Mountain building reorganizes drainage networks, influencing riverine biodiversity. Northern Italy offers a natural experiment in the impact of tectonic and geomorphic processes on aquatic species distributions. We combined geomorphic analysis with environmental DNA from rivers to assess the influence of tectonically driven drainage reorganization on genetic diversity, targeting an endemic fish species, Telestes muticellus (A. Risso, 1827). In the Northern Apennines, horizontal shortening and topographic advection in an orogenic wedge have been hypothesized as leading to river capture and drainage divide migration. In addition, slab rollback has produced a spatial transition from contraction to extension, which is more pronounced from north to south, with normal faulting producing range-parallel drainage only in the southern regions. In contrast, the adjacent Ligurian Alps are a remnant of the Alpine orogen with little modern deformation. We found distinct zones of geomorphic characteristics from north to south, including divide asymmetry and frequency of range-parallel drainage. Analysis of DNA sequences shows cross-divide assemblage characteristics that correlate with the geomorphic zonation. The Northern Apennines show higher values of the directional measures of assemblage change gain, loss, and turnover; the Ligurian Alps show higher values of overlap and nestedness. There is a positive correlation between divide asymmetry and genetic distance, and gain, loss, and turnover of DNA sequences from Adriatic to Ligurian sites; there is a negative correlation with overlap and nestedness. Since the species is confined to freshwater environments, tectonically driven drainage reorganization is one of the only mechanisms that can explain its spatial genetic differentiation.

The Magdalena River basin harbors a large biodiversity of vertebrates, with numerous endemic species, many of which are threatened with extinction. Following the same trend as most freshwater ecosystems globally, the Magdalena faces threats from human activities, causing habitat degradation and the decline of its biodiversity. Monitoring the freshwater biodiversity is crucial to detect early impacts and guide conservation actions in this river system, which is of vital ecological importance for Colombia. Here, we used environmental DNA (eDNA) metabarcoding, with two primer sets designed to target mitochondrial DNA regions, specifically the 12S ribosomal RNA gene, targeting fish as well as amphibians, reptiles, birds, and mammals in the Magdalena River. We detected a total of 158 vertebrate taxa, not only aquatic but also terrestrial, arboreal, and aerial. The diversity of these vertebrates increases as the river mouth is approached, accompanied by a change in the composition of the aquatic vertebrate assemblages, with two distinct groups linked to the geomorphology of the lower Magdalena basin. The assemblage was characterized by a high turnover of taxa between the sites closest to the mouth of the river and a marked nesting of taxa when comparing the sites closest to the river mouth with those farther away. We conclude that eDNA metabarcoding allows characterizing vertebrate assemblages in large rivers, assessing conservation status, and elucidating biodiversity patterns with minimal ecosystem disturbance. The information obtained through this approach can contribute to the sustainable management and preservation of vital freshwater ecosystems and their associated biodiversity.

The Hengduan Mountains (HM) are located on the southeastern edge of the Tibetan Plateau (TP) and feature high mountain ridges (> 6000 m a.s.l.) separated by deep valleys. The HM region also features an exceptionally high biodiversity, believed to have emerged from the topography interacting with the climate. To investigate the role of the HM topography on regional climate, we conduct simulations with the regional climate model COSMO at high horizontal resolutions (at ~12 km and a convection-permitting scale of ~4.4 km) for the present-day climate. We conduct one control simulation with modern topography and two idealised experiments with modified topography, inspired by past geological processes that shaped the mountain range. In the first experiment, we reduce the HM’s elevation by applying a spatially non-uniform scaling to the topography. The results show that, following the uplift of the HM, the local rainy season precipitation increases by ~25%. Precipitation in Indochina and the Bay of Bengal (BoB) also intensifies. Additionally, the cyclonic circulation in the BoB extends eastward, indicating an intensification of the East Asian summer monsoon. In the second experiment, we remove the deep valley by applying an envelope topography to quantify the effects of terrain undulation with high amplitude and frequency on climate. On the western flanks of the HM, precipitation slightly increases, while the remaining fraction of the mountain range experiences ~20% less precipitation. Simulations suggest an overall positive feedback between precipitation, erosion, and valley deepening for this region, which could have influenced the diversification of local organisms.

Understanding the intricate dynamics of biodiversity within and across riverine ecosystems, influenced by geological history and environmental factors, is crucial for effective conservation and management strategies. Italy, particularly the Ligurian region, harbors diverse freshwater fish communities and populations shaped by unique geological and hydrological conditions. Here, we investigated the suitability of eDNA-metabarcoding to identify inter- and intraspecific diversity patterns of riverine fish populations along the main drainage divide (MDD) between the Adriatic and Ligurian basins in Northern Italy. We collected 96 aquatic eDNA samples across 48 riverine sites, amplified them using a cytb primer pair and denoised the sequences to retrieve amplicon sequence variants (ASV). We calculated communities’ phylogenetic distance with betaMPD based on genetic distances derived from the ASVs, combined them with conductance-based landscape metrics and applied generalized dissimilarity models (GDM) to assess spatial genetic structure. Our results reveal genetic differentiation among populations of several fish species, with some displaying clustering patterns across the drainage divide and isolation by distance patterns. Overall, taxon richness was significantly higher in the Ligurian sites (25) than in the Adriatic side of the MDD (22), as was ASV richness (205 vs. 196). Our findings highlight the effectiveness of eDNA-metabarcoding in uncovering various facets of diversity, shedding light on hidden genetic diversity within ASVs, and revealing significant spatial genetic structuring in freshwater fish populations across multiple species.

1. Metabarcoding of environmental DNA (eDNA) has recently improved our understanding of biodiversity patterns in marine and terrestrial ecosystems. However, the complexity of these data prevents current methods to extract and analyze all the relevant ecological information they contain. Therefore, ecological modeling could greatly benefit from new methods providing better dimensionality reduction and clustering. 2. Here we present two new deep learning-based methods that combine different types of neural networks to ordinate eDNA samples and visualize ecosystem properties in a two-dimensional space: the first is based on variational autoencoders (VAEs) and the second on deep metric learning (DML). The strength of our new methods lies in the combination of several inputs: the number of sequences found for each molecular operational taxonomic unit (MOTU), together with the genetic sequence information of each detected MOTU within an eDNA sample. 3. Using three different datasets, we show that our methods represent well three different ecological indicators in a two-dimensional latent space: MOTU richness per sample, sequence α-diversity per sample, and sequence ꞵ-diversity between samples. We show that our nonlinear methods are better at extracting features from eDNA datasets while avoiding the major biases associated with eDNA. Our methods outperform traditional dimension reduction methods such as Principal Component Analysis, t-distributed Stochastic Neighbour Embedding, and Uniform Manifold Approximation and Projection for dimension reduction. 4. Our results suggest that neural networks provide a more efficient way of extracting structure from eDNA metabarcoding data, thereby improving their ecological interpretation and thus biodiversity monitoring.

Human activities can degrade the quality of coral reefs, cause a decline in fish species richness and functional diversity and an erosion of the ecosystem services provided. Environmental DNA metabarcoding (eDNA) has been proposed as an alternative to Underwater Visual Census (UVC) to offer more rapid assessment of marine biodiversity to meet management demands for ecosystem health indices. Taxonomic information derived from sequenced eDNA can be combined with functional traits and phylogenetic positions to generate a variety of ecological indices describing ecosystem functioning. Here, we inventoried reef fish assemblages of two contrasted coastal areas of Curaçao, (i) in close proximity to the island’s capital city and (ii) in a more remote area under more limited anthropogenic pressure. We sampled eDNA by filtering large volumes of sea water (2 x 30L) along 2km boat transects, which we coupled with species ecological properties related to habitat use, trophic level and body size to investigate the difference in fish taxonomic composition, functional and phylogenetic indices recovered from eDNA metabarcoding between these two distinct coastal areas. Despite no marked difference in species richness, we found a higher phylogenetic diversity in proximity to the city, but a higher functional diversity on the more isolated reef. Composition differences between coastal areas were associated with different frequencies of reef fish families. Because of a partial reference database, eDNA only partly matched those detected with UVC, but eDNA surveys nevertheless provided rapid and robust species occupancy responses to contrasted environments. eDNA metabarcoding coupled with functional and phylogenetic diversity assessment can serve the management of coastal habitats under increasing threat from global changes.

Forecasting the trajectories of species assemblages in response to ongoing climate change requires quantifying the time lags in the demographic and ecological processes through which climate impacts species' abundances. Since experimental climate manipulations are typically abrupt, the observed species responses may not match their responses to gradual climate change. We addressed this problem by transplanting alpine grassland turfs to lower elevations, recording species' demographic responses to climate and competition, and using these data to parameterize community dynamics models forced by scenarios of gradual climate change. We found that shifts in community structure following an abrupt climate manipulation were not simply accelerated versions of shifts expected under gradual warming, especially when they missed the rise of species benefiting from moderate warming. Time lags in demography and species interactions controlled the pace and trajectory of changing species' abundances under simulated 21st century climate change, and thereby prevented immediate diversity loss.

Understanding the traits mediating species' responses to climate change is a cornerstone for predicting future community composition and ecosystem function. Although species' eco-physiological properties determine their response to environmental change, most trait-based studies focus on a small subset of easily-measured morphological traits as proxies for physiology. This choice may limit our ability to predict the impacts of climate change on species' demography, and obscure the underlying mechanisms. We conducted a transplantation experiment along a 1000 m Alpine elevation gradient to quantify the degree to which plant demographic responses to climate were predicted by eco-physiological performance versus common morphological traits. Although physiological measurements revealed that warming favored species with a conservative water use strategy, the predictive power of physiological traits did not exceed that of morphological traits. Our results show that while easily-measured morphological traits can successfully predict demographic responses to climate, eco-physiological approaches are needed to understand mechanism.

Ecological gradients are expected to be associated with structural rewiring of species interaction networks. The study of network structures along geographic and ecological gradients, however, remains marginal because documenting species interactions at multiple sites is a methodological challenge. Using a standardized DNA metabarcoding method applied to feces, we examined how structural properties of plant--orthoptera networks reflecting specialization and resilience vary with elevation. We found an increase in levels of generality and nestedness with decreasing temperature, and the correlation was stronger than in null models. These relationships corresponded to greater robustness and reduced importance of keystone species in alpine habitats. In cold environments, plant--herbivore networks are wired in a way that may reinforce the resilience of the system to species extinction. Documenting ecological networks along ecological gradients allows a better understanding of the influence of climate on the structure of ecosystems.