Biology subjects

De Barba, M.

Publications and source records attributed to De Barba, M..

4 recordsLinked to original sources

bioRxiv2026

Workflow for multiplex microsatellite panel development and sample preparation for robust amplicon sequencing of low-template and degraded DNA: validation for non-invasive genotyping in three large carnivore species

High-throughput amplicon sequencing has transformed microsatellite (STR) genotyping by overcoming many of the limitations of fragment-length analysis, enabling more accurate, cost-effective, and standardized genotyping. Yet, protocols specifically designed for high-throughput sequencing (HTS)-based STR genotyping from low-template and degraded DNA remain scarce, despite the prevalence of these challenging sample types in ecological and conservation contexts. We present a methodology for the de novo development of robust STR multiplex panels together with a laboratory protocol for efficient and reliable STR genotyping by sequencing with low quantity and quality DNA samples. The protocol comprises (i) an automated bioinformatic pipeline to design large sets of short tetranucleotide markers optimized for multiplex amplicon sequencing of degraded and low-template DNA; (ii) guidelines for efficient in vitro optimization of multiplex amplification using directly low quantity/quality template DNA; and (iii) a library preparation procedure that improves detection of low-level allele signal while enabling quality assessment of STR amplicon sequencing under limiting DNA conditions. We demonstrate the approach by developing and validating STR panels for non-invasive genotyping of three large carnivore species: a 44-plex for the grey wolf (Canis lupus), a 41-plex for the Eurasian lynx (Lynx lynx), and a 30-plex for the brown bear (Ursus arctos). Multiplex performance was high, with [≥]91% of samples successfully genotyped at [≥]50% of loci (allele size range 28-110 bp across panels) and correctly assigned to known individuals, negligible levels of noise in the controls, and high discriminatory power (PIDsibs [≤]2.4 x 1e-12), also owing to sequence variation among same-length alleles at 15-50% of loci. The approach is broadly applicable to animal and plant species, a wide range of sample types, and large-scale analysis such as genetic monitoring. Our study reinforces the value of STR amplicon sequencing for ecological and conservation applications while highlighting the importance of marker design and laboratory workflows tailored to HTS-based genotyping for accurate and efficient implementation.

ecology↗

bioRxiv2024

Human footprint and forest disturbance reduce space use of brown bears across Europe.

Three-quarters of the planets land surface has been altered by humans, with consequences for animal ecology, movements and related ecosystem functioning. Species often occupy wide geographical ranges with contrasting human disturbance and environmental conditions, yet, limited data availability across species ranges has constrained our understanding of how human impact and resource availability jointly shape intraspecific variation of animal space use. Leveraging a unique dataset of 752 annual GPS movement trajectories from 370 brown bears (Ursus arctos) across the species range in Europe, we investigated the effects of human impact (i.e., human footprint index), resource availability, forest cover and disturbance, and area-based conservation measures on brown bear space use. We quantified space use at different spatio-temporal scales during the growing season (May - September): home range size; representing general space requirements, 10-day long-distance displacement distances, and routine 1-day displacement distances. We found large intraspecific variation in brown bear space use across all scales, which was profoundly affected by human footprint index, vegetation productivity, and recent forest disturbances creating opportunity for resource pulses. Bears occupied smaller home ranges and moved less in more anthropized landscapes and in areas of higher resource availability. Forest disturbances reduced space use while contiguous forest cover promoted longer daily movements. The amount of strictly protected and roadless areas within bear home ranges were too small to affect space use. Anthropized landscapes may hinder the expansion of small and isolated populations, such as the Apennine and Pyrenean, and obstruct population connectivity, for example between the Alpine or Carpathian with the Dinaric Pindos populations. Our findings call for actions to maintain bear movements across landscapes with high human footprint, for example by maintaining forest integrity, to support viable bear populations and their ecosystem functions.

ecology↗

bioRxiv2023

Including biotic interactions in species distribution models improves the understanding of species niche: a case of study with the brown bear in Europe

Biotic interactions are expected to influence species responses to climate change, but they are usually not included when predicting future range shifts. We assessed the importance of biotic interactions to understand future consequences of climate and land use change for biodiversity using as a model system the brown bear (Ursus arctos) in Europe. By including biotic interactions using the spatial variation of energy contribution and habitat models of each food species, we showed that the use of biotic factors considerably improves our understanding of the distribution of brown bears. Predicted future range shifts, which included changes in the distribution of food species, varied greatly when considering various scenarios of change in biotic factors, warning about future indirect climate change effects. Our study confirmed that advancing our understanding of ecological networks of species interactions will improve future scenarios of biodiversity change, which is key for conserving biodiversity and ecosystem services.

ecology↗

bioRxiv2017

Soil community assembly varies across body sizes in a tropical forest

The relative influence of deterministic niche-based (i.e. abiotic conditions, biotic interactions) and stochastic-distance dependent neutral processes (i.e. demography, dispersal) in shaping communities has been extensively studied for various organisms, but is far less explored jointly across the tree of life, in particular in soil environments. Here, using a thorough DNA-based census of the whole soil biota in a large tropical forest plot, we show that soil aluminium, topography, and plant species identity are all important drivers of soil richness and community composition. Body size emerges as an important feature of the comparative ecology of the different taxa at the studied spatial scale, with microorganisms being more importantly controlled by environmental factors, while soil mesofauna rather display random spatial distribution. We infer that niche-based processes contribute differently to community assembly across trophic levels due to spatial scaling. Body size could hence help better quantifying important properties of multitrophic assemblages.

ecology↗