Massimo Lorenzoni

Bio: Massimo Lorenzoni is an academic researcher from University of Perugia. The author has contributed to research in topics: Population & Salmo. The author has an hindex of 21, co-authored 126 publications receiving 1458 citations.

Spatial heterogeneity in the Mediterranean Biodiversity Hotspot affects barcoding accuracy of its freshwater fishes.

Abstract: Incomplete knowledge of biodiversity remains a stumbling block for conservation planning and even occurs within globally important Biodiversity Hotspots (BH). Although technical advances have boosted the power of molecular biodiversity assessments, the link between DNA sequences and species and the analytics to discriminate entities remain crucial. Here, we present an analysis of the first DNA barcode library for the freshwater fish fauna of the Mediterranean BH (526 spp.), with virtually complete species coverage (498 spp., 98% extant species). In order to build an identification system supporting conservation, we compared species determination by taxonomists to multiple clustering analyses of DNA barcodes for 3165 specimens. The congruence of barcode clusters with morphological determination was strongly dependent on the method of cluster delineation, but was highest with the general mixed Yule-coalescent (GMYC) model-based approach (83% of all species recovered as GMYC entity). Overall, genetic morphological discontinuities suggest the existence of up to 64 previously unrecognized candidate species. We found reduced identification accuracy when using the entire DNA-barcode database, compared with analyses on databases for individual river catchments. This scale effect has important implications for barcoding assessments and suggests that fairly simple identification pipelines provide sufficient resolution in local applications. We calculated Evolutionarily Distinct and Globally Endangered scores in order to identify candidate species for conservation priority and argue that the evolutionary content of barcode data can be used to detect priority species for future IUCN assessments. We show that large-scale barcoding inventories of complex biotas are feasible and contribute directly to the evaluation of conservation priorities.

Native and exotic fish species in the tiber river watershed (umbria - italy) and their relationship to the longitudinal gradient

Abstract: In this study we examine the spatial variations in the fish communities in the Tiber River watershed, including both native and exotic species. Its main objectives were to assess the quality of fish communities of this area and to verify if factors of fish community disturbance are constant over the basin or if they change along the river gradient. The level of degradation was evaluated according to the ratio between the number of native fish species and total number of species (ZIC = Zoogeographic Integrity Coefficient). A total of 37 fish species was found, 13 native and 24 exotic (64.86%). Cyprinid is the prevailing family with 15 species (7 native, 8 exotic). The species most frequently introduced are cyprinids, followed by salmonids (4 species) and gobids (3 species). Of the 24 exotic species only 11 (45.83%) can be considered intentionally introduced by man: the proportion of intentionally introduced transplanted species (66.67%) is considerably higher than the translocated species (33.33%). There is a correlation between the longitudinal gradient of the river, the morphological evolution of the riverbed and decline in water quality. High ZIC values were related to higher elevation, greater slope and better water quality. As the size of the river increases the fish communities appear to be ever-more dominated by species of exotic origin, whose number progressively increases with the worsening of the water quality and downstream movement. The number of native species is the greatest in the middle reaches of the rivers, and decreases both upstream and downstream. Compared to the introduced species, the native species tend to stay upstream and are often the only species found in the headwaters. The number of introduced species increases downstream. We have also found differences among translocated and transplanted species: the first ones tend to favor the middle reaches of the rivers, while transplanted species seem to prefer the downstream sectors. In almost all cases, the sampling station immediately below an impoundment has the lowest ZIC values in comparison to the river stretches above the dam. Our preliminary results suggest that characteristics of fish community alterations depend on the type of river sector involved; the small rivers of the basin are a refuge zone for the native community and are currently of fundamental importance for maintaining biodiversity.

Biology of Procambarus clarkii (Girard, 1852) in Lake Trasimeno

Abstract: The aim of this study was to gather more informations about the biological characteristics of Procambarus clarkii and to investigate the reasons of its rapid expansion in Lake Trasimeno. Specimens of both sexes (544 males and 624 females) were collected from October 2000 to November 2001. During the sampling period physical factors such as water temperature and hydrologic level of LakeTrasimeno were recorded. The study was conducted monthly in order to assess this species’ reproductive period. 1,168 specimens were analyzed for colour, sex, weight, and length. The sexual maturation of gonads was investigated in females. The results of this study evidenced that the population is in expansion, showing that Lake Trasimeno is an optimal habitat for this species.

“Bioinformatics” 특집을 내면서

Abstract: BIOE 402. Medical Technology Assessment. 2 or 3 hours. Bioentrepreneur course. Assessment of medical technology in the context of commercialization. Objectives, competition, market share, funding, pricing, manufacturing, growth, and intellectual property; many issues unique to biomedical products. Course Information: 2 undergraduate hours. 3 graduate hours. Prerequisite(s): Junior standing or above and consent of the instructor.

Fast Tree: Computing Large Minimum-Evolution Trees with Profiles instead of a Distance Matrix

Abstract: Gene families are growing rapidly, but standard methods for inferring phylogenies do not scale to alignments with over 10,000 sequences. We present FastTree, a method for constructing large phylogenies and for estimating their reliability. Instead of storing a distance matrix, FastTree stores sequence profiles of internal nodes in the tree. FastTree uses these profiles to implement neighbor-joining and uses heuristics to quickly identify candidate joins. FastTree then uses nearest-neighbor interchanges to reduce the length of the tree. For an alignment with N sequences, L sites, and a different characters, a distance matrix requires O(N^2) space and O(N^2 L) time, but FastTree requires just O( NLa + N sqrt(N) ) memory and O( N sqrt(N) log(N) L a ) time. To estimate the tree's reliability, FastTree uses local bootstrapping, which gives another 100-fold speedup over a distance matrix. For example, FastTree computed a tree and support values for 158,022 distinct 16S ribosomal RNAs in 17 hours and 2.4 gigabytes of memory. Just computing pairwise Jukes-Cantor distances and storing them, without inferring a tree or bootstrapping, would require 17 hours and 50 gigabytes of memory. In simulations, FastTree was slightly more accurate than neighbor joining, BIONJ, or FastME; on genuine alignments, FastTree's topologies had higher likelihoods. FastTree is available at http://microbesonline.org/fasttree.

The Ecology of Invasions by Animals and Plants

Abstract: Much as Rachel Carson's \"Silent Spring\" was a call to action against the pesticides that were devastating bird populations, Charles S. Elton's classic \"The Ecology of Invasions by Animals and Plants\" sounded an early warning about an environmental catastrophe that has become all too familiar today-the invasion of nonnative species. From kudzu to zebra mussels to Asian long-horned beetles, nonnative species are colonizing new habitats around the world at an alarming rate thanks to accidental and intentional human intervention. One of the leading causes of extinctions of native animals and plants, invasive species also wreak severe economic havoc, causing $79 billion worth of damage in the United States alone. Elton explains the devastating effects that invasive species can have on local ecosystems in clear, concise language and with numerous examples. The first book on invasion biology, and still the most cited, Elton's masterpiece provides an accessible, engaging introduction to one of the most important environmental crises of our time. Charles S. Elton was one of the founders of ecology, who also established and led Oxford University's Bureau of Animal Population. His work has influenced generations of ecologists and zoologists, and his publications remain central to the literature in modern biology. \"History has caught up with Charles Elton's foresight, and \"The Ecology of Invasions\" can now be seen as one of the central scientific books of our century.\"-David Quammen, from the Foreword to \"Killer Algae: The True Tale of a Biological Invasion\

Computation And Interpretation Of Biological Statistics Of Fish Populations

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