Biology subjects

Chiocchio, A.

Publications and source records attributed to Chiocchio, A..

15 recordsLinked to original sources

bioRxiv2026

Fiat lux: A hotspot of Luciola fireflies on Western Mediterranean islands

O_LIIslands are priority areas for the study and conservation of biodiversity, as they frequently harbour distinct lineages. Yet they are particularly threatened by the global change. In the frame of an accelerated biodiversity crisis, many insular species risk disappearing before they are even discovered. C_LIO_LIFireflies, despite their ecological and cultural significance, remain poorly investigated, especially in temperate regions, where they have shown marked decline over the last decades. C_LIO_LIWe investigated firefly diversity across a Mediterranean biodiversity hotspot by genotyping 114 fireflies of the genus Luciola from 29 locations across the Tuscan Archipelago and the adjacent Italian peninsula and applied phylogenetic and species delimitation methods to characterise genetic differentiation and its geographic structure. C_LIO_LIWe found an unexpectedly high level of genetic differentiation in this area. Phylogenetic inference recovered six deeply divergent and geographically structured mitochondrial lineages: three restricted to Elba Island and three to the Italian Peninsula. Genetic divergence among these lineages ranged from 1.97% to 4.58%, values comparable to or exceeding those typically observed among distinct species. Accordingly, species delimitation methods consistently supported their status as distinct species. C_LIO_LIThe coexistence of three divergent lineages on Elba Island suggests a biogeographic scenario characterised by ancient island colonisations and possible in situ diversification. These findings reveal a previously unrecognised depth of evolutionary diversity in Italian fireflies and identify the Tuscan Archipelago as a priority area for future research on firefly evolution and conservation, emphasizing that fireflies are a major gap in our knowledge of insect biodiversity in Europe. C_LI

ecology↗

bioRxiv2022

Behavioural foundation of a massive mitochondrial introgression in the fire salamander, Salamandra salamandra

Patterns of mito-nuclear discordance across secondary contact zones have been reported in a wide range of animal and plant organisms. They consist of a spatial mismatch between nuclear and mitochondrial genomes, in terms of the geographic location and/or extension of the secondary contact zone between distinct evolutionary lineages. Several theoretical and empirical studies have identified massive mitochondrial introgression as the putative source of these mismatches. Yet, we still lack a clear understanding of the potential phenotypic underpinnings of these instances of massive introgression. In this study, we addressed the hypothesis that mtDNA variation across a contact zone could be associated with variation at phenotypic traits affecting dispersal propensity. We analyzed patterns of behavioural and genetic variation across a mtDNA secondary contact zone of the fire salamander Salamandra salamandra in central Italy, which is over 600 km displaced from its nuclear counterpart. We found distinct behavioral profiles associated with the two mitotypes co-occurring in the mtDNA secondary contact zone. Counterintuitively, we found a slow-thorough dispersal profile associated with the massively introgressed mitotype. This dispersal profile was characterized by shy, less active and less exploratory personality traits, and this pattern was consistent across life-stages and contexts (i.e., aquatic larvae and terrestrial juveniles). Our results provide experimental evidence supporting the intriguing hypothesis that personality traits associated with distinct mitotypes could promote differential mitochondrial introgression within alternative nuclear backgrounds.

evolutionary biology↗

bioRxiv2022

Brain de novo transcriptome assembly of a toad species showing polymorphic anti-predatory behavior

Understanding the genomic underpinnings of antipredatory behaviors is a hot topic in eco-evolutionary research. Yellow-bellied toad of the genus Bombina are textbook examples of the deimatic display, a time-structured behavior aimed at startling predators. Here, we generated the first de novo brain transcriptome of the Apennine yellow-bellied toad Bombina pachypus, a species showing inter-individual variation in the deimatic display. Through Rna-Seq experiments on a set of individuals showing distinct behavioral phenotypes, we generated 316,329,573 reads, which were assembled and annotated. The high-quality assembly was confirmed by assembly validators and by aligning the contigs against the de novo transcriptome with a mapping percentage higher than 91.0%. The homology annotation with DIAMOND (blastx) led to 77,391 contigs annotated on Nr, Swiss Prot and TrEMBL, whereas the domain and site protein prediction made with InterProScan led to 4747 GO-annotated and 1025 KEGG-annotated contigs. The B. pachypus transcriptome described here will be a valuable resource for further studies on the genomic underpinnings of behavioral variation in amphibians.

evolutionary biology↗

bioRxiv2022

Spatial differentiation of background matching strategies along a Late Pleistocene range expansion route

Late Pleistocene climate changes have deeply impacted the range dynamics of temperate species. While the genetic legacy of these dynamics has been widely investigated, little is known about their phenotypic consequences. Anti-predatory strategies offer intriguing opportunities to study phenotypic evolution in response to dispersal dynamics since the ability to avoid predation can be pivotal for populations colonizing new environments. Here we investigated the spatial differentiation of background colour matching strategies along a Late Pleistocene range expansion route of a temperate species, the Tyrrhenian tree frog Hyla sarda. Using common-garden experiments, we investigated whether individuals sampled in the source area (Sardinia) and individuals sampled in the newly founded area (Corsica) differ in two components of the camouflage strategy: colour change abilities and background choice behaviour. We found a remarkable spatial structure in both colour change abilities and background choice behaviour, across the expansion range. Tree frogs from the source area displayed higher colour change abilities and a more pronounced preference for a greener background, with respect to tree frogs from the newly colonized area. We discuss these results in the context of the spatial and demographic components of the expansion dynamics. Our results support the intriguing hypothesis that Late Pleistocene biogeographic history might be an overlooked major player in shaping current spatial patterns of phenotypic traits variation across animal populations.

evolutionary biology↗

bioRxiv2022

First brain de-novo transcriptome of Tyrrenhian tree frog, Hyla sarda, for the study of dispersal-related behavioral variation

Dispersal is a key process in ecology and evolution as it contributes to shaping the spatial patterns of biological diversity at all its levels of organization. Growing evidence is unveiling the role of phenotypic trait variation in affecting dispersal dynamics of populations, and that substantial, rapid, and directional changes in the phenotypic makeup of populations would occur during range expansions by spatial sorting of dispersal-related traits. Accordingly, selective pressures at the front of a range expansion wave would actively promote individuals with higher dispersal abilities. Although many studies have been focusing on phenotypic trait evolution during range expansion, its genomic underpinnings are almost unexplored, hampering a thorough understanding of the evolutionary processes involved during dispersal. The Tyrrhenian tree frog Hyla sarda is a small amphibian endemic to the Tyrrhenian islands. According to previous phylogeographic studies, H. sarda underwent a northward range expansion from the north of Sardinia (western Mediterranean sea) during the last glacial phase. The colonization of the Corsica island was allowed by the temporary formation of a wide land bridge connecting Sardinia and Corsica, induced by the marine regression occurred during the last glacial maximum. The postglacial loss of this land bridge prevented any subsequent gene flow between Corsican and Sardinian populations. As a consequence, the genetic and phenotypic legacies of this range expansion event can still be detected in current populations, which makes H. sarda an interesting candidate species for the study of the genetic underpinnings of phenotypic trait evolution during range expansions. Here, we contribute to the investigation of the genetic underpinning phenotypic trait evolution during range expansion, by generating the first brain de-novo transcriptome of H. sarda. We focused on the brain transcriptome as behavioural variation at personality traits has been identified as a key component of the dispersal syndromes, substantial personality traits variation has been observed within H. sarda populations, and brain gene expression patterns have been linked to a vast number of behavioural responses to environmental stimuli.

evolutionary biology↗

bioRxiv2022

Evolution of personality and locomotory performance traits during a late Pleistocene island colonization in a treefrog

Recent empirical and theoretical studies suggest that personality and locomotory performance traits are crucial components of the dispersal syndromes, and that they can evolve during a dispersal process. Island colonisation is one the best characterized processes in dispersal biogeography, and its implication in the evolution of phenotypic traits has been investigated over a wide range of temporal scales. However, the effect of island colonization on personality and performance traits of natural populations has been little explored, and no studies have addressed these processes in the context of late-Pleistocene range expansions. Here, we investigated the contribution of island colonisations triggered by post-glacial range expansions to intraspecific variation in personality and locomotory performance traits. We compared boldness, exploration, jumping performance, and stickiness abilities, in three equidistant populations of the Tyrrhenian tree frog Hyla sarda, two from the source area and one from the colonised island. Individuals from the colonised population were significantly bolder than individuals from the source area, as they emerged sooner from a shelter (p=0.028), while individuals from the source area showed markedly higher jumping and stickiness performance (both p<0.001). We discuss these results in the context of the major microevolutionary processes at play during range expansion, including selection, spatial sorting, and founder effects. However, irrespective of the processes contributing the most, our results clearly indicate that late Pleistocene climatic changes have had major consequences not just on species range dynamics, but also on the spatial patterns of phenotypic variation within species, including personality and locomotory traits variation.

evolutionary biology↗

bioRxiv2022

Shock or jump: deimatic behaviour is repeatable and polymorphic in a yellow-bellied toad

Inter-individual variation in antipredatory strategies has long attracted curiosity among scientists. Deimatisms is a complex and time-structured antipredatory strategy consisting in prey suddenly unleashing unexpected defences to frighten predators and stop their attack. Being deimatism traditionally considered as a stereotyped antipredatory response, the inter-individual variation in phenotypic traits related to deimatic displays is almost unexplored. In this study, we employed common garden experiments on 71 yellow-bellied toad Bombina pachypus to investigate the extent and pattern of inter-individual variation in the unken-reflex behaviour, a deimatic display performed by some amphibians. Results show that deimatic displays consistently differ among individuals. Only about half of the individuals reacted to the predation stimuli by exhibiting the display, which varied in responsiveness, duration and intensity. All the investigated descriptors were repeatable (R > 0.50, p < 0.01). Finally, we found significant correlations between the measured parameters, defining two alternative behavioural profiles: individuals quickly doing unken-reflex, with high intensity and long duration of the display, and individuals avoiding unken-reflex but rather escaping. Such dichotomy resembles respectively the proactive and reactive coping styles. Such an unexpected variation in deimatic behaviour raises intriguing questions on the evolutionary processes shaping multiple adaptive responses to predation within populations.

ecology↗

bioRxiv2021

From STRs to SNPs via ddRAD-seq: geographic assignment of confiscated tortoises at reduced costs

Assigning individuals to their source populations is crucial for conservation research, especially for endangered species threatened by illegal trade and translocations. Genetic assignment can be achieved with different types of molecular markers, but technical advantages and cost saving are recently promoting the shift from short tandem repeats (STRs) to single nucleotide polymorphisms (SNPs). Here, we designed, developed, and tested a small panel of SNPs for cost-effective geographic assignment of individuals with unknown origin of the endangered Mediterranean tortoise Testudo hermanni. We started by performing a ddRAD-seq experiment on 70 wild individuals of T. hermanni from 38 locations. Results obtained using 3,182 SNPs are comparable to those previously obtained using STR markers in terms of genetic structure and power to identify the macro-area of origin. However, our SNPs revealed further insights into the substructure in Western populations, especially in Southern Italy. A small panel of highly informative SNPs was then selected and tested by genotyping 190 individuals using the KASP genotyping chemistry. All the samples from wild populations of known geographic origin were genetically re-assigned with high accuracy to the original population. This reduced SNPs panel represents an efficient molecular tool that enables individuals to be genotyped at low cost (less than {euro}15 per sample) for geographical assignment and identification of hybrids. This information is crucial for the management in-situ of confiscated animals and their possible re-allocation in the wild. Our methodological pipeline can easily be extended to other species.

genomics↗

bioRxiv2021

The unresolved phylogenomic tree of butterflies and moths (Lepidoptera): assessing the potential causes and consequences

The field of molecular phylogenetics is being revolutionised with next-generation sequencing technologies making it possible to sequence large numbers of genomes for non-model organisms ushering us into the era of phylogenomics. The current challenge is no longer how to get enough data, but rather how to analyse the data and how to assess the support for the inferred phylogeny. We focus on one of the largest animal groups on the planet - butterflies and moths (order Lepidoptera). We clearly demonstrate that there are unresolved issues in the inferred phylogenetic relationships of the major lineages, despite several recent phylogenomic studies of the group. We assess the potential causes and consequences of the conflicting phylogenetic hypotheses. With a dataset consisting of 331 protein-coding genes and the alignment length over 290 000 base pairs, including 200 taxa representing 81% of lepidopteran superfamilies, we compare phylogenetic hypotheses inferred from amino acid and nucleotide alignments. The resulting two phylogenies are discordant, especially with respect to the placement of the superfamily Gelechioidea, which is likely due to compositional bias of both the nucleotide and amino acid sequences. With a series of analyses, we dissect our dataset and demonstrate that there is sufficient phylogenetic signal to resolve much of the lepidopteran tree of life. Overall, the results from the nucleotide alignment are more robust to the various perturbations of the data that we carried out. However, the lack of support for much of the backbone within Ditrysia makes the current butterfly and moth tree of life still unresolved. We conclude that taxon sampling remains an issue even in phylogenomic analyses, and recommend that poorly sampled highly diverse groups, such as Gelechioidea in Lepidoptera, should receive extra attention in the future.

evolutionary biology↗

bioRxiv2020

Paso doble: A two-step Late Pleistocene range expansion in the Tyrrhenian tree frog Hyla sarda

The Tyrrhenian tree frog, Hyla sarda, is an amphibian endemic to the Tyrrhenian islands (Western Mediterranean). Previous investigations of its Pleistocene evolutionary history suggested that it colonised the northern portion of its current range, through a spatial diffusion process from the Sardinia island, during the last glaciation. However, southern and northern portions of the species range experienced markedly different climatic conditions during the Late Pleistocene, suggesting the possibility of an unusual two-step process of demographic expansion. Here, we use Bayesian phylogeographic approaches to locate the ancestral area in Sardinia and to characterise better the demographic component of this expansion event. These analyses located the ancestral area for H. sarda populations along the central-eastern coast of the Sardinia island, within an area previously shown to host suitable bioclimatic conditions for H. sarda populations throughout the Late Pleistocene. Historical demographic reconstructions clearly showed that a two-step process of demographic growth fits well the data, with northern populations expanding later than Sardinia populations. The harsher climatic conditions occurred in northern islands during the glacial epoch, as compared to Sardinia, likely delayed tree frog colonisation of northern territories, and the associated demographic growth.

evolutionary biology↗

bioRxiv2019

Unveiling cryptic diversity among Mullerian co-mimics: insights from the Western Palaearctic Syntomis moths (Lepidoptera: Erebidae)

Accurate species delimitation is of primary importance in biodiversity assessments and in reconstructing patterns and processes in the diversification of life. However, the discovery of cryptic species in virtually all taxonomic groups unveiled major gaps in our knowledge of biodiversity. Mimicry complexes are good candidates to source for cryptic species. Indeed, members of mimicry complexes undergo selective pressures on their habitus, which results in strong resemblance between both distantly and closely related species. In this study, we used a multi-locus genetic approach to investigate the presence of cryptic diversity within a group of mimetic day-flying moths whose systematics has long been controversial, the Euro-Anatolian Syntomis. Results showed incongruence between species boundaries and currently accepted taxonomy of the group. Both mitochondrial and nuclear markers indicate presence of four, well-distinct genetic lineages. The genetic distance and time of divergence between the Balkan and Italian populations of S. marjana are the same as those found between S. phegea and S. ragazzii, the last two being well-distinct, broadly sympatrically occurring species. The divergence between the two lineages of S. marjana dates back to the Early Pleistocene, which coincided with substantial changes in climatic conditions and vegetation cover in Southern Europe that have likely induced geographic and ecological vicariance. Our results show that the species richness of mimicry complexes inhabiting temperate regions might still be severely underestimated. Syntomis populations up to now designated as S. marjana albionica, S. m. quercii and S. marjana kruegeri s. str. are here considered to represent a separate species from nominate marjana and are distinguished as Syntomis quercii Verity, 1914, bona sp., stat. nov.

zoology↗

bioRxiv2018

Population genetic structure of the bank vole Myodes glareolus within its glacial refugium in peninsular Italy

It is now well established that Southern European peninsulas have been major glacial refugia for temperate species during Pleistocene climatic oscillations. However, substantial environmental changes occurred also within these peninsulas throughout the Pleistocene, rising questions about the role and interplay of various of micro-evolutionary processes in shaping patterns of intraspecific diversity within these areas. Here, we investigate the patterns of genetic variation in the bank vole Myodes glareolus within the Italian peninsula. By using a panel of 13 microsatellite loci, we found more intra-specific variation than expected based on previous assessments. Indeed, both Bayesian and ordination-based clustering analyses of variation recovered five main geographic/genetic clusters along the peninsula, with three clusters geographically restricted to the southern portion of the study area. This pattern supports the occurrence of multiple sub-refugia for the bank vole in peninsular Italy, likely promoted by the major paleo-environmental changes which affected forested habitats within this area during the Pleistocene. Thus, our results support a scenario whereby the high levels of intraspecific diversity observed within major glacial refugia are better explained by dynamic micro-evolutionary processes occurred within these areas, rather than by long-term demographic stability of refugial population. Finally, the narrow and isolated distribution of some of the identified lineages, suggest the need for future assessments of their conservation and taxonomic status.

evolutionary biology↗

bioRxiv2018

Drilling down hotspots of intraspecific diversity to bring them into on-ground conservation of threatened species

Unprecedented rates of biodiversity loss rise the urgency for preserving species ability to cope with ongoing global changes. An approach in this direction is to target intra-specific hotspots of genetic diversity as conservation priorities. However, these hotspots are often identified by sampling at a spatial resolution too coarse to be useful in practical management of threatened species, hindering the long-appealed dialog between conservation stakeholders and conservation genetic researchers. Here, we investigated the spatial and temporal variation in species presence, genetic diversity, as well as potential risk factors, within a previously identified hotspot of genetic diversity for the endangered Apennine yellow bellied toad Bombina pachypus. Our results show that this hotspot is neither a geographically homogeneous nor a temporally stable unit. Over a time-window spanning 10-40 years since previous assessments, B. pachypus populations declined in large portions of its hotspot, and their genetic diversity levels decreased. Considering the demographic trend, genetic and epidemiological data, and models of current and future climatic suitability, populations at the extreme south of the hotspot area still qualify for urgent in-situ conservation actions, whereas northern populations would be better managed through a mix of in-situ and ex-situ actions. Our results emphasize that identifying hotspot of genetic diversity, albeit essential step, does not suffice to warrant on-ground conservation of threatened species. Hotspots should be analysed at finer geographic and temporal scales, to provide conservation stakeholders with key knowledge to best define conservation priorities, and to optimize resource allocation to alternative management practices.

evolutionary biology↗

bioRxiv2017

Forest Dormouse (Dryomys nitedula) populations in southern Italy belong to a deeply divergent evolutionary lineage

The Forest Dormouse (Dryomys nitedula) is a small rodent with a wide, albeit severely fragmented distribution, ranging from central Europe to central Asia. Within the Italian region, D. nitedula populations are restricted to forested mountain areas of two largely disconnected regions, the eastern Alps and the Calabria region, where two distinct subspecies (D. nitedula intermedius and D. nitedula aspromontis, respectively) have been described on the basis of phenotypic characters (i.e., fur colour). Here we analysed D. nitedula samples from both regions, to investigate patterns of genetic divergence and phylogenetic relationship among these two populations. Genetic variation was studied at the level of one mitochondrial (cytochrome b gene) and three nuclear gene fragments (exon1 of the interstitial retinoid-binding protein, exon 10 of the growth hormone receptor, and recombination activating gene 1). Phylogenetic analyses were performed using Maximum Likelihood and Bayesian inference methods. D. n. aspromontis and D. n. intermedius were found to be reciprocally monophyletic in all the phylogenetic analyses, and the genetic divergence observed between them at the mitochondrial CYTB gene was conspicuous (HKY: 0.044) when compared to previously observed values among many sister species of rodents. Our results clearly show that D. nitedula aspromontis is a deeply divergent, narrow endemic evolutionary lineage, and its conservation needs should be carefully evaluated in the near future. Moreover, such deep genetic divergence, together with phenotypic differentiation between D. n. intermedius and D. n. aspromontis, suggest that D. nitedula populations in southern Italy might belong to a distinct, previously unrecognized species.

evolutionary biology↗

bioRxiv2016

Climate change promotes hybridisation between deeply divergent species of European toads

Rare hybridisations between deeply divergent animal species have been reported for decades in a wide range of taxa, but have often remained unexplained, mainly considered chance events and reported as anecdotal. Here, we combine field observations with long-term data concerning natural hybridizations, climate, land-use, and field-validated species distribution models for two deeply divergent and naturally sympatric toad species in Europe (Bufo bufo and Bufotes viridis species groups). We show that climate warming and seasonal extreme temperatures are conspiring to set the scene for these maladaptive hybridisations, by differentially affecting life-history traits of both species. Our results identify and provide evidence of an ultimate cause for such events, and reveal that the potential influence of climate change on interspecific hybridisations goes far beyond closely related species. Furthermore, climate projections suggest that the chances for these events will steadily increase in the near future.

evolutionary biology↗