation suggest that A. thaliana colonized central and northern Europe from Asia and from Mediterranean Pleistocene refugia, a trend which has been identified in other species. Statistically significant levels of multilocus linkage disequilibrium suggest intermediate levels of disequilibrium among subsets of loci, and analysis of genetic relationships among accessions reveal a star or bush‐like dendrogram with low bootstrap support. Taken together, it appears that there has been sufficient historical recombination in the A. thaliana genome such that accessions do not conform to a tree‐like, bifurcating pattern of evolution – there is no ‘ecotype phylogeny.’ Nonetheless, significant isolation by distance provides a framework upon which studies of natural variation in A. thaliana may be designed and interpreted.
The genetic architecture of disease resistance in plants and the maintenance of recombination by parasites
Authors: Kover Paula X. , Caicedo Ana Lucia 
Published: March 2003

AbstractParasites represent strong selection on host populations because they are ubiquitous and can drastically reduce host fitness. It has been hypothesized that parasite selection could explain the widespread occurrence of recombination because it is a coevolving force that favours new genetic combinations in the host. A review of deterministic models for the maintenance of recombination reveals that for recombination to be favoured, multiple genes that interact with each other must be under selection. To evaluate whether parasite selection can explain the maintenance of recombination, we review 85 studies that investigated the genetic architecture of plant disease resistance and discuss whether they conform to the requirements that emerge from theoretical models. General characteristics of disease resistance in plants and problems in evaluating resistance experimentally are also discussed. We found strong evidence that disease resistance in plants is determined by multiple loci. Furthermore, in most cases where loci were tested for interactions, epistasis between loci that affect resistance was found. However, we found weak support for the idea that specific allelic combinations determine resistance to different host genotypes and there was little data on whether epistasis between resistance genes is negative or positive. Thus, the current data indicate that it is possible that parasite selection can favour recombination, but more studies in natural populations that specifically address the nature of the interactions between resistance genes are necessary. The data summarized here suggest that disease resistance is a complex trait and that environmental effects and fitness trade‐offs should be considered in future models of the coevolutionary dynamics of host and parasites.
Speciation, hybrid zones and phylogeography — or seeing genes in space and time
Authors: Hewitt Godfrey M. 
Published: March 2003

AbstractThe origins and development of the study of speciation, hybrid zones and phylogeography are outlined using evolutionary iconography. This traces the ideas in this field from Lamarck and Darwin through to the present as represented in diagrams and figures. A ‘tree of trees’ summarizes this growth and current vitality. The new facility to use various DNA sequences from nuclear, mitochondrial and chloroplast genomes to determine genetic variation throughout a species range is examined particularly. There is great genomic subdivision across species distributions, which can be interpreted in the light of the recent demonstrations of severe palaeoclimatic oscillations. Refugia and postglacial colonization routes are proposed for several organisms across Europe. The role of geography in speciation through the Pleistocene is considered. These emerging principles and analyses are applied to data available on a variety of organisms in other regions of the world, such as the Arctic, North America and the Tropics, and including the progress of Homo sapiens through the last ice age. Some suggestions are made for future research directions.
The annual number of breeding adults and the effective population size of syntopic newts (Triturus cristatus, T. marmoratus)
Authors: Jehle R. , Arntzen J. W. , Burke T. , Krupa A. P. , Hödl W. 
Published: March 2003

AbstractPond‐breeding amphibians are deme‐structured organisms with a population genetic structure particularly susceptible to demographic threats. We estimated the effective number of breeding adults (Nb) and the effective population size (Ne) of the European urodele amphibians Triturus cristatus (the crested newt) and T. marmoratus (the marbled newt), using temporal shifts in microsatellite allele frequencies. Eight microsatellite loci isolated from a T. cristatus library were used, five of which proved polymorphic in T. marmoratus, albeit with high frequencies of null alleles at two loci. Three ponds in western France were sampled, situated 4–10 kilometres apart and inhabited by both species. Parent–offspring cohort comparisons were used to measure Nb; samples collected at time intervals of nine or 12 years, respectively, were used to measure Ne. The adult population census size (N) was determined by mark–recapture techniques. With one exception, genetic distances (FST) between temporal samples were lower than among populations. Nb ranged between 10.6 and 101.8 individuals, Ne ranged between 9.6 and 13.4 individuals. For the pond where both parameters were available, Nb/N (overall range: 0.10–0.19) was marginally larger than Ne/N (overall range: 0.09–0.16), which is reflected in the temporal stability of N. In line with the observed differences in reproductive life‐histories between the species, Nb/N ratios for newts were about one order of magnitude higher than for the anuran amphibian Bufo bufo. Despite of the colonization of the study area by T. cristatus only some decades ago, no significant genetic bottleneck could be detected. Our findings give rise to concerns about the long‐term demographic viability of amphibian populations in situations typical for European landscapes.
Phylogeography of the dusky shrew,Sorex monticolus(Insectivora, Soricidae): insight into deep and shallow history in northwestern North America
Authors: Demboski John R. , Cook Joseph A. 
Published: March 2003

AbstractPhylogenetic relationships among the dusky shrew (Sorexmonticolus) and eight related species (S.bairdi,S.bendirii,S.neomexicanus,S.ornatus,S.pacificus,S.palustris,S.sonomaeandS.vagrans) were assessed using sequences from the mitochondrial cytochromebgene (801 bp). Analyses using parsimony and maximum likelihood revealed significant molecular variation not reflected in previous morphological studies of these species. Conversely, three morphologically defined species (S.bairdi,S.neomexicanusandS.pacificus) were poorly differentiated.SorexornatusandS.vagransrepresented basal taxa for a more inclusive group that included: (i) a widespread Continental clade containingS.monticolus(Arizona to Alaska, includingS.neomexicanus); (ii) a Coastal clade containingS.monticolus(Oregon to south‐east Alaska, includingS.bairdiandS.pacificus); (iii) the semiaquatic species (S. bendiriiandS.palustris); and (iv)S.sonomae. Additional subdivision was observed within the Continental clade corresponding to populations from the northern and southern Rocky Mountains. Average uncorrected sequence divergence between the Coastal and Continental clades was 5.3% (range 4.5–6.2%), which exceeds many interspecific comparisons within this species complex and within the genusSorex. Lack of resolution of internal nodes within topologies suggests a deep history of rapid diversification within this group. Late Pleistocene/Holocene glacial perturbations are reflected in the shallow phylogeographic structure within these clades in western North America. Our results suggest also thatS. monticolusis not monophyletic under current taxonomic nomenclature. This perspective on phylogeographic history was developed within a growing comparative framework for other organisms in western North America.
The extent of clonality and genetic diversity in lingonberry (Vaccinium vitis‐idaea L.) revealed by RAPDs and leaf‐shape analysis
Authors: Persson H. A. , Gustavsson B. A. 
Published: March 2003

AbstractNumerous plant species reproduce mainly by clonal growth, implying that levels of genetic variation may be comparatively low. In this study we describe the genetic and genotypic diversity within and between four Swedish populations of the clonal shrub lingonberry, Vaccinium vitis‐idaea L. Two approaches were used to assess the amount and partitioning of variation: automated image analysis of leaf shape and random amplified polymorphic DNA (RAPD) analysis. Morphometric analyses, using moment invariants and elliptic Fourier coefficients, revealed that most of the variation could be attributed to within‐population variation. With the use of 43 polymorphic RAPD markers, we were able to identify 29 different genotypes (i.e. putative clones) among 129 plants from two populations. The genotypic diversity (D: mean 0.84) and evenness (E: mean 0.81) were higher than the average for clonal plant species. Within‐population gene diversity was similar to values reported in nonclonal plants, suggesting that sexual reproduction has played a significant role in these populations despite low levels of seedling recruitment in present‐day populations. An analysis of molecular variance revealed that most of the variation (89.2%) resided within populations. Comparisons between the different suites of characters indicated a congruent pattern of partitions of diversity, particularly when comparing moment invariants and RAPDs. When comparing the ability of the two descriptor suites to assign the plants to the RAPD‐defined clones, elliptic Fourier coefficients yielded the best result; a classification test correctly reassigned 96.9% and 98.1% of the plant material in the two respective populations.
A comparison of microsatellite‐based pairwise relatedness estimators
Authors: Van De Casteele T. , Galbusera P. , Matthysen E. 
Published: March 2003

AbstractStudies of inbreeding depression or kin selection require knowledge of relatedness between individuals. If pedigree information is lacking, one has to rely on genotypic information to infer relatedness. In this study we investigated the performance (absolute and relative) of 10 marker‐based relatedness estimators using allele frequencies at microsatellite loci obtained from natural populations of two bird species and one mammal species. Using Monte Carlo simulations we show that many factors affect the performance of estimators and that different sets of loci promote the use of different estimators: in general, there is no single best‐performing estimator. The use of locus‐specific weights turns out to greatly improve the performance of estimators when marker loci are used that differ strongly in allele frequency distribution. Microsatellite‐based estimates are expected to explain between 25 and 79% of variation in true relatedness depending on the microsatellite dataset and on the population composition (i.e. the frequency distribution of relationship in the population). We recommend performing Monte Carlo simulations to decide which estimator to use in studies of pairwise relatedness.
Molecular identification of fine roots of trees from the Alps: reliable and fast DNA extraction and PCR–RFLP analyses of plastid DNA
Authors: Brunner I. , Brodbeck S. , BÜchler U. , Sperisen C. 
Published: March 2003

AbstractFine roots of trees are intensively used as indicators to assess soil alterations, e.g. those owing to atmospheric inputs of acidifying substances, but their identification to species with morphological criteria is difficult. In this study, we established molecular techniques in order to identify fine roots of the 30 most common tree species of the Alps. We developed a protocol for efficient isolation of DNA from fine roots with extraction of DNA in the presence of polyvinylpyrrolidone (PVP) and polyvinylpolypyrrolidone (PVPP). The trnL (UAA) intron of plastid DNA was used as a marker for fine root identification. We amplified and sequenced this intron with plant universal primers. The size of the sequences ranged from 444 to 672 bp. A synoptic key for species identification was designed on the basis of restriction fragment patterns predicted from sequence data. Using the restriction enzyme TaqI as key enzyme, and where necessary HinfI, RsaI and CfoI, 16 taxa, including Picea abies, Larix decidua, Abies alba, and Fagus sylvatica, the dominant tree species of the Alpine region could be identified by agarose gel electrophoresis of restriction fragments. Fourteen taxa could be identified to the genus level, among them Quercus, Salix and Populus species. In a field study, conducted in a 20 × 30 m plot of a mixed forest with five tree species, fine roots of 43 out of 46 samples were identified and their distributions were mapped. These results demonstrate the utility of our DNA extraction method and of the trnL intron for the identification of fine tree roots.
Postglacial colonization of Northern Europe by distinct phylogeographic lineages of the bullhead, Cottus gobio
Authors: Kontula Tytti , VÄinölä Risto 
Published: March 2003

AbstractThree major phylogeographic lineages of the cottid fish Cottus gobio (bullhead) were identified in northern Europe from mitochondrial DNA sequences and allozyme data. The largely separate freshwater distributions of the lineages demonstrate distinct postglacial colonization histories. West of the Baltic Sea, Swedish lakes were invaded from the southwest (Germany). Another, eastern lineage has colonized the inland waters northeast and east of the Baltic, from refugia in northwest Russia; this lineage comprises a distinct subgroup found only from Estonia. The third lineage, found south and southeast of the Baltic, probably descended from rivers draining to the Black Sea from the north (e.g. Dnepr). In coastal waters of the Baltic Sea, and in near‐coast inland waters, the lineages are now found intermixed in various combinations. The alternating fresh‐ and saltwater phases of the Baltic basin have variously enabled and disabled the use of coastal waters as colonization routes. Hypotheses on the chronology of dispersal and lineage mixing can be based on the distribution of the marker genes and the palæohydrographical record. The diversity of the Fennoscandian bullhead thus comprises anciently diverged (probably mid‐Pleistocene) refugial lineages that in their freshwater range constitute distinct evolutionarily significant units. The thorough mixing of the various genomic origins in and around the Baltic, however, refutes the controversial view of distinct species status for the western and eastern (‘Cottus koshewnikowi’) bullheads. The postglacial contact of the lineages has created new diversity that cannot be interpreted in a conventional hierarchical framework of taxonomic or conservation units.