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61.
Howe GT; Bucciaglia PA; Hackett WP; Furnier GR; Cordonnier-Pratt MM; Gardner G 《Molecular biology and evolution》1998,15(2):160-175
The phytochrome photoreceptors play important roles in the photoperiodic
control of vegetative bud set, growth cessation, dormancy induction, and
cold-hardiness in trees. Interestingly, ecotypic differences in
photoperiodic responses are observed in many temperate- zone tree species.
Northern and southern ecotypes of black cottonwood (Populus trichocarpa
Torr. & Gray), for example, exhibit marked differences in the timing of
short-day-induced bud set and growth cessation, and these responses are
controlled by phytochrome. Therefore, as a first step toward determining
the molecular genetic basis of photoperiodic ecotypes in trees, we
characterized the phytochrome gene (PHY) family in black cottonwood. We
recovered fragments of one PHYA and two PHYB using PCR-based cloning and by
screening a genomic library. Results from Southern analyses confirmed that
black cottonwood has one PHYA locus and two PHYB loci, which we arbitrarily
designated PHYB1 and PHYB2. Phylogenetic analyses which included PHY from
black cottonwood, Arabidopsis thaliana and tomato (Solanum lycopersicum)
suggest that the PHYB/D duplications in these species occurred
independently. When Southern blots were probed with PHYC, PHYE, and PHYE
heterologous probes, the strongest bands that we detected were those of
black cottonwood PHYA and/or PHYB. These results suggest that black
cottonwood lacks members of the PHYC/F and PHYE subfamilies. Although black
cottonwood could contain additional PHY that are distantly related to known
angiosperm PHY, our results imply that the PHY family of black cottonwood
is less complex than that of other well-characterized dicot species such as
Arabidopsis and tomato. Based on Southern analyses of five black cottonwood
genotypes representing three photoperiodic ecotypes, substantial
polymorphism was detected for at least one of the PHYB loci but not for the
PHYA locus. The novel character of the PHY family in black cottonwood, as
well as the differences in polymorphism we observed between the PHYA and
PHYB subfamilies, indicates that a number of fundamental macro- and
microevolutionary questions remain to be answered about the PHY family in
dicots.
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62.
Infection of the fittest: devil facial tumour disease has greatest effect on individuals with highest reproductive output 下载免费PDF全文
Konstans Wells Rodrigo K. Hamede Douglas H. Kerlin Andrew Storfer Paul A. Hohenlohe Menna E. Jones Hamish I. McCallum 《Ecology letters》2017,20(6):770-778
Emerging infectious diseases rarely affect all members of a population equally and determining how individuals’ susceptibility to infection is related to other components of their fitness is critical to understanding disease impacts at a population level and for predicting evolutionary trajectories. We introduce a novel state‐space model framework to investigate survival and fecundity of Tasmanian devils (Sarcophilus harrisii) affected by a transmissible cancer, devil facial tumour disease. We show that those devils that become host to tumours have otherwise greater fitness, with higher survival and fecundity rates prior to disease‐induced death than non‐host individuals that do not become infected, although high tumour loads lead to high mortality. Our finding that individuals with the greatest reproductive value are those most affected by the cancer demonstrates the need to quantify both survival and fecundity in context of disease progression for understanding the impact of disease on wildlife populations. 相似文献
63.
A. G. Jones R. Bürger S. J. Arnold P. A. Hohenlohe J. C. Uyeda 《Journal of evolutionary biology》2012,25(11):2210-2231
Theoretical and empirical results demonstrate that the G ‐matrix, which summarizes additive genetic variances and covariances of quantitative traits, changes over time. Such evolution and fluctuation of the G ‐matrix could potentially have wide‐ranging effects on phenotypic evolution. Nevertheless, no studies have yet addressed G ‐matrix stability and evolution when movement of an intermediate optimum includes large, episodic jumps or stochasticity. Here, we investigate such scenarios by using simulation‐based models of G ‐matrix evolution. These analyses yield four important insights regarding the evolution and stability of the G ‐matrix. (i) Regardless of the model of peak movement, a moving optimum causes the G ‐matrix to orient towards the direction of net peak movement, so that genetic variance is enhanced in that direction (the variance enhancement effect). (ii) Peak movement skews the distribution of breeding values in the direction of movement, which impedes the response to selection. (iii) The stability of the G ‐matrix is affected by the overall magnitude and direction of peak movement, but modes and rates of peak movement have surprisingly small effects (the invariance principle). (iv) Both episodic and stochastic peak movement increase the probability that a population will fall below its carrying capacity and go extinct. We also present novel equations for the response of the trait mean to multivariate selection, which take into account the higher moments of the distribution of breeding values. 相似文献
64.
65.
Next-generation RAD sequencing identifies thousands of SNPs for assessing hybridization between rainbow and westslope cutthroat trout 总被引:1,自引:0,他引:1
Hohenlohe PA Amish SJ Catchen JM Allendorf FW Luikart G 《Molecular ecology resources》2011,11(Z1):117-122
The increased numbers of genetic markers produced by genomic techniques have the potential to both identify hybrid individuals and localize chromosomal regions responding to selection and contributing to introgression. We used restriction-site-associated DNA sequencing to identify a dense set of candidate SNP loci with fixed allelic differences between introduced rainbow trout (Oncorhynchus mykiss) and native westslope cutthroat trout (Oncorhynchus clarkii lewisi). We distinguished candidate SNPs from homeologs (paralogs resulting from whole-genome duplication) by detecting excessively high observed heterozygosity and deviations from Hardy-Weinberg proportions. We identified 2923 candidate species-specific SNPs from a single Illumina sequencing lane containing 24 barcode-labelled individuals. Published sequence data and ongoing genome sequencing of rainbow trout will allow physical mapping of SNP loci for genome-wide scans and will also provide flanking sequence for design of qPCR-based TaqMan(?) assays for high-throughput, low-cost hybrid identification using a subset of 50-100 loci. This study demonstrates that it is now feasible to identify thousands of informative SNPs in nonmodel species quickly and at reasonable cost, even if no prior genomic information is available. 相似文献
66.
Amish SJ Hohenlohe PA Painter S Leary RF Muhlfeld C Allendorf FW Luikart G 《Molecular ecology resources》2012,12(4):653-660
Hybridization with introduced rainbow trout threatens most native westslope cutthroat trout populations. Understanding the genetic effects of hybridization and introgression requires a large set of high-throughput, diagnostic genetic markers to inform conservation and management. Recently, we identified several thousand candidate single-nucleotide polymorphism (SNP) markers based on RAD sequencing of 11 westslope cutthroat trout and 13 rainbow trout individuals. Here, we used flanking sequence for 56 of these candidate SNP markers to design high-throughput genotyping assays. We validated the assays on a total of 92 individuals from 22 populations and seven hatchery strains. Forty-six assays (82%) amplified consistently and allowed easy identification of westslope cutthroat and rainbow trout alleles as well as heterozygote controls. The 46 SNPs will provide high power for early detection of population admixture and improved identification of hybrid and nonhybridized individuals. This technique shows promise as a very low-cost, reliable and relatively rapid method for developing and testing SNP markers for nonmodel organisms with limited genomic resources. 相似文献
67.
68.
Mice of the TO Swiss strain received diets containing different amounts of saturated or unsaturated fat throughout life. These diets produced characteristic changes in cardiac phospholipid fatty acid composition, but produced no significant differences in fatty acid composition of phospholipids from a crude membrane fraction of brain. When littermates of these animals were exposed to ethanol vapour in an inhalation chamber it was observed that mice which had received a diet high in saturated fat lost the righting reflex at an estimated concentration of ethanol in blood higher than that required for mice receiving a control diet, or a diet rich in polyunsaturated fat. Analysis of the brain membrane fraction from those animals which had received ethanol revealed that mice receiving the highly saturated fat diet now had a significantly greater proportion of saturated fatty acids in brain membrane phospholipids. These results are discussed in relation to the hypothesis that brain membrane lipid composition may influence the behavioural response to ethanol. 相似文献
69.
Sze SH; Roytberg MA; Gelfand MS; Mironov AA; Astakhova TV; Pevzner PA 《Bioinformatics (Oxford, England)》1998,14(1):14-19
MOTIVATION: Gene annotation is the final goal of gene prediction
algorithms. However, these algorithms frequently make mistakes and
therefore the use of gene predictions for sequence annotation is hardly
possible. As a result, biologists are forced to conduct time-consuming gene
identification experiments by designing appropriate PCR primers to test
cDNA libraries or applying RT-PCR, exon trapping/amplification, or other
techniques. This process frequently amounts to 'guessing' PCR primers on
top of unreliable gene predictions and frequently leads to wasting of
experimental efforts. RESULTS: The present paper proposes a simple and
reliable algorithm for experimental gene identification which bypasses the
unreliable gene prediction step. Studies of the performance of the
algorithm on a sample of human genes indicate that an experimental protocol
based on the algorithm's predictions achieves an accurate gene
identification with relatively few PCR primers. Predictions of PCR primers
may be used for exon amplification in preliminary mutation analysis during
an attempt to identify a gene responsible for a disease. We propose a
simple approach to find a short region from a genomic sequence that with
high probability overlaps with some exon of the gene. The algorithm is
enhanced to find one or more segments that are probably contained in the
translated region of the gene and can be used as PCR primers to select
appropriate clones in cDNA libraries by selective amplification. The
algorithm is further extended to locate a set of PCR primers that uniformly
cover all translated regions and can be used for RT-PCR and further
sequencing of (unknown) mRNA.
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70.
Zimmerman PA; Katholi CR; Wooten MC; Lang-Unnasch N; Unnasch TR 《Molecular biology and evolution》1994,11(3):384-392
Polymerase chain reaction (PCR) products were characterized for a repeated
sequence family (designated "O-150") of the human filarial parasite
Onchocerca volvulus. In phylogenetic inferences, the O-150 sequences
clustered into closely related groups, suggesting that concerted evolution
maintains sequence homology in this family. Using a novel mathematical
model based on a nested application of an analysis of variance, we
demonstrated that African rainforest and savannah strain parasite
populations are significantly different. In contrast, parasites collected
in the New World are indistinguishable from African savannah strains of O.
volvulus. This finding supports the hypothesis that onchocerciasis was
recently introduced into the New World, possibly as a result of the slave
trade.
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