Amphibian Biology. Volume 11, Part 4: Status of Conservation and Decline of Amphibians: Eastern Hemisphere. Southern Europe and Turkey

Heatwole, H. and J. W. Wilkinson (eds.). 2015. Amphibian Biology. Volume 11, Part 4: Status of Conservation and Decline of Am­phibians: Eastern Hemisphere. Southern Europe and Turkey. 158 pp. Pelagic Publishing, Exeter, UK

Numerical methods for sedimentary‐ancient‐DNA‐based study on past biodiversity and ecosystem functioning

Abstract Sedimentary ancient DNA (SedaDNA) is an emerging tool to reconstruct past biodiversity with high taxonomic resolution. Its growing popularity has stimulated an increasing complexity of SedaDNA data production (e.g., DNA extraction, amplification, and sequencing; authentication of molecules; bioinformatics). Conversely, less attention has been devoted to how appropriate statistical analyses can help to extract ecological information from SedaDNA. Until now, ecological studies based on SedaDNA have taken limited advantage of the multiple statistical and numerical methods available for analysis. Here, we present a range of numerical approaches that can be particularly useful to multispecies ecological analysis on SedaDNA, with a special focus on biodiversity studies on macroorganisms. We discuss the advantages and complexity of such methods and describe how some of them can be optimized for ecological analyses of SedaDNA‐based metabarcoding data, with a special focus on SedaDNA studies. First, site occupancy‐detection models can help to better ascertain the variation through time of the occurrence of target species and to identify the factors determining their detection through time. Second, several approaches can be used to estimate variation of relative abundance. Even though methods for abundance estimation have major limitations, they can provide useful information on temporal variation of ecosystem functions. Third, approaches exist to obtain better measures of species diversity, while taking into account the uncertainties of species abundance and identification. Fourth, techniques of clustering, ordination, and constrained ordination allow identification of temporal trends and testing of candidate drivers of community variation. Finally, structural equation models can be used to assess complex causal relationships among biodiversity, human activities, and environment. SedaDNA studies can make use of a broad panel of analytical approaches, which can improve our understanding of long‐term biodiversity changes, maximizing the information we can obtain from past ecosystems

Switching from mesopredator to apex predator: how do responses vary in amphibians adapted to cave living?

AbstractThe effective detection of both prey and predators is pivotal for the survival of mesopredators. However, the condition of being a mesopredator is strongly context dependent. Here we focus on two aquatic caudate species that have colonised caves: the Pyrenean newt (Calotriton asper) and the olm (Proteus anguinus). The former maintains both surface and subterranean populations, while only cave-adapted populations of the latter exist. Both species are apex predators in underground waterbodies, while the Pyrenean newt is a mesopredator in surface waterbodies. Shifting to a higher level of the trophic web through colonising caves may promote the loss of anti-predator response against surface apex predators, and an increase in the ability to detect prey. To test these two non-exclusive hypotheses, we integrated classical behavioural characterisations with a novel approach: the assessment of lateralisation (i.e. preference for one body side exposure). Behavioural experiments were performed using laboratory-reared individuals. We performed 684 trials on 39 Pyrenean newts and eight olms. Under darkness and light conditions, we tested how exposure to different chemical cues (predatory fish, prey and unknown scent) affected individuals' activity and lateralisation. Both cave and surface Pyrenean newts responded to predator cues, while olms did not. In Pyrenean newts, predator cues reduced the time spent in movement and time spent in lateralisation associated with hunting. Our results show that predator recognition is maintained in a species where recently separated populations inhabit environments lacking of higher predators, while such behaviour tends to be lost in populations with longer history of adaptation.Significance statementPredator recognition can be maintained in animals adapted to predator free habitats, but varies with their history of adaptation. Species that are not at the apex of the food web can become top predators if they colonise subterranean environments. We compared the behavioural responses of the olm, a strictly cave species with a long underground evolutionary history, and of the Pyrenean newt, a facultative cave species that also has stream-dwelling populations. Moreover, we integrated a classical behavioural characterisation, such as movement detection, with a novel approach: the assessment of lateralisation. While olms do not respond to external predators scent, cave-dwelling newts still recognise it. This clearly indicates that predator recognition is still maintained in species that have colonised predator-free environments more recently

Thirty years of invasion: the distribution of the invasive crayfish Procambarus clarkii in Italy

The presence of the red swamp crayfish Procambarus clarkii in Italy is documented since 1989, but no comprehensive data are available on its spread through time at the national scale. New confirmed records for Procambarus clarkii are continuously arising in recent years across the country. By reviewing the scientific and grey literature, we obtained an up-to-date map of the species invasion in Italy. This information can help to monitor and understand the spread of this highly invasive crayfish and to implement more effective management measures.

Amplified fragment length homoplasy: in silico analysis for model and non-model species

<p>Abstract</p> <p>Background</p> <p>AFLP markers are widely used in evolutionary genetics and ecology. However the frequent occurrence of non-homologous co-migrating fragments (homoplasy) both at the intra- and inter-individual levels in AFLP data sets is known to skew key parameters in population genetics. Geneticists can take advantage of the growing number of full genome sequences available for model species to study AFLP homoplasy and to predict it in non-model species.</p> <p>Results</p> <p>In this study we performed <it>in silico </it>AFLPs on the complete genome of three model species to predict intra-individual homoplasy in a prokaryote (<it>Bacillus thuringiensis </it>ser. <it>konkukian</it>), a plant (<it>Arabidopsis thaliana</it>) and an animal (<it>Aedes aegypti</it>). In addition, we compared <it>in silico </it>AFLPs to empirical data obtained from three related non-model species (<it>Bacillus thuringiensis </it>ser. <it>israelensis, Arabis alpina </it>and <it>Aedes rusticus</it>). Our results show that homoplasy rate sharply increases with the number of peaks per profile. However, for a given number of peaks per profile, genome size or taxonomical range had no effect on homoplasy. Furthermore, the number of co-migrating fragments in a single peak was dependent on the genome richness in repetitive sequences: we found up to 582 co-migrating fragments in <it>Ae. aegypti</it>. Finally, we show that <it>in silico </it>AFLPs can help to accurately predict AFLP profiles in related non-model species.</p> <p>Conclusions</p> <p>These predictions can be used to tackle current issues in the planning of AFLP studies by limiting homoplasy rate and population genetic estimation bias. ISIF (In SIlico Fingerprinting) program is freely available at <url>http://www-leca.ujf-grenoble.fr/logiciels.htm</url>.</p

TetraDENSITY: a database of population density estimates in terrestrial vertebrates

Motivation: Population density is a key demographic parameter influencing many ecological processes, and macroecology has described both intra‐ and interspecific patterns of variation. Population density data are expensive to collect and contain many forms of noise and potential bias; these factors have impeded investigation of macroecological patterns, and many hypotheses remain largely unexplored. Population density also represents fundamental information for conservation, because it underlies population dynamics and, ultimately, extinction risk. Here we present TetraDENSITY, an extensive dataset with >18,000 records of density estimates for terrestrial vertebrates, in order to facilitate new research on this topic. Main types of variable contained: The dataset includes taxonomic information on species, population density estimate, year of data collection, season, coordinates of the locality, locality name, habitat, sampling method and sampling area. Spatial location and grain: Global. Spatial accuracy varies across studies; conservatively, it can be considered at 1°, but for many data it is much finer. Time period and grain: From 1926 to 2017. Temporal accuracy is yearly in most cases, but studies with higher temporal resolution (season, month) are also present. Major taxa and level of measurement: Amphibians in terrestrial phase, reptiles, birds and mammals. Estimates derive from multiple methods, reflecting the study taxon, location and techniques available at the time of density estimation

Predator cues and risky habitats affect foraging activity in salamanders

peer reviewe

Microplastic pollution in the Trieste Karst (Italy) protected habitats: preliminary analysis of cave and spring water sediments

Microplastic (MP) pollution in karst and subterranean areas is still poorly studied and research are generally focused on the water matrix. The Trieste Karst, Italy, is rich in peculiar karst habitats and species, including some endemics. To preserve these ecological heritages, different European, national and local laws are present. In this preliminary study we collected and investigated several sediment samples from aquatic environments in different protected habitats (three caves and a spring) of the Trieste Karst. Sediment samples were subjected to organic matter removal with 1:1 30% H2O2 solution and for each sample, three subsamples of 15g dried sediment were selected via coning and quartering. MPs were extracted from sediment via density separation and filtered. Particles on filters (5-0.1 mm) were counted and characterized by size, color and shape via visual identification under a microscope, with and without UV light, exploiting fluorescence given by additives added in many plastic materials. Finally, spectroscopic analyses were carried out on random particles on each filter. The concentration of MPs in cave water sediments varied from 911 to 2178 items/kg, instead, in the sediments of the spring it was of 889 items/kg. Fibre represented the most abundant shape (67.5%), followed by fragment (21.6%), bead (10%), and film (0.9%). Most MPs (86.4%) were smaller than 1 mm. The majority of the MPs were fluorescent under UV light (69.1%) and have 77.1% blue fluorescence, 8.1% red fluorescence, 6.1% green fluorescence and 8.7% other colors. Fluorescent particles were mainly transparent (63.8%), instead, in non-fluorescent ones predominated the black (56.2%) and brown (15.1%) MPs. Our results show the presence of MPs in all examined aquatic habitats, providing essential information for future research. The studied areas are adjacent to highways, roads and railways, therefore, most of the particles found in water sediment samples could come from surface pollution, transported by water and/or air. In addition, the waters of the sampling points are often stationary or poorly moved, therefore, there may be an accumulation of pollutants in the sediments. Vulnerable and troglobitic species hosted in these habitats could consume or assimilate MPs, which can irreversibly damage ecosystems and contaminate water resources too. Analyses on a greater number of aquatic surface and subterranean habitats should be done to better understand this kind of problem. Monitoring MPs pollution in karst areas should become a priority for the habitat conservation, the species protection and the water resources management

Estimating abundance and habitat suitability in a micro-endemic snake: the Walser viper

Recently described species suffer lack of information that hampers setting up appropriate conservation strategies. The situation is particularly complex with micro-endemic snakes, for which detection and monitoring are particularly challenging. The Walser viper Vipera walser is a recently described snake inhabiting a small area of the SW Italian alps. We combined information on species distribution with repeated monitoring to identify the areas most suitable for the species, and to obtain estimates of species abundance. Species distribution models were used to identify the topographical, climatic, and land-cover features related to the occurrence of vipers. Furthermore, repeated transects and N-mixture models were used to estimate abundance and to identify factors related to the variation of abundance. The available data suggested that the species has a disjunct range, with a Northern range of ~45 km2 , and a southern range of ~225 km2. Distribution models suggested that vipers are associated with areas with open egetation,altitude between 1300 and 2300 m, high precipitation, low forest cover, low slope, and southern aspect. N-mixture models confirmed very low detection probability of these vipers, and suggested that the species has a low abundance,with the highest abundance in south-facing plots. We provide the first quantitative information on habitats and abundance variation for Walser vipers. The broad confidence intervals of abundance estimates exemplify the complexity of providing range-wide measures of abundance for secretive species. Given the narrow range of these vipers, continuous monitoring is required to understand how they respond to ongoing environmental changes in mountainous areas

Batrachochytrium dendrobatidis in amphibians from the Po River Delta, Northern Italy

Batrachochytrium dendrobatidis is a pathogen infecting amphibians at the global scale and causing their decline, but knowledge of the distribution of this pathogen is far from complete. We sampled amphibians from three species (Hyla intermedia, Rana dalmatina and Pelophylax synklepton esculentus) to evaluate whether B. dendrobatidis infects amphibians in the Po River Delta Natural Park, Northern Italy. We detected the pathogen in one population of P. sk. esculentus (prevalence: 0.33). These findings expand the known distribution of B. dendrobatidis in Italy and add further concern to the conservation of amphibians in this area