Search

Intense research efforts over the last two decades have renewed our understanding of plant phylogeography and domestication in the Mediterranean basin. Here we aim to investigate the evolutionary history and the origin of domestication of the carob tree (Ceratonia siliqua), which has been cultivated for millennia for food and fodder. We used >1000 microsatellite genotypes to delimit seven carob evolutionary units (CEUs). We investigated genome-wide diversity and evolutionary patterns of the CEUs with 3557 single nucleotide polymorphisms generated by restriction-site associated DNA sequencing (RADseq). To address the complex wild vs. cultivated status of sampled trees, we classified 56 sampled populations across the Mediterranean basin as wild, seminatural or cultivated. Nuclear and cytoplasmic loci were identified from RADseq data and separated for analyses. Phylogenetic analyses of these genomic-wide data allowed us to resolve west-to-east expansions from a single long-term refugium probably located in the foothills of the High Atlas Mountains near the Atlantic coast. Our findings support multiple origins of domestication with a low impact on the genetic diversity at range-wide level. The carob was mostly domesticated from locally selected wild genotypes and scattered long-distance westward dispersals of domesticated varieties by humans, concomitant with major historical migrations by Romans, Greeks and Arabs. Ex situ efforts to preserve carob genetic resources should prioritize accessions from both western and eastern populations, with emphasis on the most differentiated CEUs situated in southwest Morocco, south Spain and eastern Mediterranean. Our study highlights the relevance of wild and seminatural habitats in the conservation of genetic resources for cultivated trees., (© 2022 The Authors. Molecular Ecology published by John Wiley & Sons Ltd.)

The onset of the Acheulean, marked by the emergence of large cutting tools (LCTs), is considered a major technological advance in the Early Stone Age and a key turning point in human evolution. The Acheulean originated in East Africa at ~ 1.8-1.6 Ma and is reported in South Africa between ~ 1.6 and > 1.0 Ma. The timing of its appearance and development in North Africa have been poorly known due to the near-absence of well-dated sites in reliable contexts. The ~ 1 Ma stone artefacts of Tighennif (Algeria) and Thomas Quarry I-Unit L (ThI-L) at Casablanca (Morocco) are thus far regarded as documenting the oldest Acheulean in North Africa but whatever the precision of their stratigraphical position, both deserve a better chronology. Here we provide a chronology for ThI-L, based on new magnetostratigraphic and geochemical data. Added to the existing lithostratigraphy of the Casablanca sequence, these results provide the first robust chronostratigraphic framework for the early North African Acheulean and firmly establish its emergence in this part of the continent back at least to ~ 1.3 Ma., (© 2021. The Author(s).)

The demography of a population is often reduced to the apparent (or local) survival of individuals and their realised fecundity within a study area defined according to logistical constraints rather than landscape features. Such demographics are then used to infer whether a local population contributes positively to population dynamics across a wider landscape context. Such a simplistic approach ignores a fundamental process underpinning population dynamics: dispersal. Indeed, it has long been accepted that immigration contributed by dispersers that emigrated from neighbouring populations may strongly influence the net growth of a local population. To date however, we lack a clear picture of how widely immigration rate varies both among and within populations, in relation to extrinsic and intrinsic ecological conditions, even for the best-studied avian and mammalian populations. This empirical knowledge gap precludes the emergence of a sound conceptual framework that ought to inform conservation and population ecology. This review, conducted on both birds and mammals, has thus three complementary objectives. First, we describe and evaluate the relative merits of methods used to quantify immigration and how they relate to widely applicable metrics. We identify two simple and unifying metrics to measure immigration: the immigration rate i t defined as the ratio of the number of immigrants present in the population at time t + 1 and the total breeding population in year t, and π t , the proportion of immigrants among new recruits (i.e. new breeders). Two recently developed methods are likely to provide the most valuable data on immigration in the near future: individual parentage (rather than population) assignments based on genetic sampling, and spatially explicit integrated population models combining multiple sources of demographic data (survival, fecundity and population counts). Second, we report on a systematic literature review of studies providing a quantitative measure of immigration. Although the diversity of methods employed precludes detailed analyses, it appears that the number of immigrants exceeds locally born individuals in recruitment for most avian populations (median π t  = 0.57, N = 45 estimates from 37 studies), a figure twofold higher than estimated for mammalian populations (median π t  = 0.26, N = 33 estimates from 11 studies). Third, recent quantitative studies reveal that immigration can be the main driver of temporal variation in population growth rates, across a wide array of demographic and spatial contexts. To what extent immigration acts as a regulatory process has however been considered only rarely to date and deserves more attention. Overall, it is likely that most populations benefit from immigrants without necessarily being sink populations. Furthermore, we suggest that quantitative estimates of immigration should be core to future demographic studies and plead for more empirical evidence about the ways in which immigration interacts with local demographic processes to shape population dynamics. Finally, we discuss how to tackle spatial population dynamics by exploring, beyond the classical source-sink framework, the extent to which populations exchange individuals according to spatial scale and type of population distribution throughout the landscape., (© 2019 Cambridge Philosophical Society.)

A mass mortality event is devastating the populations of the endemic bivalve Pinna nobilis in the Mediterranean Sea from early autumn 2016. A newly described Haplosporidian endoparasite (Haplosporidium pinnae) is the most probable cause of this ecological catastrophe placing one of the largest bivalves of the world on the brink of extinction. As a pivotal step towards Pinna nobilis conservation, this contribution combines scientists and citizens' data to address the fast- and vast-dispersion and prevalence outbreaks of the pathogen. Therefore, the potential role of currents on parasite expansion was addressed by means of drift simulations of virtual particles in a high-resolution regional currents model. A generalized additive model was implemented to test if environmental factors could modulate the infection of Pinna nobilis populations. The results strongly suggest that the parasite has probably dispersed regionally by surface currents, and that the disease expression seems to be closely related to temperatures above 13.5 °C and to a salinity range between 36.5-39.7 psu. The most likely spread of the disease along the Mediterranean basin associated with scattered survival spots and very few survivors (potentially resistant individuals), point to a challenging scenario for conservation of the emblematic Pinna nobilis, which will require fast and strategic management measures and should make use of the essential role citizen science projects can play.

The black caiman is one of the largest neotropical top predators, which means that it could play a structuring role within swamp ecosystems. However, because of the difficulties inherent to studying black caimans, data are sorely lacking on many aspects of their general biology, natural history, and ecology, especially in French Guiana. We conducted a detailed study of the Agami Pond black caiman population using a multidisciplinary approach. The aim was to better understand the species' dietary ecology and movements in the pond, and thus its functional role in pond system. We gathered natural history data, tracked caiman movements using satellite transmitters, and characterized feeding ecology via stable isotope analysis. Our study was carried out over three sampling periods and spanned both wet and dry seasons, which differ in their hydrological and ecological conditions. Our results show that black caiman abundance and age demographics differed between seasons in Agami Pond. In the dry season, Agami Pond is one of the only areas within the marsh to hold water. It thus contains large quantities of different fish species, which form the basis of the black caiman's diet. Caiman body size, a proxy for age class, was around 1.5 meters. During the wet season, which corresponds to the breeding period for migratory birds (e.g., Agami herons), adult black caimans are present in Agami Pond. Adults were most abundant in the inundated forest. There, most individuals measured up to 2 meters. They also exhibited a particular "predatory" behavior near bird nests, preying on fallen chicks and adults. Juveniles and subadults were present during both seasons in the pond's open waters. These behavioral observations were backed up by stable isotope analysis, which revealed ontogenetic variation in the caiman's isotopic values. This isotopic variation reflected variation in diet that likely reduced intraspecific competition between adults and young. The telemetry and microchip data show that different age classes had different movement patterns and that seasonal variation in the pond may influence caiman prey availability and reproductive behavior. The new information gathered should help predict this species' responses to potential ecosystem disturbance (e.g., water pollution, habitat destruction) and inform the development of an effective conservation plan that involves locals and wildlife officials., Competing Interests: The authors have declared that no competing interests exist.

Molybdoenzymes are ubiquitous in living organisms and catalyze, for most of them, oxidation-reduction reactions using a large range of substrates. Periplasmic nitrate reductase (NapAB) from Rhodobacter sphaeroides catalyzes the 2-electron reduction of nitrate into nitrite. Its active site is a Mo bis-(pyranopterin guanine dinucleotide), or Mo-bisPGD, found in most prokaryotic molybdoenzymes. A [4Fe-4S] cluster and two c-type hemes form an intramolecular electron transfer chain that deliver electrons to the active site. Lysine 56 is a highly conserved amino acid which connects, through hydrogen-bonds, the [4Fe-4S] center to one of the pyranopterin ligands of the Mo-cofactor. This residue was proposed to be involved in the intramolecular electron transfer, either defining an electron transfer pathway between the two redox cofactors, and/or modulating their redox properties. In this work, we investigated the role of this lysine by combining site-directed mutagenesis, activity assays, redox titrations, EPR and HYSCORE spectroscopies. Removal of a positively-charged residue at position 56 strongly decreased the redox potential of the [4Fe-4S] cluster at pH 8 by 230 mV to 400 mV in the K56H and K56M mutants, respectively, thus affecting the kinetics of electron transfer from the hemes to the [4Fe-4S] center up to 5 orders of magnitude. This effect was partly reversed at acidic pH in the K56H mutant likely due to protonation of the imidazole ring of the histidine. Overall, our study demonstrates the critical role of a charged residue from the second coordination sphere in tuning the reduction potential of the [4Fe-4S] cluster in RsNapAB and related molybdoenzymes., (Copyright © 2019. Published by Elsevier B.V.)

Astragalus tragacantha is a protected plant species in France that grows even in the trace metal and metalloid (TMM) polluted soils of the Calanques National Park (PNCal). Soils are mainly contaminated by lead, copper, zinc and arsenic. An ex situ experiment was conducted, firstly to determine the molecular responses and root traits involved in the TMM tolerance of this plant species by growing individuals in a soil from the surroundings of one of the brownfields of the PNCal, known as l'Escalette, where this plant species grows spontaneously. Secondly, in order to determine the plasticity of these responses, seeds were collected from three different populations, at l'Escalette (polluted site), one from the Frioul archipelago (non-polluted, insular site) and one from La Seyne (non-polluted, littoral site). The results of this study confirmed the capacity of A. tragacantha to germinate and grow in TMM contaminated soils. Only moderate significant variations in chlorophyll and flavonol indices, proline content and antioxidant activities were detected between polluted and control soil conditions for all populations. The main driver for A. tragacantha TMM tolerance seemed to be its ability to be associated with root symbionts i.e. arbuscular mycorrhizal fungi and dark septate endophytes, corresponding to a nutrient-uptake strategy trait. This work provides support for the challenge of A. tragacantha conservation along the littoral of the PNCal, because increasing the number of A. tragacantha individuals would both increase vegetation cover of the polluted soils to reduce the pollution transfer and reinforce the populations of this species., (Copyright © 2018 Elsevier Ltd. All rights reserved.)

Sponges harbor characteristic microbiomes derived from symbiotic relationships shaping their lifestyle and survival. Haliclona fulva is encrusting marine sponge species dwelling in coralligenous accretions or semidark caves of the Mediterranean Sea and the near Atlantic Ocean. In this work, we characterized the abundance and core microbial community composition found in specimens of H. fulva by means of electron microscopy and 16S amplicon Illumina sequencing. We provide evidence of its low microbial abundance (LMA) nature. We found that the H. fulva core microbiome is dominated by sequences belonging to the orders Nitrosomonadales and Cenarchaeales. Seventy percent of the reads assigned to these phylotypes grouped in a very small number of high-frequency operational taxonomic units, representing niche-specific species Cenarchaeum symbiosum and uncultured Betaproteobacteria HF1, a new eubacterial ribotype variant found in H. fulva. The microbial composition of H. fulva is quite distinct from those reported in sponge species of the same Haliclona genus. We also detected evidence of an excretion/capturing loop between these abundant microorganisms and planktonic microbes by analyzing shifts in seawater planktonic microbial content exposed to healthy sponge specimens maintained in aquaria. Our results suggest that horizontal transmission is very likely the main mechanism for symbionts' acquisition by H. fulva. So far, this is the first shallow water sponge species harboring such a specific and predominant assemblage composed of these eubacterial and archaeal ribotypes. Our data suggests that this symbiotic relationship is very stable over time, indicating that the identified core microbial symbionts may play key roles in the holobiont functioning.

Four Haploops species collected in the North Atlantic Ocean are studied. One of them, H. islandica is a new species for the science. The three other species, H. carinata, H. setosa, H. robusta, were described from a long time, but many confusions exist about these species because their morphological nearness. The four species are described and illustrated in detail, and their distribution around the Iceland is specified. A key of the 23 species known nowadays is given permetting to separate the different species of the Haploops genus.

Ecological interactions in the marine environment are now recognized to be partly held by chemical cues produced by marine organisms. In particular, sponges are sessile animals thought to rely on the bioactive substances they synthesize to ensure their development and defense. However, the mechanisms leading the sponges to use their specialized metabolites as chemical cues remain unknown. Here we report the constant release of bioactive polycyclic guanidinic alkaloids by the Mediterranean sponge Crambe crambe into the dissolved and the particulate phases using a targeted metabolomics study. These compounds were proven to be stored into already described specialized (spherulous) sponge cells and dispersed into the water column after release through the sponge exhaling channels (oscula), leading to a chemical shield surrounding the sponge. Low concentrations of these compounds were demonstrated to have teratogenic effects on embryos of a common sea squirt (ascidian). This mechanism of action called spherulization may therefore contribute to the ecological success of encrusting sponges that need to extend their substrate cover to expand.

Epidemiological studies have associated environmental exposure to polychlorinated biphenyls (PCBs) with an increased risk of type 2 diabetes; however, little is known about the underlying mechanisms involved in the metabolic side-effects of PCB. Our study evaluated the transcriptional effects of a subchronic exposure (gavage at Day 0 and Day 15 with 10 or 100 μmol/Kg bw) to PCB118 (dioxin-like PCB), PCB153 (non-dioxin-like PCB), or an equimolar mixture of PCB118 and PCB153 on various tissues (liver, visceral adipose tissue, muscle, and colon) in mice. Our results showed that a short-term exposure to PCB118 and/or PCB153 enhanced circulating triglyceride levels but did not affect glycemia. Among the studied tissues, we did not observe any modification of the expression of inflammation-related genes, such as cytokines or chemokines. The main transcriptional effects were observed in visceral adipose and liver tissues. We found a downregulation of lipin1 and glut4 expression in these two target organs. In adipose tissue, we also showed a downregulation of Agpat2, Slc25a1, and Fasn. All of these genes are involved in lipid metabolism and insulin resistance. In muscles, we observed an induction of CnR1 and Foxo3 expression, which may be partly involved in PCB metabolic effects. In summary, our results suggest that lipin1 and glut4, notably in adipose tissue, are the main targeted genes in PCB-induced metabolic disorders, however, further studies are required to fully elucidate the mechanisms involved.