bluuebunny/crossref_metadata_2025_split huggingface dataset:
Microsatellite diversity and conservation of a relic trout population: McCloud River redband trout
Authors: Nielsen J. L. , Crow K. D. , Fountain M. C. 
Published: March 2003

AbstractRainbow trout native to the McCloud River, California, USA (Oncorhynchus mykiss stonei) are thought to represent a relic, nonanadromous trout adapted to harsh, fragmented environments. These fish, commonly named McCloud River ‘redband’ trout, survive in their most primitive form in a small, spring‐fed stream, Sheepheaven Creek, in the upper McCloud River drainage. Turn‐of‐the‐century fisheries records document both coastal anadromous steelhead and freshwater resident trout within the McCloud River drainage. The phylogenetic position of the McCloud River redband trout within O. mykiss has been debated for over 50 years. Based on phenotypic evidence, these fish were first reported as ‘southern Sierra golden trout’ by Wales in 1939.
Behnke (1970) considered them a relic subspecies of nonanadromous, fine‐scaled trout. Allozyme and mitochondrial DNA evidence suggested a coastal lineage. In this study, we examined within‐ and among‐basin genetic associations for Sheepheaven Creek redband trout using 11 microsatellite loci. Within‐basin analyses supported unique genetic characteristics in Sheepheaven Creek’s trout in comparisons with other McCloud River rainbow trout. Microsatellite data supported significant independence between Sheepheaven Creek fish and hatchery rainbow trout. Inter‐basin genetic distance analyses positioned Sheepheaven Creek fish with samples collected from Lassen Creek, a geographically proximate stream containing inland redband trout. California’s redband trout shared a close genetic association with Little Kern River golden trout (O.m. whitei) and isolated rainbow trout from Rio Santo Domingo, Baja, Mexico (O.m. nelsoni), suggesting a vicariant distribution of microsatellite diversity throughout the southern range of this species.
Mitochondrial DNA phylogeography and population history of the grey wolfCanis lupus
Authors: Vilà C. , Amorim I. R. , Leonard J. A. , Posada D. , Castroviejo J. , Petrucci‐Fonseca F. , Crandall K. A. , Ellegren H. , Wayne R. K. 
Published: March 2003

AbstractThe grey wolf (Canis lupus) and coyote (C. latrans) are highly mobile carnivores that disperse over great distances in search of territories and mates. Previous genetic studies have shown little geographical structure in either species. However, population genetic structure is also influenced by past isolation events and population fluctuations during glacial periods. In this study, control region sequence data from a worldwide sample of grey wolves and a more limited sample of coyotes were analysed. The results suggest that fluctuating population sizes during the late Pleistocene have left a genetic signature on levels of variation in both species. Genealogical measures of nucleotide diversity suggest that historical population sizes were much larger in both species and grey wolves were more numerous than coyotes. Currently, about 300 000 wolves and 7 million coyotes exist. In grey wolves, genetic diversity is greater than that predicted from census population size, reflecting recent historical population declines. By contrast, nucleotide diversity in coyotes is smaller than that predicted by census population size, reflecting a recent population expansion following the extirpation of wolves from much of North America. Both species show little partitioning of haplotypes on continental or regional scales. However, a statistical parsimony analysis indicates local genetic structure that suggests recent restricted gene flow.
Genetic relationships in the peregrine falcon (Falco peregrinus) analysed by microsatellite DNA markers
Authors: Nesje M. , Røed K. H. , Lifjeld J. T. , Lindberg P. , Steen O. F. 
Published: March 2003

AbstractMicrosatellite DNA markers were developed from a peregrine falcon (Falco peregrinus) and genetic relationships among peregrine falcons in southern Norway were analysed using the markers. The genomic DNA library was screened for the presence of dinucleotide microsatellite repeats. Twelve loci revealed polymorphism through the initial analysis of 24 unrelated peregrine falcons, and Mendelian inheritance was confirmed in two peregrine falcon families bred in captivity. The estimated mean probability of identical genotypes in two unrelated individuals was 3 × 10−8, and the combined exclusion probability for parentage testing was 0.99 and 0.94 for one or both parents unknown, respectively. The markers were used to investigate the parentage of peregrine broods from the same nest site from different breeding seasons, and subsequently the nest‐site fidelity of the breeding peregrines. High nest‐site fidelity was found by studying pairwise comparisons of relatedness (rxy) estimates among chicks at six nest sites from three different breeding seasons. Cross‐species amplifications showed that most loci also appeared to amplify polymorphic products in the gyrfalcon (F. rusticolus), merlin (F. columbarius), hobby (F. subbuteo) and kestrel (F. tinnunculus), demonstrating that the loci will provide powerful genetic markers in these falcons too.
Glacial refugia of limber pine (Pinus flexilisJames) inferred from the population structure of mitochondrial DNA
Authors: Mitton J. B. , Kreiser B. R. , Latta R. G. 
Published: March 2003

AbstractTo make inferences about the glacial refugia that harboured the limber pine,Pinus flexilisJames, we examined the range‐wide population structure of mitochondrial DNA (mtDNA) with eight size variants in the second intron ofnad1. The data consisted of haplotypes from 704 trees collected from 40 localities. The value ofFSTfor these populations was 0.80, which is a much larger value than has been reported for allozymes and chloroplast DNA (cpDNA) in limber pine, and it suggests that the number of seeds moving among localities per generation is ≈ 0.12. Gene flow of this magnitude would allow mutation and subsequent genetic drift to have a substantial impact on the population structure of mtDNA. The majority of the mtDNA haplotypes are restricted to minor portions of the geographical range. The data are consistent with mtDNA differentiation in seven glacial refugia, followed by dispersal out of those refugia.
Geographic distribution and frequency of a taurine Bos taurus and an indicine Bos indicus Y specific allele amongst sub‐Saharan African cattle breeds
Authors: Hanotte O. , Tawah C. L. , Bradley D. G. , Okomo M. , Verjee Y. , Ochieng J. , Rege J. E. O. 
Published: March 2003

AbstractWe report for the first time, and for the whole of sub‐Saharan Africa, the geographical distribution and the frequency of an indicine and a taurine Y specific allele amongst African cattle breeds. A total of 984 males from 69 indigenous African populations from 22 countries were analysed at the microsatellite locus INRA 124. The taurine allele is probably the oldest one on the continent. However, the taurine and the indicine alleles were present in 291 males (30%), and 693 males (70%), respectively. More particularly, 96% of zebu males (n = 470), 50% of taurine males (n = 263), 29% of sanga males (crossbreed Bos taurus × Bos indicus, n = 263) and 95% of zebu × sanga crossbred males (n = 56) had the indicine allele. The Borgou, a breed classified as zebu × taurine cross showed only the zebu allele (n = 12). The indicine allele dominates today in the Abyssinian region, a large part of the Lake Victoria region and the sahelian belt of West Africa. All the sanga males (n = 64) but only one from the Abyssinian region had the indicine allele. The taurine allele is the commonest only among the sanga breeds of the southern African region and the trypanotolerant taurine breeds of West Africa. In West Africa and in the southern Africa regions, zones of introgression were detected with breeds showing both Y chromosome alleles. Our data also reveal a pattern of male zebu introgression in Mozambique and Zimbabwe, probably originating from the Mozambique coast. The sanga cattle from the Lake Victoria region and the Kuri cattle of Lake Chad, cattle populations surrounded by zebu breeds were, surprisingly, completely devoid of the indicine allele. Human migration, phenotypic preferences by the pastoralists, adaptation to specific habitats and to specific diseases are the main factors explaining the present‐day distribution of the alleles in sub‐Saharan Africa.
Do discrepancies between microsatellite and allozyme variation reveal differential selection between sea and lagoon in the sea bass (Dicentrarchus labrax)?
Authors: Lemaire C. , Allegrucci G. , Naciri M. , Bahri‐Sfar L. , Kara H. , Bonhomme F. 
Published: March 2003

AbstractIn the present study the genetic structure of Dicentrarchus labrax (14 samples from the Mediterranean) was analysed at six microsatellite loci, in order to test the hypothesis that some enzymatic loci undergo selection between marine and lagoon habitat. Eight of the 14 samples were analysed at both microsatellite and allozyme markers. The analysis of the genetic variation among the Mediterranean samples showed that (i) FST values obtained with the six microsatellite loci were much smaller than those obtained with the 28 allozymes and (ii) microsatellite loci seemed to reflect more the geographical proximity than an ecological one. Thirteen enzymatic loci exhibited moderate to high values compared with microsatellites. This was interpreted as evidence that these allozymes are non‐neutral. However, only six loci seemed to be implicated in differentiation between marine and lagoon samples, the causes of selection being unknown for the others. A possible scenario of population dynamics of the sea bass between marine and lagoon habitat is suggested.
Reciprocal hybrid formation ofSpartinain San Francisco Bay
Authors: Anttila C. K. , King R. A. , Ferris C. , Ayres D. R. , Strong D. R. 
Published: March 2003

AbstractDiversity in the tRNALEU1intron of the chloroplast genome ofSpartinawas used to study hybridization of native California cordgrass,Spartina foliosa, withS. alterniflora, introduced to San Francisco Bay ≈ 25 years ago. We sequenced 544 bases of the tRNALEU1intron and found three polymorphic sites, a pyrimidine transition at site 126 and transversions at sites 382 and 430.Spartinafrom outside of San Francisco Bay, where hybridization between these species is impossible, gave cpDNA genotypes of the parental species.S. foliosahad a single chloroplast haplotype, CCT, and this was unique to California cordgrass.S. alterniflorafrom the native range along the Atlantic coast of North America had three chloroplast haplotypes, CAT, TAA, and TAT. Hybrids were discriminated by random amplified polymorphic DNA (RAPD) phenotypes developed in a previous study. We found one hybrid that contained a cpDNA haplotype unknown in either parental species (TCT). The most significant finding was that hybridization proceeds in both directions, assuming maternal inheritance of cpDNA; 26 of the 36 hybridSpartinaplants from San Francisco Bay contained theS. foliosahaplotype, nine contained haplotypes of the invadingS. alterniflora, and one had the cpDNA of unknown origin. Furthermore, cpDNA of both parental species was distributed throughout the broad range of RAPD phenotypes, suggesting ongoing contributions to the hybrid swarm from both. The preponderance ofS. foliosacpDNA has entered the hybrid swarm indirectly, we propose, from F1s that backcross toS. foliosa. Flowering of the native precedes by several weeks that of the invading species, with little overlap between the two. Thus, F1 hybrids would be rare and sired by the lastS. foliosapollen upon the firstS. alterniflorastigmas. The native species produces little pollen and this has low viability. An intermediate flowering time of hybrids as well as pollen that is more vigourous and abundant than that of the native species would predispose F1s to high fitness in a vast sea of native ovules. Thus, spread of hybrids to otherS. foliosamarshes could be an even greater threat to the native species than introductions of alienS. alterniflora.
Dynamics of genotypic structure in clonal Rhododendron ferrugineum (Ericaceae) populations
Authors: Pornon A. , Escaravage N. , Thomas P. , Taberlet P. 
Published: March 2003

AbstractTwo populations of Rhododendron ferrugineum growing at subalpine level in the Pyrenees (France) were studied in two sites (Bethmale and Mourtis). Identification and delimitation of genets were inferred from amplified fragment length polymorphism (AFLP) markers, along a closure gradient (from meadow to more closed heath) in each site. Surface and age of genets, genotypic diversity (Simpson’s index D), ‘proportion distinguishable’ genotypes and genetic relationships between genets were then estimated. Amplification of the 312 DNA samples with three selective primer pairs gave a mean of 98 detectable peaks (i.e. bands) per sample, with size ranging from 60 to 300 bp. In total 60% (Bethmale) and 70% (Mourtis) of the peaks were polymorphic, and a total of 31 and 23 multilocus genotypes were identified, in Bethmale and Mourtis, respectively. We inferred that pioneer genotypes began arriving 110 years ago mainly over a 40‐year period in the Mourtis meadow, and began about 130 years ago over a 100‐year period in the Bethmale meadow. After this pioneer stage, populations extended vegetatively. Two different patterns of genotypic dynamics can be identified. At Bethmale, population closure could have led to a dramatic loss of genets and to the selection of highly genetically related genotypes. In contrast, at Mourtis, genotypic diversity and genet density did not change fundamentally along the closure gradient. However the range of genetic diversity diminished from the open to the closed situation, suggesting that thinning could have occurred in the past.
Offspring sex ratios in tree swallows: females in better condition produce more sons
Authors: Whittingham Linda A. , Dunn Peter O. 
Published: March 2003

AbstractOrganisms are expected to adjust the sex ratio of their offspring in relation to the relative fitness benefits of sons and daughters. We used a molecular sexing technique that amplifies an intron of the CHD1 gene in birds to examine the sex ratio at egg‐laying in socially monogamous tree swallows (Tachycineta bicolor). We examined all individuals in 40 broods (210 young), including all unhatched eggs and nestlings. Thus, the sex ratio we measured was the same as the sex ratio at laying. Overall, the mean sex ratio per brood (± SD) was biased significantly towards males (57 ± 2% male). Within broods, male‐biased sex ratios were associated with females in better body condition, and these females were more likely to produce sons in better condition. Tree swallows have one of the highest known levels of extra‐pair paternity in birds (38–76% extra‐pair young), and, as a consequence, variance in male reproductive success is greater than that of females. Thus, in tree swallows, investment in sons has the potential for higher fitness returns than investment in daughters, assuming that sons in better condition have greater reproductive success.
Genetic variation and population structure in the endangered greater horseshoe bat Rhinolophus ferrumequinum
Authors: Rossiter Stephen J. , Jones Gareth , Ransome Roger D. , Barratt Elizabeth M. 
Published: March 2003

AbstractFollowing a dramatic decline last century, the British population of the endangered greater horseshoe bat Rhinolophus ferrumequinum is highly fragmented. To examine the consequences of fragmentation and limited dispersal on patterns of genetic structure and variation, we used microsatellite markers to screen bats from around 50% of the known maternity colonies in Britain, and two areas from continental Europe. Analyses revealed that Welsh and English colonies were genetically isolated. This, and lower variability in Britain than north France, may result from either genetic drift, or the species’ colonization history. Gene flow among most neighbouring colonies was not generally restricted, with one exception. These findings have important implications for the ongoing conservation management of this species.
Absence of evidence for isolation by distance in an expanding cane toad (Bufo marinus) population: an individual‐based analysis of microsatellite genotypes
Authors: Leblois Raphael , Rousset François , Tikel Dani , Moritz Craig , Estoup Arnaud 
Published: March 2003

AbstractThe cane toad (Bufo marinus) was introduced in 1935 in Australia, where it spread rapidly. We have tested for isolation by distance by analysing at a local geographical scale a continuous population using seven microsatellite markers and an individual‐based method. The matrix of pairwise individual differentiation was not significantly correlated with that of geographical distance. Regression analyses gave a low positive slope of 0.00072 (all individuals) or a negative slope of 0.0017 (individuals with a distance higher than the previously estimated mean dispersal distance). The absence of evidence for isolation by distance favours the hypothesis that the substantial differentiation and autocorrelation previously observed at enzyme loci, mainly results from discontinuities in the colonization process with founder effects occurring at the time of the establishment of new populations.
Identifying key cereal aphid predators by molecular gut analysis
Authors: Chen Y. , Giles K. L. , Payton M. E. , Greenstone M. H. 
Published: March 2003

AbstractWe describe polymerase chain reaction (PCR) primers for gut analysis of aphid predators. The primers amplify aphid mitochondrial COII fragments ranging in size from 77 to 386 bp. Using these primers, we were able to distinguish six species of US Great Plains cereal aphids, including two congeners,Rhopalosiphum maidis(Fitch) andR. padi(L.), and to detect them in extracts of coccinellid and chrysopid predators. We devised a protocol for deriving half‐lives of detectability for the DNA of a single aphid consumed by predators maintained under simulated field dietary and temperature conditions. Using this protocol and primers that amplify a 198‐bp fragment, we determined statistically different half‐lives of detectability for a singleR. maidisof 3.95 h inChrysoperla plorabunda(Fitch) and 8.78 h inHippodamia convergensGuerin. The detectability half‐life for a 339‐bpR. maidisfragment was statistically longer inC. plorabundabut not inH. convergens. The sensitivity of the assay for the 198‐bp fragment is 10−7aphid equivalents. For species‐specific predator gut analysis, PCR is superior to monoclonal antibody technology, giving comparable detectability half‐lives with lower expense, much shorter development times, and greater certainty of a successful outcome.
Morphological and molecular differentiation of invasive freshwater species of the genus Corbicula (Bivalvia,Corbiculidea) suggest the presence of three taxa in French rivers
Authors: Renard E. , Bachmann V. , Cariou M. L. , Moreteau J. C. 
Published: March 2003

AbstractAsiatic Clams are common in brackish and fresh water in Asia, and they were introduced into North America in 1924 and have now spread throughout the continent. During the last two decades they have been reported in Europe, but the number of species here is uncertain. Populations of Corbicula from France and the Netherlands were analysed morphologically and genetically to quantify the degree of species and/or population differentiation. The morphological and genetic data, based on allozymes and mitochondrial sequences, were in full agreement. They indicate that there are two distinct species, identified as C. fluminalis and C. fluminea, in the two countries. Analyses of the mitochondrial COI gene revealed an unexpected divergent population of Corbicula in the Rhône. All these individuals were morphologically identified as C. fluminea, but had a COI sequence different from the two previous species. This population may, therefore, be a more ancient population, or a distinct species introduced via a different colonization route.
Diversity and abundance of resupinate thelephoroid fungi as ectomycorrhizal symbionts in Swedish boreal forests
Authors: Kõljalg U. , Dahlberg A. , Taylor A. F. S. , Larsson E. , Hallenberg N. , Stenlid J. , Larsson K.‐H. , Fransson P. M. , Kårén O. , Jonsson L. 
Published: March 2003

AbstractResupinate thelephoroid fungi (hereafter called tomentelloid fungi) have a world‐wide distribution and comprise ≈70 basidiomycete species with inconspicuous, resupinate sporocarps. It is only recently that their ability to form ectomycorrhizas (EM) has been realized, so their distribution, abundance and significance as mycobionts in forest ecosystems is still largely unexplored. In order to provide baseline data for future ecological studies of tomentelloid fungi, we explored their presence and abundance in nine Swedish boreal forests in which the EM communities had been analysed. Phylogenetic analyses were used to compare the internal transcribed spacer of nuclear ribosomal DNA (ITS rDNA) sequence data obtained from mycobionts on single ectomycorrhizal tips with that obtained from sporocarps of identified tomentelloid fungi. Five species of Tomentella and one species of Pseudotomentella were identified as ectomycorrhizal fungi. The symbiotic nature of Tomentella bryophila, T. stuposa, T. badia and T. atramentaria is demonstrated for the first time. T. stuposa and Pseudotomentellatristis were the most commonly encountered tomentelloid fungi, with the other species, including T. sublilacina, only being recorded from single stands. Overall, tomentelloid fungi were found in five of the studies, colonizing between 1 and 8% of the mycorrhizal root tips. Two of the five sites supported several tomentelloid species. Tomentelloid fungi appear to be relatively common ectomycorrhizal symbionts with a wide distribution in Swedish coniferous forests. The results are in accordance with accumulating data that fungal species which lack conspicuous sporocarps may be of considerable importance in EM communities.
Genetic (RAPD) diversity inPeromyscus maniculatuspopulations in a naturally fragmented landscape
Authors: Vucetich L. M. , Vucetich J. A. , Joshi C. P. , Waite T. A. , Peterson R. O. 
Published: March 2003

AbstractWe assessed the effects of long‐term habitat fragmentation on genetic (random amplified polymorphic DNA) diversity in 11Peromyscus maniculatuspopulations in the Lake Superior watershed. We analysed genetic structure at two spatial scales and the effect of island size and isolation on genetic diversity. At the regional scale, island populations differed from mainland populations (FST = 0.36), but mainland populations did not differ from each other (FST = 0.01). At the local scale, populations of the main island of Isle Royale differed from adjacent islet populations (P < 0.001; Monte Carlo approximation of Fisher’s exact test), but not from each other (combinedP = 0.63). Although geographical distance and genetic distance were positively correlated (P < 0.01; Mantel test), cluster analysis revealed some inconsistencies. Finally, genetic diversity was inversely related to isolation (P = 0.01), but had an unexpectedly negative relationship with island area (P = 0.03). The genetic structure ofP. maniculatuspopulations in portions of the Lake Superior watershed appears to have been affected by long‐term habitat fragmentation.