Biology subjects

De Sanctis, B.

Publications and source records attributed to De Sanctis, B..

4 recordsLinked to original sources

bioRxiv2026

Molecular Clock Dating of Ancient Environmental DNA Reveals Damage Beyond Deamination

Ancient environmental DNA (aeDNA) from permafrost, lake, cave, and marine sediments provides a rich source of genetic data that captures broad perspectives of past biodiversity. Accurate dating is crucial for discovering ecologically relevant patterns from aeDNA, and molecular clock dating would allow for sample ages to be estimated from the recovered genetic material itself instead of the geological components. However, the fragmented and damaged nature of short-read ancient DNA (aDNA) from multiple taxonomic sources poses significant challenges and has limited this dating approach for aeDNA. Here we developed ratePlacer, a phylogeny-based method for analyzing aeDNA that can combine information from many short reads in a sample while accounting for DNA damage to provide maximum likelihood estimates of sample ages. Simulations demonstrate that ratePlacer accurately dates samples even under the fragmented, damaged conditions characteristic of aeDNA and outperforms Bayesian tip-dating approaches for taxonomically mixed samples commonly found in aeDNA. Yet age estimates from re-dating Kap Kobenhavn varied across taxa, highlighting the difficulty of molecular clock dating in aeDNA. This dating also revealed elevated G [->] T and C [->] A mismatches consistent with oxidative damage. These patterns reveal aDNA damage beyond deamination and that remains understudied, suggesting that aeDNA should be carefully evaluated in genomic and evolutionary analyses. The new dating method, ratePlacer, extends molecular clock dating of aDNA from single-specimen to pooled environmental DNA data, where traditional methods struggle.

bioinformatics↗

bioRxiv2025

Ancient metagenomics reveals subglacial microbiomes driven by oxygen availability

Beneath Earths glaciers and ice sheets lies an aquatic realm where ice, water, rock, and microbial life interact, driving chemical reactions that can collectively influence the global carbon cycle, polar oceans, and climate. Efforts to describe subglacial microbiomes have been limited by the challenge of cleanly drilling through hundreds of meters of ice, such that only a few sites have ever been directly sampled. Here we use ancient metagenomics to present the first spatiotemporal characterization of subglacial bacteria and archaea. We extracted DNA from 25 subglacial precipitate samples, sedimentary accumulations of minerals that form in subglacial waters prior to exposure on the surface. The precipitates studied here formed between 16,000 and 570,000 years ago beneath the Antarctic and Laurentide Ice Sheets. We show that postmortem DNA damage patterns can reliably distinguish between ancient subglacial and modern surface taxa, and that this approach can enable reconstruction of subglacial microbiomes across poles and ice ages. Our analysis suggests that subglacial microbiomes are dominated by chemolithoautotrophs, ultra-small microbes, and taxa closely related to those found in deep subsurface or extreme cold and hypersaline environments. These microbiomes split into two distinct clusters distinguished by oxygen availability and redox conditions, irrespective of geography or age. Geochemical measurements of subglacial redox state, measured either indirectly via precipitate calcite Fe and Mn concentrations or directly via water reduction potential, reproduce these same two clusters exactly. Our findings describe how subglacial water redox states are held in balance by microbes, hydrology, and oxygen input from fresh subglacial meltwater, that we interpret to be controlled by the ice sheet response to past climate variations.

genomics↗

bioRxiv2022

How does the mode of evolutionary divergence affect reproductive isolation?

When divergent populations interbreed, the outcome will be affected by the genomic and phenotypic differences that they have accumulated. In this way, the mode of evolutionary divergence between populations may have predictable consequences for the fitness of their hybrids, and so for the progress of speciation. To investigate these connections, we present a new analysis of hybridization under Fishers geometric model, making few assumptions about the allelic effects that differentiate the hybridizing populations. Results show that the strength and form of postzygotic reproductive isolation (RI) depend on just two properties of the evolutionary changes, which we call the "total amount" and "net effect" of change, and whose difference quantifies the similarity of the changes at different loci, or their tendency to act in the same phenotypic direction. It follows from our results that identical patterns of RI can arise in different ways, since different evolutionary histories can lead to the same total amount and net effect of change. Nevertheless, we show how these estimable quantities do contain some information about the history of divergence, and that - thanks to Haldanes Sieve - the dominance and additive effects contain complementary information. Impact SummaryWhen populations of animals or plants evolve differences in their genomes or traits, the nature of the differences will help to determine whether they can continue to interbreed. For example, the hybrid offspring may be infertile, or unlikely to survive to reproductive age, meaning that the two populations remain distinct from one another even after mating. However, in some cases the hybrids may be more fertile than their parents or have some other reproductive advantage. In this study, we use a mathematical model to relate hybrid fitness to the evolved differences separating the parents. We find that the outcome depends on just two properties of these differences, which capture the "total amount" and the "net effect" of evolutionary change. We then show that different evolutionary divergence scenarios or modes can lead to the exact same hybrid fitness. On the other hand, we can still make some inferences about the history of divergence by observing certain properties of hybrid fitness. Determining the relationship between hybrid fitness and the mode of evolutionary divergence will help to understand how new species form, to plan conservation interventions such as moving individuals between isolated populations to increase their adaptive potential, and to understand how existing species might interact when their habitats overlap, for example due to climate change or other human impacts.

evolutionary biology↗

bioRxiv2019

The Geometry and Genetics of Hybridization

We develop an analytical framework for predicting the fitness of hybrid genotypes, based on Fishers geometric model. We first show that all of the model parameters have a simple geometrical and biological interpretation. Hybrid fitness decomposes into intrinsic effects of hybridity and heterozygosity, and extrinsic measures of the (local) adaptedness of the parental lines; and all of these correspond to distances in a phenotypic space. We also show how these quantities change over the course of divergence, with convergence to a characteristic pattern of intrinsic isolation. Using individual-based simulations, we then show that the predictions apply to a wide range of population genetic regimes, and divergence conditions, including allopatry and parapatry, local adaptation and drift. We next connect our results to the quantitative genetics of line crosses in variable or patchy environments. This relates the geometrical distances to quantities that can be estimated from cross data, and provides a simple interpretation of the "composite effects" in the quantitative genetics partition. Finally, we develop extensions to the model, involving selectively-induced disequilibria, and variable phenotypic dominance. The geometry of fitness landscapes provides a unifying framework for understanding speciation, and wider patterns of hybrid fitness.

evolutionary biology↗