Julien Renaud

During the last decades, describing, analysing and understanding the phylogenetic structure of species assemblages has been a central theme in both community ecology and macro‐ecology. Among the wide variety of phylogenetic structure metrics, three have been predominant in the literature: Faith's phylogenetic diversity (PD _Faith ), which represents the sum of the branch lengths of the phylogenetic tree linking all species of a particular assemblage, the mean pairwise distance between all species in an assemblage (MPD) and the pairwise distance between the closest relatives in an assemblage (MNTD). Comparisons between studies using one or several of these metrics are difficult because there has been no comprehensive evaluation of the phylogenetic properties each metric captures. In particular it is unknown how PD _Faith relates to MDP and MNTD. Consequently, it is possible that apparently opposing patterns in different studies might simply reflect differences in metric properties. Here, we aim to fill this gap by comparing these metrics using simulations and empirical data. We first used simulation experiments to test the influence of community structure and size on the mismatch between metrics whilst varying the shape and size of the phylogenetic tree of the species pool. Second we investigated the mismatch between metrics for two empirical datasets (gut microbes and global carnivoran assemblages). We show that MNTD and PD _Faith provide similar information on phylogenetic structure, and respond similarly to variation in species richness and assemblage structure. However, MPD demonstrate a very different behaviour, and is highly sensitive to deep branching structure. We suggest that by combining complementary metrics that are sensitive to processes operating at different phylogenetic depths (i.e. MPD and MNTD or PD _Faith ) we can obtain a better understanding of assemblage structure.

In analogy to the species–area relationship (SAR), one of the few laws in ecology, the phylogenetic diversity–area relationship (PDAR) describes the tendency of phylogenetic diversity (PD) to increas...

Despite numerous studies suggesting that amphibians are highly sensitive to cumulative anthropogenic stresses, the role pollutants play in the decline of amphibian populations remains unclear. Amongst the most common aquatic contaminants, polycyclic aromatic hydrocarbons (PAHs) have been shown to induce several adverse effects on amphibian species in the larval stages. Conversely, adults exposed to high concentrations of the ubiquitous PAH, benzo[a]pyrene (BaP), tolerate the compound thanks to their highly efficient hepatic detoxification mechanisms. Due to this apparent lack of toxic effect on adults, no studies have examined in depth the potential toxicological impact of PAH on the physiology of adult amphibian livers. This study sheds light on the hepatic responses of Xenopus tropicalis when exposed to high environmentally relevant concentrations of BaP, by combining a high throughput transcriptomic approach (mRNA deep sequencing) and a characterization of cellular and physiological modifications to the amphibian liver. Transcriptomic changes observed in BaP-exposed Xenopus were further characterized using a time-dependent enrichment analysis, which revealed the pollutant-dependent gene regulation of important biochemical pathways, such as cholesterol biosynthesis, insulin signaling, adipocytokines signaling, glycolysis/gluconeogenesis and MAPK signaling. These results were substantiated at the physiological level with the detection of a pronounced metabolic disorder resulting in a possible insulin resistance-like syndrome phenotype. Hepatotoxicity induced by lipid and cholesterol metabolism impairments was clearly identified in BaP-exposed individuals. Our data suggested that BaP may disrupt overall liver physiology, and carbohydrate and cholesterol metabolism in particular, even after short-term exposure. These results are further discussed in terms of how this deregulation of liver physiology can lead to general metabolic impairment in amphibians chronically exposed to contaminants, thereby illustrating the role xenobiotics might play in the global decline in amphibian populations.

Aim: To define biome‐scale hotspots of phylogenetic and functional mammalian biodiversity (PDandFD, respectively) and compare them with ‘classical’ hotspots based on species richness (SR) alone.Location: Global.Methods: SR,PDandFDwere computed for 782 terrestrial ecoregions using the distribution ranges of 4616 mammalian species. We used a set of comprehensive diversity indices unified by a recent framework incorporating the relative species coverage in each ecoregion. We built large‐scale multifaceted diversity–area relationships to rank ecoregions according to their levels of biodiversity while accounting for the effect of area on each facet of diversity. Finally we defined hotspots as the top‐ranked ecoregions.Results: While ignoring relative species coverage led to a fairly good congruence between biome‐scale top rankedSR,PDandFDhotspots, ecoregions harbouring a rich and abundantly represented evolutionary history and FD did not match with the top‐ranked ecoregions defined bySR. More importantlyPDandFDhotspots showed important spatial mismatches. We also found thatFDandPDgenerally reached their maximum values faster thanSRas a function of area.Main conclusions: The fact thatPD/FDreach their maximum value faster thanSRcould suggest that the two former facets might be less vulnerable to habitat loss than the latter. While this point is expected, it is the first time that it has been quantified at a global scale and should have important consequences for conservation. Incorporating relative species coverage into the delineation of multifaceted hotspots of diversity led to weak congruence betweenSR,PDandFDhotspots. This means that maximizing species number may fail to preserve those nodes (in the phylogenetic or functional tree) that are relatively abundant in the ecoregion. As a consequence it may be of prime importance to adopt a multifaceted biodiversity perspective to inform conservation strategies at a global scale.