Publications

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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.
    Biodiversity and Conservation 07/2014; 23(10). · 2.26 Impact Factor
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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.
    Biological Conservation 02/2014; · 3.79 Impact Factor
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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.
    Journal of Experimental Marine Biology and Ecology 01/2014; 450:98-108. · 2.26 Impact Factor
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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.
    Molecular Ecology 03/2013; · 6.28 Impact Factor
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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.
    Mammalian Biology - Zeitschrift für Säugetierkunde. 01/2013; 78(5):374–378.
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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.
    PLoS ONE 01/2013; 8(3):e58800. · 3.53 Impact Factor
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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.
    Journal of Insect Conservation 01/2013; · 1.80 Impact Factor
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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.
    Aquatic Conservation Marine and Freshwater Ecosystems 01/2013; · 1.92 Impact Factor
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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.
    PLoS ONE 01/2013; 8(6):e65746. · 3.53 Impact Factor
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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.
    Conservation Genetics Resources 05/2012; · 1.14 Impact Factor
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    Current biology: CB 01/2012; 22(1):R10-1. · 10.99 Impact Factor
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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.
    PLoS ONE 01/2012; 7(9):e45398. · 3.53 Impact Factor
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    ABSTRACT: Multiplex PCR assays for the coamplification of microsatellite loci allow rapid and cost-effective genetic analyses and the production of efficient screening protocols for international breeding programs. We constructed a partial genomic library enriched for di-nucleotide repeats and characterized 14 new microsatellite loci for the Komodo monitor (or Komodo dragon, Varanus komodoensis). Using these novel microsatellites and four previously described loci, we developed multiplex PCR assays that may be loaded on a genetic analyser in three separate panels. We tested the novel set of microsatellites for polymorphism using 69 individuals from three island populations and evaluated the resolving power of the entire panel of 18 loci by conducting (i) a preliminary assignment test to determine population(s) of origin and (ii) a parentage analysis for 43 captive Komodo monitors. This panel of polymorphic loci proved useful for both purposes and thus can be exploited for fine-scale population genetic analyses and as part of international captive breeding programs directed at maintaining genetically viable ex situ populations and reintroductions.
    Molecular Ecology Resources 05/2011; 11(3):550-6. · 7.43 Impact Factor
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    ABSTRACT: Background: The Manila clam, Ruditapes philippinarum, is one of the major aquaculture species in the world and a potential sentinel organism for monitoring the status of marine ecosystems. However, genomic resources for R. philippinarum are still extremely limited. Global analysis of gene expression profiles is increasingly used to evaluate the biological effects of various environmental stressors on aquatic animals under either artificial conditions or in the wild. Here, we report on the development of a transcriptomic platform for global gene expression profiling in the Manila clam. Results: A normalized cDNA library representing a mixture of adult tissues was sequenced using a ultra high-throughput sequencing technology (Roche 454). A database consisting of 32,606 unique transcripts was constructed, 9,747 (30%) of which could be annotated by similarity. An oligo-DNA microarray platform was designed and applied to profile gene expression of digestive gland and gills. Functional annotation of differentially expressed genes between different tissues was performed by enrichment analysis. Expression of Natural Antisense Transcripts (NAT) analysis was also performed and bi-directional transcription appears a common phenomenon in the R. philippinarum transcriptome. A preliminary study on clam samples collected in a highly polluted area of the Venice Lagoon demonstrated the applicability of genomic tools to environmental monitoring. Conclusions: The transcriptomic platform developed for the Manila clam confirmed the high level of reproducibility of current microarray technology. Next-generation sequencing provided a good representation of the clam transcriptome. Despite the known limitations in transcript annotation and sequence coverage for non model species, sufficient information was obtained to identify a large set of genes potentially involved in cellular response to environmental stress.
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    ABSTRACT: Background: The Manila clam, Ruditapes philippinarum, is one of the major aquaculture species in the world and a potential sentinel organism for monitoring the status of marine ecosystems. However, genomic resources for R. philippinarum are still extremely limited. Global analysis of gene expression profiles is increasingly used to evaluate the biological effects of various environmental stressors on aquatic animals under either artificial conditions or in the wild. Here, we report on the development of a transcriptomic platform for global gene expression profiling in the Manila clam. Results: A normalized cDNA library representing a mixture of adult tissues was sequenced using a ultra high-throughput sequencing technology (Roche 454). A database consisting of 32,606 unique transcripts was constructed, 9,747 (30%) of which could be annotated by similarity. An oligo-DNA microarray platform was designed and applied to profile gene expression of digestive gland and gills. Functional annotation of differentially expressed genes between different tissues was performed by enrichment analysis. Expression of Natural Antisense Transcripts (NAT) analysis was also performed and bi-directional transcription appears a common phenomenon in the R. philippinarum transcriptome. A preliminary study on clam samples collected in a highly polluted area of the Venice Lagoon demonstrated the applicability of genomic tools to environmental monitoring. Conclusions: The transcriptomic platform developed for the Manila clam confirmed the high level of reproducibility of current microarray technology. Next-generation sequencing provided a good representation of the clam transcriptome. Despite the known limitations in transcript annotation and sequence coverage for non model species, sufficient information was obtained to identify a large set of genes potentially involved in cellular response to environmental stress.
    BMC Genomics 03/2011; 12(1). · 4.40 Impact Factor
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    ABSTRACT: The Manila clam, Ruditapes philippinarum, is one of the major aquaculture species in the world and a potential sentinel organism for monitoring the status of marine ecosystems. However, genomic resources for R. philippinarum are still extremely limited. Global analysis of gene expression profiles is increasingly used to evaluate the biological effects of various environmental stressors on aquatic animals under either artificial conditions or in the wild. Here, we report on the development of a transcriptomic platform for global gene expression profiling in the Manila clam. A normalized cDNA library representing a mixture of adult tissues was sequenced using a ultra high-throughput sequencing technology (Roche 454). A database consisting of 32,606 unique transcripts was constructed, 9,747 (30%) of which could be annotated by similarity. An oligo-DNA microarray platform was designed and applied to profile gene expression of digestive gland and gills. Functional annotation of differentially expressed genes between different tissues was performed by enrichment analysis. Expression of Natural Antisense Transcripts (NAT) analysis was also performed and bi-directional transcription appears a common phenomenon in the R. philippinarum transcriptome. A preliminary study on clam samples collected in a highly polluted area of the Venice Lagoon demonstrated the applicability of genomic tools to environmental monitoring. The transcriptomic platform developed for the Manila clam confirmed the high level of reproducibility of current microarray technology. Next-generation sequencing provided a good representation of the clam transcriptome. Despite the known limitations in transcript annotation and sequence coverage for non model species, sufficient information was obtained to identify a large set of genes potentially involved in cellular response to environmental stress.
    BMC Genomics 01/2011; 12:234. · 4.40 Impact Factor
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    ABSTRACT: A set of 13 polymorphic microsatellite markers were isolated and characterized from a genomic library enriched for dinucleotide repeats in the European pine marten Martes martes. Microsatellite loci amplification was tested on a panel of 12 tissue samples and 9 distinct hair samples collected from either road-killed or trapped animals in Tuscany, Italy. Allelic diversity was 6 and the number of alleles per locus ranged from 2 to 10. Mean observed and expected heterozygosity were 0.610 (range: 0.238–0.905) and 0.698 (range: 0.400–0.856), respectively. This novel set of microsatellite loci will be particularly useful for non-invasive genetic studies to assess population distribution and patterns of population structure and dispersal of M. martes in woodlands and fragmented habitats. KeywordsPine marten-Mustelidae-Microsatellites-Population genetics-Non-invasive genetics
    Conservation Genetics Resources 01/2010; 2:397-399. · 1.14 Impact Factor
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    ABSTRACT: Evolution of population structure on islands is the result of physical processes linked to volcanism, orogenic events, changes in sea level, as well as habitat variation. We assessed patterns of genetic structure in the giant tortoise of the Aldabra atoll, where previous ecological studies suggested population subdivisions as a result of landscape discontinuity due to unsuitable habitat and island separation. Analysis of mitochondrial DNA (mtDNA) control region sequences and allelic variation at 8 microsatellite loci were conducted on tortoises sampled in 3 locations on the 2 major islands of Aldabra. We found no variation in mtDNA sequences. This pattern corroborated earlier work supporting the occurrence of a founding event during the last interglacial period and a further reduction in genetic variability during historical time. On the other hand, significant population structure recorded at nuclear loci suggested allopatric divergence possibly due to geographical barriers among islands and ecological partitions hindering tortoise movements within islands. This is the first attempt to study the population genetics of Aldabra tortoises, which are now at carrying capacity in an isolated terrestrial ecosystem where ecological factors appear to have a strong influence on population dynamics.
    The Journal of heredity 01/2010; 102(1):29-37. · 2.05 Impact Factor
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    ABSTRACT: A set of eight highly polymorphic microsatellite markers was isolated and characterized from a genomic library enriched for dinucleotide repeats in the European pond turtle, Emys orbicularis. The markers were tested for polymorphism in a total of 33 turtles sampled in two natural ponds in the nature reserve of Kerkini, northern Greece. Number of alleles varied from 10 to 18, and expected heterozygosity ranged between 0.738 and 0.921. This novel set of loci will be particularly useful to assess fine-scale population structure and for parentage analysis in E. orbicularis.
    Molecular Ecology Resources 01/2009; 9(1):189-91. · 7.43 Impact Factor

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