Biology subjects

Bertorelle, G.

Publications and source records attributed to Bertorelle, G..

12 recordsLinked to original sources

bioRxiv2026

Autozygosity and genetic load as sensitive early warnings of butterfly population decline

Insects are commonly expected to be protected from genomic erosion by high fecundity, short generation times, and large census sizes. Yet, insect populations can decline and eventually go extinct, underscoring the need for genomic indicators that provide actionable early warnings of population collapse. Here, we test this expectation by comparing contemporary and historical genomes of the Ponza grayling, Hipparchia sbordonii, an endangered butterfly endemic to the Pontine Islands in the Mediterranean, with the genomes of a widespread European congeneric species, H. semele. Using whole-genome resequencing, outgroup-based variant polarization, demographic reconstruction, runs of homozygosity, selection scans, and annotation-based genetic-load analyses, we show that H. sbordonii has undergone sustained demographic contraction, including a sharp recent decline. Despite limited temporal change in mean genome-wide heterozygosity, we observe extensive autozygosity, elevated inbreeding, and a clear shift from masked to realized genetic load in contemporary H. sbordonii. R'XY analysis revealed similar relative frequencies of high-impact derived variants in H. sbordonii and H. semele, suggesting ineffective purging during population collapse, whereas low- and moderate-impact variants were relatively enriched in H. sbordonii, particularly within candidate regions under selection. This indicates a more complex dynamic, in which functional variation has been shaped by the combined effects of drift, relaxed purifying selection, and possible local adaptation. Our study shows that declining butterfly populations bear distinctive signatures of genomic erosion, mirroring patterns well documented in vertebrates. Yet recent demographic collapse in H. sbordonii is more clearly captured by long runs of homozygosity and realized genetic load than by changes in mean genome-wide heterozygosity, highlighting their potential as early warning indicators for monitoring declining insect populations.

evolutionary biology↗

bioRxiv2026

The relationship between genomic variation and genetic load: insights from small island populations

Small populations face high extinction risks. This can be explained by several non-genetic and genetic factors, the latter including the loss of genetic diversity and evolutionary potential, as well as the accumulation of harmful mutations (genetic load). Using whole-genome data from island populations with different effective sizes, we estimated genetic variation and load and explored the relationship between these quantities. An extremely small population of the Aeolian wall lizard, Podarcis raffonei, likely isolated for tens of thousands of years, shows the lowest genome-wide heterozygosity observed in wild eukaryotes (one polymorphic site every 300 kb on average). Despite this, its realized genetic load is comparable to that observed in another larger and more genetically variable population. Both populations have lower variation and higher load than the much more abundant sister species, the Sicilian wall lizard. These observations are consistent with the hypothesis that populations experiencing severe bottlenecks may persist for extended periods with extremely low genomic variation, provided that their burden of deleterious mutations remains within tolerable bounds.

genomics↗

bioRxiv2025

Coexisting with humans: genomic and behavioural consequences in a small and isolated bear population

Climate and land use change have increased human-wildlife interactions, potentially reducing wild species density and prompting behavioural adaptations to urbanised environments. It is still debated if behavioural responses are mainly the result of phenotypic plasticity or if they were driven by anthropic selective pressures, especially in small populations. Our study focused on the Apennine brown bear population (Ursus arctos marsicanus), which has coexisted with humans in Central Italy for millennia. We characterised genomic diversity and identified adaptation signals distinctive to this population by comparing whole genome resequencing data across the Holarctic species range. We show that Apennine brown bears possess a unique genomic diversity pattern including selective signatures at genes associated with reduced aggressiveness, possibly involving alternative splicing mechanism. Our findings suggest that even in small and long-isolated populations, selection may shape behavioural traits. We hypothesise that human-induced selection has influenced these changes, reducing conflicts and contributing to the long-term persistence of the Apennine bear and its coexistence with humans.

genomics↗

bioRxiv2023

Gene expression is the main driver of purifying selection in large penguin populations

Purifying selection is the most pervasive type of selection, as it constantly removes deleterious mutations arising in populations, directly scaling with population size. Highly expressed genes appear to accumulate fewer deleterious mutations between divergent species lineages (known as E-R anticorrelation), pointing towards gene expression as an additional driver of purifying selection. However, estimates of the effect of gene expression on segregating deleterious variants in natural populations are scarce, as is an understanding of the relative contribution of population size and gene expression to purifying selection. Here, we analyse genomic and transcriptomic data from two natural populations of closely related sister species with different demographic histories, the Emperor penguin (Aptenodytes forsteri) and the King penguin (A. patagonicus), and show that purifying selection at the population-level depends on gene expression rate, resulting in very high selection coefficients at highly expressed genes. Leveraging realistic forward simulations, we estimate that the top 10% of the most highly expressed genes in a genome experience a selection pressure corresponding to an average selection coefficient of -0.1, which decreases to a selection coefficient of -0.01 for the top 50%. Gene expression rate can be regarded as a fundamental parameter of protein evolution in natural populations, maintaining selection effective even at small population size. We suggest it could be used as a proxy for gene selection coefficients, which are notoriously difficult to derive in non-model species under real-world conditions.

evolutionary biology↗

bioRxiv2023

Unravelling the mystery of endemic versus translocated populations of the endangered Australian lungfish (Neoceratodus forsteri)

The Australian lungfish is a primitive and endangered representative of the subclass Dipnoi. The distribution of this species is limited to south-east Queensland, with some populations considered endemic and others possibly descending from translocations in the late nineteenth century shortly after European discovery. Attempts to resolve the historical distribution for this species have met with conflicting results based on descriptive genetic studies. Understanding if all populations are endemic or some are the result of, or influenced by, translocation events, has implications for conservation management. In this work, we analysed the genetic variation at three types of markers (mtDNA genomes, 11 STRs, and 5,196 nuclear SNPs) using the Approximate Bayesian Computation algorithm to compare several demographic models. We postulated different contributions of Mary River and Burnett River gene pools into the Brisbane River and North Pine River populations, related to documented translocation events. We ran the analysis for each marker separately, and we also estimated the posterior probabilities of the models combining the markers. Nuclear SNPs have the highest power to correctly identify the true model amongst the simulated datasets (where the model was known), but different markers typically provided similar answers. The most supported demographic model able to explain the real dataset implies that an endemic gene pool is present in the Brisbane and North Pine Rivers where past translocations are documented. These results will inform ongoing conservation efforts for this endangered and iconic species and warrant careful consideration of future genetic management of the Australian lungfish populations.

evolutionary biology↗

bioRxiv2022

Evidence of backcross inviability and mitochondrial DNA paternal leakage in sea turtle hybrids

Hybridization is known to be part of many species evolutionary history. Sea turtles have a fascinating hybridization system in which species separated by as much as 43 million years are still capable of hybridizing. Indeed, the largest nesting populations in Brazil of loggerheads (Caretta caretta) and hawksbills (Eretmochelys imbricata) have a high incidence of hybrids between these two species. A third species, olive ridleys (Lepidochelys olivacea), is also known to hybridize although at a smaller scale. Here we used restriction site-associated DNA sequencing (RAD-Seq) markers, mitogenomes, and satellite-telemetry to investigate the patterns of hybridization and introgression in the Brazilian sea turtle population and their relationship with the migratory behaviors between feeding and nesting aggregations. We also explicitly test if the mixing of two divergent genomes in sea turtle hybrids causes mitochondrial paternal leakage. We developed a new species-specific PCR-assay capable of detecting mitochondrial DNA (mtDNA) inheritance from both parental species and performed ultra-deep sequencing to estimate the abundance of each mtDNA type. Our results show that all adult hybrids are first generation (F1) and most display a loggerhead migratory behavior. We detected paternal leakage in F1 hybrids and different proportions of mitochondria from maternal and paternal species. Although previous studies showed no significant fitness decrease in hatchlings, our results support genetically-related hybrid breakdown possibly caused by cytonuclear incompatibility. Further research on hybrids from other populations besides Brazil and between different species will show if backcross inviability and mitochondrial paternal leakage is observed across sea turtle species.

evolutionary biology↗

bioRxiv2022

Selection and adaptive introgression guided the complex evolutionary history of European common bean

Domesticated crops have been disseminated by humans over vast geographic areas. After 1492, the common bean (Phaseolus vulgaris L.) was introduced in Europe. Here, we combine whole-genome profiling, metabolic fingerprinting and phenotypic characterisation, and we show that the first common bean cultigens successfully introduced into Europe were of Andean origin, after Francisco Pizarros expedition to northern Peru in 1529. We show that hybridisation, selection and recombination have shaped the genomic diversity of the European common bean in parallel with political constraints. There is clear evidence of adaptive introgression into the Mesoamerican-derived European genotypes, with 44 Andean introgressed genomic segments shared by more than 90% of European accessions and distributed across all chromosomes except PvChr11. Genomic scans for signatures of selection highlight the role of genes relevant to flowering and environmental adaptation, suggesting that introgression has been crucial for the dissemination of this tropical crop to the temperate regions of Europe.

genomics↗

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↗

bioRxiv2020

Unveiling diffusion pattern and structural impact of the most invasive SARS-CoV-2 spike mutation

Starting in Wuhan, China, SARS-CoV-2 epidemics quickly propagated worldwide in less than three months, geographically sorting genomic variants in newly established propagules of infections. Stochasticity in transmission within and between countries and/or actual advantage in virus transmissibility could explain the high frequency reached by some genomic variants during the course of the outbreak. Using a suite of statistical, population genetics, and theoretical approaches, we show that the globally most represented spike protein variant (i.e., the G clade, A [->] G nucleotide change at genomic position 23,403; D [->] G amino acid change at spike protein position 614) i) underwent a significant demographic expansion in most countries not explained by stochastic effects or enhanced pathogenicity; ii) affects the spike S1/S2 furin-like site increasing its conformational plasticity (short range effect), and iii) modifies the internal motion of the receptor-binding domain affecting its cross-connection with other functional domains (long-range effect). Our study unambiguously links the spread of the G614 with a non-random process, and we hypothesize that this process is related to the selective advantage produced by a specific structural modification of the spike protein. We conclude that the different conformation of the S1/S2 proteolytic site is at the basis of the higher transmission rate of this invasive SARS-CoV-2 variant, and provide structural information to guide the design of selective and efficient drugs.

evolutionary biology↗

bioRxiv2019

Ancient genomes reveal early Andean farmers selected common beans while preserving diversity

All crops are the product of a domestication process that started less than 12,000 years ago from one or more wild populations [1, 2]. Farmers selected desirable phenotypic traits, such as improved energy accumulation, palatability of seeds or reduced natural shattering [3], while leading domesticated populations through several more or less gradual demographic contractions [2, 4]. As a consequence, erosion of wild genetic variation [5] is typical of modern cultivars making them highly susceptible to pathogens, pests and environmental change [6,7]. The loss of genetic diversity hampers further crop improvement programs to increase food production in a changing world, posing serious threats to food security [8,9]. Using both ancient and modern seeds, we analyzed the temporal dynamic of genetic variation and selection during the domestication process of the common bean (Phaseolus vulgaris) that occurred in the Southern Andes. Here we show that most domestic traits were selected for prior to 2,500 years ago, with no or only minor loss of whole-genome variation. In fact, i) all ancient domestic genomes dated between 600 and 2,500 years ago are highly variable - at least as variable as a modern genome from the wild; the genetic erosion that we observe in modern cultivars is therefore a recent process that occurred in the last centuries; ii) the majority of changes at coding genes that differentiate wild and domestic genomes are already present in the ancient genomes analyzed here. Considering that most desirable phenotypic traits are likely controlled by multiple polymorphic genes [10], a likely explanation of this decoupling of selection and genomic erosion is that early farmers applied a relatively weak selection pressure [2] by using many phenotypically similar but genomically diverse individuals as breeders. Selection strategies during the last few centuries were probably less sustainable and produced further improvements focusing on few plants carrying the traits of interest, at the cost of marked genetic erosion.

genomics↗

bioRxiv2018

Who’s who in the western Hermann’s tortoise conservation: a STR toolkit and reference database for wildlife forensic genetic analyses

Illegal trade is threatening tortoise populations worldwide since decades. Nowadays, however, DNA typing and forensic genetic approaches allow to investigate geographic origin of confiscated animals and to relocate them into the wild, provided that suitable molecular tools and reference data are available. Here we assess the suitability of a small panel of microsatellite markers to investigate patterns of illegal translocations and to assist forensic genetic applications in the endangered Mediterranean land tortoise Testudo hermanni hermanni. We used the microsatellite panel to (i) increase the understanding of the population genetic structure in wild populations with new data from previously unsampled geographic areas (overall 461 wild individuals from 28 sampling sites); (ii) detect the presence of non-native individuals in wild populations; and (iii) identify the most likely geographic area of origin of 458 confiscated individuals hosted in Italian seizure and recovery centers. Our analysis initially identified six major genetic clusters corresponding to different geographic macro-areas along the Mediterranean range. Long-distance migrants among wild populations, due to translocations, were found and removed from the reference database. Assignment tests allowed us to allocate approximately 70% of confiscated individuals of unknown origin to one of the six Mediterranean macro-areas. Most of the assigned tortoises belonged to the genetic cluster corresponding to the area where the respective captivity center was located. However, we also found evidence of long-distance origin of confiscated individuals, especially in centers along the Adriatic coast and facing the Balkan regions, a well-known source of illegally traded individuals. Our results clearly show the role for reintroduction projects of the microsatellite panel, which was useful to re-assign most of the confiscated individuals to the respective macro-area of origin. At the same time, the microsatellite panel can assist future forensic genetic applications to detect illegal trade and possess of Testudo hermanni individuals.

genetics↗

bioRxiv2018

Genetic structure in the wood mouse and the bank vole: contrasting patterns in a human-modified and highly fragmented landscape

Habitat fragmentation related to human activities modifies the distribution and the demographic trajectory of a species, often leading to genetic erosion and increased extinction risks. Understanding the impact of fragmentation on different species that co-exist in the same area becomes extremely important. Here we estimated the impact produced by different natural and anthropic landscape features on gene flow patterns in two sympatric species sampled in the same locations. Our main goal was to identify shared and private factors in the comparison among species. 199 bank voles and 194 wood mice were collected in 15 woodlands in a fragmented landscape, and genotyped at 8 and 7 microsatellites, respectively. Genetic variation and structure were analysed with standard approaches. Effective migration surfaces, isolation by resistance analysis, and regression with randomization were used to study isolation by distance and to estimate the relative importance of land cover elements on gene flow. Genetic structure was similarly affected by isolation by distance in these species, but the isolation-by-resistance analysis suggests that i) the wood mouse has constrained patterns of dispersal across woodland patches and facilitated connectivity in cultivated areas; ii) the bank vole connectivity is hindered by urban areas, while permeability is facilitated by the presence of woodlands, and cultivated terrains. Habitat loss and fragmentation can therefore influence genetic structure of small sympatric mammal species in different ways, and predicting the genetic consequences of these events using only one species may be misleading.

genetics↗