Genetic and genomic data from single or multiple individuals contain a lot of useful information to reconstruct the past and predict the future evolution of species or populations. In our group, we want to understand what happened in the past, what is the impact of human-altered environments on the evolution and survival of a species, what is the genomic architecture of specific adaptations.
In a few words, we are fascinated by the genetics consequences of evolution and by the use of genetic polymorphisms to reconstruct the past and to possibly prevent the extinction of endangered species, lineages, and traits. To do that, we study processes like selection events at specific genes, variation in population size during environmental change, habitat fragmentation and reduction of gene flow, accumulation of deleterious mutations.
Keywords: evolution, population genetics/genomics, conservation genetics/genomics, bioinformatics, genetic/genomic variation, genetic drift, selection, adaptation.
Ongoing research
Our research spans diverse topics, although the predominant interest of the group is conservation genomics. See below our current projects by category.
Sampling and whole-genome sequencing of Italian terrestrial vertebrates
Starting: 2025 – Ending: 2026
The project aims at 1) collecting tissue samples from approximately 40 individuals in 15-20 terrestrial species in Italy; 2) producing whole-genome sequencing for all these 600-800 individuals with a coverage >30X; 3) assembling de-novo genomes for 5 of these species; 4) computing basic diversity and structure statistics for each species/individuals. The project is supported by the Ministry of the Environment and managed by the CFR (Consorzio Futuro in Ricerca).
Team: Giorgio Bertorelle (Coordinator), Andrea Benazzo, Roberto Biello, Silvia Fuselli, Valentina Giongo, Amiel Masarap
External team members: Emiliano Trucchi (Marche Polytechnic University)
Global warming now and then: the speed and load factors affecting the success or failure of a range expansion
Starting: 2023– Ending: 2026
Several interacting environmental and biological factors contribute to the success (or failure) of a geographic expansion. In this project we focus on the colonization rate and the genetic load, and we use an Italian endangered endemic species (the Apennine yellow-bellied toad, Bombina pachypus) as a model species. This toad expanded northwards along the peninsula after the last glaciation. Using genomic data, we will estimate the expansion load in our model species and develop a realistic simulation model capable of generating genomic patterns compatible with those observed in the real system. We will also use spatially explicit genomic simulations to understand more in general how the rate of climate change and the velocity of a species to colonize new suitable habitats affect the expansion load and thus the probability of success of the colonization.
Team: Giorgio Bertorelle (Coordinator), Victor Muñoz Mora, Silvia Fuselli, Roberto Biello, Giulia Fabbri
External team members: Claudio Ciofi (University of Florence), Alessio Iannucci (University of Florence), Leonardo Girlanda (University of Florence), Daniele Canestrelli (Univesity of Tuscia), Andrea Chiocchio (Univesity of Tuscia), Emiliano Trucchi (Marche Polytechnic University), Sebastiano Fava (Marche Polytechnic University), Marco Gargano (Marche Polytechnic University)
Genomic diversity, demography and local adaptations of the Apennine brown bear
Starting: 2024– Ending: 2027
Supported by the National Park of Abruzzo, Lazio and Molise, this project analyzes whole genome sequences of the Apennine brown bear (Ursus arctos marsicanus) with the primary objective of identifying the genetic factors that distinguish it from other brown bear populations. We will describe what makes its genetic heritage unique by identifying specific genetic differences and studying regulatory regions. The results will constitute crucial information for its conservation.
Team: Giorgio Bertorelle (Coordinator), Elisa Desiato, Giulia Fabbri, Roberto Biello, Andrea Benazzo, Beatrice Sammarco
External team members: Carolyn G. Mahan (Penn State University)
Genomic insights into the conservation of the endangered Hermann’s tortoise
Starting: 2022– Ending: 2026
This project focuses on the conservation genomics of the endangered Hermann’s tortoise (Testudo hermanni), which is threatened by habitat loss, agriculture, fires, and pet trade. We will generated a high-quality genome assembly and analyse whole-genome data from the two subspecies, to reveal historical divergence, population bottlenecks, and areas of low genetic diversity and high inbreeding. We will explore genomic regions involved in immunity and sensory functions aim to inform translocation and hybridization risks, guiding conservation strategies based on functional genetic insights.
Team: Giorgio Bertorelle (Coordinator), Roberto Biello, Silvia Fuselli, Andrea Benazzo
External team members: Patricia Santos (University of Ferrara), Elena Ramella Levis (Eurafrica Conservation Projects)
Genomic diversity and inbreeding levels of the endangered Secretarybird within Tanzania and South Africa
Starting: 2024– Ending: 2028
This project uses genomic data to support Secretarybird (Sagittarius serpentarius) conservation by assessing population diversity, inbreeding, and genetic load in Tanzania and South Africa. We aim to investigate population structure, define conservation units, and guide translocation efforts. By evaluating inbreeding and deleterious mutations, we can assess genetic risks and inform actions like corridor creation and targeted relocations. The genomic data will also enable long-term monitoring and evaluation of conservation strategies.
Team: Andrea Benazzo (Coordinator), Roberto Biello, Silvia Fuselli, Giorgio Bertorelle
External team members: Elena Ramella Levis (Eurafrica Conservation Projects), Federico Romani (Eurafrica Conservation Projects), Leonardo Congiu (University of Padua), Alessio Iannucci (University of Florence), Melissa Whitecross (University of Witwatersrand), Wesley Gush (University of Pretoria), Ben Novak (Revive&Restore)
Population genomics of fin whales in the Mediterranean Sea
Starting: 2022– Ending: 2025
This project will produce the first comprehensive genomic analysis of the endangered Mediterranean fin whale (Balaenoptera physalus), a population under growing threat from habitat degradation, climate change, and human activity. Despite its conservation status, little is known about its genetic structure, or capacity to adapt to environmental stress. By generating and analyzing whole-genome data and comparing it with global populations, we aim to assess genetic diversity, detect population structure, evaluate isolation levels, and estimate vulnerability to genomic erosion. These insights will guide conservation planning and establish a foundation for long-term genetic monitoring.
Team: Silvia Fuselli (Coordinator), Roberto Biello, Elisa Desiato
External team members: Annalaura Mancia (Coordinator, Jacksonville University), Alessio Iannucci (University of Florence), Maria Cristina Fossi (University of Siena), Cristina Panti (University of Siena), Jorge Urban R. (Universidad Autónoma de Baja California Sur )
Fish biodiversity in the lower course of the Po River: a study model of the effects of global changes in large rivers (BioPo)
Starting: 2024 – Ending: 2025
The BioPo project aims to provide an overview of the current ecological status of the lower course of the Po River, supporting targeted actions for its protection and sustainable management. To this end, three complementary approaches are being implemented: 1) the creation of a database integrating knowledge about the species present in this part of the river over the past 20 years, 2) the characterization of intraspecific diversity at the neurobehavioral level, and 3) a population genomics approach. Our group is responsible for the latter, which involves analyzing the genomic variability of four species, two endemic (Tinca tinca and Anguilla anguilla) and two invasive (Ictalurus punctatus and Abramis brama) to determine their evolutionary potential, reconstruct demographic history, and understand the invasion dynamics of the different species. The project is supported by European Union – NextGenerationEU via the National Biodiversity Future Center - NBFC.
Team: Andrea Benazzo, Silvia Fuselli, Giorgio Bertorelle, Luigia Possemato, Marta Lago
External team members: Cristiano Bertolucci (Coordinator, Unife), Giuseppe Castaldelli (Unife)
Illuminating range shifts through evolutionary FIASCO: contrasting FaIling And Successful ColOnizations in replicated wild populations
Starting: 2023– Ending: 2026
Human impacts and climate change drive species declines or adaptations, but responses vary unpredictably. We explore repeated range shifts in a marine snail using genomic, phenotypic, and ecological data to uncover why some succeed and others fail. The model species of this project is the sea snail rough periwinkle (Littorina saxatilis). These findings will improve biodiversity conservation and guide policy to address global biodiversity loss. The project is supported by European Union – NextGenerationEU.
Team: Andrea Benazzo (Co-Coordinator), Beatrice Sammarco, Roberto Biello
External team members: Francesca Raffini (Coordinator, SZN), David Carmelet-Rescan (SZN)
For more information visit the website of the project at: https://raffinifrancescalab.weebly.com/
Lupin bean (PRIN 2022)
Starting: 2023 – Ending: 2025
This projects scope is to reconstruct the pangenome of the white lupin (Lupinus albus) as a mean to better represent the genetic landscape for this agronomically important species for both animal and human consumption. In particular, besides some preliminary population genetics analyses aimed at determining the genetic diversity for this species (in terms of small and structural variants) and at identifying the genetic variation "artificially" selected during the domestication process, another important contribution will be to infer the underlying demographic events leading to modern-day cultivar species — through the same domestication process aimed at selecting specific genes (or genetic regions) with relevant, functional impact on desirable agronomic traits. The latter will be carried out ...
Team: Andrea Benazzo, Matteo Ungaro
External team members: Umberto Rosani (Co-coordinator, Unipd), Enrico Bortoletto (Co-ccordinator, Unipd), Elena Bitocchi (Co-coordinator, Univpm), Karolina Susek (Co-coordinator, Polish Academy of Sciences), Magdalena Korc (Polish Academy of Sciences)
Ancient genomes reveal early Andean farmers selected common bean
During domestication, the selection made by farmers on crops for desired traits implied a demographic contraction of the original wild population(s), and that led to genomic erosion. As a result, modern cultivars are highly susceptible to pathogens, pests and environmental change. Using both ancient and modern seeds of the common bean (Phaseolus vulgaris) in the southern Andes, we showed that only during the past few centuries an intensified round of selection led to genomic erosion in the modern cultivars compared with the ancient Andean landraces.
Genomic susceptibility to extinction: a whole-genome approach to study and protect endangered Italian endemics (ENDEMIXIT)
Using five Italian iconic endangered endemics as model species (a mammal, a reptile, an amphibian, a fish, and an insect) this conservation genomics project had the major goal to understand the dynamics of the accumulation of deleterious mutations in small populations, and its impact on individual fitness and extinction risks. We also aimed at increasing public awareness about biodiversity erosion and innovative molecular tools to prevent it.
For more information visit: www.endemixit.com
Geographic assignment of samples of unknown origin from the terrestrial tortoise Testudo hermanni
We developed two tools for mapping the geographic origin of Hermann's tortoises focusing on major genetic clusters corresponding to geographic macro-areas: first we tested a panel of 7 microsatellite markers (STRs) and assigned approximately 70% of confiscated individuals to these areas. Building on this, we developed and validated a more cost-effective panel of 48 single nucleotide polymorphisms (SNPs) for the same species, demonstrating that the SNPs provided finer genetic structure than the previously used STRs and allowed for geographic assignment at low cost (less than €15 per sample).
Hybridization in sea turtles
This study aimed to reconstruct past hybridization events and changes in population size among sea turtles to better understand their evolutionary history and inform conservation strategies. Whole genome data revealed widespread historical hybridization and long-term gene flow among species, along with a general decline in effective population sizes—except for the leatherback turtle—highlighting that hybridization may be a natural part of sea turtle evolution.
For more information visit: https://cordis.europa.eu/project/id/844756
Relaxation of natural selection in the evolution of the giant lungfish genomes
Nonadaptive hypotheses on the evolution of eukaryotic genome size predict an expansion when purifying selection is weaker. By studying lungfish genomes and transcriptomes we identified signature of relaxation of selection, and we propose that the largest known animal genomes evolved in a nearly neutral scenario whereby genome expansion is less efficiently constrained.
Unravelling the mystery of endemic versus translocated populations of the endangered Australian lungfish
This study investigated the genetic history of the endangered Australian lungfish to determine whether current populations are endemic or influenced by past translocation events. Using three types of genetic markers and approximate Bayesian computation, we found that the most supported model indicates both endemic and translocated gene pools coexist in the Brisbane and North Pine Rivers. These findings highlight the value of genetic modeling in understanding species history and guiding conservation strategies.