Biology subjects

Fontani, F.

Publications and source records attributed to Fontani, F..

3 recordsLinked to original sources

bioRxiv2025

Ecology and demographic structure of an extinct ibex population in Upper Palaeolithic Italian Alps

Alpine Upper Palaeolithic contexts exhibit specialised subsistence strategies, heavily dependent on Capra ibex. Among them, the rock shelter Riparo Dalmeri stands out, with C. Ibex dominating faunal remains across all occupation phases, spanning the Pleistocene/Holocene transition. This evidence positions Riparo Dalmeri as a key site for exploring the interdependence between human groups and C. ibex during one of the most critical climatic and cultural shifts in human evolution. Here, we present the first multidisciplinary study on Late Palaeolithic C. ibex teeth from Riparo Dalmeri, integrating direct radiocarbon dating, isotope (87Sr/86Sr, {delta}13C, {delta}18O), proteomic, and aDNA analyses. We generated the earliest aDNA sequences for C. ibex and contextual evidence on mobility, seasonality, and sex ratios. We found that most C. ibex were local to the area despite consistent human presence. They reveal significant dietary differences between sexes as well as increased seasonality at the Pleistocene-Holocene transition. Our results identify Riparo Dalmeri as an extinct branch of the ibex mtDNA phylogeny, offering unprecedented insights into ibex ecology and evolution that resonate with present-day issues on the conservation of this species in the face of climate change.

ecology↗

bioRxiv2024

Ancient DNA reveals historical demographic decline and genetic erosion in the Atlantic bluefin tuna

Overexploitation has depleted fish stocks during the past century, nonetheless its genomic consequences remain poorly understood. Characterising the spatiotemporal patterns of these consequences may provide baseline estimates of past diversity and productivity to aid management targets, help predict future dynamics, and facilitate the identification of evolutionary factors limiting fish population recovery. Here, we evaluate human impacts on the evolution of the iconic Atlantic bluefin tuna (Thunnus thynnus), one of the longest and most intensely exploited marine fishes, with a tremendous cultural and economic importance. We sequenced whole genomes from modern (n=49) and ancient (n=41) specimens dating up to 5000 years ago, uncovering several novel findings. First, we identify temporally stable patterns of population admixture, as bluefin tuna caught off Norway and in the eastern Mediterranean share a greater degree of ancestry with Gulf of Mexico bluefin tuna than western and central Mediterranean bluefin tuna. This suggests that Atlantic spawning areas are important mixing grounds for the genetic diversity of Mediterranean bluefin tuna. We model effective population size to show that Mediterranean bluefin tuna began to undergo a demographic decline by the year 1900 to an extent not observed across the previous millennia. Coinciding with this, we found that heterozygosity and nucleotide diversity was significantly lower in modern (2013-2020), than ancient (pre-1941) Mediterranean bluefin tuna, suggesting bluefin tuna underwent a genetic bottleneck. With this work we show how ancient DNA provides novel perspectives on ecological complexity with the potential to inform the management and conservation of fishes. SignificanceAchieving the aim of the current UN Ocean Decade to "protect and restore ecosystems and biodiversity" is stymied by a lack of historical knowledge on how human exploitation has impacted and therefore what should be restored. Here, we sequence DNA in ancient fish bones to evaluate the historical diversity of the Atlantic bluefin tuna; which has been of great commercial importance for centuries. We find that bluefin tuna began to undergo demographic decline by 1900, 70 years earlier than currently recognised. Correspondingly, we find modern bluefin tuna had lower levels of genetic diversity than historical ones. This suggests that human impacts on the diversity of marine fishes are likely to have begun earlier and be more complex than previously thought.

ecology↗

bioRxiv2024

Five millennia of mitochondrial introgression in Atlantic bluefin tuna identified using ancient DNA

Mitogenomic (MT) introgression between species is readily documented in marine fishes. Such introgression events may either be long-term natural phenomena or the result of human-driven shifts in spatial distributions of previously separated species. Determining the drivers behind MT introgression is stymied by the difficulty of directly observing patterns of interbreeding over long timescales. Using ancient DNA spanning five millennia, we here investigate the long-term presence of MT introgression from Pacific bluefin tuna (Thunnus orientalis) and albacore (Thunnus alalunga) into Atlantic bluefin tuna (Thunnus thynnus), a species with extensive exploitation history and observed shifts in abundance, and demographic distribution. Comparing ancient (n=130) and modern (n=78) mitogenomes of specimens covering most of the range of Atlantic bluefin tuna we detect no significant spatial or temporal population structure. This lack of spatiotemporal genomic differentiation is indicative of ongoing gene flow between populations and large effective population sizes over millennia. Moreover, we identify introgressed MT genomes in ancient specimens up to 5000 years old and find that this rate of introgression has remained similar through time. We therefore conclude that MT introgression in the Atlantic bluefin tuna is to date unaffected by anthropogenic impacts. By providing the oldest example of directly observed MT introgression in the marine environment, our results highlight the utility of ancient DNA to obtain temporal insights in the long-term persistence of such phenomena.

evolutionary biology↗