Biology subjects

Hauffe, H. C.

Publications and source records attributed to Hauffe, H. C..

7 recordsLinked to original sources

bioRxiv2026

Intra- and interspecific relationships of alpine ungulates reorganise along a wolf recolonisation gradient

Apex predators are recovering across many ecosystems after decades of decline, yet whether their return can restore ecological interactions disrupted by their loss remains poorly understood. Here, we used the ongoing recolonisation of grey wolves (Canis lupus) in the south-eastern Alps as a natural gradient of predator recovery to examine how predation risk and human disturbance shape relationships among red deer (Cervus elaphus), roe deer (Capreolus capreolus), and Alpine chamois (Rupicapra rupicapra). Across a gradient of time since wolf establishment, roe deer increasingly occupied sites without red deer, suggesting predator recovery alters relationships between prey species. Red deer also formed larger groups, consistent with a shift in collective behaviour under increased predation risk. Human disturbance also affected group formation in red deer and chamois. Together, these findings show that prey community structure can vary with wolf recovery, even in human-dominated landscapes, through altered associations among species and grouping within species.

ecology↗

bioRxiv2026

From prehistory to present-day: How isolation shaped the distinct genomic makeup of Italian Alpine valleys

Historically, the eastern Italian Alps have provided crucial geographic corridors for cultural and genetic exchange between the Mediterranean region and Central and Northern Europe. Although recent archaeogenomic data suggest a strong regional persistence of Anatolian Neolithic ancestry followed by the arrival of Yamnaya-related components during the Bronze Age, the genomic landscape of modern Alpine populations remains largely unmapped. In this study, we verified the persistence of these signals in the present-day Rendena and Ledro Valleys by integrating novel complete mitochondrial genomes (N=185) and genome-wide SNP data (N=96), the latter combined with a novel Italian genomic dataset (N=139). Our findings show that the Rendena and Ledro populations form a distinct "modern Alpine" genomic group, which retains a significant proportion of early European Neolithic ancestry, aligning with ancient eastern Italian Alpine individuals and modern Sardinians. More recently, geographic isolation and localized genetic drift appear to have shaped the two valleys differently. Demographic reconstructions reveal asynchronous population declines over the past two millennia, followed by a sharp, synchronized bottleneck 200-300 years ago, which coincided with historical plague outbreaks. Remarkably, this structured drift persisted at an extremely fine microgeographic scale within the valleys, resulting in internal genetic subclusters that directly correlate with local topography. This micro-differentiation was likely maintained by steep geographic barriers and/or local endogamous practices. This study ultimately underscores how geographic barriers and isolation can preserve ancient genomic components and shape highly localized genetic structures over centuries even to the modern day.

evolutionary biology↗

bioRxiv2026

Multidimensional isotopic niches inform coexistence mechanisms in an Alpine ungulate community

O_LIUnderstanding functional community structure and the niche-based mechanisms that enable coexistence among sympatric species is essential for explaining how biodiversity is maintained in natural systems, and for anticipating how ecological communities will respond to ongoing environmental change. Stable isotope analysis provides a process-oriented perspective on resource use by integrating information across time and space, thereby allowing reconstruction of realised isotopic niches that reflect multiple dimensions of ecological differentiation. C_LIO_LIWe applied this framework to a community of ungulates in the Central-Eastern Italian Alps, including red deer (Cervus elaphus), roe deer (Capreolus capreolus), and Alpine chamois (Rupicapra rupicapra). Using stable isotope ratios in summer-grown hair segments ({delta}13C, {delta}15N, {delta}34S, {delta}18O, {delta}2H), we quantified species-specific n-dimensional niche hypervolumes within a Bayesian framework and estimated niche regions, overlap probabilities, univariate differentiation and multivariate structure. C_LIO_LIDespite broad dietary overlap typically observed among these ungulates, we found clear isotopic niche segregation, with mean pairwise overlap consistently remaining below 40%. Three dimensions emerged as primary drivers of differentiation: water sourcing ({delta}18O), diet quality ({delta}15N), and habitat openness ({delta}13C). Specifically, chamois appeared to derive more water from plants in their diet rather than from drinking, and to consume a higher-quality diet compared to Cervids. Red deer relied more heavily on forested habitats for resource use compared to roe deer and chamois, and additional isotopic differences between red deer and roe deer may stem from fine-scale abiotic conditions like microclimate and topography. We found no isotopic evidence for differential niche breadth among the three ungulate species. C_LIO_LITogether, these patterns highlight functional differentiation across multiple ecological axes, offering mechanistic insight into how these ungulates segregate realised niche space despite substantial potential for resource overlap. This multi-element isotope perspective underscores the value of integrative, process-based approaches for understanding current coexistence as well as improving predictions of how mammal communities may reorganise under accelerating environmental change. C_LI

ecology↗

bioRxiv2024

Movement responses to lethal risk: an integrative analysis of proactive and reactive antipredator behaviours in a large herbivore

Prey species can display antipredation movement behaviours to reduce predation risk including proactive responses to chronic or predictable risk, and reactive responses to acute or unpredictable risk. Thus, at any given time, prey movement choice may reflect the trade-off between proaction and reaction. In previous studies, proaction and reaction have generally been considered separately, which neglects their simultaneous influence on animal decisions. In this study, we analysed how proaction and reaction interact to shape the movements of GPS-collared red deer (Cervus elaphus), in response to human hunting of conspecifics. Our results show that red deer proactively selected canopy cover where and when risk was predictably high. However, when they were unable to avoid risk, canopy cover was no longer selected, but only modulated a reactive response along a freeze-to-escape continuum. This reaction was even more evident when the environment was unfamiliar, underlining the importance of memory in such reaction patterns. Therefore, to our knowledge, for the first time, we describe how proaction and reaction fuse in an antipredation sequence of interconnected movement decisions in a large herbivore, and we lay the foundations for further investigations into the evolutionary origins of similarities and differences between proactive and reactive behaviours.

ecology↗

bioRxiv2022

Comparison of microbial communities from diverse biological matrices using mock community as an in situ positive control

Metataxonomy has become the standard for characterizing the diversity and composition of microbial communities associated with multicellular organisms and their environment. Understanding the interactions between the microbiotas within the same ecosystem is essential for fully understanding the role of microorganisms in evolutionary and ecological processes; however, such comparative studies across diverse biological samples are rare. In particular, currently available protocols assume a uniform DNA extraction, amplification and sequencing efficiency for all sample types and taxa. The addition of a mock community (MC) to biological samples before the DNA extraction step could aid identification of technical biases, but the impact of MC on diversity estimates is unknown. Here, standardized aliquots of bovine faecal samples with high or low biomass were extracted with high or low doses of MC, characterized using standard Illumina technology for metataxonomics, and analysed with custom bioinformatic pipelines. We showed that a MC was an informative in situ positive control provided an estimate of 16S rRNA sample gene copies (which allowed a more direct measure of community size), and detected sample outliers. However, we also demonstrated that if the recommended dose of MC is added to a sample with low biomass, diversity estimates were distorted. Using our results, we recommend MC doses for a range of sample types, including rhizosphere soil, whole invertebrates, and vertebrate faecal samples. ImportanceThe simultaneous processing of the sample microbiota with a known number of readily identifiable MC cells (co-extracted with the sample cells) or SNA (co-amplified with the sample DNAs) can be a valuable in situ positive control. However, guidelines regarding their application are very limited and do not consider the effect of these controls on sample diversity estimates. We demonstrate that a MC co-extracted with the study sample provides several advantages, such as highlighting bias in DNA extraction of gram positive, identifying potential sample outliers and inferring the number of 16S rRNA gene copies in the sample. However, the incorporation of a MC requires prior knowledge of sample biomass, as high ratios of MC to sample microbiota lead to biased sample diversity estimates. Practical advice on determining the appropriate MC dose for a wide range of sample types, including rhizosphere soil, whole invertebrates and mammalian faecal samples are provided.

ecology↗

bioRxiv2021

A highly endemic area of Echinococcus multilocula is identified through a comparative re-assessment of prevalence in red fox (Vulpes vulpes), Alto Adige (Italy: 2019-2020)

BackgroundSurveillance of E. multilocularis at the edge of its range is hindered by fragmented distributional patterns and low prevalence and burden in definitive hosts. Thus, tests with adequate levels of sensitivity are especially important for discriminating between infected and non-infected areas. AimWe reassessed the prevalence of E. multilocularis at the southern border of its distribution in Alto Adige (Italy), to improve surveillance in wildlife and provide more accurate estimates of exposure risk. MethodsWe compared results from the diagnostic test currently implemented for surveillance (based on Coproscopy+Multiplex PCR - CMPCR), against a real-time quantitative PCR (qPCR) for 235 fox faeces collected in 2019-2020. The performances of the two tests were estimated using a scraping technique (SFCT) as the gold standard applied to the small intestines of a subsample (n=123) of the same hosts. True prevalence was calculated and sample size required by each faecal test for the detection of the parasite was then estimated. ResultsTrue prevalence of E. multilocularis in foxes (14.3%) was definitely higher than reported in the last decade (never >5% from 2012 to 2018). The qPCR also had a higher sensitivity (83%) compared to CMPCR (21%). Agreement with the gold standard was far higher for qPCR (0.816) than CMPCR (0.298) as well, determining a smaller sample size required to detect the disease. ConclusionsAlto Adige should be considered a highly endemic area. Surveillance at the edges of E. multilocularis distribution should adopt qPCR diagnostics on definitive hosts on a small geographic scale. AUTHOR SUMMARYEchinococcus multilocularis is an intestinal flatworm, whose adult stage in Europe is harboured mainly by the red fox (Vulpes vulpes), which spreads parasites eggs by faeces. This parasite is the agent of a severe and potentially lethal zoonosis, the alveolar echinococcosis, affecting humans after accidental ingestion of parasites eggs. In the Italian Alpine area, which represents the southernmost border of E. multilocularis European range, surveillance is hindered by a fragmented distributional pattern, where presence in foxes has been consistently reported only in few isolated foci in Alto Adige (Bolzano province - Italy) of low prevalence. In order to improve the efficiency of monitoring efforts, we tested the performances of two diagnostic protocols on fox faeces (sedimentation, filtration, counting technique followed by standard PCR, and whole stool real-time PCR) against a benchmark technique on fox intestines (scraping, filtration, counting technique - considered as the gold standard). This allowed not only to determine qPCR as a far more sensitive and sample-efficient diagnostic tool for E. multilocularis detection in marginally affected areas, but also to re-assess its prevalence in Alto Adige, which should be considered a highly endemic area. Consequent actions in the field and modifications in the surveillance strategy should be therefore considered.

molecular biology↗

bioRxiv2020

From local spectral species to global spectral communities: a benchmark for ecosystem diversity estimate by remote sensing

In the light of unprecedented change in global biodiversity, real-time and accurate ecosystem and biodiversity assessments are becoming increasingly essential. Nevertheless, estimation of biodiversity using ecological field data can be difficult for several reasons. For instance, for very large areas, it is challenging to collect data that provide reliable information. Some of these restrictions in Earth observation can be avoided through the use of remote sensing approaches. Various studies have estimated biodiversity on the basis of the Spectral Variation Hypothesis (SVH). According to this hypothesis, spectral heterogeneity over the different pixel units of a spatial grid reflects a higher niche heterogeneity, allowing more organisms to coexist. Recently, the spectral species concept has been derived, following the consideration that spectral heterogeneity at a landscape scale corresponds to a combination of subspaces sharing a similar spectral signature. With the use of high resolution remote sensing data, on a local scale, these subspaces can be identified as separate spectral entities, the so called "spectral species". Our approach extends this concept over wide spatial extents and to a higher level of biological organization. We applied this method to MODIS imagery data across Europe. Obviously, in this case, a spectral species identified by MODIS is not associated to a single plant species in the field but rather to a species assemblage, habitat, or ecosystem. Based on such spectral information, we propose a straightforward method to derive - (local relative abundance and richness of spectral species) and {beta}-diversity (turnover of spectral species) maps over wide geographical areas.

ecology↗