bluuebunny/crossref_metadata_2025_split huggingface dataset:
Dynamics ofMhcevolution in birds and crocodilians: amplification of class II genes with degenerate primers
Authors: EDWARDS S. V. , GRAHN M. , POTTS W. K. 
Published: April 2008

AbstractGenes of the major histocompatibility complex (Mhc) are the most polymorphic functional loci in mammalian populations, but little is known ofMhcvariability in natural populations of nonmammalian vertebrates. To help extend such studies to birds and relatives, we present a pair of degenerate primers that amplify polymorphic segments of one chain (the β chain) of the class II genes from the major histocompatibility complex (Mhc) of archosaurs (birds + crocodilians). The primers target two conserved regions lying within portions of the antigen‐binding site (ABS) encoded by the second exon and amplify multiple genes from both genomic DNA and cDNA. The pattern of nucleotide substitution in ABS codons of 51 sequences amplified and cloned from five species of passerine birds and an alligator (Alligator mississippiensis) indicates that archosaurian class II β genes are subject to selective forces similar to those operating in mammalian populations. Hybridization of a genomic clone generated by the primers revealed highly polymorphic bands in a sample of Florida scrub jays (Aphelocoma coerulescens coerulescens). Because the primers amplify only part of the ABS from multiple class II genes, they will be useful primarily for generating species specific clones, thereby providing a critical inroad to more detailed structural and evolutionary studies.
Mitochondrial DNA variation in Atlantic capelin, Mallotus villosus: a comparison of restriction and sequence analyses
Authors: BIRT T. P. , FRIESEN V. L. , BIRT R. D. , GREEN J. M. , DAVIDSON W. S. 
Published: April 2008

AbstractDivergence estimates were calculated using restriction analysis and cytochrome‐b sequences for capelin Mallotus villosus mitochondrial genomes sampled from Newfoundland and Norwegian populations. On average, pairwise divergence values based on cytochrome‐b sequences were 2.7 times greater than those based on restriction data. Since the rate of evolution in the cytochrome‐b gene is low, it appears that restriction analysis underestimated divergence values, possibly due to limited sensitivity of this method when variable nucleotide positions are not randomly distributed. Mitochondrial genotypes were not shared among the two populations.
Distribution and abundance of trypanosome (subgenus Nannomonas) infections of the tsetse fly Glossina pallidipes in southern Africa
Authors: WOOLHOUSE M. E. J. , MCNAMARA J. J. , HARGROVE J. W. , BEALBY K. A. 
Published: April 2008

AbstractOver 10000 Glossina pallidipes tsetse flies were collected during two field studies in the Zambezi Valley, Zimbabwe and one in the Luangwa Valley, Zambia. These were screened for mature trypanosome infections and 234 dot‐blot preparations were made of infected midguts, which were screened using DNA probes or PCR with primers specific to different species or types of the trypanosome subgenus Nannomonas. Over 70% of midgut infections were successfully identified as either Trypanosoma godfreyi, T. simiae or three types of T. congolense, savannah, riverine‐forest and Kilifi. The relative abundance of species and types did not vary significantly between study locations, habitat, season or tsetse age or sex, although there were differences between DNA probe and PCR results. Mixed species and/or mixed type infections were common and were more often detected using PCR. The distribution of infections among flies was highly aggregated, but there was no tendency for multiple infections to accumulate in older flies, implying that sequential superinfection may be uncommon. Possible explanations for these patterns are discussed.
Genetic differentiation of continental and island populations of Bombus terrestris (Hymenoptera: Apidae) in Europe
Authors: ESTOUP A. , SOLIGNAC M. , CORNUET J. M. , GOUDET J. , SCHOLL A. 
Published: April 2008

AbstractTen microsatellite loci and a partial sequence of the COII mitochondrial gene were used to investigate genetic differentiation in B. terrestris, a bumble bee of interest for its high‐value crop pollination. The analysis included eight populations from the European continent, five from Mediterranean islands (six subspecies altogether) and one from Tenerife (initially described as a colour form of B. terrestris but recently considered as a separate species, B. canariensis). Eight of the 10 microsatellite loci displayed high levels of polymorphism in most populations. In B. terrestris populations, the total number of alleles detected per polymorphic locus ranged from 3 to 16, with observed allelic diversity from 3.8 ± 0.5 to 6.5 ± 1.4 and average calculated heterozygosities from 0.41 ± 0.09 to 0.65 ± 0.07. B. canariensis showed a significantly lower average calculated heterozygosity (0.12 ± 0.08) and observed allelic diversity (1.5 ± 0.04) as compared to both continental and island populations of B. terrestris. No significant differentiation was found among populations of B. terrestris from the European continent. In contrast, island populations were all significantly and most of them strongly differentiated from continental populations. B. terrestris mitochondrial DNA is characterized by a low nucleotide diversity: 0.18%± 0.07%, 0.20%± 0.04% and 0.27%± 0.04% for the continental populations, the island populations and all populations together, respectively. The only haplotype found in the Tenerife population differs by a single nucleotide substitution from the most common continental haplotype of B. terrestris. This situation, identical to that of Tyrrhenian islands populations and quite different from that of B. lucorum (15 substitutions between terrestris and lucorum mtDNA) casts doubts on the species status of B. canariensis. The large genetic distance between the Tenerife and B. terrestris populations estimated from microsatellite data result, most probably, from a severe bottleneck in the Canary island population. Microsatellite and mitochondrial DNA data call for the protection of the island populations of B. terrestris against importation of bumble bees of foreign origin which are used as crop pollinators.
The phylogeographic pattern of mitochondrial DNA variation in the Dall's porpoise Phocoenoides dalli
Authors: MCMILLAN W. O. , BERMINGHAM E. 
Published: April 2008

AbstractWe used 11 restriction endonucleases to study mtDNA variation in 101 Dall's porpoises Phocoenoides dalli from the Bering Sea and western North Pacific. There was little phylogeographic patterning among the 34 mtDNA haplotypes identified in this analysis, suggesting a strong historical connection among populations across this region. Nonetheless, mtDNA variation does not appear to be randomly distributed in this species. Both GST and AMOVA uncovered significant differences in the distribution of mtDNA variation between the Bering Sea and western North Pacific populations. These mtDNA results, coupled with differences in allozyme variation and parasite infestation, support the demographic distinctiveness of Bering Sea and western North Pacific stocks of Dall's porpoise. The lack of a strong phylogeographic orientation of mtDNA haplotypes within the Dall's porpoise is similar to the pattern reported in other vertebrates such as coyotes, blackbirds, chickadees, marine catfish, and catadromous eels. Like Dall's porpoise, these species are broadly distributed, and have large populations linked by moderate to high levels of gene flow. However, the more complex, deeply branched phylogenetic network of mtDNA haplotypes within Dall's porpoise, relative to these other vertebrates, suggests important differences between these species in the forces shaping mtDNA variation. One such force is the effective size of female populations, which appears to have been comparatively large and stable in Dall's porpoise.
Founder effects and sex ratio in the gynodioecious Thymus vulgaris L.
Authors: MANICACCI D. , COUVET D. , BELHASSEN E. , GOUYON P. H. , ATLAN A. 
Published: April 2008

Abstract Thymus vulgaris is a gynodioecious species (in which females and hermaphrodites coexist) with a highly variable frequency of females among natural populations (5–95%) and a high average female frequency (60%). Sex determination involves both cytoplasmic genes responsible for male sterility, i.e. the female phenotype, and specific nuclear factors responsible for the restoration of male fertility, and thus a hermaphrodite phenotype. In this study, molecular markers of the mitochondrial genome have been used to quantify the cytoplasmic diversity in 11 clumps of individuals observed in four recently founded populations. The very low diversity within patches in conjunction with the strong diversity among patches strongly suggests that clumps of individuals are the result of single matrilinear families. In clumps that contain mainly females, all the analysed females showed the same cytoplasmic pattern. This pattern differed from that shown by neighbouring hermaphrodites, indicating that the determination of sex is locally cytoplasmic. A comparison of genetic diversity before and after fire in one population showed that disturbances may cause a reduction in genetic diversity and a concurrent induction of local cytoplasmic determination of sex. Such cytoplasmic determination of sex in colonizing populations, together with the greater seed set of females, may largely improve the colonizing ability of the species.
Compatibility of systemic acquired resistance and microbial biocontrol for suppression of plant disease in a laboratory assay
Authors: CHEN J. , JACOBSON L. M. , HANDELSMAN J. , GOODMAN R. M. 
Published: April 2008

AbstractSystemic acquired resistance (SAR) and microbial biocontrol each hold promise as alternatives to pesticides for control of plant diseases. SAR and Bacillus cereus UW85, a microbial biocontrol agent, separately suppress seedling damping‐off diseases caused by oomycete pathogens. The purposes of this study were to investigate how expression of SAR affected the efficacy of biocontrol by UW85 and if UW85 treatment of plants induced SAR. We devised a laboratory assay in which seedling damping‐off disease, induction of SAR, and growth of UW85 could be quantified. Seedlings of Nicotiana tabacum Xanthi nc were germinated on moist filter paper and transferred after 7 days to water agar plates (40 seedlings per plate). Zoospores of oomycete pathogens (Pythium torulosum, Pythium aphanidermatum, or Phytophthora parasitica) were applied at concentrations that caused 80% seedling mortality within 10 days. Seedling mortality was dependent on zoospore inoculum concentration. The level of disease suppression caused by treatment with UW85 depended on the UW85 dose applied. SAR was induced with 0.5‐mM salicylic acid or 0.1‐mM 2,6‐dichloroisonicotinic acid. Expression of an SAR‐related gene was confirmed by northern analysis with a probe prepared from a tobacco PR‐1a cDNA. Induction of SAR suppressed disease caused by each of the oomycete pathogens, but did not alter the growth of UW85 on roots. Treatment of seedlings with UW85 did not induce the expression of PR‐1a. The combination of induction of SAR and treatment with UW85 resulted in additive suppression of disease as measured by seedling survival.
Homology among RAPD fragments in interspecific comparisons
Authors: RIESEBERG L. H. 
Published: April 2008

AbstractThe use of RAPDs for comparative purposes relies on the assumption that similarity of fragment size is a dependable indicator of homology. To test the validity of this assumption, homology among 220 pairs of comigrating fragments from three wild sunflower species was determined. Ninety‐one per cent cross‐hybridized and/or displayed congruent restriction fragment profiles suggestive of homology. However, comparative linkage mapping data indicated that 13% of the homologous loci mapped to genomic locations that were incongruent with the majority of loci, suggestive of paralogous rather than orthologous relationships. Thus, of the 220 pairwise comparisons, only 174 (79.1%) identified loci that are useful for comparative genetic studies. These problems, as well as several other factors discussed in the text, will introduce noise into RAPD data sets and thereby reduce the probability of generating accurate estimates of genetic relationships. Recommended methods for reducing noise in RAPD data sets include increasing gel resolution and/or testing fragment homology. However, implementation of these approaches will not eliminate all uncertainties, and it is also recommended that RAPD data sets be tested for structure and reliability.
Molecular characterization of clonal population structure and biogeography of arctic apomictic Daphnia from Greenland and Iceland
Authors: WEIDER L. J. , HOBÆK A. , CREASE T. J. , STIBOR H. 
Published: April 2008

AbstractAs part of a continuing international project to characterize the population genetic (clonal) structure of arctic members of the Daphnia pulex complex, 34 populations from western Iceland (N= 1373), and 76 populations from western Greenland (N= 2917), were surveyed for allozymic variation at six polymorphic enzyme loci. Mean clonal richness (±SE) was 1.91±0.19 and 1.50±0.12 for Iceland and Greenland populations, respectively. Mean clonal diversity (±1 SE) was 1.20±0.07 and 1.13±0.04 for Iceland and Greenland populations, respectively. Four widely distributed clones constituted 92.2% of the total animals surveyed from Iceland, while three locally abundant clones constituted 80.1% of the total animals collected primarily from Disko Island, western Greenland. Selected populations were screened for mitochondrial (mt)DNA variation using PCR‐based RFLP analysis of a 2100 bp fragment containing part of the ND4 and ND5 genes. One mtDNA haplotype was very widespread in both western Greenland and western Iceland, although, a number of mutational derivatives were also detected. These data indicate the potential for long‐distance dispersal of mtDNA lineages, of the order of hundreds or thousands of kilometers across the arctic. Phylogenetic analysis of the sequence of a 254 base pair (bp) fragment of the control region of the mtDNA molecule revealed two major clades one of which consisted solely of non‐melanic lineages, and the other of which consisted almost exclusively of melanic lineages (i.e. one non‐melanic lineage also clustered in this clade). Sequence divergence between the two clades averaged 7.3%. Both mitochondrial analyses did not reveal any distinct intraregional clustering of lineages. We discuss our results in reference to previous molecular work done on this arctic Daphnia complex, and we attempt to infer phylogeographic patterning based on geological/glaciological historical events in this region of the arctic.
Molecular diversity of fungi from ericoid mycorrhizal roots
Authors: PEROTTO S. , ACTIS‐PERINO E. , PERUGINI J. , BONFANTE P. 
Published: April 2008

AbstractIn order to investigate the diversity of fungal endophytes in ericoid mycorrhizal roots, about 150 mycelia were isolated from surface‐sterilized roots of 10 plants of Calluna vulgaris. Each mycelium was reinoculated to C. vulgaris seedlings under axenic conditions, and the phenotype of the plant‐fungus association assessed by light and electron microscopy. Many isolates that were able in vitro to produce typical ericoid mycorrhizae did not form reproductive structures under our culture conditions, whereas others could be identified as belonging to the species Oidiodendron maius. Morphological and molecular analysis of the fungal isolates showed that the root system of a single plant of C. vulgaris is a complex mosaic of several populations of mycorrhizal and non mycorrhizal fungi. PCR‐RFLP techniques, used to investigate the mycorrhizal endophytes, revealed up to four groups of fungi with different PCR‐RFLP patterns of the ITS ribosomal region from a single plant. Some of the mycorrhizal fungi sharing the same PCR‐RFLP pattern showed high degree of genetic polymorphism when analysed with the more sensitive RAPD technique; this technique may prove a useful tool to trace the spread of individual mycorrhizal mycelia, as it has allowed us to identify isolates with identical RAPD fingerprints on different plants.
Dissemination of thestrA‐strBstreptomycin‐resistance genes among commensal and pathogenic bacteria from humans, animals, and plants
Authors: SUNDIN G. W. , BENDER C. L. 
Published: April 2008

AbstractGene transfer within bacterial communities has been recognized as a major contributor in the recent evolution of antibiotic resistance on a global scale. The linkedstrA‐strBgenes, which encode streptomycin‐inactivating enzymes, are distributed worldwide and confer streptomycin resistance in at least 17 genera of gram‐negative bacteria. Nucleotide sequence analyses suggest thatstrA‐strBhave been recently disseminated. In bacterial isolates from humans and animals,strA‐strBare often linked with thesulIIsulfonamide‐resistance gene and are encoded on broad‐host‐range nonconjugative plasmids. In bacterial isolates from plants,strA‐strBare encoded on the Tn3‐type transposon Tn5393 which is generally borne on conjugative plasmids. The wide distribution of thestrA‐strBgenes in the environment suggests that gene transfer events between human, animal, and plant‐associated bacteria have occurred. Although the usage of streptomycin in clinical medicine and animal husbandry has diminished, the persistence ofstrA‐strBin bacterial populations implies that factors other than direct antibiotic selection are involved in maintenance of these genes.
Low frequency of extra‐pair paternity in two colonies of the socially monogamous short‐tailed shearwater Puffinus tenuirostris
Authors: AUSTIN J. J. , PARKIN D. T. 
Published: April 2008

AbstractThe short‐tailed shearwater is a colonially nesting, socially monogamous seabird. Little is known about mate fidelity and breeding behaviour in this species because breeding birds are nocturnal on land and spend much of their time within subterranean nesting burrows. Colonial breeding and extended sperm storage create opportunities for extra‐pair copulations which may form a significant component of the mating strategy in this species. Multilocus DNA fingerprinting was used to examine the genetic relationship between nestlings and the male and female nest attendants in 83 burrows from two distinct breeding colonies. Genetic analyses identified nine nestlings, approximately equally distributed between the two colonies, that were not related to the attendant pair male in those burrows, implying extra‐pair paternity through extra‐pair copulations. These results are used retrospectively to discuss the characteristics of extra‐pair copulations and extra‐pair fertilizations and the implications for estimates of life‐time reproductive success in the short‐tailed shearwater.
Genetic exchange and recombination in populations of the root‐infecting fungus Armillaria gallica
Authors: SAVILLE B. J. , YOELL H. , ANDERSON J. B. 
Published: April 2008

AbstractGenetic individuals, or genets, of Armillaria and other root‐infecting basidiomycetes are usually found in discrete patches that often include the root systems of several adjacent trees. Each diploid individual is thought to arise in an unique mating event and then grow vegetatively in an expanding territory over a long period of time. Our objective in this study was to describe the population from which such genetic individuals are drawn. In a sample including 274 collections representing 121 genetic individuals of A. gallica (synonym A. bulbosa) from two sites in each of four regions of eastern North America, genotype frequencies at seven nuclear loci were not significantly different from Hardy‐Weinberg expectations. Furthermore, allele frequencies at the seven loci were not significantly different between regions. Additional allelic data from four non‐contiguous regions of mitochondrial DNA showed little or no population subdivision over the four regions. Analysis of the distribution of multilocus mtDNA haplotypes revealed some clonal transmission of mtDNAs between genets and nonrandom mating within sites. Despite the sharing of mtDNA types by some individuals, the overall sample contained a high level of genotypic diversity. The apparent linkage equilibrium between some pairs of loci and the high level of phylogenetic inconsistency among all four loci suggest the occurrence heteroplasmy and recombination among mtDNAs of A. gallica in nature. In laboratory matings of two haploid strains with different mtDNA types, a low frequency of recombination in mtDNA was detected.
RAPD marker estimation of genetic structure among isolated northern leopard frog populations in the south‐western USA
Authors: KIMBERLING D. N. , FERREIRA A. R. , SHUSTER S. M. , KEIM P. 
Published: April 2008

AbstractAmphibians in the south‐western United States are currently experiencing population declines. Causal explanations for these population changes as well as the implementation of sound management practices requires an understanding of the genetic structure of natural amphibian populations. To this end, we estimated genetic differences within and among seven isolated populations of northern leopard frogs, Rana pipiens, from Arizona and southern Utah using random amplified polymorphic DNA (RAPD) analyses. Fourteen arbitrarily designed primers detected 38 polymorphic loci in 85 individual frogs. Three types of population structure were observed in this study, (i) Two populations showed low genetic diversity (D= 0.10 and 0.04) and may have been established by relatively recent events, (ii) Two were not genetically distinct and exhibited a high degree of within‐population diversity (D= 0.35). The possibility of gene flow between these populations is high due to their geographical proximity and their shared genetic structure, (iii) Three populations were genetically distinct from each other and the other populations, and exhibited intermediate within‐population variation (D= 0.19, 0.17, 0.14). Genetic distances among the seven populations ranged from 0.00 to 0.20, suggesting that some of these leopard frog populations are genetically distinct. Although based on relatively small samples, these data suggest that leopard frog populations in the south‐west are likely to represent unique genetic entities worthy of conservation. The management implications of these results are that isolated leopard frog populations should be evaluated on an individual basis to best preserve them.
Indo‐Pacific population structure and evolutionary history of the coconut crab Birgus latro
Authors: LAVERY S. , MORITZ C. , FIELDER D. R. 
Published: April 2008

AbstractMitochondrial DNA variation was used to examine population structure in a widespread, marine‐dispersed species, Birgus latro. Crabs were collected from eight locations throughout the species' Indo‐Pacific distribution. Purified mtDNA from 160 individuals was cut with five restriction enzymes, revealing high haplotype diversity (0.96) and moderate nucleotide diversity (0.75%). Island populations from the Indian Ocean (Christmas I.) and Pacific Ocean were significantly different (GST= 0.37) and had distinct mtDNA lineages with a net sequence divergence of 1.4%. Pacific island populations had diverged in a manner consistent with isolation by distance, with only the most peripheral populations being significantly different. The results for mtDNA are largely concordant with those from allozymes, although estimates of gene flow between the Indian and Pacific Oceans were much lower when based on mtDNA. The mtDNA phylogeny also permitted a deeper examination of the evolutionary and demographic history of Birgus latro. Long‐term separation of populations is evident in the complete phylogenetic subdivision of mtDNA lineages between the Indian and Pacific Ocean populations sampled. The starlike phylogeny of alleles from the Pacific suggests a rapid population expansion in the Pacific during the Pleistocene. Including information about allele phylogeny, as well as distribution and frequency, obscured contemporary population structure, but provided unique insights into the evolutionary history of the species.