bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genetic analysis of the mating system of the common brushtail possum (Trichosurus vulpecula) in New Zealand farmland
Authors: Taylor A. C. , Cowan P. E. , Fricke B. L. , Cooper D. W. 
Published: March 2003

AbstractWe examined male reproductive success in a common brushtail possum population in New Zealand farmland. Paternity was assigned to 66 of 91 pouch young (maternity known), using a likelihood approach applied to genotypes at six microsatellite loci having an overall average exclusion probability of around 99%. The distribution of number of offspring per male was L‐shaped with a standardized variance of 1.52. At least 46% of the 76 sampled reproductively mature males, bred, siring between one and four offspring each. Although breeding males were on average older and larger than nonbreeding males, the small differences did not result in a significant overall difference between the two groups in a multivariate permutation test analagous to a t‐test. Paternity analysis of 22 sibling pairs (resulting from experimental removal of pouch young early in the breeding season, inducing a second oestrous) suggested that sequential mating of females with the same male was uncommon (≈ 16–27%). Whilst there was a tendency for female possums to mate with nearby males, consistent with previous observations of territorial mating behaviour in Australian populations, some interhabitat matings were also inferred. The study population displayed only a low degree of polygyny, which may in part reflect population and habitat characteristics of the study site. A comprehensive understanding of the mating system of Trichosurus vulpecula awaits genetic paternity analysis in additional populations from both Australia and New Zealand, using quantitative approaches undertaken in this study.
Hybrid origins of honeybees from Italy (Apis mellifera ligustica) and Sicily (A. m. sicula)
Authors: Franck P. , Garnery L. , Celebrano G. , Solignac M. , Cornuet J.‐M. 
Published: March 2003

AbstractThe genetic variability of honeybee populations Apis mellifera ligustica, in continental Italy, and of A. m. sicula, in Sicily, was investigated using nuclear (microsatellite) and mitochondrial markers. Six populations (236 individual bees) and 17 populations (664 colonies) were, respectively, analysed using eight microsatellite loci and DraI restriction fragment length polymorphism (RFLP) of the cytochrome oxidase I (COI)–cytochrome oxidase II (COII) region. Microsatellite loci globally confirmed the southeastern European heritage of both subspecies (evolutionary branch C). However, A. m. ligustica mitochondrial DNA (mtDNA) appeared to be a composite of the two European (M and C) lineages over most of the Italian peninsula, and only mitotypes from the African (A) lineage were found in A. m. sicula samples. This demonstrates a hybrid origin for both subspecies. For A. m. ligustica, the most widely exported subspecies, this hybrid origin has long been obscured by the fact that in the main area of queen production (from which most of the previous ligustica bee samples originated) the M mitochondrial lineage is absent, whereas it is present almost everywhere else in Italy. This presents a new view of the evolutionary history of European honeybees. For instance, the Iberian peninsula was considered as the unique refuge for the M branch during the quaternary ice periods. Our results show that the Apennine peninsula played a similar role. The differential distribution of nuclear and mitochondrial markers observed in Italy seems to be a general feature of introgressed honeybee populations. Presumably, it stems from the social nature of the species in which both genome compartments are differentially affected by the two (individual and colonial) reproduction levels.
Rapid identification of cyst (Heterodera spp., Globodera spp.) and root‐knot (Meloidogyne spp.) nematodes on the basis of ITS2 sequence variation detected by PCR‐single‐strand conformational polymorphism (PCR‐SSCP) in cultures and field samples
Authors: Clapp J. P. , Stoel C. D. van der , Putten W. H. van der 
Published: March 2003

AbstractCyst and root‐knot nematodes show high levels of gross morphological similarity. This presents difficulties for the study of their ecology in natural ecosystems. In this study, cyst and root‐knot nematode species, as well as some ectoparasitic nematode species, were identified using the second internal transcribed spacer (ITS2) sequence variation detected by polymerase chain reaction‐single‐strand conformational polymorphism (PCR‐SSCP). The ITS2 region was sufficiently variable within the taxa investigated to allow species to be separated on the basis of minor sequence variation. The PCR primers used in this study were effective for 12 species with three genera within the Heteroderinae (Globodera pallida, G. rostochiensis, Heterodera arenaria/avenae, H. ciceri, H. daverti, H. hordecalis, H. mani, H. schachtii, H. trifolii, Meloidogyne ardenensis, M. duytsi and M. maritima). However, pathotypes of Globodera pallida and G. rostochiensis could not be distinguished. The method was tested at two coastal dune locations in The Netherlands (one in the lime‐poor dunes of the north and one in calcareous dunes of the south) to determine the population structure of cyst nematodes. At each site, cyst nematodes were associated with three plant species: two plant species on the foredune (Elymus farctus and Ammophila arenaria) and one plant species occurring further inland (Calamagrostis epigejos). Two species of cyst nematodes, H. arenaria and H. hordecalis, were found. H. arenaria associated with vigorous A. arenaria and H. hordecalis in association with degenerating A. arenaria and C. epigejos. The field survey demonstrated that in coastal dunes abiotic factors may be the important affecting the distribution of cyst nematodes.
Estimating the probability of identity among genotypes in natural populations: cautions and guidelines
Authors: Waits Lisette P. , Luikart Gordon , Taberlet Pierre 
Published: March 2003

AbstractIndividual identification using DNA fingerprinting methods is emerging as a critical tool in conservation genetics and molecular ecology. Statistical methods that estimate the probability of sampling identical genotypes using theoretical equations generally assume random associations between alleles within and among loci. These calculations are probably inaccurate for many animal and plant populations due to population substructure. We evaluated the accuracy of a probability of identity (P(ID)) estimation by comparing the observed and expected P(ID), using large nuclear DNA microsatellite data sets from three endangered species: the grey wolf (Canis lupus), the brown bear (Ursus arctos), and the Australian northern hairy‐nosed wombat (Lasiorinyus krefftii). The theoretical estimates of P(ID) were consistently lower than the observed P(ID), and can differ by as much as three orders of magnitude. To help researchers and managers avoid potential problems associated with this bias, we introduce an equation for P(ID) between sibs. This equation provides an estimator that can be used as a conservative upper bound for the probability of observing identical multilocus genotypes between two individuals sampled from a population. We suggest computing the actual observed P(ID) when possible and give general guidelines for the number of codominant and dominant marker loci required to achieve a reasonably low P(ID) (e.g. 0.01–0.0001).
Detection of reduction in population size using data from microsatellite loci
Authors: Garza J. C. , Williamson E. G. 
Published: March 2003

AbstractWe demonstrate that the mean ratio of the number of alleles to the range in allele size, which we term M, calculated from a population sample of microsatellite loci, can be used to detect reductions in population size. Using simulations, we show that, for a general class of mutation models, the value of M decreases when a population is reduced in size. The magnitude of the decrease is positively correlated with the severity and duration of the reduction in size. We also find that the rate of recovery of M following a reduction in size is positively correlated with post‐reduction population size, but that recovery occurs in both small and large populations. This indicates that M can distinguish between populations that have been recently reduced in size and those which have been small for a long time. We employ M to develop a statistical test for recent reductions in population size that can detect such changes for more than 100 generations with the post‐reduction demographic scenarios we examine. We also compute M for a variety of populations and species using microsatellite data collected from the literature. We find that the value of M consistently predicts the reported demographic history for these populations. This method, and others like it, promises to be an important tool for the conservation and management of populations that are in need of intervention or recovery.
Molecular barcodes for soil nematode identification
Authors: Floyd Robin , Abebe Eyualem , Papert Artemis , Blaxter Mark 
Published: March 2003

AbstractUsing a molecular barcode, derived from single‐specimen polymerase chain reaction (PCR) and sequencing of the 5′ segment of the small subunit ribosomal RNA (SSU) gene, we have developed a molecular operational taxonomic unit (MOTU) scheme for soil nematodes. Individual specimens were considered to belong to the same MOTU when the sequenced segment of 450 bases was > 99.5% identical. A Scottish upland Agrostis‐Festuca grassland soil was sampled, using both culture‐based and random selection methods. One hundred and sixty‐six cultured isolates were sequenced, and clustered into five MOTU. From 74 randomly sampled individuals across the study site, 19 MOTU were defined. A subsequent sample of 18 individuals from a single subplot contained eight MOTU, four of which were unique to the single subplot sample. Interestingly, seven of these MOTU were not present in the culture‐independent sampling. Overall, a total of 23 MOTU were defined from only 240 sequences. Many MOTU could readily be assigned to classical, morphologically defined taxonomic units using a database of SSU sequences from named nematode species. The MOTU technique allows a rapid assessment of nematode taxon diversity in soils. Correlation with a database of sequences from known species offers a route to application of the technique in ecological surveys addressing biological as well as genetic diversity.
Genetic, ecological, and behavioural divergence between two sibling snapping shrimp species (Crustacea: Decapoda:Alpheus)
Authors: Mathews L. M. , Schubart C. D. , Neigel J. E. , Felder D. L. 
Published: March 2003

AbstractExamination of genetic and ecological relationships within sibling species complexes can provide insights into species diversity and speciation processes.Alpheus angulatusandA. armillatus, two snapping shrimp species with overlapping ranges in the north‐western Atlantic, are similar in morphology, exploit similar ecological niches and appear to represent recently diverged sibling species. We examined phylogenetic and ecological relationships between these two species with: (i) sequence data from two mitochondrial genes (16SrRNA andCOI); (ii) data on potential differences in microhabitat distribution forA. armillatusandA. angulatus; and (iii) data from laboratory experiments on the level of reproductive isolation between the two species. DNA sequence data suggestA. armillatusandA. angulatusare sister species that diverged subsequent to the close of the Isthmus of Panama, and that haplotype diversity is lower inA. armillatusthan inA. angulatus. Both species are distantly related toA. heterochaelisandA. estuariensis, two species with whichA. angulatusshares some similarities in coloration. Ecological data on the distribution ofA. angulatusandA. armillatusfrom two locations revealed differences in distribution of the two species between habitat patches, with each patch dominated by one or the other species. However, there was no apparent difference in distribution of the two species within habitat patches with respect to microhabitat location. Ecological data also revealed that heterospecific individuals often occur in close proximity (i.e. within metres or centimetres) where sympatric. Behavioural data indicated that these species are reproductively isolated, which is consistent with speciation in transient allopatry followed by post‐divergence secondary contact. Our data further resolve taxonomic confusion between the sibling species,A. armillatusandA. angulatus, and suggest that sympatry in areas of range overlap and exploitation of similar ecological niches by these two recently diverged species have selected for high levels of behavioural incompatibility.
Intraspecific molecular variation in the seaweed fly Coelopa frigida consistent with behavioural distinctness of British and Swedish populations
Authors: MacDonald C. , Brookfield J. F. Y. 
Published: March 2003

AbstractThe major aim of this study was to compare the intraspecific variation and genetic structure of the behaviourally distinct British and Swedish populations of the seaweed fly Coelopa frigida. C. frigida has been the subject of intense study into the basis of female choice. The behaviour of British females is consistent with a ‘good genes’ model, whereas that of the Swedish flies suggests a Fisher process, in which the difference between the former and the latter is defined by female choice increasing offspring viability in ‘good genes’ models. Through a study of variability in the mitochondrial cytochrome oxidase II gene from more than 600 flies, we show that there is clear differentiation at the molecular level between the two countries’ populations, with an FST of > 75% and no shared haplotypes. Tajima's test reveals an excess of rare variants relative to expectation, which, if not the result of selective sweep, indicates either a population expansion or purifying selection against weakly deleterious variants. Within the two populations, substantial subpopulation differentiation is observed in the UK, where there is also evidence of isolation by distance. Swedish populations exhibit lower variability, and no evidence of isolation by distance, with the latter result possibly being related to the continuous distribution of suitable habitat. The pattern of intraspecific variation is explainable by a combination of contemporary and also historical factors. British and Swedish populations may have been descended from at least two separate founding populations during the recolonization of these areas following Pleistocene glaciations.
Genealogical exclusivity in geographically proximate populations of Hypochilus thorelli Marx (Araneae, Hypochilidae) on the Cumberland Plateau of North America
Authors: Hedin M. , Wood D. A. 
Published: March 2003

AbstractThe issue of sampling sufficiency is too infrequently explored in phylogeographical analysis, despite both theoretical work and analytical methods that stress the importance of sampling effort. Regarding the evolutionary pattern of reciprocal monophyly, both the probability of recovering this pattern and the possible inferences derived from this pattern, are highly contingent upon the density and geographical scale of sampling. Here, we present an empirical example that relates directly to this issue. We analyse genetic structure in the southern Appalachian spider Hypochilus thorelli, using an average sample of 5 mitochondrial DNA (mtDNA) sequences per location for 19 locations. All sampled sites are reciprocally monophyletic for mtDNA variation, even when separated by geographical distances as small as 5 km. For populations separated by greater geographical distances of 20–50 km, mtDNA sequences are not only exclusive, but are also highly divergent (uncorrected p‐distances exceeding 5%). Although these extreme genealogical patterns are most seemingly consistent with a complete isolation model, both a coalescent method and nested cladistic analysis suggest that other restricted, but nonzero, gene flow models may also apply. Hypochilus thorelli appears to have maintained morphological cohesion despite this limited female‐based gene flow, suggesting a pattern of stasis similar to that observed at higher taxonomic levels in Hypochilus.
Evaluating the effects of historic bottleneck events: an assessment of microsatellite variability in the endangered, North Atlantic right whale
Authors: Waldick R. C. , Kraus S. , Brown M. , White B. N. 
Published: March 2003

AbstractCommercial exploitation reduced the North Atlantic right whale (Eubalaena glacialis) population from c. 12 000 in the 11th century to around 300 by the 21st century. We examine the effect of this population decline on levels of genetic variation at 16 microsatellite loci and contrast levels of variability to that in a closely related species (E. australis). Of the 13 loci developed from the E. glacialis genome, 100% were polymorphic in E. australis. In contrast, nine loci were polymorphic in E. glacialis and four were fixed. Both allelic diversity (A) and heterozygosity (H) were significantly lower in E. glacialis than E. australis (A = 3.2 ± 2.6 vs. A= 6.9 ± 3.3, P < 0.001; H= 0.31 ± 0.25 vs. H= 0.72 ± 0.23, P < 0.001, respectively). Bottleneck anlayses indicate that the population is in mutation‐drift equilibrium and that a genetic bottleneck did not occur during the most recent decline (18th–20th centuries). Nevertheless, low frequency alleles are relatively uncommon in E. glacialis, suggesting that genetic variability has been reduced in this population. Possible origins of low genetic variability are discussed, including the slow but continual erosion of alleles during the 800‐year period of decline.
History and evolution of the arctic flora: in the footsteps of Eric Hultén
Authors: Abbott Richard J. , Brochmann Christian 
Published: March 2003

AbstractA major contribution to our initial understanding of the origin, history and biogeography of the present‐day arctic flora was made by Eric Hultén in his landmark book Outline of the History of Arctic and Boreal Biota during the Quarternary Period, published in 1937. Here we review recent molecular and fossil evidence that has tested some of Hultén's proposals. There is now excellent fossil, molecular and phytogeographical evidence to support Hultén's proposal that Beringia was a major northern refugium for arctic plants throughout the Quaternary. In contrast, most molecular evidence fails to support his proposal that contemporary east and west Atlantic populations of circumarctic and amphi‐Atlantic species have been separated throughout the Quaternary. In fact, populations of these species from opposite sides of the Atlantic are normally genetically very similar, thus the North Atlantic does not appear to have been a strong barrier to their dispersal during the Quaternary. Hultén made no detailed proposals on mechanisms of speciation in the Arctic; however, molecular studies have confirmed that many arctic plants are allopolyploid, and some of them most probably originated during the Holocene. Recurrent formation of polyploids from differentiated diploid or more low‐ploid populations provides one explanation for the intriguing taxonomic complexity of the arctic flora, also noted by Hultén. In addition, population fragmentation during glacial periods may have lead to the formation of new sibling species at the diploid level. Despite the progress made since Hultén wrote his book, there remain large gaps in our knowledge of the history of the arctic flora, especially about the origins of the founding stocks of this flora which first appeared in the Arctic at the end of the Pliocene (approximately 3 Ma). Comprehensive analyses of the molecular phylogeography of arctic taxa and their relatives together with detailed fossil studies are required to fill these gaps.
Multilocus sequence typing suggests the chytrid pathogen of amphibians is a recently emerged clone
Authors: Morehouse Erica A. , James Timothy Y. , Ganley Austen R. D. , Vilgalys Rytas , Berger Lee , Murphy Peter J. , Longcore Joyce E. 
Published: March 2003

AbstractChytridiomycosis is a recently identified fungal disease associated with global population declines of frogs. Although the fungus, Batrachochytrium dendrobatidis, is considered an emerging pathogen, little is known about its population genetics, including the origin of the current epidemic and how this relates to the dispersal ability of the fungus. In this study, we use multilocus sequence typing to examine genetic diversity and relationships among 35 fungal strains from North America, Africa and Australia. Only five variable nucleotide positions were detected among 10 loci (5918 bp). This low level of genetic variation is consistent with the description of B. dendrobatidis as a recently emerged disease agent. Fixed (i.e. 100%) or nearly fixed frequencies of heterozygous genotypes at two loci suggested that B. dendrobatidis is diploid and primarily reproduces clonally. In contrast to the lack of nucleotide polymorphism, electrophoretic karyotyping of multiple strains demonstrated a number of chromosome length polymorphisms.
Sequence and expression of a halobacterial β‐galactosidase gene
Authors: Holmes Melissa L. , Dyall‐Smith Michael L. 
Published: March 2003

Studies of gene expression in haloarchaea have been greatly hindered by the lack of a convenient reporter gene. In a previous study, a β‐galactosidase from Haloferax alicantei was purified and several peptide sequences determined. The peptide sequences have now been used to clone the entire β‐galactosidase gene (designated bgaH) along with some flanking chromosomal DNA. The deduced amino acid sequence of BgaH was 665 amino acids (74 kDa) and showed greatest amino acid similarity to members of glycosyl hydrolase family 42 [classification of Henrissat, B., and Bairoch, A. (1993) New families in the classification of glycosyl hydrolases based on amino acid sequence similarities. Biochem J 293: 781–788]. Within this family, BgaH was most similar (42–43% aa identity) to enzymes from extremely thermophilic bacteria such as Thermotoga and Thermus. Family 42 enzymes are only distantly related to the Sulfolobus LacS and Escherichia coli LacZ enzymes (families one and two respectively). Three open reading frames (ORFs) upstream of bgaH were readily identified by database searches as glucose–fructose oxidoreductase, 2‐dehydro‐3‐deoxyphosphogluconate aldolase and 2‐keto‐3‐deoxygluconate kinase, enzymes that are also involved in carbohydrate metabolism. Downstream of bgaH there was an ORF which contained a putative fibronectin III motif. The bgaH gene was engineered into a halobacterial plasmid vector and introduced into Haloferax volcanii, a widely used strain that lacks detectable β‐galactosidase activity. Transformants were shown to express the enzyme; colonies turned blue when sprayed with Xgal and enzyme activity could be easily quantitated using a standard ONPG assay. In an accompanying publication, Patenge et al. (2000) have demonstrated the utility of bgaH as a promoter reporter in Halobacterium salinarum.