Preparedness to fight an averted, yet possible next "Disease X" pandemics would require many actions along different dimensions. The WHO One Health framework has strongly highlighted the major threat posed by zoonotic infectious diseases - transmitted from animal to human hosts - and the necessity to reduce their risk of disease spillover and spread. An integrated framework that envisions all the ecological actors involved in the transmission cycle can inform policies to efficiently act well before the next “Disease X” pandemic event. Here, we target a set of zoonotic viruses brought to attention by the WHO, with critical epidemic potential and lacking effective countermeasures. Based on a performed review of almost 500 papers, we identify a taxonomy of prototypical models describing the local-scale spatiotemporal transmission of the target pathogens. The comprehensive approach of the analysis can provide relevant insights into the yet-unknown identity of Disease X: one of the target viruses, a related virus emerging from one of the target viral families, or -more generally - one of these viruses that evolves the ability to transmit in a new way or in an alternative host in unaffected and unprepared locations. We show the substantial differences that exist among diseases with distinct epidemiological characteristics and highlight the relative importance of the wildlife compartment for both human infection and viral maintenance. Specifically, we distinguish between viruses that can sporadically spill from animal hosts but then mainly circulate in humans (e.g. SARS-CoV1), viruses that efficiently co-circulate in humans and animals (e.g. LASV), and viruses for which humans are merely the dead-end host of a predominantly animal chain (e.g. RVF). This review serves a twofold objective: it represents an essential component for further modelling developments and provides a clear overview of the intrinsic benefits of simultaneously safeguarding human and environmental health.

The leopard (Panthera pardus spp.) is a generalist species that originated in Africa and dispersed into Eurasia between 400 and 600 thousand years ago. It is commonly subdivided into one African and eight Asian subspecies, roughly corresponding to the geographic areas each of them inhabits.

It is still unclear if such categorisation also reflects an ecological differentiation of leopards across different parts of their range. Here, we use species distribution modelling/habitat suitability modelling to compare the niches of leopard subspecies. Our aim is to investigate how the species’ niche varies across its entire range and provide insight into the role of local adaptation and niche shift in its range expansion.

Our results support a general lack of niche separation between all subspecies. Most Asian subspecies have overlapping niches and occupy subsets of the African leopard's niche. Nevertheless, we found the Persian leopard, Panthera pardus saxicolor, to have the most distinct niche, giving some evidence for niche expansion in more Northern Asian subspecies.

We suggest little ecological differentiation among leopard subspecies and a lack of adaptation to novel climates after dispersal from Africa. This finding complements recent genetic studies in implying that the taxonomy of Asian leopards may not reflect biological differentiation, an important issue to resolve due to its relevance for the conservation of the species.

Addressing how individual variation within populations drives the evolution of biodiversity patterns is a major challenge in ecology and evolutionary biology. Historical biogeographic processes have had dramatic consequences on the structure of biodiversity. However, while the interplay between historical processes and genotypic variation within populations has been widely investigated, the effects of such processes on phenotypic variation remain poorly explored. Here, we investigate whether dispersal-driven processes of historical biogeographic relevance, such as late Pleistocene range dynamics, have contributed to shape the geographic patterns of phenotypic trait variation. We focus on dispersal-related personality, morphological and performance traits in the Tyrrhenian tree frog, Hyla sarda, which underwent a northward range expansion from the Sardinia island to the Corsica island during the last Glacial Maximum, when a temporary land-bridge connected these islands. We collected tree frogs from four geographic areas along the past expansion route, controlling for altitude, local habitat effects, demographic factors, and bioclimatic differences between geographic areas. Then, we scored intraspecific variation in two personality traits, two performance traits, along with morphological traits likely involved in the dispersal process. Tree frogs from Corsica were more prudent in a novel environment, they had significantly larger body size, longer limbs, wider heads, and displayed stronger take-off and adhesion performances compared to individuals from the source area in Sardinia. Overall, these results may suggest a non-random spatial sorting of the intraspecific variation in multiple phenotypic traits during the range expansion phase. In turn, they also suggest that population differentiation in phenotypic traits associations might be a legacy of past biogeographic dynamics, identifying an overlooked driver of current patterns of intraspecific variation in phenotypic integration and opening intriguing evolutionary scenarios on the processes shaping the phenotypic architecture of animal populations.

Interspecific hybridization is an evolutionary process that plays a crucial role in shaping the spatial and temporal patterns of biodiversity. Studying these processes necessitates specialized molecular techniques for recognizing and monitoring genetic introgression. In this methodological presentation, we introduce a new class of markers currently being developed at the University of Padua.

Our approach employs intron-targeted amplicon sequencing to genotype Multi-locus Intron Polymorphisms (MIPs) and evaluate genetic diversity. These highly variable intron regions, thanks to the high transferability between species provided by the highly conserved flanking exon regions, constitute powerful multi-SNP markers (microhaplotypes), suitable for various applications, including species and hybrid identification and population comparisons, even without prior knowledge of the species. We present the first highly transferable panel of MIPs across fish genomes, seeking to examine the advantages and limitations of these markers and evaluating their characteristics in relation to other available markers. Additionally, the potential of this method, developed here on teleosts, to be applied to other taxa is anticipated by various preliminary results.

Cichlids are a species-rich family of teleost fishes renowned for their explosive phenotypic diversification, rapid adaptative radiation, and sympatric speciation. This makes them an ideal system to investigate the intricate interplay between ecological divergence and trait evolution, and to elucidate the genomic basis of adaptation. Hypertrophied lips, a trait associated with feeding variation, have convergently arisen in several cichlid adaptive radiations, including the Neotropical Midas cichlid species complex (Amphilophus spp.). These thick lip phenotypes play significant ecological roles, enhancing feeding efficiency and specialized foraging strategies, thereby promoting niche differentiation and resource exploitation. A functional trade-off in feeding behavior between thick- and normal-lipped ecotypes likely fuels divergence through disruptive selection.

By integrating analyses of quantitative trait loci (QTL), genome-wide association studies (GWAS), pangenomics, transcriptomics, and topological associating domain (TAD) detection, we aimed to characterize the molecular genetic bases of the hypertrophied lip phenotype in Midas cichlids. Unlike previous studies, our findings reveal that multiple loci contribute to variation in this trophic trait, including two loci with large effect sizes. We then identified several differentially expressed (DE) genes between fishes with thick and thin lips. Notably, several of these DE genes were regulated by microRNAs also found to be DE in the same comparison. Moreover, pangenome reconstructions based on 32 chromosome-level haplotype-resolved assemblies for 16 phenotypically and genetically diverse Midas cichlid individuals resolved several ecomorph-specific structural variants that co-localize with lip GWAS and QTL intervals. Lastly, we identified altered TADs in genomic regions harboring coincident structural variants, GWAS, and QTL.

Overall, our results suggest that variation in lip size – a possible driver of sympatric speciation – is due to a complex interplay of multiple genomic factors. By elucidating the genetic architecture behind this ecologically significant trait, our study provides new insights into the molecular mechanisms driving ecologically based adaptive divergence.