bluuebunny/crossref_metadata_2025_split huggingface dataset:
A graph‐theoretic approach to the partition of individuals into full‐sib families
Authors: Beyer Jennifer , May Bernie 
Published: July 2003

AbstractWe present an algorithm to partition a single generation of individuals into full‐sib families using single‐locus co‐dominant marker data. Pairwise likelihood ratios are used to create a graph that represents the full‐sib relationships within the data set. Connected‐component and minimum‐cut algorithms from the graph theory are then employed to find the full‐sib families within the graph. The results of a large‐scale simulation study show that the algorithm is able to produce accurate partitions when applied to data sets with eight or more loci. Although the algorithm performs best when the distribution of allele frequencies and family sizes in a data set is uniform, the inclusion of more loci or alleles per locus allows accurate partitions to be created from data sets in which these distributions are highly skewed.
Population genetic structure of rock ptarmigan Lagopus mutus in Northern and Western Europe
Authors: Caizergues A. , Bernard‐Laurent A. , Brenot J.‐F. , Ellison L. , Rasplus J. Y. 
Published: July 2003

AbstractAlpine species may be losing habitat because of global warming. Setting management priorities for such species is thus urgent and cannot be achieved without data on population structure. We studied the structure of rock ptarmigan (Lagopus mutus) populations in the Pyrenees, Alps and Norway, using six microsatellites. We found that rock ptarmigan in the Pyrenees were genetically impoverished compared with those in the Alps and Norway, and displayed a greater divergence (Pyrenees vs. Alps or Norway: θST = 0.16, Alps vs. Norway, θST = 0.04). In the Alps, despite a weak genetic differentiation between localities up to 200 km apart (θST = 0.011), a significant isolation‐by‐distance (IBD) effect was detected. When computed for each sex separately this IBD effect was significant for males but not for females, suggesting that males are highly philopatric.
Long‐distance colonization, isolation by distance, and historical demography in a relictual Mexican pinyon pine (Pinus nelsoniiShaw) as revealed by paternally inherited genetic markers (cpSSRs)
Authors: Cuenca A. , Escalante A. E. , Piñero D. 
Published: July 2003

AbstractPinus nelsoniiis a relictual pinyon pine distributed across a wide altitudinal range in semiarid zones in Mexico near the border between the States of Nuevo León and Tamaulipas. It also occurs in small patches in the State of San Luis Potosí.Pinus nelsoniiis classified in the monotypic subsectionNelsoniae, separated from other pinyon pines (subsectionCembroides), because it possesses several distinctive characters including persistent fascicle sheaths, connate needles, and a distinctive wood anatomy. In the present study, chloroplast simple sequence repeats (cpSSRs) were used to estimate genetic variation in most known populations (nine) ofP. nelsonii. The genetic variation (HT = 0.73; 27 haplotypes in 256 individuals) is moderate when compared to other pine species. Population differentiation ranged between low and moderate (FST = 0.13 andRST = 0.05), as did the Nei and Goldstein genetic distances between populations. However, this pattern varied depending on whether the infinite alleles or stepwise mutation model was used. In the former case a significant isolation by distance was found, but not in the latter. A significant association between geographical and genetic structure in one clade, through a nested clade analysis, was found, which suggested long‐distance colonization between 125 000 and 309 000 years ago. We found weak evidence for a population expansion. A mismatch distribution suggests thatP. nelsoniipopulations underwent an expansion 4.25 times their size between 59 000 and 146 000 years ago. On the other hand, the populations’ star‐like phylogeny and a slight parabolic relationship between coalescence times and lineage number also suggest weak population expansion. Overall, this species appears to have been in demographic stasis for a large proportion of the time detected by the markers used.
Genetic structure of kestrel populations and colonization of the Cape Verde archipelago
Authors: Hille S. M. , Nesje M. , Segelbacher G. 
Published: July 2003

AbstractGenetic diversity and population structure were studied in eight populations of the kestrelFalco tinnunculusto identify the genetic consequences of spatial distribution and to infer the colonization patterns of the Cape Verde archipelago. We studied genetic differentiation and gene flow among seven island populations and one mainland population using nine microsatellite loci. Within the archipelago, differentiation was strong and genetic diversity and heterozygosity were low but variable among populations. Two subspeciesF. tinnunculus neglectuson the northwestern islands andF. tinnunculus alexandrion all the other islands were identified as genetically distinct units.F. t. alexandricould be further separated into two groups on eastern and southern islands. Populations are probably founded by birds originating from the mainland. Immigration is more likely to the eastern and southern populations, whereas the northwestern islands with the lowest genetic diversity and highest differentiation are likely to exhibit fewer founding events by immigrants. The number of founding events on each island may depend not only on geographical distance to neighbouring populations, but also on directional immigration due to the northeastern trade winds. This may explain differences in genetic differentiation and diversity between populations and subspecies and may enable allopatric speciation.
Lack of molecular genetic divergence between sea‐ranched and wild sea trout (Salmo trutta)
Authors: Palm S. , Dannewitz J. , Järvi T. , Petersson E. , Prestegaard T. , Ryman N. 
Published: July 2003

AbstractThe supportive breeding programme for sea trout (Salmo trutta) in the River Dalälven, Sweden, is based on a sea‐ranched hatchery stock of local origin that has been kept ‘closed’ to the immigration of wild genes since the late 1960s (about seven generations). In spite of an apparent potential for substantial uni directional gene flow from sea‐ranched to wild (naturally produced) trout, phenotypic differences with a presumed genetic basis have previously been observed between the two ‘stocks’. Likewise, two previous studies of allozyme and mitochondrial DNA variation based on a single year of sampling have indicated genetic differentiation. In the present study we used microsatellite and allozyme data collected over four consecutive years, and tested for the existence of overall genetic stock divergence while accounting for temporal heterogeneity. Statistical analyses of allele frequency variation (F‐statistics) and multilocus genotypes (assignment tests) revealed that wild and sea‐ranched trout were significantly different in three of four years, whereas no overall genetic divergence could be found when temporal heterogeneity among years within stocks was accounted for. On the basis of estimates of effective population size in the two stocks, and of FST between them, we also assessed the level of gene flow from sea‐ranched to wild trout to be ≈ 80% per generation (with a lower confidence limit of ≈ 20%). The results suggest that the reproductive success of hatchery and naturally produced trout may be quite similar in the wild, and that the genetic characteristics of the wild stock are largely determined by introgressed genes from sea‐ranched fish.
Comparison of microsatellite and blood protein diversity in sheep: inconsistencies in fragmented breeds
Authors: Tapio M. , Miceikiené I. , Vilkki J. , Kantanen J. 
Published: July 2003

AbstractFinnsheep, Romanov, Oxford Down and three local breeds from Finland or northwestern Russia were assessed at 15 microsatellite and 7 protein loci. A novel albumin allele was identified. Diversity patterns were mostly concordant between marker types, but discrepancies appeared for the local Viena and Vepsia sheep, both demonstrating frequent linkage disequilibria for both marker types and excess of homozygotes for microsatellites, and in the case of Vepsia also for proteins as signs of breed fragmentation. On the basis of microsatellite data, the neighbour‐joining tree and two‐dimensional map constructed from DA distances suggested that difference in longitude of breed origin would relate to breed relationship, whereas on the basis of protein data latitude would have this quality. These different impressions resulted because genetic distances involving Vepsia sheep were relatively low for protein variation compared with microsatellites. Microsatellite variation correlated positively with protein variation, but for the local Viena sheep protein variation was comparatively low. Populations had significant differences in allelic richness, but not in genetic diversity. Analysis implied that at least 30 polymorphic loci were needed to detect a difference in diversity between populations using a paired t‐test, if the true mean diversity difference was 0.2. In the total sample, proteins demonstrated larger θ‐values, but this was reversed for Finnsheep, for which model‐based clustering of microsatellite genotypes revealed a structure associated with coat colour. Imported and rare sheep exhibited lowered allelic variability and increased frequency of pairwise disequilibria between unlinked markers. Our results emphasize that more loci are required for studying fragmented breeds.
Out of Anatolia: longitudinal gradients in genetic diversity support an eastern origin for a circum‐Mediterranean oak gallwasp Andricus quercustozae
Authors: Rokas Antonis , Atkinson Rachel J. , Webster Lucy , Csóka György , Stone Graham N. 
Published: July 2003

AbstractMany studies have addressed the latitudinal gradients in intraspecific genetic diversity of European taxa generated during postglacial range expansion from southern refugia. Although Asia Minor is known to be a centre of diversity for many taxa, relatively few studies have considered its potential role as a Pleistocene refugium or a potential source for more ancient westward range expansion into Europe. Here we address these issues for an oak gallwasp, Andricus quercustozae (Hymenoptera: Cynipidae), whose distribution extends from Morocco along the northern coast of the Mediterranean through Turkey to Iran. We use sequence data for a fragment of the mitochondrial gene cytochrome b and allele frequency data for 12 polymorphic allozyme loci to answer the following questions: (1) which regions represent current centres of genetic diversity for A. quercustozae? Do eastern populations represent one refuge or several discrete glacial refugia? (2) Can we infer the timescale and sequence of the colonization processes linking current centres of diversity? Our results suggest that A. quercustozae was present in five distinct refugia (Iberia, Italy, the Balkans, southwestern Turkey and northeastern Turkey) with recent genetic exchange between Italy and Hungary. Genetic diversity is greatest in the Turkish refugia, suggesting that European populations are either (a) derived from Asia Minor, or (b) subject to more frequent population bottlenecks. Although Iberian populations show the lowest diversity for putatively selectively neutral markers, they have colonized a new oak host and represent a genetically and biologically discrete entity within the species.
Using faecal DNA sampling and GIS to monitor hybridization between red wolves (Canis rufus) and coyotes (Canis latrans)
Authors: Adams J. R. , Kelly B. T. , Waits L. P. 
Published: July 2003

AbstractThe US Fish and Wildlife Service's (USFWS) Red Wolf Recovery Program recognizes hybridization with coyotes as the primary threat to red wolf recovery. Efforts to curb or stop hybridization are hampered in two ways. First, hybrid individuals are difficult to identify based solely on morphology. Second, managers need to effectively search 6000 km2 for the presence of coyotes and hybrids. We develop a noninvasive method to screen large geographical areas for coyotes and hybrids with maternal coyote ancestry by combining mitochondrial DNA sequence analysis of faeces (scat) and geographic information system (GIS) technology. This method was implemented on the Alligator River National Wildlife Refuge (1000 km2) in northeastern North Carolina. A total of 956 scats were collected in the spring of 2000 and 2001 and global positioning system (GPS) coordinates were recorded. Seventy‐five percent of the scats were assigned to species and five coyote/hybrid scats were detected. Placement of scat location coordinates on a map of the experimental population area revealed that four of the coyote/hybrid scats were detected within the home ranges of sterilized hybrids. The other coyote/hybrid scat indicated the presence of a previously unknown individual. We suggest this method be expanded to include more of the experimental population area and be optimized for use with nuclear markers to improve detection of hybrid and back‐crossed individuals.
Gene dispersal and outbreeding in a philopatric mammal
Authors: Winters Jonathan B. , Waser Peter M. 
Published: July 2003

AbstractExtensive mark–recapture data from banner‐tailed kangaroo rats,Dipodomys spectabilis, have shown that both males and females are highly philopatric and suggest the possibility of close inbreeding. However, indirect analyses based on genetic structure appear to contradict direct observations, suggesting longer dispersal distances. Using microsatellite genotypes from most members of a banner‐tailed kangaroo rat population during five successive breeding seasons, we ask how relatedness is influenced by dispersal and how it in turn influences mating patterns. The data confirm that, because of philopatry, neighbours are often close relatives. However, patterns of parentage also show that the average distance between mates is large relative to natal dispersal distances and larger than the average distance between nearest opposite‐sexed neighbours. Females’ mates were often not their nearest male neighbour and many were less related than the nearest male neighbour. We detected multiple paternity in some females’ litters; both sexes produce offspring with multiple mates within and between breeding seasons. At the population level, heterozygosities were high and estimates ofFwere low, indicating that levels of inbreeding were low. Using individual inbreeding coefficients of all juveniles to estimate their parents’ relatedness, we found that parental relatedness was significantly lower than relatedness between nearest opposite‐sexed adult neighbours. Thus in philopatric populations, long breeding forays can cause genes to move further than individuals disperse, and polyandry may serve to reduce relatedness between mates.
Inferences from mitochondrial DNA patterns on the domestication history of alfalfa (Medicago sativa)
Authors: Muller M. H. , Prosperi J. M. , Santoni S. , Ronfort J. 
Published: July 2003

AbstractThe evolutionary history of a wild–cultivated complex is the outcome of different factors, among which are the domestication of the cultivated form, its geographical and demographic expansion, as well as gene flow between natural and cultivated populations. To clarify this history for alfalfa (Medicago sativa), we adopted a phylogeographical approach based on a sample of natural and cultivated populations of the M. sativa species complex. This sample was characterized for mtDNA variation through restriction fragment length polymorphisms. Twenty‐two mitotypes were identified in the whole data set (155 individuals). In the wild pool from the presumed area of origin (Near East to Central Asia), the diversity was high but the absence of geographical differentiation hinders a more precise location of the centre of domestication. Within the cultivated alfalfa, the geographical structure suggests strongly the existence of at least two independent routes of dissemination of alfalfa from its centre of origin. In particular, original mitotypes detected in some regions suggest that wild populations not sampled in this study, and located outside the presumed area of domestication, may have contributed to the diversity of the cultivated pool. Finally, analysis of the mtDNA variation shows that natural populations collected in Spain constitute an endemic wild pool now introgressed partially by cultivated alfalfa.
Genetic structure and gene flow in a metapopulation of an endangered plant species,Silene tatarica
Authors: Tero N. , Aspi J. , Siikamäki P. , Jäkäläniemi A. , Tuomi J. 
Published: July 2003

AbstractWe investigated the distribution of genetic variation within and between seven subpopulations in a riparian population ofSilene tataricain northern Finland by using amplified fragment length polymorphism (AFLP) markers. A Bayesian approach‐based clustering program indicated that the marker data contained not only one panmictic population, but consisted of seven clusters, and that each original sample site seems to consist of a distinct subpopulation. A coalescent‐based simulation approach shows recurrent gene flow between subpopulations. Relative highFSTvalues indicated a clear subpopulation differentiation. However,amovaanalysis and UPGMA‐dendrogram did not suggest any hierarchical regional structuring among the subpopulations. There was no correlation between geographical and genetic distances among the subpopulations, nor any correlation between the subpopulation census size and amount of genetic variation. Estimates of gene flow suggested a low level of gene flow between the subpopulations, and the assignment tests proposed a few long‐distance bidirectional dispersal events between the subpopulations. No apparent difference was found in within‐subpopulation genetic diversity among upper, middle and lower regions along the river. Relative high amounts of linkage disequilibrium at subpopulation level indicated recent population bottlenecks or admixture, and at metapopulation levels a high subpopulation turnover rate. The overall pattern of genetic variation within and between subpopulations also suggested a ‘classical’ metapopulation structure of the species suggested by the ecological surveys.
Phylogeography of the rock partridge (Alectoris graeca)
Authors: Randi E. , Tabarroni C. , Rimondi S. , Lucchini V. , Sfougaris A. 
Published: July 2003

AbstractWe used mitochondrial DNA control‐region and microsatellite data to infer the evolutionary history and past demographic changes in 332 rock partridges (Alectoris graeca) sampled from throughout the species’ distribution range, with the exception of the central Balkans region. Maternal and biparental DNA markers indicated concordantly that rock partridge populations are structured geographically (mtDNA φST = 0.86, microsatelliteFST = 0.35;RST = 0.31;P < 0.001). Phylogenetic analyses of 22 mtDNA haplotypes identified two major phylogroups (supported by bootstrap values = 93%), splitting partridges from Sicily vs. all the other sampled populations at an average Tamura–Nei genetic distance of 0.035, which corresponds to 65% of the average distance between closely related species ofAlectoris. Coalescent estimates of divergence times suggested that rock partridges in Sicily were isolated for more than 200 000 years. This deep subdivision was confirmed by multivariate, Bayesian clustering and population assignment analyses of microsatellite genotypes, which supported also a subdivision of partridges from the Alps vs. populations in the Apennines, Albania and Greece. Partridges in the Apennines and Albania–Greece were probably connected by gene flow since recently through a late Pleistocene Adriatic landbridge. Deglaciated Alps were probably colonized by distinct and, perhaps, not yet sampled source populations. Bottleneck and mismatch analyses indicate that rock partridges have lost variability through past population declines, and did not expand recently. Deglaciated areas could have been recolonized without any strong demographic expansion. Genetic data partially supported subspecies subdivisions, and allowed delimiting distinct conservation units. Rock partridges in Sicily, formally recognized asA. g. whitakeri, met the criteria for a distinct evolutionary significant unit.
Erfolgreiche Reduktion des SCORAD‐Scores bei Kindern mit atopischem Ekzem im 6‐Wochen‐Vergleich durch Kurzschulung mit einem vereinfachten Hautmodell
Authors: Kardorff Bernd , Schnelle‐Parker Gisela , Kardorff Maria , Wahlen Manuela , d'Orville Inga Hönig , Dorittke Peter 
Published: July 2003

Zusammenfassung Hintergund: Zur langfristigen Stabilisierung des Hautbefundes bei Patienten mit atopischem Ekzem ist die konsequente Durchführung einer Hautpflege essentiell. Im Rahmen der ambulanten dermatologischen Sprechstunde bleibt häufig zu wenig Zeit für eine intensive Aufklärung der Patienten. Zur Evaluation der Effektivität einer kurzen, aber eindrucksvollen praktischen Hautpflegeschulung mit dem „Hautmodell nach Kardorff, Schnelle‐Parker” während der normalen Sprechstunde führten wir eine randomisierte prospektive Vergleichsstudie durch. Patienten und Methodik: 30 konsekutiv in unserer Praxis als Patienten vorstellig gewordene Kinder zwischen 3 und 6 Jahren mit mittelschwerem atopischem Ekzem wurden eingeschlossen. Die Hälfte der Patienten erhielt an den Tagen 0 und 14 eine aktive Kurzzeitschulung von 10 Minuten mit dem Hautmodell, die Kontrollgruppe erhielt in der selben Zeit intensive verbale Erklärungen wie bei einer dermatologischen Routinebehandlung. Der SCORAD‐Score wurde an den Tagen 0, 14 und 42 blind ermittelt. Ergebnisse: Nach 42 Tagen hatte die mit dem „Hautmodell nach Kardorff, Schnelle‐Parker” geschulte Gruppe einen signifikant geringeren SCORAD‐Score als die Kontrollgruppe (p < 0,006). Schlußfolgerungen: Durch die auch für Vorschulkinder einleuchtende, den Tastsinn einbeziehende Schulung mit dem Hautmodell wird eine bessere Compliance in Bezug auf regelmäßige Hautpflege erzielt. Hierdurch werden positive Effekte für das langfristige Erkrankungsmanagement des atopischen Ekzems erwartet.