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Many Loci (many + locus)
Selected AbstractsAnonymous nuclear markers for the eastern fence lizard, Sceloporus undulatusMOLECULAR ECOLOGY RESOURCES, Issue 1 2007E. B. ROSENBLUM Abstract We present results from a screen for de novo variable nuclear loci using a genomic library approach in Sceloporus undulatus, the eastern fence lizard. We tested amplification success for 77 primer pairs in S. undulatus, Sceloporus occidentalis and Sceloporus grammicus. Many loci amplified in all three species suggesting that our primers will be useful for developing sequencing or single nucleotide polymorphism (SNP) genotyping markers in other sceloporine lizards. We also sequenced 19 loci, containing 158 variable sites, for 91 S. undulatus individuals. We report high levels of nucleotide variation in this species with an average of 38 SNPs per kilobase. [source] COMPARATIVE GENOMIC AND POPULATION GENETIC ANALYSES INDICATE HIGHLY POROUS GENOMES AND HIGH LEVELS OF GENE FLOW BETWEEN DIVERGENT HELIANTHUS SPECIESEVOLUTION, Issue 8 2009Nolan C. Kane While speciation can be found in the presence of gene flow, it is not clear what impact this gene flow has on genome- and range-wide patterns of differentiation. Here we examine gene flow across the entire range of the common sunflower, H. annuus, its historically allopatric sister species H. argophyllus and a more distantly related, sympatric relative H. petiolaris. Analysis of genotypes at 26 microsatellite loci in 1015 individuals from across the range of the three species showed substantial introgression between geographically proximal populations of H. annuus and H. petiolaris, limited introgression between H. annuus and H. argophyllus, and essentially no gene flow between the allopatric pair, H. argophyllus and H. petiolaris. Analysis of sequence divergence levels among the three species in 1420 orthologs identified from EST databases identified a subset of loci showing extremely low divergence between H. annuus and H. petiolaris and extremely high divergence between the sister species H. annuus and H. argophyllus, consistent with introgression between H. annuus and H. petiolaris at these loci. Thus, at many loci, the allopatric sister species are more genetically divergent than the more distantly related sympatric species, which have exchanged genes across much of the genome while remaining morphologically and ecologically distinct. [source] Variation in Reproductive Behaviour within a Sex:Neural Systems and Endocrine ActivationJOURNAL OF NEUROENDOCRINOLOGY, Issue 7 2002T. Rhen Abstract Intrasexual variation in reproductive behaviour, morphology and physiology is taxonomically widespread in vertebrates, and is as biologically and ecologically significant as the differences between the sexes. In this review, we examine the diverse patterns of intrasexual variation in reproductive behaviours within vertebrates. By illustrating the genetic, cellular, hormonal and/or neural mechanisms underlying behavioural variation in a number of species, another level of complexity is added to studies of brain organization and function. Such information increases our understanding of the unique and conserved mechanisms underlying sex and individual differences in behaviour in vertebrates as a whole. Here, we show that intrasexual variation in behaviour may be discrete or continuous in nature. Moreover, this variation may be due to polymorphism at a single genetic locus or many loci, or may even be the result of phenotypic plasticity. Phenotypic plasticity simply refers to cases where a single genotype (or individual) can produce (or display) different phenotypes. Defined in this way, plasticity subsumes many different types of behavioural variation. For example, some behavioural phenotypes are established by environmental factors during early ontogeny, others are the result of developmental transitions from one phenotype early in life to another later in life, and still other strategies are facultative with different behaviours displayed in different social contexts. [source] Genetic variability is unrelated to growth and parasite infestation in natural populations of the European eel (Anguilla anguilla)MOLECULAR ECOLOGY, Issue 22 2009J. M. PUJOLAR Abstract Positive correlations between individual genetic heterozygosity and fitness-related traits (HFCs) have been observed in organisms as diverse as plants, marine bivalves, fish or mammals. HFCs are not universal and the strength and stability of HFCs seem to be variable across species, populations and ages. We analysed the relationship between individual genetic variability and two different estimators of fitness in natural samples of European eel, growth rate (using back-calculated length-at-age 1, 2 and 3) and parasite infestation by the swimbladder nematode Anguillicola crassus. Despite using a large data set of 22 expressed sequence tags-derived microsatellite loci and a large sample size of 346 individuals, no heterozygote advantage was observed in terms of growth rate or parasite load. The lack of association was evidenced by (i) nonsignificant global HFCs, (ii) a Multivariate General Linear Model showing no effect of heterozygosity on fitness components, (iii) single-locus analysis showing a lower number of significant tests than the expected false discovery rate, (iv) sign tests showing only a significant departure from expectations at one component, and, (v) a random distribution of significant single-locus HFCs that was not consistent across fitness components or sampling sites. This contrasts with the positive association observed in farmed eels in a previous study using allozymes, which can be explained by the nature of the markers used, with the allozyme study including many loci involved in metabolic energy pathways, while the expressed sequence tags-linked microsatellites might be located in genes or in the proximity of genes uncoupled with metabolism/growth. [source] Inbreeding depression and multiple regions showing heterozygote advantage in Drosophila melanogaster exposed to stressMOLECULAR ECOLOGY, Issue 13 2006ÁLVARO G. A. FERREIRA Abstract Recent studies that reveal a correlation between heterozygosity and fitness in natural populations have rekindled interest in whether balancing selection is widespread or an evolutionary oddity. We therefore quantified heterozygote advantage at 12 microsatellite markers in both inbred and outbred crosses of Drosophila grown under different forms of environmental stress. As expected, inbreeding depression reduces fitness relative to the outbred controls. In addition, many loci exhibit heterozygote advantage over and above any effect due to inbreeding, with ,30% of markers showing an effect in any given culture condition and ,75% of markers showing an effect in at least one of the four culture conditions. To explore the extent of linkage disequilibrium surrounding these loci we further typed four new markers close to each of the three strongest hits. We find a pattern where the extent of heterozygote excess tends to decline to nonsignificance within around 1.5 megabases (Mb) either side of the original hit. Crude extrapolation suggests 12 genes or regions experience detectable levels of heterozygote advantage in any one condition and as many as 25 overall. Thus, balancing selection is widespread and is likely to play an important role in maintaining genetic variability. [source] Patterns, sources and ecological implications of clonal diversity in apomictic Ranunculus carpaticola (Ranunculus auricomus complex, Ranunculaceae)MOLECULAR ECOLOGY, Issue 4 2006O. PAUN Abstract Sources and implications of genetic diversity in agamic complexes are still under debate. Population studies (amplified fragment length polymorphisms, microsatellites) and karyological methods (Feulgen DNA image densitometry and flow cytometry) were employed for characterization of genetic diversity and ploidy levels of 10 populations of Ranunculus carpaticola in central Slovakia. Whereas two diploid populations showed high levels of genetic diversity, as expected for sexual reproduction, eight populations are hexaploid and harbour lower degrees of genotypic variation, but maintain high levels of heterozygosity at many loci, as is typical for apomicts. Polyploid populations consist either of a single AFLP genotype or of one dominant and a few deviating genotypes. genotype/genodive and character incompatibility analyses suggest that genotypic variation within apomictic populations is caused by mutations, but in one population probably also by recombination. This local facultative sexuality may have a great impact on regional genotypic diversity. Two microsatellite loci discriminated genotypes separated by the accumulation of few mutations (,clone mates') within each AFLP clone. Genetic diversity is partitioned mainly among apomictic populations and is not geographically structured, which may be due to facultative sexuality and/or multiple colonizations of sites by different clones. Habitat differentiation and a tendency to inhabit artificial meadows is more pronounced in apomictic than in sexual populations. We hypothesize that maintenance of genetic diversity and superior colonizing abilities of apomicts in temporally and spatially heterogeneous environments are important for their distributional success. [source] The ,rare allele phenomenon' in a ribosomal spacerMOLECULAR ECOLOGY, Issue 5 2001Menno Schilthuizen Abstract We describe the increased frequency of a particular length variant of the internal transcribed spacer 1 (ITS-1) of the ribosomal DNA in a hybrid zone of the land snail Albinaria hippolyti. The phenomenon that normally rare alleles or other markers can increase in frequency in the centre of hybrid zones is not new. Under the term ,hybrizyme' or ,rare allele' phenomenon it has been recorded in many organisms and different genetic markers. However, this is the first time that it has been found in a multicopy locus. On the one hand, the pattern fits well with the view that purifying selection in hybrid populations works on many loci across the genome and should thus have its effect on many independent molecular markers. On the other hand, the results are puzzling, given that the multiple copies of rDNA are not expected to respond in unison. We suggest two possible explanations for these conflicting observations. [source] Statistical confidence in parentage analysis with incomplete sampling: how many loci and offspring are needed?MOLECULAR ECOLOGY, Issue 5 2000B. D. Neff Abstract We have recently presented models to estimate parentage in breeding systems with multiple mating and incomplete sampling of the candidate parents. Here we provide formulas to calculate the statistical confidence and the optimal trade-off between the number of loci and offspring. These calculations allow an understanding of the statistical significance of the parentage estimates as well as the appropriate sampling regime required to obtain a desired level of confidence. We show that the trade-off generally depends on the parentage of the putative parents. When parentage is low, sampling effort should concentrate on increasing the number of loci. Otherwise, there are similar benefits from increasing the number of loci or offspring. We demonstrate these methods using genetic data from a nest of the bluegill sunfish (Lepomis macrochirus). [source] Inheritance of heading time in spring barley evaluated in multiple environmentsPLANT BREEDING, Issue 3 2001L. W. Gallagher Abstract The inheritance of heading time of spring barley was studied in three extremely early genotypes IB, RL and ,Mona' (M), which is homozygous recessive for the early maturity ea8 (=eak) gene conferring extreme earliness under short daylengths and is relatively photoperiod insensitive, and five (GP, MA, PS, NU and BA) spring genotypes that are early to intermediate for heading time. Frequency distributions of F2 generations grown at Ouled Gnaou, Morocco (32°15, N), an environment which maximizes differences between photoperiod-insensitive and photoperiod-sensitive genotypes, indicated that across populations many loci were segregating in a complex Mendelian manner. IB and RL were both homozygous recessive for the ea8 gene, which conferred an early heading time. RL had partially dominant alleles at second locus (Enea8), which enhanced its earliness. Recovery of only progeny within the parental range of genotypes for heading time from the crosses of RL/M and IB/M suggests that numerous loci remained suppressed, perhaps latent, given their diverse parentage. The ea8 recessive homozygote in RL suppressed another unidentified locus which, when homozygous recessive in the absence of the ea8 recessive homozygote, conferred extreme earliness in one short daylength environment (Ouled Gnaou, Morocco) but was undetected in another environment (Davis, CA, USA). Epistatic gene action and genotype × environment effects strongly influenced heading time. In addition to a genetic system consisting of single-locus recessive homozygotes conferring photoperiod insensitivity, a second genetic system, based on dominant alleles at one or a few loci, derived from the early heading Finnish landrace ,Olli', also confers extremely early heading time under short daylengths and relative photoperiod insensitivity in the genotype GP. [source] Brief communication: The Thule migration: Rejecting population histories using computer simulationAMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY, Issue 2 2007E.E. Marchani Abstract Locked within our genetic code are the histories of our genes and the genes of our ancestors. Deciphering a population's history from genetic data often involves lengthy investigations of many loci for many individuals. We test hypothetical population histories of the Thule expansion using a new coalescent simulation method that uses little more than mitochondrial haplogroup data. This new methodology rejects a severe bottleneck at expansion and reveals the range of probable population histories on which to focus future research. Am J Phys Anthropol, 2007. © 2007 Wiley-Liss, Inc. [source] Fine-scale genetic structure overrides macro-scale structure in a marine snail: nonrandom recruitment, demographic events or selection?BIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY, Issue 1 2007SÓNIA C. S. ANDRADE The planktotrophic littorinid species Littoraria flava occupies a continuous habitat on rocky shores close to brackish and freshwater sources. Previous studies of this species have shown a moderate genetic structure over a broad geographical scale, with high deviations from Hardy,Weinberg expectations in many allozymic loci. Local-scale subdivision in marine species with a long dispersal phase is unexpected, but occasionally found. Using a horizontal transect at three locations, we examined whether microscale and short-term subdivision also occurred in L. flava populations and, if so, whether this could explain the Hardy,Weinberg deviations. Littoraria flava showed even more structuring on a microgeographical scale (4,300 m) than on a large-scale (> 200 km). The Ewens,Watterson neutrality test showed that 18% of the tests deviated significantly from the neutrality model. A homogeneity test for each locus across samples within transects showed homogeneous and high FIS values in many loci. These results and the apparent genetic patchiness within transects suggest that asynchronous spawning associated with recurrent colonizations in L. flava can explain the local differentiation without a recognizable pattern. In addition, there could be a balance between these factors and diversifying selection acting on different loci at different times and localities. © 2007 The Linnean Society of London, Biological Journal of the Linnean Society, 2007, 91, 23,36. [source] | ||||||||||