Biology subjects

Hugueny, B.

Publications and source records attributed to Hugueny, B..

4 recordsLinked to original sources

bioRxiv2025

Climate-driven habitat loss and natural fragmentation increase extinction risk and compromise population viability in freshwater fish

Climate change is one of the major drivers of the current extinction crisis. In this context, determining the probability of species extinction is crucial. In aquatic ecosystems, basin area is a key factor influencing extinction risk. Habitat fragmentation can significantly reduce river basin size and lead to both deterministic and stochastic extinctions. Deterministic extinctions occur when climatic conditions become unfavorable across the entire area of occupancy of populations, while stochastic extinctions result from temporal variability in population size driven by stochasticity events. In this study, we developed an extinction model incorporating species presence probability, basin area, and biological parameters. Using species distribution modeling to estimate current and future species distributions, we applied the extinction model to freshwater fish species in France to quantify deterministic and stochastic extinctions as well as population viability under future climatic conditions. Our results showed a significant effect of climate change on deterministic extinction rates, depending on the species considered and their spawning thermal preferences. We also observed spatial patterns in extinction rates, with small coastal rivers being particularly impacted. Furthermore, our results showed an effect of climate change on population viability, especially for cold-water species. While our results did not indicate high extinction rates for most species, they revealed that cold-water species could be severely affected by habitat loss due to climate change and natural fragmentation, with potentially greater impacts under anthropogenic fragmentation. The application of this model could be highly valuable for identifying both priority areas and species of concern in conservation planning.

ecology↗

bioRxiv2021

Drivers of phylogenetic structure in Amazonian freshwater fish assemblages

AimCommunity phylogenetics provides important information about the evolutionary and ecological factors help structure regional species assemblages. Here, we analyze phylogenetic diversity (phylodiversity) patterns among fish species in 97 sub-drainages of the Amazon basin, to evaluate the roles of historical and contemporary processes in generating and maintaining the exceptional richness and endemism of Amazonian fish species assemblages. LocationAmazon River basin TaxonFreshwater fishes MethodsUsing a large comprehensive database of freshwater fish species distributions, and a well-sampled molecular phylogeny of ray-finned (actinopterygian) fishes, we develop of multivariate statistical model to correlate estimated historical and contemporary environmental parameters with sub-drainage phylodiversity patterns. The model employs three phylogenetic metrics: i.e.: phylogenetic diversity (PD) sensu stricto, mean pairwise phylogenetic distance (MPD) between species capturing phylodiversity variation at older evolutionary timescales), and mean nearest taxon distance (MNTD) capturing variation in phylodiversity at younger evolutionary timescales. ResultsThe model recovered significant effects of elevation gradients, contemporary climate, habitat fragmentation, water types, and past marine incursions on assemblage phylodiversity patterns. The model also found significantly negative relationships among the three phylogenetic metrics, and between these metrics and distance to mouth of the Amazon, representing a West-East longitudinal gradient. Main conclusionsOur study revealed a highly non-random spatial and environmental distribution of our three phylogenetic diversity metrics across the 97 sub-drainages of the Amazon basin. Beyond significant regional effects of several environmental and historical drivers, we also found a significant West-East gradient of increasing phylogenetic diversity and phylogenetic relatedness, both patterns suggesting deeper evolutionary divergences among taxa located to the east, and more diverse, more recent radiations in the western sub-drainages. We conclude that western Amazonia can be seen as an evolutionary "cradle" of biodiversity for freshwater fishes in the Amazon basin as a whole. Significance StatementThis manuscript reveals spatial patterns of freshwater fish phylogenetic diversity and relatedness and explains its major contemporary and historical drivers in the Amazon basin. Amazon basin contains the highest freshwater biodiversity on Earth, as so investigate phylogenetic dimension of diversity is extremally relevant from the perspective of understanding the information on the evolutionary processes that had shaped Amazonian contemporary fish assemblages.

ecology↗

bioRxiv2018

Global biogeographical regions of freshwater fishes

AimTo define the major biogeographical regions and transition zones for freshwater fish species.\n\nTaxonStrictly freshwater species of actinopterygian fish (i.e., excluding marine and amphidromous fish families).\n\nMethodsWe based our bioregionalisation on a global database of freshwater fish species occurrences in drainage basins, which, after filtering, includes 11 295 species in 2 581 basins. On the basis of this dataset, we generated a bipartite (basin-species) network upon which we applied a hierarchical clustering algorithm (the Map Equation) to detect regions. We tested the robustness of regions with a sensitivity analysis. We identified transition zones between major regions with the participation coefficient, indicating the degree to which a basin has species from multiple regions.\n\nResultsOur bioregionalisation scheme showed two major supercontinental regions (Old World and New World, 50% species of the world and 99.96% endemics each). Nested within these two supercontinental regions lie six major regions (Nearctic, Neotropical, Palearctic, Ethiopian, Sino-Oriental and Australian) with extremely high degrees of endemism (above 96% except for the Palearctic). Transition zones between regions were of limited extent compared to other groups of organisms. We identified numerous subregions with high diversity and endemism in tropical areas (e.g. Neotropical), and a few large subregions with low diversity and endemism at high latitudes (e.g. Palearctic).\n\nMain conclusionsOur results suggest that regions of freshwater fish species were shaped by events of vicariance and geodispersal which were similar to other groups, but with freshwater-specific processes of isolation that led to extremely high degrees of endemism (far exceeding endemism rates of other continental vertebrates), specific boundary locations, and limited extents of transition zones. The identified bioregions and transition zones of freshwater fish species reflect the strong isolation of freshwater fish faunas for the past 10 to 20 million years. The extremely high endemism and diversity of freshwater fish fauna raises many questions about the biogeographical consequences of current introductions and extinctions.

ecology↗

bioRxiv2017

Theoretical solutions for the evaluation of discrimination capacity of species distribution models

The discriminating capacity (i.e., ability to correctly classify presences and absences) of species distribution models (SDMs) is commonly evaluated with metrics such as the Area Under the Receiving Operating Characteristic Curve, the Kappa statistic and the True Skill Statistic (TSS). AUC and Kappa have been repeatedly criticised, but the TSS has fared relatively well since its introduction, mainly because it has been considered as independent of prevalence. In addition, discrimination metrics have been contested because they should be calculated on presence-absence data, but are often used on presence-only or presence-background data. Here, we investigate the TSS and an alternative set of metrics -similarity indices, also known as F-measures. We first show that even in ideal conditions (i.e., perfectly random presence-absence sampling), TSS can be misleading because of its dependence on prevalence, whereas similarity/F-measures provide adequate estimations of model discrimination capacity. Second, we show that in real-world situations where sample prevalence is different from true species prevalence (i.e., biased sampling or presence-pseudoabsence), no discrimination capacity metric provide adequate estimations of model discrimination capacity, including metrics specifically designed for presence-pseudoabsence. Our conclusions are twofold. First, they unequivocally appeal SDM users to understand the potential shortcomings of discrimination metrics when quality presence-absence data are lacking, and we provide recommendations to obtain such data. Second, in the specific case of virtual species, which are increasingly used to develop and test SDM methodologies, we strongly recommend the use of similarity/F-measures, which were not biased by prevalence, contrary to TSS.

ecology↗