bluuebunny/crossref_metadata_2025_split huggingface dataset:
Landscape connectivity influences gene flow in a roe deer population inhabiting a fragmented landscape: an individual–based approach
Authors: COULON A. , COSSON J. F. , ANGIBAULT J. M. , CARGNELUTTI B. , GALAN M. , MORELLET N. , PETIT E. , AULAGNIER S. , HEWISON A. J. M. 
Published: August 2004

AbstractChanges in agricultural practices and forest fragmentation can have a dramatic effect on landscape connectivity and the dispersal of animals, potentially reducing gene flow within populations. In this study, we assessed the influence of woodland connectivity on gene flow in a traditionally forest‐dwelling species — the European roe deer — in a fragmented landscape. From a sample of 648 roe deer spatially referenced within a study area of 55 × 40 km, interindividual genetic distances were calculated from genotypes at 12 polymorphic microsatellite loci. We calculated two geographical distances between each pair of individuals: the Euclidean distance (straight line) and the ‘least cost distance’ (the trajectory that maximizes the use of wooded corridors). We tested the correlation between genetic pairwise distances and the two types of geographical pairwise distance using Mantel tests. The correlation was better using the least cost distance, which takes into account the distribution of wooded patches, especially for females (the correlation was stronger but not significant for males). These results suggest that in a fragmented woodland area roe deer dispersal is strongly linked to wooded structures and hence that gene flow within the roe deer population is influenced by the connectivity of the landscape.
Quantitative trait locus analyses and the study of evolutionary process
Authors: ERICKSON DAVID L. , FENSTER CHARLES B. , STENØIEN HANS K. , PRICE DONALD 
Published: August 2004

AbstractThe past decade has seen a proliferation of studies that employ quantitative trait locus (QTL) approaches to diagnose the genetic basis of trait evolution. Advances in molecular techniques and analytical methods have suggested that an exact genetic description of the number and distribution of genes affecting a trait can be obtained. Although this possibility has met with some success in model systems such as Drosophila and Arabidopsis, the pursuit of an exact description of QTL effects, i.e. individual gene effect, in most cases has proven problematic. We discuss why QTL methods will have difficulty in identifying individual genes contributing to trait variation, and distinguish between the identification of QTL (or marker intervals) and the identification of individual genes or nucleotide differences within genes (QTN). This review focuses on what ecologists and evolutionary biologists working with natural populations can realistically expect to learn from QTL studies. We highlight representative issues in ecology and evolutionary biology and discuss the range of questions that can be addressed satisfactorily using QTL approaches. We specifically address developing approaches to QTL analysis in outbred populations, and discuss practical considerations of experimental (cross) design and application of different marker types. Throughout this review we attempt to provide a balanced description of the benefits of QTL methodology to studies in ecology and evolution as well as the inherent assumptions and limitations that may constrain its application.
The impact of microsatellite electromorph size homoplasy on multilocus population structure estimates in a tropical tree (Corythophora alta) and an anadromous fish (Morone saxatilis)
Authors: ADAMS RACHEL I. , BROWN KYLE M. , HAMILTON MATTHEW B. 
Published: August 2004

AbstractMicrosatellite allelic states are determined by electrophoretic sizing of polymerase chain reaction fragments to define electromorphs. Numerous studies have documented that identical microsatellite electromorphs are potentially heterogeneous at the DNA sequence level, a phenomenon called electromorph size homoplasy. Few studies have examined the impact of electromorph size homoplasy on estimates of population genetic parameters. We investigated the frequency of microsatellite electromorph size homoplasy for 12 loci in the tropical treeCorythophora altaand 11 loci in the anadromous fishMorone saxatilisby sequencing 14–23 homozygotes per locus sampled from multiple populations for a total of 453 sequences. Sequencing revealed no homoplasy forM. saxatilisloci. SevenC. altaloci exhibited homoplasy, including single and compound repeat motifs both with and without interruptions. Between 12.5 and 42.9% of electromorphs sampled per locus showed size homoplasy. Two methods of correction for homoplasy inC. altagenerally produced little or no change in single‐locus estimates ofRST, except for two loci in which some additional differentiation among populations was revealed. Twelve‐locus estimates ofRST(including the seven loci corrected for homoplasy) were slightly greater than estimates from uncorrected data, although the 95% confidence intervals overlapped. The frequency of methodological errors such as clerical mistakes or sample mislabelling per genotype scored was estimated at 5.4 and 7.3% forC. altaandM. saxatilis, respectively. Simulations showed that the increase inRSTproduced by homoplasy correction was only slightly larger than variation inRSTestimates expected to be caused by methodological errors.
Genetic structure of desert ground squirrels over a 20‐degree‐latitude transect from Oregon through the Baja California peninsula
Authors: WHORLEY JOSHUA R. , ALVAREZ‐CASTAÑEDA S. TICUL , KENAGY G. J. 
Published: August 2004

AbstractThe genetic structure of populations over a wide geographical area should reflect the demographic and evolutionary processes that have shaped a species across its range. We examined the population genetic structure of antelope ground squirrels (Ammospermophilus leucurus) across the complex of North American deserts from the Great Basin of Oregon to the cape region of the Baja California peninsula. We sampled 73 individuals from 13 major localities over this 2500‐km transect, from 43 to 22° north. Our molecular phylogeographical analysis of 555 bp of the mitochondrial cytochrome bgene and 510 bp of the control region revealed great genetic uniformity in a single clade that extends from Oregon to central Baja California. A second distinct clade occupies the southern half of the peninsula. The minimal geographical structure of the northern clade, its low haplotype diversity and the distribution of pairwise differences between haplotypes suggest a rapid northward expansion of the population that must have followed a northward desert habitat shift associated with the most recent Quaternary climate warming and glacial retreat. The higher haplotype diversity within the southern clade and distribution of pairwise differences between haplotypes suggest that the southern clade has a longer, more stable history associated with a southern peninsular refugium. This system, as observed, reflects both historical and contemporary ecological and evolutionary responses to physical environmental gradients within genetically homogeneous populations.
Variation in mitochondrial DNA reveals multiple distant glacial refugia in black spruce (Picea mariana), a transcontinental North American conifer
Authors: JARAMILLO‐CORREA JUAN P. , BEAULIEU JEAN , BOUSQUET JEAN 
Published: August 2004

AbstractRange‐wide genetic variation of black spruce (Picea mariana) was studied using polymerase chain reaction‐random fragment length polymorphism markers of the mitochondrial genome. Four polymorphic mitochondrial DNA (mtDNA) loci were surveyed and two or three alleles were detected at each locus, resulting in 10 multilocus mtDNA types or mitotypes. A significant subdivision of population genetic diversity was detected (GST = 0.671; NST = 0.726), suggesting low levels of gene flow among populations. The distribution of mitotypes was not random (NST > GST; P < 0.05) and revealed four partially overlapping zones, presumably representative of different glacial populations. Comparison of the genetic structure derived from mtDNA markers and the colonization paths previously deduced from the fossil and pollen records allow us to infer at least three southern and one northeastern glacial populations for black spruce. The patterns revealed in this study suggest that black spruce shares its biogeographical history with other forest‐associated North American species.
Temporal changes in allele frequencies and low effective population size in greater prairie‐chickens
Authors: JOHNSON JEFF A. , BELLINGER M. RENEE , TOEPFER JOHN E. , DUNN PETER 
Published: August 2004

AbstractThe number of greater prairie‐chickens in Wisconsin has decreased by 91% since 1932. The current population of approximately 1500 birds exists primarily in four isolated management areas. In previous studies of the Wisconsin populations we documented low levels of genetic variation at microsatellite loci and the mitochondrial DNA control region. Here we investigate changes in genetic structure between the four management areas in Wisconsin over the last 50 years. We estimated the harmonic mean effective population size (Ne) over the last 50 years by comparing allele frequencies from the early 1950s with those from contemporary samples. Using a pseudo‐likelihood approach that accounted for migration, estimates ofNe(15–32 prairie‐chickens within each management area) were 10 times lower than census numbers from booming‐ground counts. These low estimates ofNeare consistent with increased habitat fragmentation and an increase in genetic isolation between management areas over the last 50 years. The reduction of gene flow between areas has reducedNe, increased genetic drift and, consequently, reduced genetic variation. These results have immediate consequences for the conservation of the prairie‐chicken, and highlight the importance of how mating systems and limited dispersal may exacerbate the loss of genetic variation in fragmented populations.
Testing the utility of internally transcribed spacer sequences in coral phylogenetics
Authors: VOLLMER STEVEN V. , PALUMBI STEPHEN R. 
Published: August 2004

AbstractReef‐building corals often possess high levels of intraindividual and intraspecific ribosomal DNA (rDNA) variation that is largely polyphyletic between closely related species. Polyphyletic rDNA phylogenies coupled with high intraindividual rDNA variation have been taken as evidence of introgressive hybridization in corals. Interpreting the data is problematic because the rDNA cluster evolves in a complex fashion and polyphyletic lineages can be generated by a variety of processes — such as incomplete lineage sorting and slow concerted evolution — in addition to hybridization. Using the genetically characterized Caribbean Acropora hybridization system, we evaluate how well rDNA data perform in revealing patterns of recent introgressive hybridization in contrast to genetic data from four single‐copy loci. While the rDNA data are broadly consistent with the unidirectional introgression seen in other loci, we show that the phylogenetic signature of recent introgressive hybridization is obscured in the Caribbean Acropora by ancient shared rDNA lineages that predate the divergence of the species.
Ex situ population management in the absence of pedigree information
Authors: RUSSELLO M. A. , AMATO G. 
Published: August 2004

AbstractFor captive breeding to play a significant role in conservation, ex situ populations must be scientifically managed to meet objective goals for retaining representative genetic variation. Imperfect genealogical information requires fundamental assumptions to be made that may bias downstream measures of genetic importance, upon which management decisions are based. The impacts of such assumptions are most pronounced within breeding programmes characterized by a high proportion of individuals of unknown ancestry, as exemplified by the large captive population of the St Vincent parrot (Amazona guildingii). The degree to which microsatellite‐based estimates of relatedness may improve upon the assumptions of conventional pedigree‐based management was investigated using genotypic data collected at eight microsatellite loci and two marker‐based relatedness estimators. The measure, rxyLR, was found to explain the highest amount of variation in true relatedness. Integration of pairwise estimates of founder relatedness with studbook data transformed current understanding of the relatedness structure of the A. guildingii population from two subgroups characterized by a high and low degree of relatedness, respectively, to a situation where all 72 individuals are prioritized for breeding according to their estimated mean kinships. Furthermore, the discovery of opposing, directional bias exhibited by rxyLR and rxyQG in assigning dyads to a given relationship category suggests that an approach that utilizes a combination of pairwise relatedness estimators may provide the most genetic information for balancing the dual considerations of maximizing gene diversity and minimizing inbreeding in developing breeding recommendations.
Spatial partitioning and asymmetric hybridization among sympatric coastal steelhead trout (Oncorhynchus mykiss irideus), coastal cutthroat trout (O. clarki clarki) and interspecific hybrids
Authors: OSTBERG CARL O. , SLATTON STACEY L. , RODRIGUEZ RUSSELL J. 
Published: August 2004

AbstractHybridization between sympatric species provides unique opportunities to examine the contrast between mechanisms that promote hybridization and maintain species integrity. We surveyed hybridization between sympatric coastal steelhead (Oncorhynchus mykiss irideus) and coastal cutthroat trout (O. clarki clarki) from two streams in Washington State, Olsen Creek (256 individuals sampled) and Jansen Creek (431 individuals sampled), over a 3‐year period. We applied 11O. mykiss‐specific nuclear markers, 11O. c. clarki‐specific nuclear markers and a mitochondrial DNA marker to assess spatial partitioning among species and hybrids and determine the directionality of hybridization. F1and post‐F1hybrids, respectively, composed an average of 1.2% and 33.6% of the population sampled in Jansen Creek, and 5.9% and 30.4% of the population sampled in Olsen Creek. A modest level of habitat partitioning among species and hybrids was detected. Mitochondrial DNA analysis indicated that all F1hybrids (15 from Olsen Creek and five from Jansen Creek) arose from matings between steelhead females and cutthroat males implicating a sneak spawning behaviour by cutthroat males. First‐generation cutthroat backcrosses containedO. c. clarkimtDNA more often than expected suggesting natural selection against F1hybrids. More hybrids were backcrossed toward cutthroat than steelhead and our results indicate recurrent hybridization within these creeks. Age analysis demonstrated that hybrids were between 1 and 4 years old. These results suggest that within sympatric salmonid hybrid zones, exogenous processes (environmentally dependent factors) help to maintain the distinction between parental types through reduced fitness of hybrids within parental environments while divergent natural selection promotes parental types through distinct adaptive advantages of parental phenotypes.
High degree of population subdivision in a widespread amphibian
Authors: PALO JUKKA U. , SCHMELLER DIRK S. , LAURILA ANSSI , PRIMMER CRAIG R. , KUZMIN SERGIUS L. , MERILÄ JUHA 
Published: August 2004

AbstractIn general, amphibians are known to exhibit a higher degree of population subdivision than any other major animal taxa, but large‐scale population genetic surveys of widely distributed species are still scarce, especially in the Eurasian continent. Using microsatellite markers and mitochondrial DNA sequences, we investigated the large‐scale population genetic structure of the common frog (Rana temporaria) — one of the most widespread amphibians of the Palearctic region. Analyses of cytochrome b sequences revealed evidence for two distinct lineages inhabiting western and eastern parts of Europe. The separation of these lineages c. 700 000 years ago may have been induced by the onset of the Middle Pleistocene continental glaciations. Analyses of the variability of microsatellite loci within each of the clades revealed evidence for evolution of a high degree of population subdivision (FST ∼ 0.23) even in northern Fennoscandia, colonized less than 10 000 years ago. The high level of substructuring is puzzling in the face of an apparently high dispersal capacity, as evidenced by the rather rapid recolonization of northern Europe. This suggests that processes other than restricted dispersal capacity need to be explored as explanations for the high degree of population subdivision in amphibians. The colonization of northern Europe has been accompanied by loss of genetic variability as evidenced by decreasing levels of intrapopulational genetic variability in microsatellite loci from south to north across Europe.
Population‐structure and genetic diversity in a haplochromine fish cichlid of a satellite lake of Lake Victoria
Authors: ABILA ROMULUS , BARLUENGA MARTA , ENGELKEN JOHANNES , MEYER AXEL , SALZBURGER WALTER 
Published: August 2004

AbstractThe ∼500 species of the cichlid fish species flock of Lake Victoria, East Africa, have evolved in a record‐setting 100 000 years and represent one of the largest adaptive radiations. We examined the population structure of the endangered cichlid species Xystichromis phytophagus from Lake Kanyaboli, a satellite lake to Lake Victoria in the Kenyan Yala wetlands. Two sets of molecular markers were analysed — sequences of the mitochondrial control region as well as six microsatellite loci — and revealed surprisingly high levels of genetic variability in this species. Mitochondrial DNA sequences failed to detect population structuring among the three sample populations. A model‐based population assignment test based on microsatellite data revealed that the three populations most probably aggregate into a larger panmictic population. However, values of population pairwise FST indicated moderate levels of genetic differentiation for one population. Eleven distinct mitochondrial haplotypes were found among 205 specimens of X. phytophagus, a relatively high number compared to the total number of 54 haplotypes that were recovered from hundreds of specimens of the entire cichlid species flock of Lake Victoria. Most of the X. phytophagus mitochondrial DNA haplotypes were absent from the main Lake Victoria, corroborating the putative importance of satellite lakes as refugia for haplochromine cichlids that went extinct from the main lake in the last decades and possibly during the Late Pleistocene desiccation of Lake Victoria.
Size distribution and genetic structure in relation to clonal growth within a population ofMagnolia tomentosaThunb. (Magnoliaceae)
Authors: SETSUKO S. , ISHIDA K. , TOMARU N. 
Published: August 2004

AbstractTo establish a baseline for conservation of a threatened clonal tree,Magnolia tomentosa, we investigated size distribution and genetic structure within a population, using six microsatellite markers. Within the study site, 1044 living ramets (stems) were distinguished into 175 genets (individuals). The mean number of ramets per genet was 5.97, and 76% of all genets had multiple ramets. Genets, which apparently produced new ramets through sprouting and layering, were generally composed of several large ramets and many small ramets. Spatial autocorrelation analysis of microsatellite alleles revealed positive autocorrelation over short distances for both ramets and genets. The Moran'sI‐value of ramets in the shortest distance class was 3.8 times larger than that of genets, reflecting the effect of clonal growth. To analyse the size‐class differences in genetic structure, the 175 genets were separated into two size classes, small and large. The correlogram for the small genets exhibited positive spatial autocorrelation in the shortest distance class, but this was not the case for the correlogram for the large genets, indicating that genetic structure is weakened or lost through self‐thinning as the genets grow. TheFISvalue over all loci for the small genets was positive and deviated significantly from zero, while the corresponding value for the large genets was close to zero. The excess homozygotes in the small genets may be the result of genetic substructuring and/or inbreeding, and the reduction in homozygote frequency from the small to large genets may be because of loss of genetic structure and/or inbreeding depression.
Molecular signals for Late Tertiary/Early Quaternary range splits of an Eurasian steppe plant: Clausia aprica (Brassicaceae)
Authors: FRANZKE A. , HURKA H. , JANSSEN D. , NEUFFER B. , FRIESEN N. , MARKOV M. , MUMMENHOFF K. 
Published: August 2004

AbstractSeveral vegetation belts stretch continuously from Europe to Asia, taiga and steppe being most prominent. Numerous plant species within these belts share a conspicuous distribution area, which is longitudinally contracted or disrupted approximately along longitude 70° E. To date no hypothesis for this intriguing distribution pattern has been put forward. We detected molecular footprints in the contemporary genetic composition in nuclear DNA (ITS1, ITS2) and chloroplast DNA (trnL–trnF spacer region) of the steppe element Clausia aprica (Brassicaceae) providing evidence for a severe longitudinal range split and genetic differentiation east of the Ural Mountains about 1 million years ago caused by Quaternary climatic oscillations. Clausia aprica provides the first phylogeographical analysis on the intraspecific evolution of an Eurasian steppe plant.
Sex‐specific correlation between heterozygosity and clone size in the trematode Schistosma mansoni
Authors: PRUGNOLLE FRANCK , CHOISY MARC , THÉRON ANDRÉ , DURAND PATRICK , DE MEEÛS THIERRY 
Published: August 2004

AbstractThe mode of reproduction (sexual and/or asexual) and the mating system determine the patterns of gene transmission and genotype formation across generations. Schistosoma mansoni is a dioecious trematode that necessarily alternates sexual and asexual reproduction during its life cycle. In a previous study of the distribution of S. mansoni genetic variability within and between definitive host individuals, we noticed that deleting multilocus genotypes from each infrapopulation so as to keep only one copy of each multilocus genotype, seemed to have a substantial effect on FIS values. More precisely, female FIS increased when repeated genotypes were removed whereas no effect was observed on male FIS. This suggested that multilocus genotypes at high frequency tended to be more heterozygous. The aim of the present study is specifically to test and analyse this phenomenon. We demonstrate that the number of repetitions per clone correlates with individual heterozygosity. This effect is however, sex‐specific: only female clone size correlates with heterozygosity. We discuss this phenomenon in relation to the heterozygosity–fitness relationship and the sex‐specific response to inbreeding depression.