http://www.dspace.cam.ac.uk:80/handle/1810/194889 Scholarly papers in Archaeology Sat, 18 May 2013 09:12:58 GMT 2013-05-18T09:12:58Z http://www.dspace.cam.ac.uk:80/handle/1810/241601 Title: Evolutionary history of barley cultivation in Europe revealed by genetic analysis of extant landraces Authors: Jones, Huw; Civan, Peter; Cockram, James; Leigh, Fiona J; Smith, Lydia MJ; Jones, Martin K; Charles, Michael P; Molina-Cano, Jose-Luis; Powell, Wayne; Jones, Glynis; Brown, Terence A Abstract: Abstract Background Understanding the evolution of cultivated barley is important for two reasons. First, the evolutionary relationships between different landraces might provide information on the spread and subsequent development of barley cultivation, including the adaptation of the crop to new environments and its response to human selection. Second, evolutionary information would enable landraces with similar traits but different genetic backgrounds to be identified, providing alternative strategies for the introduction of these traits into modern germplasm. Results The evolutionary relationships between 651 barley landraces were inferred from the genotypes for 24 microsatellites. The landraces could be divided into nine populations, each with a different geographical distribution. Comparisons with ear row number, caryopsis structure, seasonal growth habit and flowering time revealed a degree of association between population structure and phenotype, and analysis of climate variables indicated that the landraces are adapted, at least to some extent, to their environment. Human selection and/or environmental adaptation may therefore have played a role in the origin and/or maintenance of one or more of the barley landrace populations. There was also evidence that at least some of the population structure derived from geographical partitioning set up during the initial spread of barley cultivation into Europe, or reflected the later introduction of novel varieties. In particular, three closely-related populations were made up almost entirely of plants with the daylength nonresponsive version of the photoperiod response gene PPD-H1, conferring adaptation to the long annual growth season of northern Europe. These three populations probably originated in the eastern Fertile Crescent and entered Europe after the initial spread of agriculture. Conclusions The discovery of population structure, combined with knowledge of associated phenotypes and environmental adaptations, enables a rational approach to identification of landraces that might be used as sources of germplasm for breeding programs. The population structure also enables hypotheses concerning the prehistoric spread and development of agriculture to be addressed. Description: RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are. Wed, 02 Nov 2011 00:00:00 GMT http://www.dspace.cam.ac.uk:80/handle/1810/241601 2011-11-02T00:00:00Z http://www.dspace.cam.ac.uk:80/handle/1810/238260 Title: Origins of chromosomal rearrangement hotspots in the human genome: evidence from the AZFadeletion hotspots Authors: Hurles, Matthew E; Willey, David; Matthews, Lucy; Hussain, Syed Sufyan Abstract: Abstract Background The origins of the recombination hotspots that are a common feature of both allelic and non-allelic homologous recombination in the human genome are poorly understood. We have investigated, by comparative sequencing, the evolution of two hotspots of non-allelic homologous recombination on the Y chromosome that lie within paralogous sequences known to sponsor deletions resulting in male infertility. Results These recombination hotspots are characterized by signatures of concerted evolution, which indicate that gene conversion between paralogs has been predominant in shaping their recent evolution. By contrast, the paralogous sequences that surround the hotspots exhibit little evidence of gene conversion. A second feature of these rearrangement hotspots is the extreme interspecific sequence divergence (around 2.5%) that places them among the most divergent orthologous sequences between humans and chimpanzees. Conclusions Several hominid-specific gene conversion events have rendered these hotspots better substrates for chromosomal rearrangements in humans than in chimpanzees or gorillas. Monte Carlo simulations of sequence evolution suggest that extreme sequence divergence is a direct consequence of gene conversion between paralogs. We propose that the coincidence of signatures of concerted evolution and recurrent breakpoints of chromosomal rearrangement (mapped at the sequence level) may enable the identification of putative rearrangement hotspots from analysis of comparative sequences from great apes. Description: RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are. Tue, 13 Jul 2004 23:00:00 GMT http://www.dspace.cam.ac.uk:80/handle/1810/238260 2004-07-13T23:00:00Z http://www.dspace.cam.ac.uk:80/handle/1810/238135 Title: Gene conversion homogenizes the CMT1A paralogous repeats Authors: Hurles, Matthew E Abstract: Abstract Background Non-allelic homologous recombination between paralogous repeats is increasingly being recognized as a major mechanism causing both pathogenic microdeletions and duplications, and structural polymorphism in the human genome. It has recently been shown empirically that gene conversion can homogenize such repeats, resulting in longer stretches of absolute identity that may increase the rate of non-allelic homologous recombination. Results Here, a statistical test to detect gene conversion between pairs of non-coding sequences is presented. It is shown that the 24 kb Charcot-Marie-Tooth type 1A paralogous repeats (CMT1A-REPs) exhibit the imprint of gene conversion processes whilst control orthologous sequences do not. In addition, Monte Carlo simulations of the evolutionary divergence of the CMT1A-REPs, incorporating two alternative models for gene conversion, generate repeats that are statistically indistinguishable from the observed repeats. Bounds are placed on the rate of these conversion processes, with central values of 1.3 × 10-4 and 5.1 × 10-5 per generation for the alternative models. Conclusions This evidence presented here suggests that gene conversion may have played an important role in the evolution of the CMT1A-REP paralogous repeats. The rates of these processes are such that it is probable that homogenized CMT1A-REPs are polymorphic within modern populations. Gene conversion processes are similarly likely to play an important role in the evolution of other segmental duplications and may influence the rate of non-allelic homologous recombination between them. Description: RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are. Tue, 11 Dec 2001 00:00:00 GMT http://www.dspace.cam.ac.uk:80/handle/1810/238135 2001-12-11T00:00:00Z http://www.dspace.cam.ac.uk:80/handle/1810/195777 Title: A bird’s eye view - of a leopard’s spots. The Çatalhöyük ‘map’ and the development of cartographic representation in prehistory. Authors: Meece, Stephanie Abstract: The striking wall paintings uncovered in the excavations at Çatalhöyük have fascinated archaeologists and non-archaeologists alike, and many interpretations of their content and meaning have been proposed. This article re-evaluates the claim that one of these paintings is a map of the village, with Hasan Dağ erupting above it. It is argued that the excavator’s first interpretation of the objects depicted in the painting, i.e., that they are a leopard skin above a panel of geometric design, is in fact a far more reasonable one, when this painting is contextualised within the entire corpus of painting and other art objects found at the site. Implications of this re-interpretation for our understanding of Neolithic spatial and symbolic representation, and the origin of map-making are considered, as well as the importance of the depiction of animals and felines in the Neolithic period. Sun, 01 Jan 2006 00:00:00 GMT http://www.dspace.cam.ac.uk:80/handle/1810/195777 2006-01-01T00:00:00Z