http://www.dspace.cam.ac.uk:80/handle/1810/219480 Mon, 20 May 2013 09:35:26 GMT 2013-05-20T09:35:26Z http://www.dspace.cam.ac.uk:80/handle/1810/244307 Title: The biostratigraphy, palaeoecology and geochemistry of a long lacustrine sequence from NW Greece Authors: Frogley, Michael Reginald Abstract: Examination of an important new 319m core of lake sediment recovered from Ioannina in NW Greece has attempted to relate changes in the lake to variations in the regional climate of south-central Europe over the last 600,000 years. The site is known to have been extremely sensitive to past climatic change for three reasons: (i) temperate vegetation persisted throughout glacial stages (albeit at low frequencies), so the vegetational response to climatic change would therefore have been almost immediate; (ii) the extreme thickness of the sediments suggests that accumulation rates were high (at times, > 1m per thousand years), which has enabled high-resolution palaeoclimatic reconstructions; and (iii) precipitation of authigenic carbonate has preserved a remarkably sensitive proxy record of productivity variations for most of the lake's history. Well-defined shifts from glacial - interglacial mode have been correlated with vegetational changes identified in a core previously analysed from the same basin (using magnetic susceptibility profiles), enabling tentative correlations to be suggested with other European terrestrial sequences and with the marine oxygen isotope record, back to marine isotope stage 16. Twelve AMS radiocarbon determinations from the upper part of the core, together with the identification of a series of reversed palaeomagnetic events within the Brunhes chron, support the proposed age model for the sequence. The sediments at Ioannina, unlike most of the other long terrestrial European sequences, are calcareous and contain mollusc and ostracod assemblages. Part of this project has involved a comprehensive review of Quaternary and modem aquatic faunas from the lake, as well as the description, illustration and critical assessment of several poorly-known endemic taxa. Faunal assemblage data have been used to provide valuable information concerning the variable response of lake-level to climatic change over time. Convincing new mollusc an evidence indicates low lake-levels at the Last Glacial Maximum, agreeing with regional pollen data, but conflicting with geomorphological evidence derived from Kastritsa, a well-documented nearby Palaeolithic cave site. It is suggested that this discrepancy may be a result of subsequent tectonic uplift of the rockshelter. In addition, stable isotopic analyses of both the ostracods and the bulk carbonate within the sediments have contributed towards deriving a comprehensive palaeoenvironmental history for the site. Although the study analysed physical, biological and geochemical aspects of the entire core, two distinct parts of the record were selected for more detailed investigation. High-resolution analysis over the last interglacial (the Eemian) has revealed evidence for a clear, two-step deglaciation at the beginning of the period, known from elsewhere as the Zeifen-Kattegat Oscillation. Climatic instability has also been detected within the full interglacial. Comparisons are drawn with a range of other Eemian records from across Europe, as well as the Greenland ice cores. High-resolution analysis of the period from the end of the last glacial to the present day has also revealed evidence for climatic instability. A cool and arid oscillation is demonstrated by several climatic proxies that may constitute the first recognition of the Younger Dryas stadial from Greece. A shorter, but more subdued cooling event has also been detected during the first half of the Holocene, which may correspond with a widespread climatic oscillation from high-resolution terrestrial, marine and ice core records that has been dated to between 7,500 and 8,000 years BP. Thu, 01 Jan 1998 00:00:00 GMT http://www.dspace.cam.ac.uk:80/handle/1810/244307 1998-01-01T00:00:00Z http://www.dspace.cam.ac.uk:80/handle/1810/243405 Title: Extraterritorial prospecting and territory defence in cooperatively breeding meerkats Authors: Mares, Rafael Abstract: In group living animals where natal dispersal is delayed, prospecting allows individuals to asses their future dispersal and breeding opportunities and, in males of some species, may minimize the costs of delaying dispersal by enabling extra-group breeding while still resident in the natal group. While evidence of prospecting is widespread, comparatively little is known about the development of this behaviour and few studies have investigated the factors that may affect investment in prospecting, as it is typically difficult to monitor such mobile individuals. Prospectors typically encounter neighbouring groups during extraterritorial forays and resident individuals in these groups respond aggressively to approaches by extra- group males, given the potential loss in direct and indirect fitness that prospectors may inflict. As with prospecting behaviour, few studies have investigated the causes of individual differences in investment in repelling prospectors and measured the costs of such territory defence. In this dissertation, I exploit our ability to closely monitor prospecting males in meerkats, to investigate the causes of individual variation in extraterritorial prospecting effort and aggressive responses to prospector intrusions. In Chapter 3, I show that, as adults, heavier males invest more in prospecting than lighter ones, and that males time their forays in order to maximize their chances of dispersal, while minimizing the associated costs by prospecting when neighbouring groups are in close proximity to their own. In Chapter 4, I demonstrate that males that are heavier in early life start prospecting at a younger age and contribute less to helping later in life, than lighter males. In Chapter 5, I show that the threats posed by prospectors towards residents are associated with high investment by resident males in repelling intruders, which has measurable costs in terms of weight gain and cooperative contributions to offspring care. Finally, in Chapter 6, the experimental presentation of scent cues reveals that meerkats discriminate between resident and extra-group male scent cues, and that resident dominant males exhibit stronger responses to indirect evidence of prospectors than other group members. Tue, 06 Mar 2012 00:00:00 GMT http://www.dspace.cam.ac.uk:80/handle/1810/243405 2012-03-06T00:00:00Z http://www.dspace.cam.ac.uk:80/handle/1810/243353 Title: The evolutionary genetics of sexually selected plumage colour traits in the galliform birds Authors: Nadeau, Nicola Jacqueline Abstract: Extravagant male plumage traits in birds are a classic example of sexual selection. However we know very little about the units that selection is acting upon, the genes themselves – what are they and how are they influenced by sexual selection? In this study I focused on in the evolution and genetics of colouration the galliform birds. Several novel loci were used to create a well resolved phylogeny of this group. This was then used to investigate and reconstruct the evolution of sexual plumage dichromatism. Four pigmentation genes were sequenced in an array of galliform species. A measure of the rate of evolutionary change (dN/dS) at these loci was then compared between lineages with different strengths of sexual selection, using sexual dichromatism as the main index of sexual selection. I found evidence for sexual selection acting at the MC1R locus, in the form of a robust correlation between dN/dS and sexual plumage dichromatism that was not found at any of the other loci. I then went on to investigate the evolution and population genetics of MC1R in the grouse, focusing on the strongly dichromatic black grouse and the relatively monochromatic red grouse. I found some evidence for an adaptive change at this locus between these species. Finally I used a candidate gene approach to investigate the role of several genes in avian pigmentation using the Japanese quail (Coturnix japonica) as a model system. I found evidence that the avian agouti gene is involved in dorso-ventral pigmentation patterning and a regulatory mutation at this locus that produces a yellow phenotype. In addition point mutations at MC1R and TYRP1 were found to be responsible for producing pigmentation variants. I then compared the expression of several of these candidate genes in male and female common pheasants (Phasianus colchicus) and found lower TYRP1 expression in males. Knowledge of the genetic basis of secondary sexual traits and the action of sexual selection at this level could have important implications for our understanding of the process of sexual selection as a whole. Tue, 16 Jan 2007 00:00:00 GMT http://www.dspace.cam.ac.uk:80/handle/1810/243353 2007-01-16T00:00:00Z http://www.dspace.cam.ac.uk:80/handle/1810/243230 Title: Evolutionary history of the recruitment of conserved developmental genes in association to the formation and diversification of a novel trait Authors: Shirai, Leila T; Saenko, Suzanne V; Keller, Roberto A; Jeronimo, Maria A; Brakefield, Paul M; Descimon, Henri; Wahlberg, Niklas; Beldade, Patricia Abstract: Abstract Background The origin and modification of novel traits are important aspects of biological diversification. Studies combining concepts and approaches of developmental genetics and evolutionary biology have uncovered many examples of the recruitment, or co-option, of genes conserved across lineages for the formation of novel, lineage-restricted traits. However, little is known about the evolutionary history of the recruitment of those genes, and of the relationship between them -for example, whether the co-option involves whole or parts of existing networks, or whether it occurs by redeployment of individual genes with de novo rewiring. We use a model novel trait, color pattern elements on butterfly wings called eyespots, to explore these questions. Eyespots have greatly diversified under natural and sexual selection, and their formation involves genetic circuitries shared across insects. Results We investigated the evolutionary history of the recruitment and co-recruitment of four conserved transcription regulators to the larval wing disc region where circular pattern elements develop. The co-localization of Antennapedia, Notch, Distal-less, and Spalt with presumptive (eye)spot organizers was examined in 13 butterfly species, providing the largest comparative dataset available for the system. We found variation between families, between subfamilies, and between tribes. Phylogenetic reconstructions by parsimony and maximum likelihood methods revealed an unambiguous evolutionary history only for Antennapedia, with a resolved single origin of eyespot-associated expression, and many homoplastic events for Notch, Distal-less, and Spalt. The flexibility in the (co-)recruitment of the targeted genes includes cases where different gene combinations are associated with morphologically similar eyespots, as well as cases where identical protein combinations are associated with very different phenotypes. Conclusions The evolutionary history of gene (co-)recruitment is consistent with both divergence from a recruited putative ancestral network, and with independent co-option of individual genes. The diversity in the combinations of genes expressed in association with eyespot formation does not parallel diversity in characteristics of the adult phenotype. We discuss these results in the context of inferring homology. Our study underscores the importance of widening the representation of phylogenetic, morphological, and genetic diversity in order to establish general principles about the mechanisms behind the evolution of novel traits. 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, 15 Feb 2012 00:00:00 GMT http://www.dspace.cam.ac.uk:80/handle/1810/243230 2012-02-15T00:00:00Z http://www.dspace.cam.ac.uk:80/handle/1810/241665 Title: Deep mitochondrial divergence within a Heliconius butterfly species is not explained by cryptic speciation or endosymbiotic bacteria Authors: Munoz, Astrid G; Baxter, Simon W; Linares, Mauricio; Jiggins, Chris D Abstract: Abstract Background Cryptic population structure can be an indicator of incipient speciation or historical processes. We investigated a previously documented deep break in the mitochondrial haplotypes of Heliconius erato chestertonii to explore the possibility of cryptic speciation, and also the possible presence of endosymbiont bacteria that might drive mitochondrial population structure. Results Among a sample of 315 individuals from 16 populations of western Colombia, two principal mtDNA clades were detected with 2.15% divergence and we confirmed this structure was weakly associated with geography. The first mtDNA clade included 87% of individuals from northern populations and was the sister group of H. erato members of Andes western, while the second clade contained most individuals from southern populations (78%), which shared haplotypes with an Ecuadorian race of H. erato. In contrast, analysis using AFLP markers showed H. e. chestertonii to be a genetically homogeneous species with no association between mitochondrial divergence and AFLP structure. The lack of congruence between molecular markers suggests that cryptic speciation is not a plausible explanation for the deep mitochondrial divergence in H. e chestertonii. We also carried out the first tests for the presence of endosymbiontic bacteria in Heliconius, and identified two distinct lineages of Wolbachia within H. e. chestertonii. However, neither of the principal mitochondrial clades of H. e. chestertonii was directly associated with the patterns of infection. Conclusions We conclude that historical demographic processes are the most likely explanation for the high mitochondrial differentiation in H. e. chestertonii, perhaps due to gene flow between Cauca valley H. e. chestertonii and west Pacific slope populations of H. erato. 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. Mon, 12 Dec 2011 00:00:00 GMT http://www.dspace.cam.ac.uk:80/handle/1810/241665 2011-12-12T00:00:00Z http://www.dspace.cam.ac.uk:80/handle/1810/241602 Title: Motion dazzle and camouflage as distinct anti-predator defenses Authors: Stevens, Martin; Searle, William TL; Seymour, Jenny E; Marshall, Kate LA; Ruxton, Graeme D Abstract: Abstract Background Camouflage patterns that hinder detection and/or recognition by antagonists are widely studied in both human and animal contexts. Patterns of contrasting stripes that purportedly degrade an observer's ability to judge the speed and direction of moving prey ('motion dazzle') are, however, rarely investigated. This is despite motion dazzle having been fundamental to the appearance of warships in both world wars and often postulated as the selective agent leading to repeated patterns on many animals (such as zebra and many fish, snake, and invertebrate species). Such patterns often appear conspicuous, suggesting that protection while moving by motion dazzle might impair camouflage when stationary. However, the relationship between motion dazzle and camouflage is unclear because disruptive camouflage relies on high-contrast markings. In this study, we used a computer game with human subjects detecting and capturing either moving or stationary targets with different patterns, in order to provide the first empirical exploration of the interaction of these two protective coloration mechanisms. Results Moving targets with stripes were caught significantly less often and missed more often than targets with camouflage patterns. However, when stationary, targets with camouflage markings were captured less often and caused more false detections than those with striped patterns, which were readily detected. Conclusions Our study provides the clearest evidence to date that some patterns inhibit the capture of moving targets, but that camouflage and motion dazzle are not complementary strategies. Therefore, the specific coloration that evolves in animals will depend on how the life history and ontogeny of each species influence the trade-off between the costs and benefits of motion dazzle and camouflage. 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. Fri, 25 Nov 2011 00:00:00 GMT http://www.dspace.cam.ac.uk:80/handle/1810/241602 2011-11-25T00:00:00Z http://www.dspace.cam.ac.uk:80/handle/1810/241413 Title: Appendage development and early Distal-less regulation in arthropods: A study of the chelicerate Tetranychus urticae (Acarida) Authors: Cyrus-Kent, Chloë Abstract: A major goal of evolutionary developmental biology is to explore mechanisms and events underlying evolution of the myriad body plan morphologies expressed both genetically and phenotypically within the animal kingdom. Arthropods exhibit an astounding array of morphological diversity both within and between representative sub-phyla, thus providing an ideal phylum through which to address questions of body plan innovation and diversification. Major arthropod groups are recognised and defined by the distinct form and number of articulated appendages present along the antero-posterior axis of their segmented bodies. A great deal is known about the developmental genetics of limb development in the model insect Drosophila melanogaster, added to which, much comparative gene expression data and a growing body of functional genetic data is emerging for other arthropod species. Arthropod limb primordia are consistently marked by expression of the homeobox gene Distal-less (Dll), and the focus of this thesis is to compare signalling mediated by early Dll regulatory genes activity along antero-posterior and dorso-ventral embryonic axes during limb specification in Drosophila, with the activity of their orthologs in the widely disparate chelicerate, the spider mite Tetranychus urticae – interpreting new data with that available for other arthropods. Having made a detailed study of spider mite embryonic (and post-embryonic) development, to provide a basis for understanding mRNA transcription and protein activity patterns, I confirmed typical expression of Tetranychus Dll in prosomal limb primordia. I obtained limited results for the candidate antero-posterior positioning genes wingless and engrailed, although one of the two engrailed paralogs I identified is reportedly expressed in posterior segmental compartments, consistent with possible conservation of Engrailed-Wingless interactions in metameric patterning and positive regulation of Dll in arthropod limb specification. In Drosophila, wingless-dependent Dll transcription is restricted along the dorso-ventral axis by dorsal Dpp-mediated and ventral EGFR-mediated signalling gradients. Based on data from Tetranychus and other arthropods, neither dorsal nor ventral signalling regimes appear conserved outside the Drosophila system. Dll suppression in fly abdominal segments occurs due to powerful Hox (Ubx/AbdA) repression of the early Dll cis-regulatory element; this is discussed in relation to the independently evolved limbless chelicerate opisthosoma, informed by hypothetical scenarios of cis (regulatory DNA) and trans (coding sequence) evolution. Given practical difficulties and limitations encountered while working with spider mites, I offer a final assessment of the place of Tetranychus urticae as a non-model, and yet still valuable chelicerate species to consider carrying into the exciting future of evolutionary developmental biology. Sat, 08 Dec 2007 00:00:00 GMT http://www.dspace.cam.ac.uk:80/handle/1810/241413 2007-12-08T00:00:00Z http://www.dspace.cam.ac.uk:80/handle/1810/240654 Title: Inbreeding depression in red deer calves Authors: Walling, Craig A; Nussey, Daniel H; Morris, Alison; Clutton-Brock, Tim H; Kruuk, Loeske EB; Pemberton, Josephine M Abstract: Abstract Background Understanding the fitness consequences of inbreeding is of major importance for evolutionary and conservation biology. However, there are few studies using pedigree-based estimates of inbreeding or investigating the influence of environment and age variation on inbreeding depression in natural populations. Here we investigated the consequences of variation in inbreeding coefficient for three juvenile traits, birth date, birth weight and first year survival, in a wild population of red deer, considering both calf and mother's inbreeding coefficient. We also tested whether inbreeding depression varied with environmental conditions and maternal age. Results We detected non-zero inbreeding coefficients for 22% of individuals with both parents and at least one grandparent known (increasing to 42% if the dataset was restricted to those with four known grandparents). Inbreeding depression was evident for birth weight and first year survival but not for birth date: the first year survival of offspring with an inbreeding coefficient of 0.25 was reduced by 77% compared to offspring with an inbreeding coefficient of zero. However, it was independent of measures of environmental variation and maternal age. The effect of inbreeding on birth weight appeared to be driven by highly inbred individuals (F = 0.25). On the other hand first year survival showed strong inbreeding depression that was not solely driven by individuals with the highest inbreeding coefficients, corresponding to an estimate of 4.35 lethal equivalents. Conclusions These results represent a rare demonstration of inbreeding depression using pedigree-based estimates in a wild mammal population and highlight the potential strength of effects on key components of fitness. 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. Mon, 31 Oct 2011 00:00:00 GMT http://www.dspace.cam.ac.uk:80/handle/1810/240654 2011-10-31T00:00:00Z http://www.dspace.cam.ac.uk:80/handle/1810/238662 Title: Epigenetic remodelling of brain, body and behaviour during phase change in locusts Authors: Burrows, Malcolm; Rogers, Stephen M; Ott, Swidbert R Abstract: Abstract The environment has a central role in shaping developmental trajectories and determining the phenotype so that animals are adapted to the specific conditions they encounter. Epigenetic mechanisms can have many effects, with changes in the nervous and musculoskeletal systems occurring at different rates. How is the function of an animal maintained whilst these transitions happen? Phenotypic plasticity can change the ways in which animals respond to the environment and even how they sense it, particularly in the context of social interactions between members of their own species. In the present article, we review the mechanisms and consequences of phenotypic plasticity by drawing upon the desert locust as an unparalleled model system. Locusts change reversibly between solitarious and gregarious phases that differ dramatically in appearance, general physiology, brain function and structure, and behaviour. Solitarious locusts actively avoid contact with other locusts, but gregarious locusts may live in vast, migrating swarms dominated by competition for scarce resources and interactions with other locusts. Different phase traits change at different rates: some behaviours take just a few hours, colouration takes a lifetime and the muscles and skeleton take several generations. The behavioural demands of group living are reflected in gregarious locusts having substantially larger brains with increased space devoted to higher processing. Phase differences are also apparent in the functioning of identified neurons and circuits. The whole transformation process of phase change pivots on the initial and rapid behavioural decision of whether or not to join with other locusts. The resulting positive feedback loops from the presence or absence of other locusts drives the process to completion. Phase change is accompanied by dramatic changes in neurochemistry, but only serotonin shows a substantial increase during the critical one- to four-hour window during which gregarious behaviour is established. Blocking the action of serotonin or its synthesis prevents the establishment of gregarious behaviour. Applying serotonin or its agonists promotes the acquisition of gregarious behaviour even in a locust that has never encountered another locust. The analysis of phase change in locusts provides insights into a feedback circuit between the environment and epigenetic mechanisms and more generally into the neurobiology of social interaction. 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. Mon, 25 Jul 2011 23:00:00 GMT http://www.dspace.cam.ac.uk:80/handle/1810/238662 2011-07-25T23:00:00Z http://www.dspace.cam.ac.uk:80/handle/1810/238319 Title: Learning alters theta amplitude, theta-gamma coupling and neuronal synchronization in inferotemporal cortex Authors: Kendrick, Keith M; Zhan, Yang; Fisher, Hanno; Nicol, Alister U; Zhang, Xuejuan; Feng, Jianfeng Abstract: Abstract Background How oscillatory brain rhythms alone, or in combination, influence cortical information processing to support learning has yet to be fully established. Local field potential and multi-unit neuronal activity recordings were made from 64-electrode arrays in the inferotemporal cortex of conscious sheep during and after visual discrimination learning of face or object pairs. A neural network model has been developed to simulate and aid functional interpretation of learning-evoked changes. Results Following learning the amplitude of theta (4-8 Hz), but not gamma (30-70 Hz) oscillations was increased, as was the ratio of theta to gamma. Over 75% of electrodes showed significant coupling between theta phase and gamma amplitude (theta-nested gamma). The strength of this coupling was also increased following learning and this was not simply a consequence of increased theta amplitude. Actual discrimination performance was significantly correlated with theta and theta-gamma coupling changes. Neuronal activity was phase-locked with theta but learning had no effect on firing rates or the magnitude or latencies of visual evoked potentials during stimuli. The neural network model developed showed that a combination of fast and slow inhibitory interneurons could generate theta-nested gamma. By increasing N-methyl-D-aspartate receptor sensitivity in the model similar changes were produced as in inferotemporal cortex after learning. The model showed that these changes could potentiate the firing of downstream neurons by a temporal desynchronization of excitatory neuron output without increasing the firing frequencies of the latter. This desynchronization effect was confirmed in IT neuronal activity following learning and its magnitude was correlated with discrimination performance. Conclusions Face discrimination learning produces significant increases in both theta amplitude and the strength of theta-gamma coupling in the inferotemporal cortex which are correlated with behavioral performance. A network model which can reproduce these changes suggests that a key function of such learning-evoked alterations in theta and theta-nested gamma activity may be increased temporal desynchronization in neuronal firing leading to optimal timing of inputs to downstream neural networks potentiating their responses. In this way learning can produce potentiation in neural networks simply through altering the temporal pattern of their inputs. 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, 08 Jun 2011 23:00:00 GMT http://www.dspace.cam.ac.uk:80/handle/1810/238319 2011-06-08T23:00:00Z http://www.dspace.cam.ac.uk:80/handle/1810/238234 Title: Zebrafish promoter microarrays identify actively transcribed embryonic genes Authors: Wardle, Fiona C; Odom, Duncan T; Bell, George W; Yuan, Bingbing; Danford, Timothy W; Wiellette, Elizabeth L; Herbolsheimer, Elizabeth; Sive, Hazel L; Young, Richard A; Smith, James C Abstract: Abstract We have designed a zebrafish genomic microarray to identify DNA-protein interactions in the proximal promoter regions of over 11,000 zebrafish genes. Using these microarrays, together with chromatin immunoprecipitation with an antibody directed against tri-methylated lysine 4 of Histone H3, we demonstrate the feasibility of this method in zebrafish. This approach will allow investigators to determine the genomic binding locations of DNA interacting proteins during development and expedite the assembly of the genetic networks that regulate embryogenesis. 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. Thu, 03 Aug 2006 23:00:00 GMT http://www.dspace.cam.ac.uk:80/handle/1810/238234 2006-08-03T23:00:00Z http://www.dspace.cam.ac.uk:80/handle/1810/238198 Title: Metabolic changes in schizophrenia and human brain evolution Authors: Khaitovich, Philipp; Lockstone, Helen E; Wayland, Matthew T; Tsang, Tsz M; Jayatilaka, Samantha D; Guo, Arfu J; Zhou, Jie; Somel, Mehmet; Harris, Laura W; Holmes, Elaine; Paabo, Svante; Bahn, Sabine Abstract: Abstract Background Despite decades of research, the molecular changes responsible for the evolution of human cognitive abilities remain unknown. Comparative evolutionary studies provide detailed information about DNA sequence and mRNA expression differences between humans and other primates but, in the absence of other information, it has proved very difficult to identify molecular pathways relevant to human cognition. Results Here, we compare changes in gene expression and metabolite concentrations in the human brain and compare them to the changes seen in a disorder known to affect human cognitive abilities, schizophrenia. We find that both genes and metabolites relating to energy metabolism and energy-expensive brain functions are altered in schizophrenia and, at the same time, appear to have changed rapidly during recent human evolution, probably as a result of positive selection. Conclusion Our findings, along with several previous studies, suggest that the evolution of human cognitive abilities was accompanied by adaptive changes in brain metabolism, potentially pushing the human brain to the limit of its metabolic capabilities. 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. Mon, 04 Aug 2008 23:00:00 GMT http://www.dspace.cam.ac.uk:80/handle/1810/238198 2008-08-04T23:00:00Z http://www.dspace.cam.ac.uk:80/handle/1810/238164 Title: Genome-wide analysis of mRNA decay patterns during early Drosophila development Authors: Thomsen, Stefan; Anders, Simon; Chandra Janga, Sarath; Huber, Wolfgang; Alonso, Claudio R Abstract: Abstract Background The modulation of mRNA levels across tissues and time is key for the establishment and operation of the developmental programs that transform the fertilized egg into a fully formed embryo. Although the developmental mechanisms leading to differential mRNA synthesis are heavily investigated, comparatively little attention is given to the processes of mRNA degradation and how these relate to the molecular programs controlling development. Results Here we combine timed collection of Drosophila embryos and unfertilized eggs with genome-wide microarray technology to determine the degradation patterns of all mRNAs present during early fruit fly development. Our work studies the kinetics of mRNA decay, the contributions of maternally and zygotically encoded factors to mRNA degradation, and the ways in which mRNA decay profiles relate to gene function, mRNA localization patterns, translation rates and protein turnover. We also detect cis-regulatory sequences enriched in transcripts with common degradation patterns and propose several proteins and microRNAs as developmental regulators of mRNA decay during early fruit fly development. Finally, we experimentally validate the effects of a subset of cis-regulatory sequences and trans-regulators in vivo. Conclusions Our work advances the current understanding of the processes controlling mRNA degradation during early Drosophila development, taking us one step closer to the understanding of mRNA decay processes in all animals. Our data also provide a valuable resource for further experimental and computational studies investigating the process of mRNA decay. 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. Mon, 20 Sep 2010 23:00:00 GMT http://www.dspace.cam.ac.uk:80/handle/1810/238164 2010-09-20T23:00:00Z http://www.dspace.cam.ac.uk:80/handle/1810/238066 Title: Explaining individual variation in patterns of mass loss in breeding birds Authors: Rands, Sean A; Cuthill, Innes C; Houston, Alasdair I Abstract: Abstract Background Studies of birds have a disproportionate representation in the literature on life-history evolution, because of the (apparent) ease with which the costs and benefits can be quantified and manipulated. During reproduction, birds frequently show a highly conserved pattern of mass change and changes in mass loss during breeding have been widely considered to be a valid short-term measure of the costs of reproduction. Experimental manipulations of the breeding attempts of birds usually argue that the presence of a response shows that a cost of reproduction exists, but there is little consensus as to how the size of these costs can be measured. Results We model this mass loss by considering how a parent can maximise its lifetime reproductive success, using a theoretical framework that is particularly suited to modelling parental care in altricial birds. If lifetime reproductive success is taken to be the sum of a parent's current and future reproductive success, we show that the exact forms of these components will influence the optimal amount of mass a parent should lose. In particular, we demonstrate that the shape of the relationship between parental investment and chick survival will lead to differing degrees of investment between parents of different initial qualities: parents with initially high levels of energy reserves could conceivably invested a lesser, similar or greater amount of resources than parents with initially low reserves, and these initially 'heavy' parents could potentially end up being lighter than the initially 'lighter' individuals. Conclusion We argue that it is difficult to make predictions about the dependence of a parent's final mass on its initial mass, and therefore mass loss should only be used as a short-term measure of the costs of reproduction with caution. The model demonstrates that we require a better understanding of the relationship between mass loss and both current and future reproductive success of the parent, before predictions about mass loss can be made and tested. We discuss steps that could be taken to increase the accuracy of our predictions. 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. Mon, 15 May 2006 23:00:00 GMT http://www.dspace.cam.ac.uk:80/handle/1810/238066 2006-05-15T23:00:00Z http://www.dspace.cam.ac.uk:80/handle/1810/238056 Title: Fast sequence evolution of Hoxand Hox-derived genes in the genus Drosophila Authors: Casillas, Sonia; Negre, Barbara; Barbadilla, Antonio; Ruiz, Alfredo Abstract: Abstract Background It is expected that genes that are expressed early in development and have a complex expression pattern are under strong purifying selection and thus evolve slowly. Hox genes fulfill these criteria and thus, should have a low evolutionary rate. However, some observations point to a completely different scenario. Hox genes are usually highly conserved inside the homeobox, but very variable outside it. Results We have measured the rates of nucleotide divergence and indel fixation of three Hox genes, labial (lab), proboscipedia (pb) and abdominal-A (abd-A), and compared them with those of three genes derived by duplication from Hox3, bicoid (bcd), zerknüllt (zen) and zerknüllt-related (zen2), and 15 non-Hox genes in sets of orthologous sequences of three species of the genus Drosophila. These rates were compared to test the hypothesis that Hox genes evolve slowly. Our results show that the evolutionary rate of Hox genes is higher than that of non-Hox genes when both amino acid differences and indels are taken into account: 43.39% of the amino acid sequence is altered in Hox genes, versus 30.97% in non-Hox genes and 64.73% in Hox-derived genes. Microsatellites scattered along the coding sequence of Hox genes explain partially, but not fully, their fast sequence evolution. Conclusion These results show that Hox genes have a higher evolutionary dynamics than other developmental genes, and emphasize the need to take into account indels in addition to nucleotide substitutions in order to accurately estimate evolutionary rates. 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, 12 Dec 2006 00:00:00 GMT http://www.dspace.cam.ac.uk:80/handle/1810/238056 2006-12-12T00:00:00Z http://www.dspace.cam.ac.uk:80/handle/1810/238005 Title: Metamorphosis of an identified serotonergic neuron in the Drosophila olfactory system Authors: Roy, Bidisha; Singh, Ajeet P; Shetty, Chetak; Chaudhary, Varun; North, Annemarie; Landgraf, Matthias; Vijay Raghavan, K; Rodrigues, Veronica Abstract: Abstract Background Odors are detected by sensory neurons that carry information to the olfactory lobe where they connect to projection neurons and local interneurons in glomeruli: anatomically well-characterized structures that collect, integrate and relay information to higher centers. Recent studies have revealed that the sensitivity of such networks can be modulated by wide-field feedback neurons. The connectivity and function of such feedback neurons are themselves subject to alteration by external cues, such as hormones, stress, or experience. Very little is known about how this class of central neurons changes its anatomical properties to perform functions in altered developmental contexts. A mechanistic understanding of how central neurons change their anatomy to meet new functional requirements will benefit greatly from the establishment of a model preparation where cellular and molecular changes can be examined in an identified central neuron. Results In this study, we examine a wide-field serotonergic neuron in the Drosophila olfactory pathway and map the dramatic changes that it undergoes from larva to adult. We show that expression of a dominant-negative form of the ecdysterone receptor prevents remodeling. We further use different transgenic constructs to silence neuronal activity and report defects in the morphology of the adult-specific dendritic trees. The branching of the presynaptic axonal arbors is regulated by mechanisms that affect axon growth and retrograde transport. The neuron develops its normal morphology in the absence of sensory input to the antennal lobe, or of the mushroom bodies. However, ablation of its presumptive postsynaptic partners, the projection neurons and/or local interneurons, affects the growth and branching of terminal arbors. Conclusion Our studies establish a cellular system for studying remodeling of a central neuromodulatory feedback neuron and also identify key elements in this process. Understanding the morphogenesis of such neurons, which have been shown in other systems to modulate the sensitivity and directionality of response to odors, links anatomy to the development of olfactory behavior. 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, 23 Oct 2007 23:00:00 GMT http://www.dspace.cam.ac.uk:80/handle/1810/238005 2007-10-23T23:00:00Z http://www.dspace.cam.ac.uk:80/handle/1810/237987 Title: The emergence of leaders and followers in foraging pairs when the qualities of individuals differ Authors: Rands, Sean A; Cowlishaw, Guy; Pettifor, Richard A; Rowcliffe, J Marcus; Johnstone, Rufus A Abstract: Abstract Background Foraging in groups offers animals a number of advantages, such as increasing their likelihood of finding food or detecting and avoiding predators. In order for a group to remain together, there has to be some degree of coordination of behaviour and movement between its members (which may in some cases be initiated by a decision-making leader, and in other cases may emerge as an underlying property of the group). For example, behavioural synchronisation is a phenomenon where animals within a group initiate and then continue to conduct identical behaviours, and has been characterised for a wide range of species. We examine how a pair of animals should behave using a state-dependent approach, and ask what conditions are likely to lead to behavioural synchronisation occurring, and whether one of the individuals is more likely to act as a leader. Results The model we describe considers how the energetic gain, metabolic requirements and predation risks faced by the individuals affect measures of their energetic state and behaviour (such as the degree of behavioural synchronisation seen within the pair, and the value to an individual of knowing the energetic state of its colleague). We explore how predictable changes in these measures are in response to changes in physiological requirements and predation risk. We also consider how these measures should change when the members of the pair are not identical in their metabolic requirements or their susceptibility to predation. We find that many of the changes seen in these measures are complex, especially when asymmetries exist between the members of the pair. Conclusion Analyses are presented that demonstrate that, although these general patterns are robust, care needs to be taken when considering the effects of individual differences, as the relationship between individual differences and the resulting qualitative changes in behaviour may be complex. We discuss how these results are related to experimental observations, and how the model and its predictions could be extended. 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. Mon, 18 Feb 2008 00:00:00 GMT http://www.dspace.cam.ac.uk:80/handle/1810/237987 2008-02-18T00:00:00Z http://www.dspace.cam.ac.uk:80/handle/1810/237982 Title: Dental eruption in afrotherian mammals Authors: Asher, Robert J; Lehmann, Thomas Abstract: Abstract Background Afrotheria comprises a newly recognized clade of mammals with strong molecular evidence for its monophyly. In contrast, morphological data uniting its diverse constituents, including elephants, sea cows, hyraxes, aardvarks, sengis, tenrecs and golden moles, have been difficult to identify. Here, we suggest relatively late eruption of the permanent dentition as a shared characteristic of afrotherian mammals. This characteristic and other features (such as vertebral anomalies and testicondy) recall the phenotype of a human genetic pathology (cleidocranial dysplasia), correlations with which have not been explored previously in the context of character evolution within the recently established phylogeny of living mammalian clades. Results Although data on the absolute timing of eruption in sengis, golden moles and tenrecs are still unknown, craniometric comparisons for ontogenetic series of these taxa show that considerable skull growth takes place prior to the complete eruption of the permanent cheek teeth. Specimens showing less than half (sengis, golden moles) or two-thirds (tenrecs, hyraxes) of their permanent cheek teeth reach or exceed the median jaw length of conspecifics with a complete dentition. With few exceptions, afrotherians are closer to median adult jaw length with fewer erupted, permanent cheek teeth than comparable stages of non-afrotherians. Manatees (but not dugongs), elephants and hyraxes with known age data show eruption of permanent teeth late in ontogeny relative to other mammals. While the occurrence of delayed eruption, vertebral anomalies and other potential afrotherian synapomorphies resemble some symptoms of a human genetic pathology, these characteristics do not appear to covary significantly among mammalian clades. Conclusion Morphological characteristics shared by such physically disparate animals such as elephants and golden moles are not easy to recognize, but are now known to include late eruption of permanent teeth, in addition to vertebral anomalies, testicondy and other features. Awareness of their possible genetic correlates promises insight into the developmental basis of shared morphological features of afrotherians and other vertebrates. 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, 18 Mar 2008 00:00:00 GMT http://www.dspace.cam.ac.uk:80/handle/1810/237982 2008-03-18T00:00:00Z http://www.dspace.cam.ac.uk:80/handle/1810/237969 Title: Gene flow and the genealogical history of Heliconius heurippa Authors: Salazar, Camilo; Jiggins, Chris D; Taylor, Jesse E; Kronforst, Marcus R; Linares, Mauricio Abstract: Abstract Background The neotropical butterfly Heliconius heurippa has a hybrid colour pattern, which also contributes to reproductive isolation, making it a likely example of hybrid speciation. Here we used phylogenetic and coalescent-based analyses of multilocus sequence data to investigate the origin of H. heurippa. Results We sequenced a mitochondrial region (CoI and CoII), a sex-linked locus (Tpi) and two autosomal loci (w and sd) from H. heurippa and the putative parental species, H. cydno and H. melpomene. These were analysed in combination with data from two previously sequenced autosomal loci, Dll and Inv. H. heurippa was monophyletic at mtDNA and Tpi, but showed a shared distribution of alleles derived from both parental lineages at all four autosomal loci. Estimates of genetic differentiation showed that H. heurippa is closer to H. cydno at mtDNA and three autosomal loci, intermediate at Tpi, and closer to H. melpomene at Dll. Using coalescent simulations with the Isolation-Migration model (IM), we attempted to establish the incidence of gene flow in the origin of H. heurippa. This analysis suggested that ongoing introgression is frequent between all three species and variable in extent between loci. Conclusion Introgression, which is a necessary precursor of hybrid speciation, seems to have also blurred the coalescent history of these species. The origin of Heliconius heurippa may have been restricted to introgression of few colour pattern genes from H. melpomene into the H. cydno genome, with little evidence of genomic mosaicism. 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. Thu, 01 May 2008 23:00:00 GMT http://www.dspace.cam.ac.uk:80/handle/1810/237969 2008-05-01T23:00:00Z http://www.dspace.cam.ac.uk:80/handle/1810/237966 Title: ParaHox gene expression in larval and postlarval development of the polychaete Nereis virens (Annelida, Lophotrochozoa) Authors: Kulakova, Milana A; Cook, Charles E; Andreeva, Tatiana F Abstract: Abstract Background Transcription factors that encode ANTP-class homeobox genes play crucial roles in determining the body plan organization and specification of different organs and tissues in bilaterian animals. The three-gene ParaHox family descends from an ancestral gene cluster that existed before the evolution of the Bilateria. All three ParaHox genes are reported from deuterostomes and lophotrochozoans, but not to date from any ecdysozoan taxa, and there is evidence that the ParaHox genes, like the related Hox genes, were ancestrally a single chromosomal cluster. However, unlike the Hox genes, there is as yet no strong evidence that the ParaHox genes are expressed in spatial and temporal order during embryogenesis. Results We isolated fragments of the three Nereis virens ParaHox genes, then used these as probes for whole-mount in situ hybridization in larval and postlarval worms. In Nereis virens the ParaHox genes participate in antero-posterior patterning of ectodermal and endodermal regions of the digestive tract and are expressed in some cells in the segment ganglia. The expression of these genes occurs in larval development in accordance with the position of these cells along the main body axis and in postlarval development in accordance with the position of cells in ganglia along the antero-posterior axis of each segment. In none of these tissues does expression of the three ParaHox genes follow the rule of temporal collinearity. Conclusion In Nereis virens the ParaHox genes are expressed during antero-posterior patterning of the digestive system (ectodermal foregut and hindgut, and endodermal midgut) of Nereis virens. These genes are also expressed during axial specification of ventral neuroectodermal cell domains, where the expression domains of each gene are re-iterated in each neuromere except for the first parapodial segment. These expression domains are probably predetermined and may be directed on the antero-posterior axis by the Hox genes, whose expression starts much earlier during embryogenesis. Our results support the hypothesis that the ParaHox genes are involved in antero-posterior patterning of the developing embryo, but they do not support the notion that these genes function only in the patterning of endodermal tissues. 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, 28 May 2008 23:00:00 GMT http://www.dspace.cam.ac.uk:80/handle/1810/237966 2008-05-28T23:00:00Z