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Publications (190)
This study presents the first results from the analysis of water mites collected in Portugal as part of the Biodiversity Genomics Europe project. 307 COI DNA barcodes clustered into 75 BINs are provided, with 38 BINs being unique and deposited for the first time in the Barcode of Life Data Systems (BOLD). 65 species have been identified, of which 3...
Islands are crucial evolutionary hotspots, providing unique opportunities for differentiation of novel biodiversity and long-term segregation of endemic species. Islands are also fragile ecosystems, where biodiversity is more exposed to environmental and anthropogenic pressures than on continents. The Ponza grayling, Hipparchia sbordonii, is an end...
Monitoring, management and conservation of rare and elusive species often requires early detection of individuals, especially for re-introduced and endangered taxa. Environmental DNA (eDNA) approaches can enhance the detection power of traditional biomonitoring methods for low-density, newly-established populations. In this study, we used species-s...
Background
Evidence of correlation between genome size, the nuclear haploid DNA content of a cell, environmental factors and life-history traits have been reported in many animal species. Genome size, however, spans over three orders of magnitude across taxa and such a correlation does not seem to follow a universal pattern. In squamate reptiles, t...
Population structure and phylogeography of the loggerhead sea turtle (Caretta caretta) have so far been assessed mainly by mitochondrial DNA (mtDNA) single-gene sequencing studies. However, phylogenetic relationships amongst matrilines, genetic characterisation of rookeries and mixed-stock analyses have suffered from the limited resolution obtained...
Megachile (Chalicodoma) parietina (Geoffroy, 1785) is a Palearctic solitary bee included in the Red List of some central European Countries. Females build durable nests, reused year after year, by mixing soil with a salivary secretion. Like for most solitary bees, the resources contained within M. parietina nests attract several other insects which...
Background and methods Population structure and phylogeography of the loggerhead sea turtle (Caretta caretta) have so far been assessed mainly by mitochondrial DNA (mtDNA) control region sequence comparison. This marker, however, shows limited resolution, due to common haplotypes being shared across populations. Analysis of whole mtDNA provides a m...
Ants are a highly diversified insect family of the order Hymenoptera, with many fascinating characteristics such as eusociality, chemical communication, farming, or social parasitism. Moreover, ants frequent a wide variety of habitats from dry deserts, grasslands and savannas to cold temperate forests. The ability of ants to inhabit such diverse ha...
The diverse physiography of the Portuguese land and marine territory, spanning from continental Europe to the Atlantic archipelagos, has made it an important repository of biodiversity throughout the Pleistocene glacial cycles, leading to a remarkable diversity of species and ecosystems. This rich biodiversity is under threat from anthropogenic dri...
The Aeolian wall lizard, Podarcis raffonei, is an endangered species endemic to the Aeolian archipelago, Italy, where it is present only in three tiny islets and a narrow promontory of a larger island. Because of the extremely limited area of occupancy, severe population fragmentation and observed decline, it has been classified as Critically Endan...
The availability of public genomic resources can greatly assist biodiversity assessment, conservation, and restoration efforts by providing evidence for scientifically informed management decisions. Here we survey the main approaches and applications in biodiversity and conservation genomics, considering practical factors, such as cost, time, prere...
The availability of public genomic resources can greatly assist biodiversity assessment, conservation, and restoration efforts by providing evidence for scientifically informed management decisions. Here we survey the main approaches and applications in biodiversity and conservation genomics, considering practical factors, such as cost, time, prere...
Globally distributed marine taxa are well suited for investigations of biogeographic impacts on genetic diversity, connectivity, and population demography. The sea turtle genus Lepidochelys includes the wide-ranging and abundant olive ridley (L. olivacea), and the geographically restricted and 'Critically Endangered' Kemp's ridley (L. kempii). To i...
Terrestrial animals in global wet-dry tropical ecosystems experience year-round high temperatures but concentrated summer rainfall. This highly seasonal precipitation is expected to have major evolutionary and ecological consequences for animals. We considered how strong seasonal patterns of rainfall might influence the environment and biological a...
Insights into the evolution of non-model organisms are often limited by the lack of reference genomes. As part of the Vertebrate Genomes Project, we present a new reference genome and a pangenome produced with High-Fidelity long reads for the barn swallow Hirundo rustica. We then generated a reference-free multialignment with other bird genomes to...
Progress in genome sequencing now enables the large-scale generation of reference genomes. Various international initiatives aim to generate reference genomes representing global biodiversity. These genomes provide unique insights into genomic diversity and architecture, thereby enabling comprehensive analyses of population and functional genomics,...
Terrestrial animals in global wet-dry tropical ecosystems experience year-round high temperatures but concentrated summer rainfall. This highly seasonal precipitation is expected to have major evolutionary and ecological consequences for animals. We considered how strong seasonal patterns of rainfall might influence the environment and biological a...
Chronic exposure to pollutants affects natural populations, creating specific molecular and biochemical signatures. In the present study, we tested the hypothesis that chronic exposure to pollutants might have substantial effects on the Manila clam hologenome long after removal from contaminated sites. To reach this goal, a highly integrative appro...
Sea turtles migrate across ocean basins to reach foraging and breeding areas but still exhibit significant population structure across nesting beaches. Although five species of sea turtles nest in West Africa, the genetic structure of many species in this region has not been adequately explored. We investigated the diversity of mitochondrial and nu...
Population and conservation genetics studies have greatly benefited from the development of new techniques and bioinformatic tools associated with next‐generation sequencing. Analysis of extensive datasets from whole‐genome sequencing of even a few individuals allows the detection of patterns of fine‐scale population structure and detailed reconstr...
The development of roads coinciding with human expansion and settlement can lead to substantial habitat degradation and biodiversity impact. For terrestrial animals, roads can also result in direct mortality or injury due to motor vehicle collisions. Flores is the largest among the five islands harboring Komodo Dragon (Varanus komodoensis) in south...
The study of vertebrate genome evolution is currently facing a revolution, brought about by next generation sequencing technologies that allow researchers to produce nearly complete and error-free genome assemblies. Novel approaches however do not always provide a direct link with information on vertebrate genome evolution gained from cytogenetic a...
Species restricted to archipelagos are often range-restricted, dispersal limited, and persist as disjunct populations. These attributes can make island populations especially vulnerable to extinction from natural or anthropogenic processes. Ascertaining causes of habitat use, population impact, and range loss is fundamental to guiding effective con...
We studied annual trends and characteristics of nesting activities and hatchling production by female Komodo Dragons (Varanus komodoensis) in Komodo National Park, Indonesia between 2002 and 2006. During this period, we recorded 12, 16, 15, 13, and 6 females nesting annually at 42 potential nesting sites. An average female nesting periodicity was e...
The Komodo dragon (Varanus komodoensis) is an endangered, island-endemic species with a naturally restricted distribution. Despite this, no previous studies have attempted to predict the effects of climate change on this iconic species. We used extensive Komodo dragon monitoring data, climate, and sea-level change projections to build spatially exp...
Brachyura is one of the most specious infra-order belonging to Decapoda
and it plays a central role from an ecological and economic point of view. Despite its
importance, cytogenetic studies on Brachyura (Decapoda) are extremely limited due
to the difficulties in obtaining chromosome preparations of good quality. Molecular
cytogenetic have proven t...
Biological invasions are a growing threat to biodiversity. The black rat, one of the worst pest in the world, is responsible for extensive population decline of many autochthonous and endemic species, particularly in island ecosystems. A number of rat eradication campaigns have been conducted, however, such endeavors do not always result in a compl...
Among eusocial Hymenoptera, ants represent an unrivalled example of diversity in number of queens and mating systems. Ant colonies may have one (monogyny) or several queens (polygyny) which can mate once (monoandry) or several times (polyandry). In this study, we analysed the genetic structure and breeding system of the Mediterranean acrobat ant Cr...
Non-synonymous mutations in the gene encoding vitamin K epoxide reductase (VKORC1) are responsible for resistance to anticoagulant rodenticides in rodents. Detection of resistant individuals is crucial to implement effective management plans and guarantee the success of eradication campaigns. Resistant individuals of the house mouse Mus musculus ha...
The study of animal diet and feeding behaviour is a fundamental tool for the illustration of the ecological role of species in the ecosystem. However, size and quality of food intake samples make it hard for researchers to describe the diet composition of many small species. In our study, we exploited genomic tools for the analysis of the diet comp...
Monitor lizards are unique among ectothermic reptiles in that they have high aerobic capacity and distinctive cardiovascular physiology resembling that of endothermic mammals. Here, we sequence the genome of the Komodo dragon Varanus komodoensis, the largest extant monitor lizard, and generate a high-resolution de novo chromosome-assigned genome as...
During the second half of the XIX century, several species of red wood ants (Formica rufa group) were used as biological control agents and introduced to the Italian Apennine mountains where they were formerly absent. Among these, Formica lugubris was the most widely introduced alien species. In 1996, however, a taxonomic revision defined two sibli...
Our knowledge of Testudines evolution is limited by the lack of modern cytogenetic data. Compared to other reptiles, there is little information even on chromosome banding, let alone molecular cytogenetic data. Here, we provide detailed information on the karyotype of the European pond turtle Emys orbicularis , a model Emydidae, employing both chro...
We developed new tools to build a high-quality chromosomal map of the Komodo dragon ( Varanus komodoensis ) available for cross-species phylogenomic analyses. First, we isolated chromosomes by flow sorting and determined the chromosome content of each flow karyotype peak by FISH. We then isolated additional Komodo dragon chromosomes by microdissect...
Monitor lizards are unique among ectothermic reptiles in that they have a high aerobic capacity and distinctive cardiovascular physiology which resembles that of endothermic mammals. We have sequenced the genome of the Komodo dragon (Varanus komodoensis), the largest extant monitor lizard, and present a high resolution de novo chromosome-assigned g...
Despite their long history with the basal split dating back to the Eocene, all species of monitor lizards (family Varanidae) studied so far share the same chromosome number of 2n = 40. However, there are differences in the morphology of the macrochromosome pairs 5–8. Further, sex determination, which revealed ZZ/ZW sex microchromosomes, was studied...
Giant tortoises are among the longest-lived vertebrate animals and, as such, provide an excellent model to study traits like longevity and age-related diseases. However, genomic and molecular evolutionary information on giant tortoises is scarce. Here, we describe a global analysis of the genomes of Lonesome George—the iconic last member of Chelono...
Loss of dispersal typifies island biotas, but the selective processes driving this phenomenon remain contentious. This is because selection via, both indirect (e.g. relaxed selection or island syndromes) and direct (e.g. natural selection or spatial sorting) processes may be involved, and no study has yet convincingly distinguished between these al...
Understanding how threatened wildlife can coexist with humans over the long term is a central issue in conservation and wildlife management. Komodo National Park in Eastern Indonesia, harbors the largest extant populations of the endemic Komodo dragon (Varanus komodoensis). Consistent with global trends, this species is expected to be increasingly...
Several hypotheses have been advanced to explain the evolution of leks, a mating system in which males aggregate at display sites where females choose their mates. Only a small proportion of males obtain copulations, and why other males join the lek remains unexplained. One hypothesis has called kin selection into play: if juvenile males join leks...
Invasive species are one of the main causes of biodiversity loss, and rodents in particular are regarded as a real threat worldwide, especially to island ecosystems. The Tuscan Archipelago National Park is the largest in the Mediterranean basin, it harbours a large number of autochthonous endemic species, mostly reptiles and insects, and hosts many...
Rotational logging practices are used with the goal of reducing forest disturbance impacts on biodiversity. However, it is poorly understood whether such forest management practices conserve the demographic and genetic composition of animal populations across logged landscapes. Here we investigated whether rotational logging practices alter pattern...
A visualization of our published study "Effects of human activities on Komodo dragons in Komodo National Park".
Migration is one of several marine vertebrate traits increasingly affected by human encroachment. The Adriatic Sea is an important foraging and wintering site for loggerhead turtles (Caretta caretta), and one of the Mediterranean regions where they are most heavily impacted, particularly by fisheries bycatch. Conservation measures concern foraging...
A correction to this article has been published and is linked from the HTML and PDF versions of this paper. The error has been fixed in the paper.
An aim of many captive breeding programs is to increase population sizes for reintroduction and establishment of self-sustaining wild populations. Genetic analyses play a critical role in these programs: monitoring genetic variation, identifying the origin of individuals, and assigning parentage to track family sizes. Here we use genetic pedigree a...
Species are being lost at an unprecedented rate due to human-driven environmental changes.
The cases in which species declared extinct can be revived are rare. However, here we report that a remote volcano in the Galápagos Islands hosts many giant tortoises with high ancestry from a species previously declared as extinct: Chelonoidis elephantopus o...
Availability and distribution of preferred trophic resources largely influence spatial distribution and abundances of small rodents in agroecosystems. Food availability in different habitats constituting agroecosystems influences diet, population density and reproduction of small mammals. As inhabitants of anthropogenic environments, small mammals...
Hgh-throughput DNA sequencing allows efficient discovery of thousands of single nucleotide polymorphisms (SNPs) in non-model species. Population genetic theory predicts that this large number of independent markers should provide detailed insights into population structure, even when only a few individuals are sampled. Still, sampling design can ha...
High-throughput DNA sequencing allows efficient discovery of thousands of single nucleotide polymorphisms (SNPs) in non-model species. Population genetic theory predicts that this large number of independent markers should provide detailed insights into population structure, even when only a few individuals are sampled. Still, sampling design can h...
Gabon hosts nesting grounds for several sea turtle species, including the world’s largest rookery for the leatherback turtle (Dermochelys coriacea), Africa’s largest rookery for the olive ridley turtle (Lepidochelys olivacea) and smaller aggregations of the hawksbill turtle (Eretmochelys imbricata) and green turtle (Chelonia mydas). To assess the l...
Species are being lost at an unprecedented rate due to human-driven environmental changes. The cases in which species declared extinct can be revived are rare. However, here we report that a remote volcano in the Galápagos Islands hosts many giant tortoises with high ancestry from a species previously declared as extinct: Chelonoidis elephantopus o...
Marine turtles are highly migratory species that establish multiple connections among distant areas, through oceanic migration corridors. To improve the knowledge on the connectivity of Atlantic green turtles Chelonia mydas, we analysed the genetic composition and contribution to juvenile aggregations of one of the world's largest rookeries at Poil...
The population genetic structure of freshwater organisms depends upon the arrangement of streams, the extent and connectivity of ponds and marshes, as well as terrestrial dispersal capability. We assessed the population genetic structure and patterns of gene flow for a total of 324 European pond turtles Emys orbicularis sampled in ponds along the S...
Natural habitats with serpentine soils are rich in heavy metal ions, which may significantly affect ecological communities. Exposure to metal pollutants results, for instance, in a reduction of population genetic diversity and a diffused higher tolerance towards heavy metals. In this study, we investigated whether chronic exposure to metals affect...
Genetic relatedness among individuals can play a major role in the socio-spatial organization of mammals. However, only a few studies have documented kin-related spatial pattern in solitary medium-sized carnivores. Using radiotelemetry and genetic data from 15 individuals (seven males and eight females), we investigated the relationship between kin...
A trophic niche overlap in native and alien turtle species can lead to competitive interactions whereby allochthonous turtles may outcompete autochthonous individuals and eventually affect viability of natural populations. The European pond turtle (Emys orbicularis) is an autochthonous species threatened by habitat encroachment and competition with...
Savi's pine vole (Microtus savii) is a fossorial rodent distributed in open areas and croplands of the Italian peninsula. Their diet is strictly herbivorous and in some contexts this species can be considered as a pest of arable crops and orchards. The aim of this study was to analyze the diet of Savi's pine vole throughout the year in a peach orch...
Ontogenetic allometries in ecological habits and niche use are key responses by which individuals maximize lifetime fitness. Moreover, such allometries have significant implications for how individuals influence population and community dynamics. Here, we examined how body size variation in Komodo dragons (Varanus komodoensis) influenced ecological...
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 sa...
