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181.
182.
Andy Fenton Sarah C.L. Knowles Owen L. Petchey Amy B. Pedersen 《International journal for parasitology》2014
Interactions among coinfecting parasites have the potential to alter host susceptibility to infection, the progression of disease and the efficacy of disease control measures. It is therefore essential to be able to accurately infer the occurrence and direction of such interactions from parasitological data. Due to logistical constraints, perturbation experiments are rarely undertaken to directly detect interactions, therefore a variety of approaches are commonly used to infer them from patterns of parasite association in observational data. However, the reliability of these various approaches is not known. We assess the ability of a range of standard analytical approaches to detect known interactions between infections of nematodes and intestinal coccidia (Eimeria) in natural small-mammal populations, as revealed by experimental perturbations. We show that correlation-based approaches are highly unreliable, often predicting strong and highly significant associations between nematodes and Eimeria in the opposite direction to the underlying interaction. The most reliable methods involved longitudinal analyses, in which the nematode infection status of individuals at one month is related to the infection status by Eimeria the next month. Even then, however, we suggest these approaches are only viable for certain types of infections and datasets. Overall we suggest that, in the absence of experimental approaches, careful consideration be given to the choice of statistical approach when attempting to infer interspecific interactions from observational data. 相似文献
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Marean CW Bar-Matthews M Fisher E Goldberg P Herries A Karkanas P Nilssen PJ Thompson E 《Journal of human evolution》2010,59(3-4):234-255
Pinnacle Point Cave 13B (PP13B) has provided the earliest archaeological evidence for the exploitation of marine shellfish, along with very early evidence for use and modification of pigments and the production of bladelets, all dated to approximately 164?ka (Marean et?al., 2007). This makes PP13B a key site in studies of the origins of modern humans, one of a handful of sites in Africa dating to Marine Isotope Stage 6 (MIS 6), and the only site on the coast of South Africa with human occupation confidently dated to MIS 6. Along with this MIS 6 occupation there are rich archaeological sediments dated to MIS 5, and together these sediments are differentially preserved in three different areas of the cave. The sediments represent a complex palimpsest of geogenic, biogenic, and anthropogenic input and alteration that are described and interpreted through the use of a variety of macrostratigraphic, micromorphologic, and geochemical techniques. Three independent dating techniques allow us to constrain the age range of these sediments and together provide the stratigraphic context for the analyses of the material that follow in this special issue. 相似文献
186.
This paper aims to identify the spatial patterning of burning and occupation within an early Middle Stone Age (MSA) sea cave in the Western Cape Province of South Africa by creating a multidimensional model of archaeomagnetic data recovered from all excavated units. Magnetic susceptibility and other mineral magnetic parameters are shown to provide an excellent proxy for the anthropogenic alteration and spread of burnt material into the surrounding unaltered cave deposits. The identification of combustion features and areas of occupation or different activities within the site can be determined because the movement of people throughout the cave mixes magnetically strong hearth material with magnetically weak unaltered sediments. This is also indicated by micromorphological analysis. The degree of enhancement is also shown to indicate the extent to which a deposit has been altered, and therefore, intensity of occupation, because multiple heatings of deposits are needed to form the concentrations of iron minerals occurring in some layers. This is further supported by a comparison with artifact density for the layers. Variation in the magnetic values between different areas of the site is noted with major occupation or fire building occurring in the front of the cave during earlier MIS 6 periods, while during later MIS 5 periods the entire cave is occupied intensively. The oldest, MIS 11 deposits at the rear of the cave indicate no evidence of enhancement and an apparent absence of any anthropogenic signature. 相似文献
187.
A global approach to crop wild relative conservation: securing the gene pool for food and agriculture 总被引:1,自引:0,他引:1
Nigel Maxted Shelagh Kell Álvaro Toledo Ehsan Dulloo Vernon Heywood Toby Hodgkin Danny Hunter Luigi Guarino Andy Jarvis Brian Ford-Lloyd 《Kew Bulletin》2010,65(4):561-576
In light of the growing concern over the potentially devastating impacts on biodiversity and food security of climate change
and the massively growing world population, taking action to conserve crop wild relatives (CWR), is no longer an option —
it is a priority. Crop wild relatives are species closely related to crops, including their progenitors, many of which have
the potential to contribute beneficial traits to crops, such as pest or disease resistance, yield improvement or stability.
They are a critical component of plant genetic resources for food and agriculture (PGRFA), have already made major contributions
to crop production and are vital for future food security; their systematic conservation in ways that ensure their continuing
availability for use is therefore imperative. This is a complex, interdisciplinary, global issue that has been addressed by
various national and international initiatives. Drawing on the lessons learnt from these initiatives we can now propose a
global approach to CWR conservation, the key elements of which are: (1) estimating global CWR numbers, (2) assessment of the
global importance of CWR diversity, (3) current conservation status, (4) threats to CWR diversity, (5) systematic approaches
to CWR conservation, (6) CWR informatics, and (7) enhancing the use of CWR diversity. 相似文献
188.
Fred A. van Eeuwijk Martin Boer L. Radu Totir Marco Bink Deanne Wright Christopher R. Winkler Dean Podlich Keith Boldman Andy Baumgarten Matt Smalley Martin Arbelbide Cajo J. F. ter Braak Mark Cooper 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》2010,120(2):429-440
Two outlines for mixed model based approaches to quantitative trait locus (QTL) mapping in existing maize hybrid selection programs are presented: a restricted maximum likelihood (REML) and a Bayesian Markov Chain Monte Carlo (MCMC) approach. The methods use the in-silico-mapping procedure developed by Parisseaux and Bernardo (2004) as a starting point. The original single-point approach is extended to a multi-point approach that facilitates interval mapping procedures. For computational and conceptual reasons, we partition the full set of relationships from founders to parents of hybrids into two types of relations by defining so-called intermediate founders. QTL effects are defined in terms of those intermediate founders. Marker based identity by descent relationships between intermediate founders define structuring matrices for the QTL effects that change along the genome. The dimension of the vector of QTL effects is reduced by the fact that there are fewer intermediate founders than parents. Furthermore, additional reduction in the number of QTL effects follows from the identification of founder groups by various algorithms. As a result, we obtain a powerful mixed model based statistical framework to identify QTLs in genetic backgrounds relevant to the elite germplasm of a commercial breeding program. The identification of such QTLs will provide the foundation for effective marker assisted and genome wide selection strategies. Analyses of an example data set show that QTLs are primarily identified in different heterotic groups and point to complementation of additive QTL effects as an important factor in hybrid performance. 相似文献
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Adam R. Boyko Pascale Quignon Lin Li Jeffrey J. Schoenebeck Jeremiah D. Degenhardt Kirk E. Lohmueller Keyan Zhao Abra Brisbin Heidi G. Parker Bridgett M. vonHoldt Michele Cargill Adam Auton Andy Reynolds Abdel G. Elkahloun Marta Castelhano Dana S. Mosher Nathan B. Sutter Gary S. Johnson John Novembre Melissa J. Hubisz Adam Siepel Robert K. Wayne Carlos D. Bustamante Elaine A. Ostrander 《PLoS biology》2010,8(8)
Domestic dogs exhibit tremendous phenotypic diversity, including a greater
variation in body size than any other terrestrial mammal. Here, we generate a
high density map of canine genetic variation by genotyping 915 dogs from 80
domestic dog breeds, 83 wild canids, and 10 outbred African shelter dogs across
60,968 single-nucleotide polymorphisms (SNPs). Coupling this genomic resource
with external measurements from breed standards and individuals as well as
skeletal measurements from museum specimens, we identify 51 regions of the dog
genome associated with phenotypic variation among breeds in 57 traits. The
complex traits include average breed body size and external body dimensions and
cranial, dental, and long bone shape and size with and without allometric
scaling. In contrast to the results from association mapping of quantitative
traits in humans and domesticated plants, we find that across dog breeds, a
small number of quantitative trait loci (≤3) explain the majority of
phenotypic variation for most of the traits we studied. In addition, many
genomic regions show signatures of recent selection, with most of the highly
differentiated regions being associated with breed-defining traits such as body
size, coat characteristics, and ear floppiness. Our results demonstrate the
efficacy of mapping multiple traits in the domestic dog using a database of
genotyped individuals and highlight the important role human-directed selection
has played in altering the genetic architecture of key traits in this important
species. 相似文献