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International audience; The distribution of marine sponges in the tropical Southwest Pacific Ocean is largely unexplored despite the vital ecological role of sponges in coral reefs and their value as sources of metabolites for drug design. Several collection campaigns to the French Polynesian archipelagos (Society, Marquesas, Tuamotu, Gambier, and Austral) were conducted to assess the bio-and chemodiversity of the island groups. In the course of these scientific expeditions, more than 200 identified sponge specimens were acquired, for which we were able to assign 102 Molecular Operational Taxonomic Units (MOTUs). Based on these MOTUs, we assessed, in the largest analysis of its kind for this area to date, the sponge composition and faunistic overlaps of the marine province Southeast Polynesia with Marquesas and Central Polynesia. We also compared the sponge fauna of these Eastern Indo-Pacific provinces with marine provinces of the adjacent Central Indo-Pacific realm. Our findings corroborate that sponge faunal similarity within marine realms is higher than among realms, and follows the marine barriers to gene flow observed for other taxa. We detected high levels of provincial endemism for marine sponges, consistent with findings from other Indo-Pacific regions. At the level of province, geographical distance and ocean surface currents influence faunal similarity, and constitute the primary factors for the connectivity of sponge faunas between the disjunct and remote island groups in the tropical Southwest Pacific Ocean. Keywords Marine provinces • Ecoregions • Marquesas • Tuamotu • Oceania • Dispersal Communicated by Khor Waiho.

Marine phytoplankton play important roles in the global ecosystem, with a limited number of cosmopolitan keystone species driving their biomass. Recent studies have revealed that many of these phytoplankton are complexes composed of sibling species, but little is known about the evolutionary processes underlying their formation. Gephyrocapsa huxleyi, a widely distributed and abundant unicellular marine planktonic algae, produces calcified scales (coccoliths), thereby significantly affects global biogeochemical cycles via sequestration of inorganic carbon. This species is composed of morphotypes defined by differing degrees of coccolith calcification, the evolutionary ecology of which remains unclear. Here, we report an integrated morphological, ecological and genomic survey across globally distributed G. huxleyi strains to reconstruct evolutionary relationships between morphotypes in relation to their habitats. While G. huxleyi has been considered a single cosmopolitan species, our analyses demonstrate that it has evolved to comprise at least three distinct species, which led us to formally revise the taxonomy of the G. huxleyi complex. Moreover, the first speciation event occurred before the onset of the last interglacial period (~140 ka), while the second followed during this interglacial. Then, further rapid diversifications occurred during the most recent ice-sheet expansion of the last glacial period and established morphotypes as dominant populations across environmental clines. These results suggest that glacial-cycle dynamics contributed to the isolation of ocean basins and the segregations of oceans fronts as extrinsic drivers of micro-evolutionary radiations in extant marine phytoplankton.

International audience; Sowing of wildflower strips has been integrated in agri-environment schemes of several European countries. Their beneficial effects on natural enemies of pest insects are well documented but (1) the desired spill-over into crop fields has not always been demonstrated, and (2) the need to adapt sown mixtures to regional climatic differences has been rarely addressed.We set up a multi-site experiment in different French climatic regions to compare effects of a wildflower strip with a grass mixture and spontaneous vegetation. The design included five regions, three to five fields per region and the three strip treatments being repeated in each field. We tested strip treatment effects on vegetation (plant species richness, plant and flower cover) and on natural enemies (hoverflies, ladybirds, aphid predation). In a subset, we further analysed the spill-over into winter wheat fields including natural enemies and pest insects (cereal aphids, leaf beetles).The wildflower strip mixture developed well in all regions and increased plant species richness and flower cover compared with grass strips and spontaneous vegetation. We found a corresponding higher hoverfly abundance and aphid predation in wildflower strips that were consistent in all regions, whereas ladybird abundance was not affected. A significantly higher hoverfly abundance, aphid predation and aphid parasitism in wheat fields close to wildflower strips indicated a spill-over. No corresponding margin treatment effects were observed for aphid and leaf beetle abundance in the field. A multivariate analysis comparing the influence of climate and vegetation parameters showed that floral cover better explained variation in natural enemy abundance and predation than climate. Our results demonstrated that similar mixtures of native plants can be used over large climatic gradients to improve biocontrol. Further research is needed to improve spill-over into crop fields and to obtain consistently strong effects in different climate zones.

Funding: Open access funding provided by Norwegian University of Science and Technology. Bioinformatics and computational analyses were supported by the University of St Andrews Bioinformatics Unit which is funded by a Wellcome Trust ISSF award [grant 105621/Z/14/Z] and ran on cluster marvin and Crop Diversity HPC. Contemporary sample DNA extractions were supported by People’s Trust for Endangered Species and the sequencing costs were supported by the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska- Curie grant agreement No. 663830 awarded to A.D.F., by the Total Foundation awarded to M.L., the University of Groningen awarded to M.C.F., and the Marine Alliance for Science and Technology for Scotland and The Russell Trust awarded to O.E.G. M.N. was funded by MASTS and the Crawford Hayes fund. A.D.F. was funded by Marie Skłodowska-Curie grant agreement No. 663830 and the European Research Council grant agreement No. ERC-COG-101045346. Parallel evolution provides strong evidence of adaptation by natural selection due to local environmental variation. Yet, the chronology, and mode of the process of parallel evolution remains debated. Here, we harness the temporal resolution of paleogenomics to address these long-standing questions, by comparing genomes originating from the mid-Holocene (8610-5626 years before present, BP) to contemporary pairs of coastal-pelagic ecotypes of bottlenose dolphin. We find that the affinity of ancient samples to coastal populations increases as the age of the samples decreases. We assess the youngest genome (5626 years BP) at sites previously inferred to be under parallel selection to coastal habitats and find it contained coastal-associated genotypes. Thus, coastal-associated variants rose to detectable frequencies close to the emergence of coastal habitat. Admixture graph analyses reveal a reticulate evolutionary history between pelagic and coastal populations, sharing standing genetic variation that facilitated rapid adaptation to newly emerged coastal habitats. Publisher PDF

The full dataset is freely available at the link below (perennial repository) for academic use or other non-commercial use: https://lab.plantnet.org/seafile/d/936fe4298a5a4f4c8dbd/; The difficulty to measure or predict species community composition at fine spatio-temporal resolution and over large spatial scales severely hampers our ability to understand species assemblages and take appropriate conservation measures. Despite the progress in species distribution modeling (SDM) over the past decades, SDM are just beginning to integrate high resolution remote sensing data and their predictions are still entailed by the many biases and heterogeneous quality of the available biodiversity observations, most often opportunistic presence only data. We designed a European scale dataset covering around 10K plant species to calibrate and evaluate SDM predictions of species composition in space and time at high spatial resolution (~10m), and study their spatial transferability. For model training, we extracted and harmonized 5 million heterogeneous presence-only observations from selected GBIF datasets and 5 thousand exhaustive presence-absence surveys both sampled during the 2017-2021. We associated them to various environmental rasters classically used in SDMs, as well as to 10x10m resolution RGB and Near-Infra-Red satellite images and 20 years-time series of climatic variables and satellite point values. The evaluation dataset is based on 20K standardized presence-absence surveys separated from the training set with a spatial block hold out procedure. The GeoLifeCLEF 2023 dataset is open access and the first benchmark for researchers aiming to improve the prediction of plant species composition at a very fine spatial grain and at continental scale. It is also a space to explore new ways of combining massive and diverse species observations with environmental information at various scales. Innovative AI-based approaches, in particular, should be among the most interesting methods to experiment with on the GeoLifeCLEF 2023 dataset.

The full dataset is freely available at the link below (perennial repository) for academic use or other non-commercial use: https://lab.plantnet.org/seafile/d/936fe4298a5a4f4c8dbd/; The difficulty to measure or predict species community composition at fine spatio-temporal resolution and over large spatial scales severely hampers our ability to understand species assemblages and take appropriate conservation measures. Despite the progress in species distribution modeling (SDM) over the past decades, SDM are just beginning to integrate high resolution remote sensing data and their predictions are still entailed by the many biases and heterogeneous quality of the available biodiversity observations, most often opportunistic presence only data. We designed a European scale dataset covering around 10K plant species to calibrate and evaluate SDM predictions of species composition in space and time at high spatial resolution (~10m), and study their spatial transferability. For model training, we extracted and harmonized 5 million heterogeneous presence-only observations from selected GBIF datasets and 5 thousand exhaustive presence-absence surveys both sampled during the 2017-2021. We associated them to various environmental rasters classically used in SDMs, as well as to 10x10m resolution RGB and Near-Infra-Red satellite images and 20 years-time series of climatic variables and satellite point values. The evaluation dataset is based on 20K standardized presence-absence surveys separated from the training set with a spatial block hold out procedure. The GeoLifeCLEF 2023 dataset is open access and the first benchmark for researchers aiming to improve the prediction of plant species composition at a very fine spatial grain and at continental scale. It is also a space to explore new ways of combining massive and diverse species observations with environmental information at various scales. Innovative AI-based approaches, in particular, should be among the most interesting methods to experiment with on the GeoLifeCLEF 2023 dataset.

International audience; The growing evidence for the role of introgression in evolution is challenging for species delimitation, taxonomy, and conservation. Here, we examine the isolation of Saxifraga delphinensis, a south-west alpine narrow endemic, from its sympatric congeners Saxifraga exarata and Saxifraga moschata. Our analyses, based on morphological, molecular and genome-wide data, were extended to taxa from Jura, Massif Central, north-east Iberian mountains and Pyrenees to broaden the phylogenetic scope of the study. Phylogenetic results support the close relationship between (i) S. delphinensis, Saxifraga cebennensis and one population of S. exarata from Queyras and (ii) between S. lamottei, S. giziana and S. moschata. Saxifraga exarata, which was extensively sampled, is composed of several clades and is paraphyletic to other taxa. While morphological and genetic data support the evolutionary distinctiveness of S. delphinensis, introgression with S. exarata is shown by various data and analyses. In addition, ABBA-BABA analyses and plastome phylogeny reveal a possible contribution of the north-east Iberian endemic Saxifraga vayredana into the history of S. delphinensis. Overall, the results show a complex evolutionary history with frequent hybridization and spanning several mountain ranges in Europe.

International audience

International audience; Humans have built ports on all the coasts of the world, allowing people to travel, exploit the sea, and develop trade. The proliferation of these artificial habitats and the associated maritime traffic are not predicted to fade in the coming decades. Ports share common characteristics: species find themselves in novel singular environments, with particular abiotic properties-e.g., pollutants, shading, protection from wave action-within novel communities in a melting-pot of invasive and native taxa. Here we discuss how this drives evolution, including setting-up of new connectivity hubs and gateways, adaptive responses to exposure to new chemicals or new biotic communities, and hybridization between lineages that would have never come into contact naturally. There are still important knowledge gaps however, such as the lack of experimental tests to distinguish adaptation from acclimation processes, the lack of studies to understand the putative threats of port lineages to natural populations, or to better understand the outcomes and fitness effects of anthropogenic hybridization. We thus call for further research examining "biological portuarization", defined as the repeated evolution of marine species in port-ecosystems under human-altered selective pressures. Furthermore, we argue that ports act as giant mesocosms often isolated from the open sea by seawalls and locks, and so provide replicated life-size evolutionary experiments essential to support predictive evolutionary sciences.

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International audience

The world's largest butterfly is the microendemic Papua New Guinean Ornithoptera alexandrae. Despite years of conservation efforts to protect its habitat and breed this up-to-28-cm butterfly, this species still figures as endangered in the IUCN Red List and is only known from two allopatric populations occupying a total of only ∼140 km². Here we aim at assembling reference genomes for this species to investigate its genomic diversity, historical demography and determine whether the population is structured, which could provide guidance for conservation programs attempting to (inter)breed the two populations. Using a combination of long and short DNA reads and RNA sequencing, we assembled six reference genomes of the tribe Troidini, with four annotated genomes of O. alexandrae and two genomes of related species Ornithoptera priamus and Troides oblongomaculatus. We estimated the genomic diversity of the three species, and we proposed scenarios for the historical population demography using two polymorphism-based methods taking into account the characteristics of low-polymorphic invertebrates. Indeed, chromosome-scale assemblies reveal very low levels of nuclear heterozygosity across Troidini, which appears to be exceptionally low for O. alexandrae (lower than 0.01%). Demographic analyses demonstrate low and steadily declining Ne throughout O. alexandrae history, with a divergence into two distinct populations about 10,000 years ago. These results suggest that O. alexandrae distribution has been microendemic for a long time. It should also make local conservation programs aware of the genomic divergence of the two populations, which should not be ignored if any attempt is made to cross the two populations.

Cultural transmission of reproductive success has been observed in many human populations as well as other animals. Cultural transmission of reproductive success consists of a positive correlation of nongenetic origin between the progeny size of parents and children. This correlation can result from various factors, such as the social influence of parents on their children, the increase of children’s survival through allocare from uncles and aunts, or the transmission of resources. Here, we study the evolution of genomic diversity over time under cultural transmission of reproductive success. Cultural transmission of reproductive success has a threefold impact on population genetics: (1) the effective population size decreases when cultural transmission of reproductive success starts, mimicking a population contraction, and increases back to its original value when cultural transmission of reproductive success stops; (2) coalescent tree topologies are distorted under cultural transmission of reproductive success, with higher imbalance and a higher number of polytomies; and (3) branch lengths are reduced nonhomogenously, with a higher impact on older branches. Under long-lasting cultural transmission of reproductive success, the effective population size stabilizes but the distortion of tree topology and the nonhomogenous branch length reduction remain, yielding U-shaped site frequency spectra under a constant population size. We show that this yields a bias in site frequency spectra-based demographic inference. Considering that cultural transmission of reproductive success was detected in numerous human and animal populations worldwide, one should be cautious because inferring population past histories from genomic data can be biased by this cultural process.

Accurate species phylogenies are a prerequisite for evolutionary research. Teleosts are by far the largest and the most diversified group of extant vertebrates, but relationships among the three oldest lineages of extant teleosts remain unresolved. Based on seven high-quality new genome assemblies in Elopomorpha (tarpons, eels), we revisited the topology of the deepest branches of the teleost phylogeny using independent gene sequence and chromosomal rearrangement phylogenomic approaches. These analyses converged to a single scenario that unambiguously places the Elopomorpha and Osteoglossomorpha (bony-tongues) in a monophyletic group sister to all other teleosts, i.e., the Clupeocephala lineage. This finding resolves over 50 years of controversy on the evolutionary relationships of these lineages and highlights the power of combining different levels of genome-wide information to solve complex phylogenies.One-Sentence SummaryWhole-genome analyses place Elopomorpha (tarpons, eels) and Osteoglossomorpha (bony-tongues) as sister groups at the deepest branching of crown teleosts.

1. Aggregated species occurrence and abundance data from disparate sources are increasingly accessible to ecologists for the analysis of temporal trends in biodiversity. However, sampling biases relevant to any given research question are often poorly explored and infrequently reported; this can undermine statistical inference. In other disciplines, it is common for researchers to complete “risk-of-bias” assessments to expose and document the potential for biases to undermine conclusions. The huge growth in available data, and recent controversies surrounding their use to infer temporal trends, indicate that similar assessments are urgently needed in ecology. 2. We introduce ROBITT, a structured tool for assessing the “Risk-Of-Bias In studies of Temporal Trends in ecology”. ROBITT has a similar format to its counterparts in other disciplines: it comprises signalling questions designed to elicit information on the potential for bias in key study domains. In answering these, users will define study inferential goal(s) and relevant statistical target populations. This information is used to assess potential sampling biases across domains relevant to the research question (e.g. geography, taxonomy, environment), and how these vary through time. If assessments indicate biases, then usersmust clearly describe them and/or explain what mitigating action will be taken.3. Everything that users need to complete a ROBITT assessment is provided: the tool,a guidance document,and a worked example. Following other disciplines, the tool and guidance document were developed through a consensus-forming process across experts working in relevant areas of ecology and evidence synthesis.4. We propose that researchers should be strongly encouraged to include a ROBITT assessment when publishing studies of biodiversitytrends, especially when usingaggregated data. This will help researchers to structure their thinking, clearly acknowledge potential sampling issues,highlight where expert consultation is required, and provides an opportunity to describe data checks that might gounreported. ROBITT will also enable reviewers, editors, and readers to establish how well research conclusions are supported given a dataset combined with some analytical approach. In turn, itshouldstrengthen evidence-based policy and practice, reduce differing interpretations of data, and provide a clearer picture of the uncertainties associated with our understanding of reality. risk-of-bias; speciesoccurrence data; temporal trends; Essential Biodiversity Variables; indicators; uncertainty; insect declines

International audience; On one hand, studies on Salmo biological variations during the last centuries have led to the morphological description of several Salmo species (>50). On the other hand, Salmo trutta is seen as a polymorphic species, i.e. including populations with different morphotypes and ecotypes, subdivided into nine genetically divergent evolutionary lineages. For 30 years, phylogeographic and phylogenetic investigations tried to solve the Salmo systematic problem using the mitochondrial control region, sometimes combined with other mitochondrial (e.g. protein coding region or rRNA genes) or nuclear (e.g. allozymes or microsatellites) markers. With the advent of high throughput next-generation sequencing, complete mitogenomes were made available for Salmo phylogenetic studies. Even better, complete genome or chromosomes with annotations as well as genes of interest can now be loaded from public database. However, in the genomic era, some challenges still need to be addressed such as an appropriate taxon sampling or the identification of orthologous genes before having an accurate phylogeny. In the present review, I examine how traditional molecular markers contributed to our knowledge of trout systematics, and what we can expect from the genomics revolution.

We investigated the controversial origin of domestic sheep (Ovis aries) using large samples of contemporary and ancient domestic individuals and their closest wild relatives: the Asiatic mouflon (Ovis gmelini), the urial (Ovis vignei) and the argali (Ovis ammon). A phylogeny based on mitochondrial DNA, including 213 new cytochrome-b sequences of wild Ovism confirmed that O. gmelini is the maternal ancestor of sheep and precluded mtDNA contributions from O. vignei (and O. gmelini × O. vignei hybrids) to domestic lineages. We also produced 54 new control region sequences showing shared haplogroups (A, B, C and E) between domestic sheep and wild O. gmelini which localized the domestication center in eastern Anatolia and central Zagros, excluding regions further east where exclusively wild haplogroups were found. This overlaps with the geographic distribution of O. gmelini gmelini, further suggesting that the maternal origin of domestic sheep derives from this subspecies. Additionally, we produced 57 new CR sequences of Neolithic sheep remains from a large area covering Anatolia to Europe, showing the early presence of at least three mitochondrial haplogroups (A, B and D) in Western colonization routes. This confirmed that sheep domestication was a large-scale process that captured diverse maternal lineages (haplogroups).

The knowledge on symbiotic microorganisms of insects has increased in recent years, yet relatively little data is available on non-pathogenic viruses. Here we studied the virome of the parasitoid wasp Anagyrus vladimiri (Hymenoptera: Encyrtidae), a biocontrol agent of mealybugs. By high-throughput sequencing of viral nucleic acids, we revealed three novel viruses, belonging to the families Reoviridae (provisionally termed AnvRV [Anagyrus vladimiri reovirus]), Iflaviridae (AnvIFV) and Dicistroviridae (AnvDV). Phylogenetic analysis further classified the AnvRV in the genus Idnoreovirus, and the AnvDV in the genus Triatovirus. The genome of AnvRV is comprised of 10 distinct genomic segments ranging in length from 1.5 to 4.2 Kbp, but only two out of the 10 open reading frames (ORFs) have a known function. AnvIFV and AnvDV each have one polypeptide ORF, which is typical to iflaviruses but very un-common among dicistroviruses. AnvRV was found to be fixed in a mass-reared population of A. vladimiri, whereas it’s prevalence in field-collected wasps was ~15%. Similarly, the prevalence of AnvIFV and AnvDV were much higher in the mass rearing population than in the field population. Transmission electron micrographs of females’ ovaries revealed clusters and viroplasms of Reovirus-like particles in follicle cells. AnvRV was not detected in the mealybugs, suggesting that this virus is truly associated with the wasps. The possible effects of these viruses on A. vladimiri’s biology, and on biocontrol agents in general are discussed. Our findings identify RNA viruses as potential players involved in the multitrophic system of mealybugs, their parasitoids and other members of the holobiont.ImportanceDifferent biological control approaches use industrially mass-reared natural enemy insects to reduce damage of arthropod pests. Such mass-reared cultures may be positively and/or negatively affected by various microorganisms, including viruses. Yet, current knowledge on virus diversity, especially in arthropods, is limited. Here, we provide the first virome characterization of a member of the wasps family Encyrtidae - the member being the parasitoid Anagyrus vladimiri - a commercially important natural enemy of mealybug pests. We describe the genome of three previously unknown RNA viruses, co-inhabiting this parasitoid, and elaborate on the prevalence of those viruses in individual wasps of both mass-reared and environmental origins. Microscopy images suggest that at least one of the viruses is transmitted maternally via the ovaries. We discuss the genomic structure of the viruses and the possible relationship between those viruses and the A. vladimiri host, with implications on improvement of biocontrol of mealybug pests.

The slow–fast continuum is a commonly used framework to describe variation in life-history strategies across species. Individual life histories have also been assumed to follow a similar pattern, especially in the pace-of-life syndrome literature. However, whether a slow–fast continuum commonly explains life-history variation among individuals within a population remains unclear. Here, we formally tested for the presence of a slow–fast continuum of life histories both within populations and across species using detailed long-term individual-based demographic data for 17 bird and mammal species with markedly different life histories. We estimated adult lifespan, age at first reproduction, annual breeding frequency, and annual fecundity, and identified the main axes of life-history variation using principal component analyses. Across species, we retrieved the slow–fast continuum as the main axis of life-history variation. However, within populations, the patterns of individual life-history variation did not align with a slow–fast continuum in any species. Thus, a continuum ranking individuals from slow to fast living is unlikely to shape individual differences in life histories within populations. Rather, individual life-history variation is likely idiosyncratic across species, potentially because of processes such as stochasticity, density dependence, and individual differences in resource acquisition that affect species differently and generate non-generalizable patterns across species.

International audience; Although diel activity time is a major axis of species' niche space, very few conservation measures focus on preserving daily periods free of anthropogenic pressures. While the spatial ecology of bats has received much attention, less is known about their temporal ecology, the knowledge being dispersed in studies of limited taxonomical, spatial and temporal range. We used data from the French bat monitoring program based on citizen science and standardised acoustic recordings (4409 sites monitored and 9807 nights monitored from 2014 to 2020) to characterise the diel activity patterns of 20 bat species so that their consideration in mitigation measures can help conservation. We designed a method to extract times of key descriptors and describe bat activity distribution throughout the night. We found that bat species could be separated in three functional groups characterised by a crepuscular activity, an activity that occurs when it is completely dark or an intermediate activity. We showed variations of diel activity patterns depending on season. We argue that accounting for these complex diel activity patterns would help design efficient mitigation measures, for instance to reduce the exposure of bats to light pollution or wind turbines. Overall, we advocate multi-taxa approaches to design conservation policies adapted to both the temporal and spatial distributions of species.

Aim:Our current understanding of the causes of global extinction risk is mostly informed by the expert knowledge-based “threats classification scheme” of the IUCN Red List of Threatened Species. Studies based on this dataset came to different conclusions about the relative importance of threats to species, depending on which taxonomic groups and levels of extinction risk were considered, and which version of the database was used. A key reason may lie in data limitations as causes of threat are well known for charismatic and well-studied species, but not for the majority of species assessed. Here, we aim to fill current knowledge gaps about the importance of drivers of global extinction risks by focusing on endemic species.Location:Global.Methods:We examined country-level variation in the proportion of globally threatened and extinct endemic species (Index of Threat, IoT) with a range of spatially explicit information about anthropogenic pressures, mitigation measures and data limitations.Results:IoT coincided with several anthropogenic pressures, with substantial differences among kingdoms, life-forms, levels of extinction risk and geographic locations. IoT of plants, particularly tropical woody plants of moderate extinction risk, was higher in countries with higher GDP and more invasive species. Furthermore, IoT of animals, particularly tropical mammals and invertebrates of moderate extinction risk, was higher in countries with higher GDP and smaller roadless areas.Main conclusions:The extinction crisis for endemic species is associated with a complex network of potential drivers that need to be considered in concert in conservation policy and practice. Although our results require careful interpretation and remain sensitive to data limitations, we encourage similar studies at smaller scales to identify potential drivers of extinction risk at a higher resolution, particularly in regions where species assessments have been conducted consistently or on organisms with a uniform response time to pressures. published

Sarraceniainsectivorous plants show a diversity of visual features in their pitchers but their perception by insects and their role in attraction, have received little attention. They also vary in prey composition, with some species trapping more flying Hymenoptera, such as bees. To test the hypothesis of a link between visual signal variability and prey segregation ability, and to identify which signal could attract flying Hymenoptera, we characterised, the colour patterns of 32 pitchers belonging to four taxa, modelled their perception by flying Hymenoptera, and examined the prey they trapped. The pitchers of the four taxa differed in colour patterns, with notably two long-leaved taxa displaying clear areoles, which contrasted strongly in colour and brightness with the vegetative background and with other pitcher areas in the eyes of flying Hymenoptera. These taxa trapped high proportion of flying hymenoptera. This suggests that contrasting areoles may act as a visual lure for flying Hymenoptera, making plants particularly visible to these insects. Prey capture also differed according to pitcher stage, morphology, season and visual characteristics. Further studies on prey visitation are needed to better understand the link between prey capture and attraction feature.

International audience; For more than a decade, high-throughput sequencing has transformed the study of marine planktonic communities and has highlighted the extent of protist diversity in these ecosystems. Nevertheless, little is known relative to their genomic diversity at the species-scale as well as their major speciation mechanisms. An increasing number of data obtained from global scale sampling campaigns is becoming publicly available, and we postulate that metagenomic data could contribute to deciphering the processes shaping protist genomic differentiation in the marine realm. As a proof of concept, we developed a findable, accessible, interoperable and reusable (FAIR) pipeline and focused on the Mediterranean Sea to study three a priori abundant protist species: Bathycoccus prasinos, Pelagomonas calceolata and Phaeocystis cordata. We compared the genomic differentiation of each species in light of geographic, environmental and oceanographic distances. We highlighted that isolation-byenvironment shapes the genomic differentiation of B. prasinos, whereas P. cordata is impacted by geographic distance (i.e. isolation-by-distance). At present time, the use of metagenomics to accurately estimate the genomic differentiation of protists remains challenging since coverages are lower compared to traditional population surveys. However, our approach sheds light on ecological and evolutionary processes occurring within natural marine populations and paves the way for future protist population metagenomic studies.

Microbial communities in the world ocean are affected strongly by oceanic circulation, creating characteristic marine biomes. The high connectivity of most of the ocean makes it difficult to disentangle selective retention of colonizing genotypes (with traits suited to biome specific conditions) from evolutionary selection, which would act on founder genotypes over time. The Arctic Ocean is exceptional with limited exchange with other oceans and ice covered since the last ice age. To test whether Arctic microalgal lineages evolved apart from algae in the global ocean, we sequenced four lineages of microalgae isolated from Arctic waters and sea ice. Here we show convergent evolution and highlight geographically limited HGT as an ecological adaptive force in the form of PFAM complements and horizontal acquisition of key adaptive genes. Notably, ice-binding proteins were acquired and horizontally transferred among Arctic strains. A comparison withTaraOceans metagenomes and metatranscriptomes confirmed mostly Arctic distributions of these IBPs. The phylogeny of Arctic-specific genes indicated that these events were independent of bacterial-sourced HGTs in Antarctic Southern Ocean microalgae.

International audience; Aim: The Andean superpáramo ecosystem, above c. 4200 m a.s.l., currently forms an archipelago of isolated "sky islands" which provides a unique setting to study biogeography. However, there is still a poor understanding of how past geological events and climatic changes have shaped the distribution of life in this ecosystem. Our aim was to investigate the importance of biogeographic barriers in local diversifications and to analyze how populations have become isolated on current "sky islands".

Background Apoptosis is a caspase regulated cell death present in all metazoans defined by a conserved set of morphological features. A well-described function of apoptosis is the removal of excessive cells during development and homeostasis. Recent studies have shown an unexpected signalling property of apoptotic cells, affecting cell fate and/or behaviour of neighbouring cells. In contrast to the apoptotic function of cell elimination, this new role of apoptosis is not well understood but seems caspase-dependent. To deepen our understanding of apoptotic functions, it is necessary to work on a biological model with a predictable apoptosis pattern affecting cell fate and/or behaviour. The tunicate Ciona intestinalis has a bi-phasic life cycle with swimming larvae which undergo metamorphosis after settlement. Previously, we have shown that the tail regression step during metamorphosis, characterized by a predictable polarized apoptotic wave, ensures elimination of most tail cells and controls primordial germ cells survival and migration. Results We performed differential transcriptomic analysis between control metamorphosing larvae and larvae treated with the pan-caspase inhibitor Z-VAD-fmk in order to explore the transcriptional control of apoptotic cells on neighbouring cells that survive and migrate. When caspase activity was impaired, genes known to be involved in metamorphosis were downregulated along with other implicated in cell migration and survival molecular pathways. Conclusion We propose these results as a confirmation that apoptotic cells can control surrounding cells fate and as a reference database to explore novel apoptotic functions in animals, including those related to migration and differentiation.

International audience; This paper describes the first record of the Sejida (= Sejina) family Sejidae (superfamily Sejoidea) from Burmese amber, based on deutonymphs. Specimens were found in the amber piece along with a wasp (Hymenoptera: Scelionidae), flies (Diptera: Ceratopogonidae) and thrips (Thysanoptera: Adiheterothripidae). This record traces the Sejida (= Sejina) back to the mid-Cretaceous (ca. 100 Ma) and represents not only the oldest valid record of Mesostigmata, but it is also one of the oldest examples of the entire Parasitiformes clade.

International audience; Functionally and evolutionarily distinct species have traits or an evolutionary history that are shared by few others in a given set, which make them priority species for biodiversity conservation. On islands, life in isolation has led to the evolution of many distinct forms and functions as well as to a high level of endemism. The aim of this study is to assess the evolutionary and functional distinctiveness of insular monocotyledons and their distribution across 126 islands worldwide. We show that evolutionary and functional distinctiveness are decoupled but that both are higher on islands than on continental areas. Anagenesis on islands followed by extinctions and/or diversification on the mainland may have led to highly evolutionarily distinct species while functionally distinct species may have arisen from ecological niche shift or niche expansion. Insular endemic species with high evolutionary distinctiveness but not with high functional distinctiveness are significantly range-restricted compared to less distinct species, possibly indicating differences in dispersal potential. By showing that distinctiveness is high on islands and that the most distinct species are range-restricted, our study has important conservation implications. Indeed, islands are among the most threatened systems of the world, and extinctions of the most distinct species could lead to significant loss of phylogenetic and functional diversity.

L'écopastoralisme est une pratique de gestion écologique en plein essor, dont les bienfaits pour le maintien ou la restauration des milieux naturels ont été largement démontrés. Mais cette solution alternative de gestion obtient-elle les mêmes résultats sur des milieux fortement anthropisés et artificialisés ? Une étude menée sur les digues artificielles du Rhône de la réserve de chasse de Donzère-Mondragon s'est intéressée aux impacts des différents troupeaux sur les communautés végétales d’écosystèmes récents. Grâce à un suivi botanique sur plusieurs années, les scientifiques ont pu démontrer que la gestion par les herbivores s'avérait efficace pour maintenir l'ouverture des milieux et augmenter significativement le nombre et la diversité des espèces par rapport à l’absence de gestion ou aux interventions mécaniques.

As a result of numerous fossil and subfossil finds of ostriches, there is great demand for a comprehensive osteometric dataset for the living species and subspecies of the genus Struthio. We meet this demand by providing a set of > 100 measurements for a sample of 18 sexed skeletons, including all living and recently extinct species and subspecies of ostriches. We provide the first mensural data for two extinct subspecies, the hitherto questioned Struthio camelus spatzi from north-western Africa and the Arabian ostrich, Struthio camelus syriacus. The unique skeletal proportions of S. c. spatzi, with a relatively short wing, broad pelvis, short tarsometatarsus and big third toe, confirm the validity of this taxon and suggest an increased stability at the expense of cursoriality, which might have contributed to its extermination by humans. Our biometric analysis of the entire sample suggests a subtle sexual dimorphism in the ostrich skeleton, with females having more robust limb bones (especially wider and/or deeper at the ends) despite being on average smaller than males. If confirmed by further research, this size-independent dimorphism might reflect the independent regulation of the longitudinal and transverse dimensions of bones as revealed by several independent studies of morphological integration (covariance among morphological traits) in the avian skeleton.

Understanding drivers of biodiversity patterns is essential to evaluate the potential impact of deep-sea mining on ecosystems resilience. While the South West Pacific forms an independent biogeographic province for hydrothermal vent fauna, different degrees of connectivity among basins were previously reported for a variety of species depending on their ability to disperse. In this study, we compared phylogeographic patterns of several vent gastropods across South West Pacific back-arc basins and the newly-discovered La Scala site on the Woodlark Ridge by analysing their genetic divergence using a barcoding approach. We focused on six genera of vent gastropods widely distributed in the region: Lepetodrilus, Symmetromphalus, Lamellomphalus, Shinkailepas, Desbruyeresia and Provanna. A wide-range sampling was conducted at different vent fields across the Futuna Volcanic Arc, the Manus, Woodlark, North Fiji, and Lau Basins, during the CHUBACARC cruise in 2019. The Cox1-based genetic structure of geographic populations was examined for each taxon to delineate putative cryptic species and assess potential barriers or contact zones between basins. Results showed contrasted phylogeographic patterns among species, even between closely related species. While some species are widely distributed across basins (i.e. Shinkailepas tollmanni, Desbruyeresia melanioides and Lamellomphalus) without evidence of strong barriers to gene flow, others are restricted to one (i.e. Shinkailepas tufari complex of cryptic species, Desbruyeresia cancellata and D. costata). Other species showed intermediate patterns of isolation with different lineages separating the Manus Basin from the Lau/North Fiji Basins (i.e. Lepetodrilus schrolli, Provanna and Symmetromphalus spp.). Individuals from the Woodlark Basin were either endemic to this area (though possibly representing intermediate OTUs between the Manus Basin and the other eastern basins populations) or, coming into contact from these basins, highlighting the stepping-stone role of the Woodlark Basin in the dispersal of the South West Pacific vent fauna. Results are discussed according to the dispersal ability of species and the geological history of the South West Pacific.

A Gram-positive staining, aerobic, endospore-forming bacterial strain, isolated from the rhizosphere of Zea mays was studied for its detailed taxonomic allocation. Based on the 16S rRNA gene sequence similarity comparisons, strain JJ-42 T was shown to be a member of the genus Paenibacillus, most closely related to the type strain of Paenibacillus pectinilyticus (98.8%). The 16S rRNA gene sequence similarity to all other Paenibacillus species was below 98.5%. The pairwise average nucleotide identity (ANI) and digital DNA−DNA hybridization (dDDH) values of the JJ-42 T genome assembly against publicly available Paenibacillus type strain genomes were below 92% and 47%, respectively. The quinone system of strain JJ-42 T consisted exclusively of menaquinone MK-7. The polar lipid profile consisted of the major components diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, three aminophospholipids (APL), and one unidentified lipid. The major fatty acids were iso- and anteiso-branched with the major compound anteiso C15:0. Physiological and biochemical characteristics allowed a further phenotypic differentiation of strain JJ-42 T from the most closely related species. Thus, JJ-42 T represents a novel species of the genus Paenibacillus, for which the name Paenibacillus allorhizoplanae sp. nov. is proposed, with JJ-42 T (= LMG 32089 T = CCM 9085 T = DSM 111786 T = CIP 111891 T) as the type strain.

[Aim]: Discerning the relative role of geographical and ecological factors in promoting diversification is central to our understanding of the origin and maintenance of biodi-versity. We explore the roles of geology and ecological tolerance in the diversification of a group of wingless beetles with low dispersal potential. [Location]: Western Mediterranean (Iberian Peninsula and North Africa)., [Taxon]: Darkling beetles (Tenebrionidae: Misolampus)., [Methods]: We sequenced nine gene fragments from the mitochondrial and nuclear genomes in all extant Misolampus species to reconstruct their phylogeny, evaluate species boundaries and potential contact zones and estimate divergence times. We modelled species distributions for different time periods to infer ecological preferences and assess the effects of climatic changes since the last interglacial. We used a time-stratified process-based biogeographical model to estimate ancestral areas of origin and the evolution of geographical ranges., [Results]: The palaeoclimatic model projections show contractions of favourable areas during the last interglacial period and mid-Holocene, and wide stretches of suitable areas during the last glacial maximum. Analyses of ancestral bioclimatic preferences reveal ecological adaptations in isolated lineages within three species. The phylog-eny of Misolampus is strongly supported and unveils deep divergences within the six species. Two well-supported clades were recovered, one distributed in North Africa- Balearic Islands and another in the Iberian Peninsula. The divergence between the North African and Iberian clades occurred during the early Miocene. The geographical ranges of species are dynamic, shaped by biotic (e.g. life history, demography, species interactions) and abiotic (e.g. tectonic events, climatic variables) factors that vary through space and time. This variation ultimately dictates differential patterns of population viability, connectivity and growth through time in dif-ferent sections of species ranges, with important consequences for species diversification processes (Bellard et al., 2012; Gouveia et al., 2014; Thuiller et al., 2005; Wiens, 2011). Following climatic changes, species can respond by contracting their ranges into cli-matic refugia and/or dispersing to areas where their environmen-tal preferences are maintained (niche tracking), by adapting to new environmental conditions in situ (niche evolution), and often by undergoing extinction in environmentally unsuitable areas (Kozak & Wiens, 2006; Yesson & Culham, 2006a). The fragmentation of ancestral distributions because of tectonic or climatic changes pro-motes allopatric speciation, sometimes associated with niche evolution, whereas demographic expansion of populations tracking climatic changes can lead to range fusion and admixture between formerly isolated population groups. Discerning the relative role of biotic and abiotic factors in promoting diversification is central to our understanding of the origin and maintenance of biodiversity (Wiens & Graham, 2005).The ability of different taxa to track climatic conditions or evolve new adaptations depends on life-history traits like dispersal. Dispersal limitation can result in geographical isolation and ecolog-ical specialization, by promoting species persistence in small areas, which could lead to some resilience to changing climatic conditions and might accelerate the consolidation of a species' ecological niche even at the population level (Baselga et al., 2011). Usually, local adaptation to extrinsic ecological factors is initiated by the presence of a barrier to gene flow. Additionally, dispersal limitation may lead to ecological specialization and reinforce restrictions to gene flow, promoting speciation even in the face of future demographic pro-cesses such as population contractions, fragmentations or expan-sions (Wiens, 2004).Addressing the question of how much lineage diversification is affected by range expansions/contractions through historical biogeography is often tackled by reconstructing ancestral range shifts using phylogenetic analyses (Ree & Smith, 2008 ; Ronquist & Sanmartín,2011). However, the question often remains partially an-swered because of the lack of information on the timing of range shifts regarding the speciation process itself (Recuero et al., 2012; Recuero & García-París, 2011). Robust, accurate estimates of di-vergence times between species and intraspecific lineages are key to consider evolutionary processes at different temporal scales that lead to diversification, which is controlled by multiple extrin-sic ecological factors and intrinsic organismal traits (Wiens, 2004). Therefore, assessing the temporal scale of demographic processes such as range contractions, fragmentations and expansions and their impact on lineage divergence provides decisive evidence to reconstruct the evolutionary history of species. Within a temperate region such as the Western Mediterranean, the influence of demographic processes under climatic oscillations has been well studied, providing evidence for two major evolutionary patterns. On the one hand, allopatric fragmentation, or demographic contraction into refugial areas during glacial periods have allowed species to persist as isolated populations over long peri-ods of time (Gutiérrez-Rodríguez et al., 2017 ; Hewitt, 2004, 2011; Martínez- Freiría et al.,2020; Martínez-Solano et al., 2006; Recuero & García-París, 2011). On the other hand, during interglacial periods many species have expanded their ranges through newly available colonization routes, sometimes forming secondary contact areas with related species or lineages (Branco et al., 2000; Gómez & Lunt, 2007 ; Gonçalves et al., 2009; Miraldo et al., 2011). These two scenarios involve periods without effective contact or gene flow be-tween isolated populations, which has consequences on the process of lineage divergence. For instance, intraspecific divergence could be either indicative of allopatric cladogenetic events (cladogenesis), or ecological specialization (niche differentiation) (Hewitt, 2011).The Western Mediterranean hunchback darkling beetles Misolampus (Tenebrionidae: Stenochiinae: Misolampinii) are well suited for studies on the contribution of geology-driven processes and ecological divergence to diversification in species groups with limited dispersal capacity. These flightless beetles are ecologically linked to woodlands and live mainly beneath the bark or inside dead logs of Pinus, Quercus and other tree species along a broad altitudinal analyses infer an ancestral range including the Iberian, Betic and Rifean Plates, with subsequent splits followed by dispersal events., [Main conclusions]: Our results favour a dual role of vicariance and dispersal in driving the historical biogeography and diversification of Misolampus since the early Miocene. We also found evidence for incipient speciation events, underscoring the role of tectonic events and adaptation to local climatic conditions in the diversification of the group., This study was supported by the Spanish government (MINECO/MIUC/AEI) and the European Fund for Regional Development (FEDER) under grants CGL2015-66571-P (collecting and Museum visits) and PID2019-110243GB-I00/AEI/10.13039/501100011033 (Ministerio de Ciencia, Innovación y Universidades, Spain) (molecular analyses) to MGP. Support of the publication fee was granted by the CSIC Open Access Publication Support Initiative through its Unit of Information Resources for Research (URICI).

The modern era of analytical and quantitative palaeobiology has only just begun, integrating methods such as morphological and molecular phylogenetics and divergence time estimation, as well as phenotypic and molecular rates of evolution. Calibrating the tree of life to geological time is at the nexus of many disparate disciplines, from palaeontology to molecular systematics and from geochronology to comparative genomics. Creating an evolutionary time scale of the major events that shaped biodiversity is key to all of these fields and draws from each of them. Different methodological approaches and data employed in various disciplines have traditionally made collaborative research efforts difficult among these disciplines. However, the development of new methods is bridging the historical gap between fields, providing a holistic perspective on organismal evolutionary history, integrating all of the available evidence from living and fossil species. Because phylogenies with only extant taxa do not contain enough information to either calibrate the tree of life or fully infer macroevolutionary dynamics, phylogenies should preferably include both extant and extinct taxa, which can only be achieved through the inclusion of phenotypic data. This integrative phylogenetic approach provides ample and novel opportunities for evolutionary biologists to benefit from palaeontological data to help establish an evolutionary time scale and to test core macroevolutionary hypotheses about the drivers of biological diversification across various dimensions of organisms., ANR-AAPG 2022. PGC2018-094122-B-100 (MICU/AEI/FEDER, EU). National Science and Engineering Research Council of Canada (NSERC) postdoctoral fellowship to T.R.S.

Context Evidence for effects of habitat loss and fragmentation on the viability of temperate forest herb populations in agricultural landscapes is so far based on population genetic studies of single species in single landscapes. However, forest herbs differ in their life histories, and landscapes have different environments, structures and histories, making generalizations difficult. Objectives We compare the response of three slow-colonizing forest herbs to habitat loss and fragmentation and set this in relation to differences in life-history traits, in particular their mating system and associated pollinators. Methods We analysed the herbs’ landscape-scale population genetic structure based on microsatellite markers from replicate forest fragments across seven European agricultural landscapes. Results All species responded to reductions in population size with a decrease in allelic richness and an increase in genetic differentiation among populations. Genetic differentiation also increased with enhanced spatial isolation. In addition, each species showed unique responses. Heterozygosity in the self-compatible Oxalis acetosella was reduced in smaller populations. The genetic diversity of Anemone nemorosa, whose main pollinators are less mobile, decreased with increasing spatial isolation, but not that of the bumblebee-pollinated Polygonatum multiflorum. Conclusions Our study indicates that habitat loss and fragmentation compromise the long-term viability of slow-colonizing forest herbs despite their ability to persist for many decades by clonal propagation. The distinct responses of the three species studied within the same landscapes confirm the need of multi-species approaches. The mobility of associated pollinators should be considered an important determinant of forest herbs’ sensitivity to habitat loss and fragmentation.

This study explores body size in sepiids (Cephalopoda, Sepiidae) on the interspecific scale and provides an overview of their geographical distribution. Results reveal a highly skewed distribution of body size variation for raw values and a nearly normal distribution for log-transformed data. However, normality is not statistically validated due to the overrepresentation of small and large species. The geographical distribution of sepiids reveals five main clusters: Atlantic, Cape Basin, Indian Ocean, Asia-Pacific, and Australian. On average, clusters display more or less the same mean body size pattern except the Cape Basin cluster, which is statistically different from the others (smaller interspecific mean body size). The reasons remain unclear but a phylogenetic effect is suspected as southwest African coastal waters concentrate species from the ‘Hemisepius’ complex which is made up of small species. Sepiids do not obey Bergmann’s rule: species from high latitudes do not tend to be larger than species from low latitudes.

Objectives To assess the spread of New Delhi metallo-β-lactamase-1 (NDM-1)-producing Klebsiella pneumoniae ST147 organisms in Poland since an introduction from Tunisia in March 2015, including their phylogenetic position in the global population of the high-risk clone. Methods Out of 8925 unique NDM-positive K. pneumoniae isolates identified in Poland from April 2015 till December 2019, 126 isolates, including the Tunisian imports, were related by PFGE and blaNDM gene-carrying Tn125 transposon derivatives. Forty-seven representative isolates were sequenced by Illumina MiSeq. The phylogeny, resistome, virulome and plasmid replicons were analysed and compared with the international ST147 strains. Plasmids of six isolates were studied by the MinION sequencing. Results A high homogeneity of the 47 isolates was observed, with minor variations in their resistomes and plasmid replicon profiles. However, the detailed SNP comparison discerned a strict outbreak cluster of 40 isolates. All of the organisms were grouped within the ST147 phylogenetic international lineage, and four NDM-1 producers from Tunisia, Egypt and France were the closest relatives of the Polish isolates. Yersiniabactin genes (YbST280 type) were located within the ICEKpn12-like element in most of the outbreak isolates, characterized by O2v1 and KL64 antigen loci. The blaNDM-1 genes were located in double-replicon IncFIIK2+IncFIBK plasmids. Conclusions The continuous spread of K. pneumoniae ST147 NDM-1 in Poland since 2015, largely in the Warsaw area, is demonstrated by this genomic analysis. The isolates showed a high degree of homogeneity, and close relatedness to organisms spreading in the Mediterranean region.

18 pages; International audience; The potential for biological colonization of Antarctic shores is an increasingly important topic in the context of anthropogenic warming. Successful Antarctic invasions to date have been recorded exclusively from terrestrial habitats. While non-native marine species such as crabs, mussels and tunicates have already been reported from Antarctic coasts, none have as yet established there. Among the potential marine invaders of Antarctic shallow waters is Halicarcinus planatus (Fabricius, 1775), a crab with a circum-Subantarctic distribution and substantial larval dispersal capacity. An ovigerous female of this species was found in shallow waters of Deception Island, South Shetland Islands in 2010. A combination of physiological experiments and ecological modelling was used to assess the potential niche of H. planatus and estimate its future southward boundaries under climate change scenarios. We show that H. planatus has a minimum thermal limit of 1°C, and that its current distribution (assessed by sampling and niche modelling) is physiologically restricted to the Subantarctic region. While this species is presently unable to survive in Antarctica, future warming under both ‘strong mitigation’ and ‘no mitigation’ greenhouse gas emission scenarios will favour its niche expansion to the Western Antarctic Peninsula (WAP) by 2100. Future human activity also has potential to increase the probability of anthropogenic translocation of this species into Antarctic ecosystems.

Whereas Mantises of Trinidad and Tobago have been comprehensively studied, species occurring on more northern islands of Lesser Antilles are little known. The present work aims at updating the curr...

Plusieurs critères permettent d’évaluer la pertinence d’une phylogénie : le nombre minimal d’événements pour la parcimonie, la probabilité des données pour la vraisemblance. Le calcul selon ces critères repose sur des algorithmes de parcours d'arbre similaires et pouvant être décrits de manière très générique. Spécifiquement à chaque critère, il est ensuite possible d’explorer ces parcours pour inférer l’histoire évolutive des données.

International audience; Deciphering the timing of lineage diversification and extinction has greatly benefited in the last decade from methodological developments in fossil-based analyses. If these advances are increasingly used to study the past dynamics of vertebrates, other taxa such as insects remain relatively neglected. Our understanding of how insect clades waxed and waned or of the impact of major paleoenvironmental changes during their periods of diversification and extinction (mass extinction) are rarely investigated. Here, we compile and analyze the fossil record of Plecoptera (1,742 vetted occurrences) to investigate their genus-level diversification and diversity dynamics using a Bayesian process-based model that incorporates temporal preservation biases. We found that the Permian-Triassic mass extinction has drastically impacted Plecoptera, while the Cretaceous Terrestrial Revolution corresponds with a turnover of plecopteran fauna. We also unveiled three major gaps in the plecopteran fossil record: the Carboniferous-Permian transition, the late Early Cretaceous, and the late Cenomanian to Bartonian, which will need to be further investigated. Based on the life history of extant Plecoptera, we investigate the correlations between their past dynamic and a series of biotic (Red Queen hypothesis) and abiotic (Court Jester hypothesis) factors. These analyses highlight the major role of continental fragmentation in the evolutionary history of stoneflies, which is in line with phylogeny-based biogeographic analyses showing how vicariance drove their diversification. Our study advocates analyzing the fossil record with caution, while attempting to unveil the diversification and extinction periods plus the likely triggers of these past dynamics of diversification.Deciphering the timing of lineage diversification and extinction has greatly benefited in the last decade from methodological developments in fossil-based analyses. If these advances are increasingly used to study the past dynamics of vertebrates, other taxa such as insects remain relatively neglected. Our understanding of how insect clades waxed and waned or of the impact of major paleoenvironmental changes during their periods of diversification and extinction (mass extinction) are rarely investigated. Here, we compile and analyze the fossil record of Plecoptera (1,742 vetted occurrences) to investigate their genus-level diversification and diversity dynamics using a Bayesian process-based model that incorporates temporal preservation biases. We found that the Permian-Triassic mass extinction has drastically impacted Plecoptera, while the Cretaceous Terrestrial Revolution corresponds with a turnover of plecopteran fauna. We also unveiled three major gaps in the plecopteran fossil record: the Carboniferous-Permian transition, the late Early Cretaceous, and the late Cenomanian to Bartonian, which will need to be further investigated. Based on the life history of extant Plecoptera, we investigate the correlations between their past dynamic and a series of biotic (Red Queen hypothesis) and abiotic (Court Jester hypothesis) factors. These analyses highlight the major role of continental fragmentation in the evolutionary history of stoneflies, which is in line with phylogeny-based biogeographic analyses showing how vicariance drove their diversification. Our study advocates analyzing the fossil record with caution, while attempting to unveil the diversification and extinction periods plus the likely triggers of these past dynamics of diversification.

Anthropogenic activities are increasingly affecting ecosystems across the globe. Meanwhile, empirical and theoretical evidence suggest that natural systems can exhibit abrupt collapses in response to incremental increases in the stressors, sometimes with dramatic ecological and economic consequences. These catastrophic shifts are faster and larger than expected from the changes in the stressors and happen once a tipping point is crossed. The primary mechanisms that drive ecosystem responses to perturbations lie in their architecture of relationships, i.e. how species interact with each other and with the physical environment and the spatial structure of the environment. Nonetheless, existing theoretical work on catastrophic shifts has so far largely focused on relatively simple systems that have either few species and/or no spatial structure. This work has laid a critical foundation for understanding how abrupt responses to incremental stressors are possible, but it remains difficult to predict (let alone manage) where or when they are most likely to occur in more complex real-world settings. Here, we discuss how scaling up our investigations of catastrophic shifts from simple to more complex—species rich and spatially structured—systems could contribute to expanding our understanding of how nature works and improve our ability to anticipate the effects of global change on ecological systems. This article is part of the theme issue ‘Ecological complexity and the biosphere: the next 30 years’.

Publication onFront. Microbiol., 23 June 2022 Sec.Evolutionary and Genomic Microbiology https://www.frontiersin.org/articles/10.3389/fmicb.2022.891902/full Abstract IS6110is an insertion sequence found in theMycobacterium tuberculosiscomplex, to whichMycobacterium bovisbelongs, which can play a role in genome plasticity and in bacterial evolution. In this study, the abundance and location of IS6110onM. bovisgenomic data of French animal field strains were studied. A first analysis was performed on a panel of 81 strains that reflect the nationalM. bovispopulation’s genetic diversity. The results show that more than one-third of them are IS6110multicopy and that 10% have IS6110in a high copy number (more than 6 copies). Multicopy strains are those circulating in the regions where prevalence was above the national average. Further study of 93 such strains, with an IS6110copy number of 10-12, showed stability of IS6110copy number and genome location over time and between host species. The correlation betweenM. bovismulticopy strains and high bovine tuberculosis (bTB) prevalence leads us to consider whether their epidemiological success could be partly due to genetic changes originated by IS6110transposition.

International audience; Competition for limited resources can yield two contrasting outcomes in community structure, namely, either (i) dominance of most competitive species (with functional convergence of the traits conferring this ability), or (ii) niche partitioning of species using distinct resources. In addition, varying resource availability in different environmental contexts is expected to yield varying community dynamics and composition between the contexts (habitat filtering). We addressed resource-based ant community structure in a tropical ecosystem. We expected ant species to display varying trophic preferences and foraging behaviors, allowing habitat selection and niche differentiation in ant assemblages. Furthermore, we expected habitat filtering to occur between open and forested areas in the landscape mosaic, and competition to further influence local species co-occurrence. We assessed resource use in nine ant assemblages distributed in two habitats (i.e., forests and croplands), devising two separate experiments using bait-traps to characterize ant species' trophic preference (e.g., eating prey, seeds, sugars) and their ability to obtain a same resource in heterogeneous forms (e.g., on vegetation, litter, with variable amounts.. .). The majority of baits offered were rapidly exploited in the two habitats suggesting important resource limitations. Forest and cropland ant communities differed, however, in the proportions of resources exploited, suggesting different competitive pressures toward specific resources between habitats. Within each habitat, ants preferentially exploited the same resources, suggesting habitat filtering, but locally, interspecific resource partitioning resulted in a reduction of resource overlap compared to habitat scale. Our study provides evidence of the effects of habitat filtering and competition for resource in tropical ant community structure. Our findings also suggest that niche filtering and niche partitioning are co-variant forces determining the identity of the species present in local assemblages.

The generic status of the species referred to Protadelomys has long been problematic. Most Protadelomys species are now considered paraphyletic, except for the type species P. cartieri and for P. lugdunensis. Here, we revised these two species from their type locality, Egerkingen (Swiss Jura) for P. cartieri and Lissieu (Rhône, France) for P. lugdunensis. For the latter species, we also consider the locality of Laprade (Tarn-et-Garonne, Quercy, France). Additionally, we revised the material attributed to Protadelomys species that is now considered paraphyletic: ?P. alsaticus from Bouxwiller (Bas-Rhin, France) and Cuzal (Lot, Quercy, France), ?P. maximini from St-Maximin (Gard, France), and ?P. nievesae from Casa Ramon (Huesca, Spain). Our detailed morphological analysis enables us to better characterize the extent of the morphological and size variability in all Protadelomys and ?Protadelomys species. We show that both P. cartieri and P. lugdunensis co-existed in Egerkingen, Lissieu, and Laprade. We also erected a new genus and species, Homœtreposciurus egerkingensis, and reported the presence of Eoelfomys from Egerkingen. Eoelfomys is here described as a new genus and species from Laprade. Size and morphological comparisons enabled us to detect large intraspecific variation in the material of ?P. alsaticus from Bouxwiller, as well as in the type population of ?P. maximini. The co-occurrence of the two Protadelomys species, at least in two localities, in addition to the revision of the features characterizing the three species of ?Protadelomys, led us to question the existence of a single evolutionary lineage (chronospecies), as previously recognized from ?P. maximini to P. lugdunensis.

Ladybirds (Coleoptera: Coccinellidae) provide services that are critical to food production, and they fulfill an ecological role as a food source for predators. The richness, abundance, and distribution of ladybirds, however, are compromised by many anthropogenic threats. Meanwhile, a lack of knowledge of the conservation status of most species and the factors driving their population dynamics hinders the development and implementation of conservation strategies for ladybirds. We conducted a review of the literature on the ecology, diversity, and conservation of ladybirds to identify their key ecological threats. Ladybird populations are most affected by climate factors, landscape composition, and biological invasions. We suggest mitigating actions for ladybird conservation and recovery. Short-term actions include citizen science programs and education, protective measures for habitat recovery and threatened species, prevention of the introduction of non-native species, and the maintenance and restoration of natural areas and landscape heterogeneity. Mid-term actions involve the analysis of data from monitoring programs and insect collections to disentangle the effect of different threats to ladybird populations, understand habitat use by taxa on which there is limited knowledge, and quantify temporal trends of abundance, diversity, and biomass along a management-intensity gradient. Long-term actions include the development of a worldwide monitoring program based on standardized sampling to fill data gaps, increase explanatory power, streamline analyses, and facilitate global collaborations.Las catarinas (Coleoptera: Coccinellidae) proporcionan servicios que son críticos para la producción de alimento, y juegan un papel ecológico como fuente de alimento para depredadores. Sin embargo, la riqueza, abundancia y distribución de catarinas están en peligro debido a muchas amenazas antropogénicas. La carencia de conocimiento sobre el estatus de conservación de la mayoría de las especies y los factores que inciden en su dinámica poblacional dificulta el desarrollo e implementación de estrategias de conservación para las catarinas. Realizamos una revisión de la literatura sobre la ecología, diversidad y conservación de catarinas para identificar sus amenazas ecológicas clave. Las poblaciones de catarinas fueron afectadas mayormente por factores climáticos, composición del paisaje e invasiones biológicas. Proponemos acciones de mitigación para la conservación y recuperación de catarinas. Acciones a corto plazo incluyen programas de ciencia y educación ciudadana, medidas de protección para la recuperación de hábitat y de especies amenazadas, prevención de la introducción de especies no nativas y el mantenimiento y restauración de áreas naturales y la heterogeneidad del paisaje. Acciones a mediano plazo implican el análisis de datos obtenidos de programas de monitoreo y colecciones de insectos para desenmarañar el efecto de las diferentes amenazas a las poblaciones de catarinas, comprender el uso del hábitat por taxa de los que se tiene conocimiento limitado y cuantifica las tendencias temporales de la abundancia, diversidad y biomasa a lo largo de un gradiente de intensidad de manejo. Acciones a largo plazo incluyen el desarrollo de un programa de monitoreo a nivel mundial basado en muestreos estandarizados para subsanar la falta de datos, incrementar el poder explicativo, optimizar los análisis y facilitar colaboraciones globales.随着世界范围内人类与野生动物的冲突不断升级, 对野生动物的宽容和接纳等概念变得越来越重要。然而, 当代保护研究表明, 人们对人类与野生动物积极互作的认识有限, 导致可能难以准确描述人类与动物的相遇。如果不解决这些局限性, 就会导致野生动物和景观管理计划的设计和实施存在不足, 以及对本土生态知识的否定。我们利用印度喀拉拉邦瓦亚纳德野生动物保护区森林中的阿迪瓦西族Kattunayakans部落的民族志证据, 来研究印度原住民对于人类与野生动物共存的观点。通过定性的实地研究(包括访谈和在森林样带调查), 我们发现Kattunayakans部落表现出对野生动物的宽容和接纳, 其特点是深入的共存, 包括三个中心思想:野生动物是有理性的交流者;野生动物是神、老师和平等的族群;野生动物是实行 “dharmam”的具有共同起源的亲戚。我们认为, 充分理解以上几点有助于将Kattunayakan部落的观点引入印度的森林管理, 并更广泛地解决人类与野生动物的冲突。.

Arboreal and flying frugivorous animals represent primary dispersers in the Neotropics. Studies suggest a possible compensation for the loss of large species by smaller ones with expanding rampant anthropogenic pressures and declining populations of larger frugivores. However, studies on seed dispersal by frugivores vertebrates generally focus on the diurnal, terrestrial, canopy, and flying species, with the nocturnal canopy ones being less studied. Setting camera traps high in the canopy of fruiting nutmeg trees revealed for the first time the high frequency of the kinkajou (Potos flavus, Schreber, 1774, Procyonidae), an overlooked nocturnal frugivore species (Order Carnivora) in the Guianas. The diversity of the fruit species consumed by the kinkajou calls for considering it as an important seed disperser. The overlap of the size of seeds dispersed by frugivores observed in nutmeg trees suggests that the small (2–5 kg) kinkajou may compensate for the loss of large (5–10 kg) frugivorous vertebrates in the canopy. Camera traps visualise how the kinkajou is adapted to forage in the nutmeg tree crown and grab the fruit. Such information is vital for conservation because compensation of seed dispersal by small frugivores is crucial in increasing anthropogenic stressors.

International audience; It is widely recognized that major transportation infrastructures such as highways degrade habitats, increase the risk of collision mortality, and cause alterations in landscape connectivity by reducing connections between habitats due to the barrier effect. Wildlife crossings (underpasses and overpasses) have therefore become standard practice to reduce these effects on wildlife. Most studies aim to identify relevant locations for the creation of new wildlife crossings, but it is very rare for results based on modeling tools or animal movement records, for example, to be confronted with expert opinion and knowledge. Our paper provides a methodological framework combining modeling tools and field expertise from a multi-scale perspective. We used complementary connectivity metrics from graph theory to accurately quantify and spatialize the most relevant areas to improve habitat connectivity with multispecies conservation goals. The connectivity analysis was coupled with field expertise to take into account the local context, and technical and land feasibility. We prioritized existing road structures for improvement, found the best locations for new wildlife crossings, and made specific, costed technical recommendations. We empirically tested this approach on a large highway network in Northern France. This allowed us to define work principles to improve 109 existing road structures and to create underpasses or overpasses on 15 road sections. This innovative study for operational purposes has been a useful tool to assist the decision-making process of land-use planners who wish to improve wildlife crossings on major transportation infrastructures.