I am broadly interested in natural sciences, particularly biology.
My research experience has revolved around understanding how biological and environmental processes within and among populations or species produce biodiversity and adaptations, and how to preserve them.
My research experience has revolved around understanding how biological and environmental processes within and among populations or species produce biodiversity and adaptations, and how to preserve them.
| Francesca_Raffini_résumé.pdf |
Genomic susceptibility to extinction: a whole-genome approach to study and protect endangered Italian endemics
Small, declining populations are prone to extinction due to inbreeding, genetic drift and reduced evolutionary potential (extinction vortex). This phenomenon is particularly threatening for endemic species, which represent a unique, unrepeatable biological heritage. Italy is a biodiversity hotspot hosting 35% of the species included in the European IUCN Red List and is particularly rich of such endangered endemics. Extinction risk can be reduced by developing conservation strategies that prevent genetic erosion; this approach requires a detailed knowledge of genetic variation and its consequences. To this aim, we focus on five iconic Italian endemics that are endangered and require urgent actions according to the IUCN: the Apennine brown bear, Aeolian wall lizard, Apennine yellow-bellied toad, Adriatic sturgeon and Ponza grayling. In each of these species, we explore evolutionary dynamics in two populations of different sizes through advanced population genomic approaches. Whole genome (re)sequencing data is used to estimate their demographic histories, genomic diversity, genomic susceptibility to extinction due to mutation load and eligibility for genetic rescue. The effect of fixed deleterious mutations on cellular functions and individual fitness are analyzed using breeding and in vitro functional studies. Our insights will aid a proper management and conservation of these and other endangered species by informing effective interventions to face the ongoing biodiversity crisis. Furthermore, they expand our knowledge of evolutionary dynamics in small populations and, more broadly, the processes underlying biodiversity and adaptation.
Follow our updates in the ENDEMIXIT's website (click here)!
Small, declining populations are prone to extinction due to inbreeding, genetic drift and reduced evolutionary potential (extinction vortex). This phenomenon is particularly threatening for endemic species, which represent a unique, unrepeatable biological heritage. Italy is a biodiversity hotspot hosting 35% of the species included in the European IUCN Red List and is particularly rich of such endangered endemics. Extinction risk can be reduced by developing conservation strategies that prevent genetic erosion; this approach requires a detailed knowledge of genetic variation and its consequences. To this aim, we focus on five iconic Italian endemics that are endangered and require urgent actions according to the IUCN: the Apennine brown bear, Aeolian wall lizard, Apennine yellow-bellied toad, Adriatic sturgeon and Ponza grayling. In each of these species, we explore evolutionary dynamics in two populations of different sizes through advanced population genomic approaches. Whole genome (re)sequencing data is used to estimate their demographic histories, genomic diversity, genomic susceptibility to extinction due to mutation load and eligibility for genetic rescue. The effect of fixed deleterious mutations on cellular functions and individual fitness are analyzed using breeding and in vitro functional studies. Our insights will aid a proper management and conservation of these and other endangered species by informing effective interventions to face the ongoing biodiversity crisis. Furthermore, they expand our knowledge of evolutionary dynamics in small populations and, more broadly, the processes underlying biodiversity and adaptation.
Follow our updates in the ENDEMIXIT's website (click here)!
Insights from hybrid zones: the repeated evolution of barriers to gene flow in Littorina
Adaptation and speciation are key processes that determine biological diversity and its distribution in space and time. Speciation requires the evolution of barriers to gene flow between diverging populations. The mechanisms underlying these processes are often unclear, particularly when they occur under gene flow. I aim to understand the factors enabling rapid divergence in the face of gene flow using the marine rough periwinkle Littorina, particularly L. saxatilis. This intertidal snail shows repeated adaptive divergence between two ecotypes associated with different rocky shore habitats: “crab”, inhabiting boulder fields exposed to crab predation, and “wave”, living on cliffs subjected to dislocation by wave. They are morphologically and behaviourally distinct and adapted to their specific micro-environment (crab/wave exposure), but hybridize in the contact zone, where the two habitats overlap. Hybrid zones are particularly useful to identify genomic loci under selection, clarify the relationship between phenotype, genotype, environment and fitness, and the mechanisms underlying (adaptive) divergence. These findings contribute to shed light into the factors and interactions that promote speciation-with-gene-flow in nature.
Follow us in the Littorina Research Team's website (click here)!
Adaptation and speciation are key processes that determine biological diversity and its distribution in space and time. Speciation requires the evolution of barriers to gene flow between diverging populations. The mechanisms underlying these processes are often unclear, particularly when they occur under gene flow. I aim to understand the factors enabling rapid divergence in the face of gene flow using the marine rough periwinkle Littorina, particularly L. saxatilis. This intertidal snail shows repeated adaptive divergence between two ecotypes associated with different rocky shore habitats: “crab”, inhabiting boulder fields exposed to crab predation, and “wave”, living on cliffs subjected to dislocation by wave. They are morphologically and behaviourally distinct and adapted to their specific micro-environment (crab/wave exposure), but hybridize in the contact zone, where the two habitats overlap. Hybrid zones are particularly useful to identify genomic loci under selection, clarify the relationship between phenotype, genotype, environment and fitness, and the mechanisms underlying (adaptive) divergence. These findings contribute to shed light into the factors and interactions that promote speciation-with-gene-flow in nature.
Follow us in the Littorina Research Team's website (click here)!
The origin and maintenance of biodiversity through the lens of cichlids and asymmetry
How the striking diversity of life forms and their adaptations to the environment they inhabit emerge and are maintained in natural populations are largely unaddressed questions. An outstanding natural system to uncover the processes underlying biodiversity and adaptation are cichlid fishes, famously known for their spectacular rapid adaptive radiation. In a relatively short timeframe, they have evolved an extraordinary phenotypic diversity reflecting adaptations to often very narrow niches. Cichlids also comprise notable cases of stable polymorphisms, such as mouth asymmetry in the scale-eating cichlid fish Perissodus microlepis from Lake Tanganyika. Here, individuals with left- and right-bending mouth are found in sympatry in approximately equal frequencies. This morphological asymmetry is accompanied by lateralized foraging behavior: left individuals preferentially feed on the scales of the right side of its prey fish, and the opposite is true for the right morph. Using a set of multidisciplinary methods, the aim is to uncover the genetic and environmental (i.e. not genetic) mechanisms underlying asymmetry and intra-specific variation in P. microlepis. This study contributes to our understanding of why cichlids are so diverse and how evolution has produced and continues generating such a spectacular and often complex diversity.
How the striking diversity of life forms and their adaptations to the environment they inhabit emerge and are maintained in natural populations are largely unaddressed questions. An outstanding natural system to uncover the processes underlying biodiversity and adaptation are cichlid fishes, famously known for their spectacular rapid adaptive radiation. In a relatively short timeframe, they have evolved an extraordinary phenotypic diversity reflecting adaptations to often very narrow niches. Cichlids also comprise notable cases of stable polymorphisms, such as mouth asymmetry in the scale-eating cichlid fish Perissodus microlepis from Lake Tanganyika. Here, individuals with left- and right-bending mouth are found in sympatry in approximately equal frequencies. This morphological asymmetry is accompanied by lateralized foraging behavior: left individuals preferentially feed on the scales of the right side of its prey fish, and the opposite is true for the right morph. Using a set of multidisciplinary methods, the aim is to uncover the genetic and environmental (i.e. not genetic) mechanisms underlying asymmetry and intra-specific variation in P. microlepis. This study contributes to our understanding of why cichlids are so diverse and how evolution has produced and continues generating such a spectacular and often complex diversity.
Repeated sympatric speciation in Neotropical cichlid fishes
What are the processes driving the evolution of new species from an ancestral one (i.e. speciation) while inhabiting the same location (i.e. in sympatry)? Why did some cichlid lineages in the Nicaraguan crater lakes originate new species in sympatry (such as Midas fishes) while others did not (as Archocentrus centrarchus)? I am also interested in the repeated evolution of similar body shapes in two sympatric species pairs of Midas cichlid fishes. The focus of this study is the genetic basis of body shape differences and the effects of this trait on swimming performances, a measure of fish fitness. Since body shape is a putatively adaptive trait, this project will shed light on one of the most persistent debates in the field of evolutionary biology, i.e. how species diverge in absence of evident isolation, and which are the mechanisms enabling adaptation and evolution.
What are the processes driving the evolution of new species from an ancestral one (i.e. speciation) while inhabiting the same location (i.e. in sympatry)? Why did some cichlid lineages in the Nicaraguan crater lakes originate new species in sympatry (such as Midas fishes) while others did not (as Archocentrus centrarchus)? I am also interested in the repeated evolution of similar body shapes in two sympatric species pairs of Midas cichlid fishes. The focus of this study is the genetic basis of body shape differences and the effects of this trait on swimming performances, a measure of fish fitness. Since body shape is a putatively adaptive trait, this project will shed light on one of the most persistent debates in the field of evolutionary biology, i.e. how species diverge in absence of evident isolation, and which are the mechanisms enabling adaptation and evolution.
Shared barriers to gene flow in marine invertebrates
What are the biological and abiotic factors affecting distribution, diversity and connectivity in Italian marine species and populations? Integrating genetic and ecological data of multiple invertebrate species at diverse geographical scales, this project greatly improves the previously scarce knowledge on connectivity and gene flow in the Italian area. This information provides a baseline for proper coastal planning and marine protected areas (MPAs) network implementation, as urgently required for the Integrated Coastal Zone Management (EU Water Framework Directive 2000) for a “ecosystem-based” management of the European shores.
What are the biological and abiotic factors affecting distribution, diversity and connectivity in Italian marine species and populations? Integrating genetic and ecological data of multiple invertebrate species at diverse geographical scales, this project greatly improves the previously scarce knowledge on connectivity and gene flow in the Italian area. This information provides a baseline for proper coastal planning and marine protected areas (MPAs) network implementation, as urgently required for the Integrated Coastal Zone Management (EU Water Framework Directive 2000) for a “ecosystem-based” management of the European shores.
Conservation genetics of a crucial marine fishery resource
Fishery genetics have greatly changed our understanding of population dynamics and structuring in marine fish. This study focuses on the Mediterranean Bluefin tuna (Thunnus thynnus), an ecologically and economically important species that has been severely impacted by overfishing. Information on population dynamics, genetic structuring and levels of genetic diversity in this fish is still scarce yet it is crucial for both stock management and conservation of marine ecosystems dominated by this apex predator. To fill this gap, I compare genetic and demographic variation across the Mediterranean Sea. These results provide accurate estimates of genetic variation in the Mediterranean populations, and suggest strategies for stock management and conservation of evolutionary potential in this severely exploited fishery resource.
Fishery genetics have greatly changed our understanding of population dynamics and structuring in marine fish. This study focuses on the Mediterranean Bluefin tuna (Thunnus thynnus), an ecologically and economically important species that has been severely impacted by overfishing. Information on population dynamics, genetic structuring and levels of genetic diversity in this fish is still scarce yet it is crucial for both stock management and conservation of marine ecosystems dominated by this apex predator. To fill this gap, I compare genetic and demographic variation across the Mediterranean Sea. These results provide accurate estimates of genetic variation in the Mediterranean populations, and suggest strategies for stock management and conservation of evolutionary potential in this severely exploited fishery resource.
