Claudio Ciofi

Ecology, Evolutionary Biology, Genetics

31.22

Publications

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    ABSTRACT: Ten microsatellite loci were developed for the northern spectacled salamander, Salamandrina perspicillata, and cross-amplification was obtained for the southern spectacled salamander, Salamandrina terdigitata. These two species are the sole representative of the genus Salamandrina, a threatened amphibian endemic to the Italian peninsula. The two salamanders show a parapatric distribution with a contact zone in Central Italy. All but one locus were polymorphic and six microsatellites were found diagnostic for species discrimination. We genotyped a total of 169 individuals. Allelic diversity was 5.1 ± 1.5 SE in S. perspicillata and 1.9 ± 0.31 SE in S. terdigitata. Mean observed and expected heterozygosity were 0.51 ± 0.06 SE and 0.61 ± 0.07 SE, respectively in the northern spectacled salamander and 0.35 ± 0.15 SE and 0.35 ± 0.09 SE, respectively in the southern spectacled salamander. These new markers will provide an excellent tool to assess population structure and genetic diversity in Salamandrina and will be used to investigate natural hybridization events between northern and southern spectacled salamanders.
    No preview · Article · Dec 2015 · Biochemical Systematics and Ecology
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    ABSTRACT: Nest-mate recognition plays a key role in the biology of ants. Although individuals coming from a foreign nest are, in most cases, promptly rejected, the degree of aggressiveness towards non nest-mates may be highly variable among species and relies on genetic, chemical and environmental factors. We analyzed intraspecific relationships among neighboring colonies of the dominant Mediterranean acrobat ant Crematogaster scutellaris integrating genetic, chemical and behavioral analyses. Colony structure, parental relationships between nests, cuticular hydrocarbons profiles (CHCs) and aggressive behavior against non nest-mates were studied in 34 nests located in olive tree trunks. Bayesian clustering analysis of allelic variation at nine species-specific microsatellite DNA markers pooled nests into 14 distinct clusters, each representing a single colony, confirming a polydomous arrangement of nests in this species. A marked genetic separation among colonies was also detected, probably due to long distance dispersion of queens and males during nuptial flights. CHCs profiles varied significantly among colonies and between nests of the same colony. No relationship between CHCs profiles and genetic distances was detected. The level of aggressiveness between colonies was inversely related to chemical and spatial distance , suggesting a 'nasty neighbor' effect. Our findings also suggest that CHCs profiles in C. scutellaris may be linked to external environmental factors rather than genetic relationships.
    Full-text · Article · Oct 2015 · PLoS ONE
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    ABSTRACT: For wild varanid populations, basic measures of reproductive ecology, such as distribution and selection of nest sites, are difficult to obtain. To date, nest distributions and nesting behavior for Komodo dragons (Varanus komodoensis) have only been reported from Komodo National Park. Here we report the first record of V. komodoensis nesting activity and hatchling emergence on Ontoloe Island, off the north coast of Flores. This is a significant finding for it suggests that this relatively small but well protected island supports a viable population of V. komodoensis.
    Full-text · Article · Sep 2015
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    ABSTRACT: 1. Habitat diversity plays a significant role in shaping the genetic structure of cetacean populations. However, the processes involved in defining the genetic differentiation of these highly mobile marine mammals are still largely unknown. 2. Levels of genetic differentiation and dispersal patterns of common bottlenose dolphins (Tursiops truncatus) were assessed in the north-eastern Mediterranean Sea, with a focus on the Adriatic Sea. This is a region characterized by diverse marine ecosystems and high levels of human-induced habitat degradation. 3. Although this species seems almost uniformly distributed throughout the Adriatic Basin, genetic evidence rejected the hypothesis of a single stock. Pairwise estimates of genetic differentiation at 12 microsatellite loci, and mitochondrial DNA (entire control region, 920bp), revealed diverse levels of genetic differentiation among five putative populations from the Tyrrhenian Sea to the Aegean Sea. 4. A fine-scale genetic structure was recorded within the Adriatic Sea, where females appear to be the principal gene flow mediators. The assessment of recent migration rates indicates a relatively high level of gene flow from the North Adriatic towards adjacent areas. 5. Indication of a fine-scale population structure across the Adriatic Sea is a factor to be carefully considered in the emerging marine management scenario set by the implementation of the EU Marine Strategy Framework Directive (2008/56/CE), particularly when it comes to assessing and managing direct mortality caused by human activities (e.g. fisheries or maritime traffic). A good knowledge of population structure at the basin level is also fundamental for the identification of potential Adriatic Special Areas of Conservation for the bottlenose dolphin under the Habitats Directive (Council Directive 92/43/EEC).
    Full-text · Article · Apr 2015 · Aquatic Conservation Marine and Freshwater Ecosystems
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    ABSTRACT: The population dynamics of island species are considered particularly sensitive to variation in environmental, demographic and/or genetic processes. However, few studies have attempted to evaluate the relative importance of these processes for key vital rates in island endemics. We integrated the results of long-term capture – mark – recapture analysis, prey surveys, habitat quality assessments and molecular analysis to determine the causes of variation in the survival rates of Komodo dragons Varanus komodoensis at 10 sites on four islands in Komodo National Park, Indonesia. Using open population capture – mark – recapture methods, we ranked competing models that considered environmental, ecological, genetic and demographic effects on site-specific Komodo dragon survival rates. Site-specific survival rates ranged from 0.49 (95% CI: 0.33 – 0.68) to 0.92 (0.79 – 0.97) in the 10 study sites. Th e three highest-ranked models (i.e. Δ QAIC c < 2) explained ∼ 70% of variation in Komodo dragon survival rates and identified interactions between inbreeding coefficients, prey biomass density and habitat quality as important explanatory variables. Th ere was evidence of additive effects from ecological and genetic (e.g. inbreeding) processes affecting Komodo dragon survival rates. Our results indicate that maintaining high ungulate prey biomass and habitat quality would enhance the persistence of Komodo dragon populations. Assisted gene fl ow may also increase the genetic and demographic viability of the smaller Komodo dragon populations.
    Full-text · Article · Feb 2015 · Ecography
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    Full-text · Dataset · Jan 2015
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    ABSTRACT: Multidisciplinary conservation initiatives are increasingly advocated as best practice for recovering endangered species. The Komodo dragon Varanus komodoensis is the world's largest lizard, of prominent conservation value as an umbrella species for protection of south-east Indonesian ecosystems. Komodo dragons have faced multiple human-related threat processes in the past 30 years and are listed on Appendix I of the Convention on International Trade in Endangered Species of Wild Fauna and Flora, and considered Vulnerable according to the International Union for Conservation of Nature Red List. We report on a protection programme conducted from 2005 to 2012 in the Wae Wuul nature reserve, on the island of Flores, Indonesia. The Wae Wuul ranger post was completely rebuilt, and community awareness and involvement of local people in habitat-protection schemes were regularly and successfully implemented. Local rangers were trained in wildlife-monitoring techniques. Monitoring results indicated that Komodo dragon densities were lower in Wae Wuul than in the adjacent Komodo National Park; however, a relatively high level of genetic diversity was recorded for this population. Ungulate prey showed a relatively stable prey population density. Community-based initiatives and regular wildlife monitoring are crucial to ensure the persistence of Komodo dragons on Flores. The Wae Wuul protection programme is providing several sustainability indicators by which informed management plans can be designed for long-term conservation of Komodo dragons.
    Full-text · Article · Jan 2015 · International Zoo Yearbook
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    ABSTRACT: Finding practical ways to robustly estimate abundance or density trends in threatened species is a key facet for effective conservation management. Further identi-fying less expensive monitoring methods that provide adequate data for robust population density estimates can facilitate increased investment into other conservation initiatives needed for species recovery. Here we evaluated and compared inference-and cost-effec-tiveness criteria for three field monitoring-density estimation protocols to improve con-servation activities for the threatened Komodo dragon (Varanus komodoensis). We undertook line-transect counts, cage trapping and camera monitoring surveys for Komodo dragons at 11 sites within protected areas in Eastern Indonesia to collect data to estimate density using distance sampling methods or the Royle–Nichols abundance induced het-erogeneity model. Distance sampling estimates were considered poor due to large confi-dence intervals, a high coefficient of variation and that false absences were obtained in 45 % of sites where other monitoring methods detected lizards present. The Royle–Nichols model using presence/absence data obtained from cage trapping and camera monitoring produced highly correlated density estimates, obtained similar measures of precision and recorded no false absences in data collation. However because costs associated with Communicated by Indraneil Das.
    Full-text · Article · Jul 2014 · Biodiversity and Conservation
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    ABSTRACT: The Komodo dragon (Varanus komodoensis) is the world's largest lizard and endemic to five islands in Eastern Indonesia. The current management of this species is limited by a paucity of demographic infor-mation needed to determine key threats to population persistence. Here we conducted a large scale trap-ping study to estimate demographic parameters including population growth rates, survival and abundance for four Komodo dragon island populations in Komodo National Park. A combined capture mark recapture framework was used to estimate demographic parameters from 925 marked individuals monitored between 2003 and 2012. Island specific estimates of population growth, survival and abun-dance, were estimated using open population capture–recapture analyses. Large island populations are characterised by near or stable population growth (i.e. k $ 1), whilst one small island population (Gili Motang) appeared to be in decline (k = 0.68 ± 0.09). Population differences were evident in apparent sur-vival, with estimates being higher for populations on the two large islands compared to the two small islands. We extrapolated island specific population abundance estimates (considerate of species habitat use) to produce a total population abundance estimate of 2448 (95% CI: 2067–2922) Komodo dragons in Komodo National Park. Our results suggest that park managers must consider island specific population dynamics for managing and recovering current populations. Moreover understanding what demographic, environmental or genetic processes act independently, or in combination, to cause variation in current population dynamics is the next key step necessary to better conserve this iconic species.
    Full-text · Article · Feb 2014 · Biological Conservation
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    ABSTRACT: Long-distance dispersal and ontogenetic shifts in habitat use are characteristic of numerous marine species and have important ecological, evolutionary, and management implications. These processes, however, are often challenging to study due to the vast areas involved. We used genetic markers and simulations of physical transport within an ocean circulation model to gain understanding into the origin of juvenile hawksbill sea turtles (Eretmochelys imbricata) found at Ascension Island, a foraging ground that is thousands of kilometers from known nesting beaches. Regional origin of genetic markers suggests that turtles are from Western Atlantic (86%) and Eastern Atlantic (14%) rookeries. In contrast, numerical simulations of transport by ocean currents suggest that passive dispersal from the western sources would be negligible and instead would primarily be from the East, involving rookeries alongWestern Africa (i.e., Principe Island) and, potentially, from as far as the Indian Ocean (e.g.,Mayotte and the Seychelles). Given that genetic analysis identified the presence of a haplotype endemic to Brazilian hawksbill rookeries at Ascension, we examined the possible role of swimming behavior by juvenile hawksbills from NE Brazil on their current-borne transport to Ascension Island by performing numerical experiments in which swimming behavior was simulated for virtual particles (simulated turtles). We found that oriented swimming substantially influenced the distribution of particles, greatly altering the proportion of particles dispersing into the North Atlantic and South Atlantic. Assigning location-dependent orientation behavior to particles allowed them to reach Ascension Island, remain in favorable temperatures, encounter productive foraging areas, and return to the vicinity of their natal site. The age at first arrival to Ascension (4.5–5.5years) of these particles corresponded well to estimates of hawksbill age based on their size.Our findings suggest that ocean currents and swimming behavior play an important role in the oceanic ecology of sea turtles and other marine animals.
    Full-text · Article · Jan 2014 · Journal of Experimental Marine Biology and Ecology
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    Full-text · Dataset · Dec 2013
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    ABSTRACT: Integration of molecular genetic techniques and geometric morphometrics represent a valuable tool in the resolution of taxonomic uncertainty and the identification of significant units for conservation. We combined mitochondrial DNA cytochrome c oxidase subunit II gene sequence data and geometric morphometric analysis to examine taxonomic status and identify units for conservation in four species of the hypogean beetle Duvalius (Coleoptera, Trechinae) using mainly museum specimens collected in central Italy. Previous taxonomic studies based on morphological traits described several subspecies often inhabiting geographically distinct caves. Phylogenetic analysis identified two well supported monophyletic lineages and a number of different clades with relatively small genetic differences, suggesting a short divergence time in line with known geological history of the study area. Geometric morphometrics, on the other hand, recovered a high level of distinctiveness among specimens. Both genetic and morphometric analyses did not entirely corroborate former taxonomic nomenclature, suggesting possible rearrangements and the definition of evolutionary significant units. Beetles of the genus Duvalius are protected by regional laws and the majority of taxa considered in this study inhabit caves located outside protected areas. Our study advocates the importance of devoting protection efforts to networks of cave ecosystems rather than single locations or species.
    Full-text · Article · Oct 2013 · Journal of Insect Conservation
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    ABSTRACT: Southern European wolves suffered from reiterated population declines during glacial periods and historically due to human persecution. Differently from other European wolf populations, a single mitochondrial DNA (mtDNA) control region haplotype (W14) has been so far described in the Italian wolves, although no intensive genetic sampling has ever been conducted in historical source populations from central and southern Italy. Using non-invasive genetic techniques, we report the occurrence of an unexpected mtDNA haplotype (W16) in the wolf population of the Abruzzo, Lazio and Molise National Park (PNALM), central Italy. This haplotype, detected in three out of 90 faecal samples from the PNALM, was previously reported in wolves from the North Carpathians, Slovakia and the Balkans only. Microsatellite analysis and molecular sex determination confirmed that the W16 samples belonged to three distinct wolves. Although alternative explanations can be formulated for the origin of this mtDNA haplotype in the otherwise monomorphic Italian wolf population, assignment procedures indicated the likely admixed ancestry of one W16 sample with East European wolves. Anthropogenic introgression with dogs has been detected in the Italian wolf population using nuclear DNA microsatellites, but no population-wide genetic survey had previously reported a mtDNA control region variant in Italian wolves. Our findings strongly suggest that, in addition to wolf × dog hybridization, captive-released wolves or wolf × dog hybrids may successfully interbreed with wolves in the wild, and that human-mediated introgression may occur even in well established protected areas.
    Full-text · Article · Sep 2013 · Mammalian Biology - Zeitschrift fur Saugetierkunde
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    ABSTRACT: There is increasing evidence that most parapatric cryptic/sister taxa are reproductively compatible across their areas of contact. Consequently, the biological species concept, which assumes absence of interbreeding, is becoming a not so effective criterion in evolutionary ecology. Nevertheless, the few parapatric sister taxa showing complete reproductive barriers represent interesting models to study speciation processes and the evolution of reproductive isolation. In this study, we examined contact populations in northwestern Italy of two butterfly species, Zerynthia polyxena and Z. cassandra, characterized by different genitalic morphotypes. We studied levels of divergence among 21 populations distributed from Sicily to France using three genetic markers (the mitochondrial COI and ND1 genes and the nuclear wingless gene) and genitalic geometric morphometrics. Moreover, we performed species distribution modelling to estimate different climatic requirements of Z. polyxena and Z. cassandra. We projected climatic data into glacial maximum scenarios in order to verify if and to which extent glacial cycles could have contributed to speciation processes. Genetic and morphometric analyses identified two main groups. All specimens showed a concordant pattern of diversification, including those individuals sampled in the contact area. Haplotype distribution and climatic models showed that during glacial maxima both species experienced a strong range contraction and presumably remained separated into different microrefugia in southern France, in the Italian Peninsula and on the islands of Elba and Sicily. Long term separation was probably favoured by reduced dispersal ability and high phylopatry, while genitalic diversification probably favoured interbreeding avoidance. Conversely, the aposematic wing pattern remained almost identical. We compared our results with those obtained in other species and concluded that Z. polyxena and Z. cassandra represent a valuable model in the study of speciation.
    Full-text · Article · Jun 2013 · PLoS ONE
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    ABSTRACT: Camera trapping has greatly enhanced population monitoring of often cryptic and low abundance apex carnivores. Effectiveness of passive infrared camera trapping, and ultimately population monitoring, relies on temperature mediated differences between the animal and its ambient environment to ensure good camera detection. In ectothermic predators such as large varanid lizards, this criterion is presumed less certain. Here we evaluated the effectiveness of camera trapping to potentially monitor the population status of the Komodo dragon (Varanus komodoensis), an apex predator, using site occupancy approaches. We compared site-specific estimates of site occupancy and detection derived using camera traps and cage traps at 181 trapping locations established across six sites on four islands within Komodo National Park, Eastern Indonesia. Detection and site occupancy at each site were estimated using eight competing models that considered site-specific variation in occupancy (ψ)and varied detection probabilities (p) according to detection method, site and survey number using a single season site occupancy modelling approach. The most parsimonious model [ψ (site), p (site*survey); ω = 0.74] suggested that site occupancy estimates differed among sites. Detection probability varied as an interaction between site and survey number. Our results indicate that overall camera traps produced similar estimates of detection and site occupancy to cage traps, irrespective of being paired, or unpaired, with cage traps. Whilst one site showed some evidence detection was affected by trapping method detection was too low to produce an accurate occupancy estimate. Overall, as camera trapping is logistically more feasible it may provide, with further validation, an alternative method for evaluating long-term site occupancy patterns in Komodo dragons, and potentially other large reptiles, aiding conservation of this species.
    Full-text · Article · Mar 2013 · PLoS ONE
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    ABSTRACT: The assessment of marine environmental health is a complex but fundamental task both for ecosystem conservation and food safety related to the human consumption of marine products. Manila clams inhabiting the Venice Lagoon constitute an excellent case study for evaluating the effects of complex mixtures of industrial and urban effluents on aquatic organisms. Clams were collected in different seasons at four locations within the Venice Lagoon. The sampling sites were characterized by a range of pollutant concentrations and included Porto Marghera, a highly polluted industrial area where clam harvesting for human consumption is strictly forbidden. Pooled soft tissues were subjected to mass spectroscopy analysis to measure the concentrations of PCDDs/PCDFs/PCBs-DL, PCBs, PBDEs, HCB and PAHs, and pooled digestive gland samples were used for gene expression profiling. While seasonal variation was found to be responsible for the largest proportion of transcriptional changes, significance analysis of microarrays quantitative correlation analysis identified 162 transcripts that were correlated with at least one class of chemicals measured in the samples from the four different sampling sites. Prediction Analysis of Microarrays (PAM) identified a minimal set of seven genes that correctly assigned samples collected in the restricted polluted area (Porto Marghera), independent of the season in which they were collected. An integrated approach combining transcriptomics and chemical analyses of the Manila clam provided a global picture of how Manila clams respond to complex mixtures of xenobiotics and their interplay with other biotic and abiotic factors. We were also able to identify gene expression signatures for different classes of chemicals and a set of robust biomarkers of exposure to these chemicals.
    Full-text · Article · Mar 2013 · Molecular Ecology
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    ABSTRACT: Somatic growth patterns represent a major component of organismal fitness and may vary among sexes and populations due to genetic and environmental processes leading to profound differences in life-history and demography. This study considered the ontogenic, sex-specific and spatial dynamics of somatic growth patterns in ten populations of the world's largest lizard the Komodo dragon (Varanus komodoensis). The growth of 400 individual Komodo dragons was measured in a capture-mark-recapture study at ten sites on four islands in eastern Indonesia, from 2002 to 2010. Generalized Additive Mixed Models (GAMMs) and information-theoretic methods were used to examine how growth rates varied with size, age and sex, and across and within islands in relation to site-specific prey availability, lizard population density and inbreeding coefficients. Growth trajectories differed significantly with size and between sexes, indicating different energy allocation tactics and overall costs associated with reproduction. This leads to disparities in maximum body sizes and longevity. Spatial variation in growth was strongly supported by a curvilinear density-dependent growth model with highest growth rates occurring at intermediate population densities. Sex-specific trade-offs in growth underpin key differences in Komodo dragon life-history including evidence for high costs of reproduction in females. Further, inverse density-dependent growth may have profound effects on individual and population level processes that influence the demography of this species.
    Full-text · Article · Sep 2012 · PLoS ONE
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    ABSTRACT: Crematogaster scutellaris is a common ant throughout the Mediterranean basin, which occupies a dominant position within competition hierarchies. Previous studies showed a clustered distribution of nests of this species and suggested a polydomous arrangement of colonies. The relationships among different colonies were investigated combining aggression experiments, genetic analysis of population structure, and chemical analysis of cuticular hydrocarbons. The study was carried out in an olive orchard near Florence (northern Tuscany, Italy), where the only available nest sites were represented by olive trees. All the nests in area of 2.5 hectares were mapped. Nests showed a clumped distribution and formed 34 well defined spatial clusters (a cluster being formed by a group of nests not separated by an empty space in between). A subsample of 10 of such clusters (for a total of 34 nests) were randomly chosen for subsequent analysis. Six workers were randomly collected from each nest (n=204) and genotyped using 9 microsatellite loci, specifically designed for C.scutellaris. Six additional workers were also collected for chemical analysis. A total of 91 aggression tests among ants from different nests were also carried out in the field. Results showed that the 34 nests belonged to 14 totally unrelated colonies. Aggression was not related to genetic distance, but was inversely correlated with spatial distance (closer unrelated nests were more aggressive to each other than distant ones) and cuticular hydrocarbon similarity among nests (aggression was more likely to occur between nests sharing similar hydrocarbon profiles).
    Full-text · Conference Paper · Aug 2012
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    ABSTRACT: We developed a set of nine polymorphic microsatellite markers from a genomic library enriched for dinucleotide repeats in the European polecat Mustela putorius. Microsatellite loci amplification was tested on fresh tissues and museum samples collected over the last 40 years in central and northern Italy. Number of alleles per locus ranged from 3 to 7. Mean observed and expected heterozygosity were 0.48 and 0.61, respectively. This novel set of species-specific microsatellite loci will be particularly useful to assess fine patterns of genetic structure and degree of isolation of European polecat populations.
    Full-text · Article · May 2012 · Conservation Genetics Resources
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    ABSTRACT: Genes from recently extinct species can live on in the genomes of extant individuals of mixed ancestry. Recently, genetic signatures of the giant Galápagos tortoise once endemic to Floreana Island (Chelonoidis elephantopus) were detected within eleven hybrid individuals of otherwise pure Chelonoidis becki on Volcano Wolf, Isabela Island [1]. Movement of tortoises between islands by pirate and whaling ships was not uncommon during the 1800s [2], representing a likely mechanism by which individuals from Floreana were translocated to northern Isabela, despite being presumed extinct soon after Charles Darwin's historic voyage to the Galápagos Islands in 1835. These eleven hybrid individuals with C. elephantopus ancestry were thought to be the last genetic vestiges of a unique evolutionary lineage in the wild. Here, we report that reproductively mature purebred tortoises of the recently ‘extinct’ C. elephantopus from Floreana Island are very likely still alive today, as identified and tracked through the genetic footprints left in the genomes of very recent hybrid offspring on Volcano Wolf. If found, these purebred C. elephantopus individuals could constitute core founders of a captive breeding program directed towards resurrecting this species.
    Full-text · Article · Jan 2012 · Current biology: CB

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