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International audience; With the advent of the Anthropocene, biological invasions have reached an unprecedented level, and the number of species introductions is still increasing in an ever-changing world. Despite major advances in invasion science, significant debate and lack of clarity remain surrounding the determinants of success of introduced species, the magnitude and dimensions of their impact, and the mechanisms sustaining successful invasions. Empirical studies show divergent impacts of alien populations on ecosystems and contrasting effects of biotic and abiotic factors on the dynamics of alien populations, which hinders the creation of a unified theory of biological invasions. Compounding these issues is the plethora of hypotheses that aim to explain invasion success, which can be unclear and contradictory. We propose a synthesis that categorizes hypotheses along a timeline of invasion. We sorted invasion hypotheses along the invasion timeline, and considered population, community and ecosystem levels. This temporal sorting of invasion concepts shows that each is relevant at a specific stage of the invasion. Although concepts and empirical findings on alien species may appear contradictory, when mapped onto an invasion timeline, they may be combined in a complementary way. An overall scheme is proposed to summarise the theoretical dynamics of ecosystems subjected to invasions. For any given case study, this framework provides a guide through the maze of theories and should help choose the appropriate concepts according to the stage of invasion.

In the isopod Armadillidium vulgare , many females produce progenies with female-biased sex ratios, owing to two feminizing sex ratio distorters (SRD): Wolbachia endosymbionts and the f element. We investigated the distribution and population dynamics of these SRD and mitochondrial DNA variation in 16 populations from Europe and Japan. Confirming and extending results from the 1990s, we found that the SRD are present at variable frequencies in populations and that the f element is overall more frequent than Wolbachia . The two SRD never co-occur at high frequency in any population, suggesting an apparent mutual exclusion. We also detected Wolbachia or the f element in some males, which probably reflects insufficient titer to induce feminization or presence of masculinizing alleles. Our results are consistent with a single integration event of a Wolbachia genome in the A. vulgare genome at the origin of the f element, which contradicts an earlier hypothesis of frequent losses and gains. We identified strong linkage between Wolbachia strains and mitochondrial haplotypes, but no association between the f element and mitochondrial background. Our results open new perspectives on SRD evolutionary dynamics in A. vulgare , the evolution of genetic conflicts and their impact on the variability of sex determination systems.

Introductions of invasive non-native species (and their subsequent impacts) are recognized as a major threat to native flora and fauna. This is especially true in island ecosystems such as the tropical island of Martinique. In 2018, one such aquatic invasive species, the suckermouth catfish Hypostomus robinii (Loricariidae), was reported for the first time in two of the islands rivers. H. robinii is a popular freshwater aquarium fish and native to tropical and sub-tropical South America. Since its initial discovery, a growing number of populations have been found, suggesting a larger distribution of this species through Martinique's hydrographic network. Here, we developed a novel survey technique (utilizing environmental DNA) and conducted a widespread survey across the island to assess the distribution of this invasive species. We were able to detect H. robinii in 22% of sites surveyed (18 out of 83) via our eDNA-based assay. The presence of these fish was confirmed using traditional trapping at 14 of these sites. Additionally, we used occupancy modeling to investigate the impact of different environmental covariates on the detection efficiency of the novel assay and the potential impacts of false positives and negatives. We highlight a decrease in the detection probability when water volume filtered increases. That said, the eDNA-based method proves a useful tool for the detection of this invasive fish species and monitoring its spread for management purposes.

In the isopodArmadillidium vulgare, many females produce progenies with female-biased sex ratios, due to two feminizing sex ratio distorters (SRD):Wolbachiaendosymbionts and thefelement. We investigated the distribution and population dynamics of these SRD and mitochondrial DNA variation in 16 populations from Europe and Japan. Confirming and extending results from the 1990’s, we found that the SRD are present at variable frequencies in populations, and that thefelement is overall more frequent thanWolbachia. The two SRD never co-occur at high frequency in any population, suggesting an apparent mutual exclusion. We also detectedWolbachiaor thefelement in some males, which likely reflects insufficient titer to induce feminization or presence of masculinizing alleles. Our results are consistent with a single integration event of aWolbachiagenome in theA. vulgaregenome at the origin of thefelement, which contradicts an earlier hypothesis of frequent losses and gains. We identified strong linkage betweenWolbachiastrains and mitochondrial haplotypes, but no association between thefelement and mitochondrial background. Our results open new perspectives on SRD evolutionary dynamics inA. vulgare, the evolution of genetic conflicts and their impact on the variability of sex determination systems.

International audience

International audience; Parasitic Aphanomyces species are a global threat to agri- and aquaculture, causing multimillion USD damage every year. Via the global trade, Aphanomyces has spread across all continents with exception of South America and Antarctica, and has become a major problem in pea, sugar beet, fish and crayfish production. The widespread A. euteiches and A. cochlioides induce root rot diseases in leguminous species and sugar beet respectively. The fish pathogen A. invadans is the causative agent of Epizootic Ulcerative Syndrome in various fish species whilst A. astaci infects crayfishes causing crayfish plague. Aphanomyces have developed an efficient transmission and infection mechanism which allows a rapid colonization and disruption of the host's infected tissues. This review presents an overview on the current research on Aphanomyces genus. We summarise the latest research efforts on four pathogenic Aphanomyces species, shedding light on the biology of these microorganisms, the pathogenicity factors of these parasites, the diseases which they cause, their distribution and finally the strategies to control the diseases.

International audience; Climate and land use/land cover (LULC) change are two major global change factors driving shifts in the location of suitable areas for many species. Here, we assessed if a low-vagility newt, Triturus marmoratus, can track displacement of suitable areas by 2100, and tested whether climate or LULC changes are primary drivers of the species’ future distribution. We combined niche modelling with the process-based model simRShift to improve biological relevance and simulate species dispersal by 2100 under scenarios of climate and LULC changes at high spatial resolution. Our results show that T. marmoratus could lose a significant part of its current French range in the coming decades, and that the range loss will primarily be driven by climate change, with LULC change playing a secondary role. The species seems unlikely to be able to track the northern shift of its suitable habitat as rapidly as required given the rate of climate warming during the 21st century. This is due to insufficient dispersal ability, which is compounded by the magnitude of habitat fragmentation in the human-dominated landscape. We highlight the need to assess vulnerability and anticipate threats arising from global change even for species that are not currently considered endangered. We identified areas where the species is most likely to occur and be extinct in the future, which can serve as a guide for population monitoring. Our framework can support conservation strategy development by defining ecological corridors that would assist species to track their required habitats in the face of global change.

International audience; We report the discovery of a new enveloped, spherical virus belonging to the Phenuiviridae family of negative ssRNA viruses associated with a massive outbreak in a French population of the endangered white-clawed crayfish Austropotamobius pallipes. We call this virus Bunya-like Brown Spot Virus (BBSV) and characterize it using transmission electronic microscopy, genome sequencing and clinical signs. Infected specimens show discolored brown spots on the cuticle. Using RNA-seq data we assembled a partial sequence for the L, M and S genome segments of BBSV. Phylogenetic analyses using all three segments show this virus is closely related to the Wenling crustacean virus 7 (China) and to a bunya-like virus found in feces of the European otter. Our survey of the mass mortality event indicates the virus is less virulent than the crayfish plague caused by Aphanomyces astaci. Overall, the discovery of BBSV provides a new important asset to monitor A. pallipes populations.

Biodiversity and wild populations are globally threatened by a wide range of actors. The genus Iguana, widely distributed throughout the Americas, is under threat by invasive species, hybridization, the global pet trade, and habitat destruction. This holds especially true for the insular lineages, with the Critically Endangered I. delicatissima having experienced a > 75% range decrease, primarily through hybridization with non-native iguanas. We collated published microsatellite data and genotyped samples from new localities to construct a distribution-wide Iguana dataset built from 190 individuals for 17 microsatellite loci. This enabled us to identify patterns of genetic differentiation within and among populations, and identify key loci and private alleles for use in conservation management. Our analyses reveal clear separation between I. delicatissima and the I. iguana complex, highlighting the power of eight key microsatellite loci for the study of hybridization dynamics. Genetic differentiation within I. delicatissima identifies four clusters that aid decision making for conservation management action. Within the I. iguana complex, we increase mainland localities by 11-fold and recover 3.5 × more alleles across all loci than previously known. Overall, we identify 112 (48% private) and 76 (25% private) alleles for mainland and island lineages, respectively. We highlight loci sets to identify (1) non-native or hybrid iguanas in insular populations and their genetic origin, and (2) genetic origin of insular iguanas in the global pet trade. Overall, we provide a reference for Iguana microsatellite loci in order to allow standardization and comparison among studies, aiding broader assessment of research and conservation hypotheses., We thank Ty Park and all donators to IguanaFest 2019 for financial support.

Low coverage genome sequencing is rapid and cost-effective for recovering complete mitochondrial genomes for crustacean phylogenomics. The recovery of high-copy-number nuclear genes, including histone H3, 18S and 28S ribosomal RNAs, is also possible using this approach based on our research with freshwater crayfishes (Astacidea). We explored the potential of genome skimming (GS) to recover additional nuclear genes from shallow sequencing projects using decapod crustaceans. Using an in silico-baited approach, we recovered three additional core histone genes (H2A, H2B, and H4) from our low-coverage decapod dataset (99 species, 69 genera, 38 families, 10 infraorders). Phylogenetic analyses using various combinations of mitochondrial and nuclear genes for the entire decapod dataset and a subset of 40 species of crayfishes showed that the evolutionary rates for different classes of genes varied widely. A very high level of congruence was nevertheless found between trees from the six nuclear genes and those derived from the mitogenome sequences for freshwater crayfish. These findings indicate that nuclear genes recovered from the same genome skimming datasets designed to obtain mitogenomes can be used to support more robust and comprehensive phylogenetic analyses. Further, a search for additional intron-less nuclear genes identified several high-copy-number genes across the decapod dataset, and recovery of NaK, PEPCK, and GAPDH gene fragments is possible at slightly elevated coverage, suggesting the potential and utility of GS in recovering even more nuclear genetic information for phylogenetic studies from these inexpensive and increasingly abundant datasets.

The stone crayfish Austropotamobius torrentium is a native European freshwater species with significant population declines caused by anthropogenic pressure onto its habitats, climate change and spreading of non-native invasive crayfish and their pathogens. Large-scale DNA barcoding based on sequencing a short fragment of the mitochondrial cytochrome c oxidase subunit I (COI) gene revealed this species represents a highly divergent taxon whose evolutionary heritage is preserved in genetically divergent mtDNA phylogroups, with majority of them having restricted distribution ranges. Guarding in mind vanishing populations trends and potential loss of genetic diversity, effective conservation planning and monitoring are needed for ensuring the persistence and long-term survival of this endangered species. Since genetic data are often critical for defining populations for conservation and management purposes, along with DNA barcoding, we employed microsatellites to examine samples of more than 400 individuals from 17 populations across its entire distribution range in Croatia, known as the stone crayfish diversity hot spot. Microsatellite analyses revealed high level of genetic diversity and differentiation among studied populations that grouped according to their geographical position and mtDNA phylogroup. Almost all sampled populations represent a distinct genetic cluster, showing high level of differentiation and reflecting long periods of isolation. Results of genetic characterisation enabled selection of suitable donor populations for future restocking and reintroduction programs. Combination of DNA barcoding and microsatellites provided good insight into genetic diversity and population structure as well as enabled sound conservation programs for this threatened species in Croatia.

Pontastacus leptodactylus is a native European crayfish species found in both freshwater and brackish environments. It has commercial importance for fisheries and aquaculture industries. Up till now, most studies concerning P. leptodactylus have focused onto gaining knowledge about its phylogeny and population genetics. However, little is known about the chromosomal evolution and genome organization of this species. Therefore, we performed clustering analysis of a low coverage genomic dataset to identify and characterize repetitive DNA in the P. leptodactylus genome. In addition, the karyogram of P. leptodactylus (2n = 180) is presented here for the first time consisting of 75 metacentric, 14 submetacentric, and a submetacentric/metacentric heteromorphic chromosome pair. We determined the genome size to be at ~18.7 gigabase pairs. Repetitive DNA represents about 54.85% of the genome. Satellite DNA repeats are the most abundant type of repetitive DNA, making up to ~28% of the total amount of repetitive elements, followed by the Ty3/Gypsy retroelements (~15%). Our study established a surprisingly high diversity of satellite repeats in P. leptodactylus. The genome of P. leptodactylus is by far the most satellite-rich genome discovered to date with 258 satellite families described. Of the five mapped satellite DNA families on chromosomes, PlSAT3-411 co-localizes with the AT-rich DAPI positive probable (peri)centromeric heterochromatin on all chromosomes, while PlSAT14-79 co-localizes with the AT-rich DAPI positive (peri)centromeric heterochromatin on one chromosome and is also located subterminally and intercalary on some chromosomes. PlSAT1-21 is located intercalary in the vicinity of the (peri)centromeric heterochromatin on some chromosomes, while PlSAT6-70 and PlSAT7-134 are located intercalary on some P. leptodactylus chromosomes. The FISH results reveal amplification of interstitial telomeric repeats (ITRs) in P. leptodactylus. The prevalence of repetitive elements, especially the satellite DNA repeats, may have provided a driving force for the evolution of the P. leptodactylus genome.

We announce the draft genome sequences of two pathogenic microsporidia of European freshwater crustaceans, Thelohania contejeani (the causative agent of porcelain disease) and Cucumispora dikerogammari. Both species are implicated in mass mortalities in natural populations of their crayfish and amphipod hosts, respectively.

The Lesser Antilles, in the Eastern Caribbean, is inhabited by threeIguanaspecies: the Lesser Antillean iguanaIguana delicatissima, which is endemic to the northernmost islands of the Lesser Antilles, the introduced common iguana from South America,Iguana iguana iguana, represented also by the two newly described endemic subspeciesIguana iguana sanctaluciaefrom Saint Lucia andIguana iguana insularisfrom Saint Vincent and the Grenadines, and Grenada, and the introducedIguana rhinolophafrom Central America. Drawing on both morphological and genetic data, this paper describes theIguanapopulations from Saba and Montserrat as a new species,Iguana melanoderma. This species is recognized on the basis of the following combination of characteristics: private microsatellite alleles, unique mitochondrial ND4 haplotypes, a distinctive black spot between the eye and tympanum, a dorsal carpet pattern on juveniles and young adults, a darkening of body coloration with aging (except for the anterior part of the snout), a black dewlap, pink on the jowl, the high number of large tubercular nape scales, fewer than ten medium sized–triangular dewlap spikes, high dorsal spikes, and lack of horns on the snout. This new melanistic taxon is threatened by unsustainable harvesting (including for the pet trade) and both competition and hybridization from escaped or released invasive alien iguanas (I. iguana iguanaandI. rhinolopha) from South and Central America, respectively. The authors call for action to conserveIguana melanodermain Saba and Montserrat and for further research to investigate its relationship to other melanistic iguanas from the Virgin Islands and coastal islands of Venezuela.

The white-clawed crayfish (Austropotamobius pallipes) is an endangered species in Europe with limited genomic information. Despite its conservation status there is no transcriptomic data available for A. pallipes in public databases. The data here represents the first transcriptome profile of the white-clawed crayfish generated using Illumina stranded RNA sequencing. Pair-end reads were assembled de novo with three separate transcriptome assemblers (Trinity, RNABloom, and RNASpades) followed by transcript assembly reduction and gene reconstruction using the EvidentialGene pipeline. The transcriptome was functionally annotated using InterProScan and genes coding for carbohydrate-active enzymes were identified through the dbCAN2 server. Raw fastq reads and the final version of the transcriptome assembly have been deposited in the NCBI-SRA (SRR10549898) and NCBI-TSA (GICG01) databases. Keywords: Austropotamobius pallipes, Transcriptome, Muscle, Illumina, Crayfish

Triturus cristatus and Triturus marmoratus are two protected and declining newts occurring in the administrative department of Vienne, in France. They have limited dispersal abilities and rely on the connectivity between habitats and their suitability. In a warming climate, the locations of suitable habitats are expected to change, as is the connectivity. Here, we wondered how climate change might affect shifts in habitat suitability and connectivity of habitat patches, as connectivity is a key element enabling species to realize a potential range shift. We used ecological niche modelling (ENM), combining large-scale climate suitability with local scale, high-resolution habitat features, to identify suitable areas for the two species, under low and high warming scenarios (RCP 2.6 and RCP 8.5). We associated it with connectivity assessment through graph theory. The variable ‘small ponds’ contributed most to land cover-only ENMs for both species. Projections with climate change scenarios revealed a potential impact of warming on suitable habitat patches for newts, especially for T. cristatus. We observed a decrease in connectivity following a decrease in patch suitability. Our results highlight the important areas for newt habitat connectivity within the study area, and define those potentially threatened by climate warming. We provide information for prioritizing sites for acquisition, protection or restoration, and to advise landscape policies. Our framework is a useful and easily reproducible way to combine global climate requirements of the species with detailed information on species habitats and occurrence when available.

International audience; 1. The white-clawed crayfish (Austropotamobius pallipes) is globally endangered due to the impacts of habitat modification and fragmentation, water pollution, climate change, and invasive species, particularly the signal crayfish (Pacifastacus leniusculus). These pressures have caused the decline of A. pallipes populations in Europe, demonstrating the importance of predicting the species' potential distribution under current and future conditions. Focusing on the watercourses of mainland France, we aimed to identify suitable areas for A. pallipes to guide the conservation of current populations and future introduction actions or protection measures.2. We applied ecological niche modelling to model the potential distribution of both A. pallipes and P. leniusculus and identified locations suitable for A. pallipes only. We also assessed the potential distribution of the species under two representative concentration pathway (RCP) scenarios: RCP 2.6 and RCP 8.5, respectively describing low-warming and high-warming conditions.3. We found that A. pallipes and P. leniusculus exploit equivalent niches in France. Despite this, under current conditions, about 5% of the study area simultaneously records a high suitability for A. pallipes and a low suitability for P. leniusculus and is therefore of significant conservation interest. This percentage remains relatively stable under RCP 2.6 for 2050 and 2100, but decreases to 2% under RCP 8.5 for 2100.4. Ecological niche modelling can supply crucial guidance for conservation actions aimed at protecting endangered species at a national scale by identifying sites most suitable for protection and sites where climate change and invasive species constitute a threat.

The redclaw crayfish, Cherax quadricarinatus, was introduced to Martinique Island for aquaculture purposes in 2004, in an attempt to revitalize the freshwater crustacean aquaculture sector. In 2015, three wild populations were discovered during an electrofishing survey on fish diversity. In 2018, a specific crayfish survey was performed at night using spotlighting and baited traps at 34 sites throughout the island. The species was mostly found in the center and northern part of the island, specifically, a total of 105 specimens were captured in eight streams and five closed water bodies. We sequenced a 491 base-pair fragment of the COI gene to understand the invasion history and pathway from the presumed source population at the Mangatal hatchery. Among the eight haplotypes found, three were dominant, of which, two occurred in the Mangatal hatchery. As crayfish are sold alive, there is a high risk of further human-mediated introductions across the island hydrographic basins. Thus, the distribution of this species could rapidly expand throughout Martinique freshwater ecosystems, with ecological impacts on native communities yet to be determined and requiring urgent investigation.

The redclaw crayfish, Cherax quadricarinatus, was introduced to Martinique Island for aquaculture purposes at the beginning of the 21st century, in an attempt to revitalize the freshwater crustacean aquaculture sector. Mainly due to its high economical value, it was intentionally released in the wild and was caught and sold by fishermen. Martinican rivers are polluted by chlordecone, considered as one of the worst Persistant Organic Pollutants (POP). Despite its dangerousness, it was used until 1993 in the French West Indies against a banana pest and was always found in the ecosystems. This study aimed to investigate the level of contamination in the muscle of crayfish caught in the wild, as well as the potential of bioconcentration and depuration in the C. quadricarinatus muscle. This study could allow us to quantify the risk for consumers but also, to evaluate a depuration process to reduce the risk related to its consumption. Using both in-vitro and in-situ experiments, results highlighted the importance of the chlordecone concentration in the water and the time of exposure to the pollutant. The bioconcentration seems to be very quick and continuous in crayfish muscle, as chlordecone can be detectable as early as 6 h of exposure, whatever the concentration tested. Finally, it appears that, even after 20 days of depuration in chlordecone-free water, chlordecone concentrations remained higher to the residual maximum limit (i.e. 20 ng/g wet weight), concluding that the decontamination of the muscle seems not very efficient, and the risk for the Martinican people could be serious.

International audience; Whereas the effects of climate change on the potential range shifts of amphibians have been modeled at various scales, exploring the future impacts of land-use changes has rarely been considered. We modeled the potential distribution of Bombina variegata, Hyla arborea, Hyla meridionalis, and Triturus cristatus using ecological niche modeling, in the French administrative region Nouvelle-Aquitaine. The species are all at range margin in the study area which makes them interesting model species to study range shifts because of their potential local adaptations to their marginal habitat. We used Dyna-CLUE modeling framework to produce land-use change scenarios and combined them with RCP 2.6 and RCP 8.5 climate change scenarios to predict their impact on local amphibian distributions. B. variegata, H. arborea, and T. cristatus were predicted to shift eastward and northward. H. meridionalis was predicted to increase its probability of presence in the study area. The effect of climate determined the general pattern of distribution and was modulated depending on the scenarios of land-use change.

Background The noble crayfish (Astacus astacus) is a native European species in decline, with a contracting range and diminishing populations and abundance. Previous studies revealed this species significant genetic diversity in the south-eastern Europe, with populations from the western and the southern part of the Balkan Peninsula being the most divergent. However, sampling of populations from the western part of the Balkans was limited and insufficient for investigating genetic diversity and population divergence for the purpose of conservation planning and management. Thus, the major aim of this study was to fill in this knowledge gap by studying mitochondrial and microsatellite DNA diversity, using 413 noble crayfish from 18 populations from waterbodies in the western part of the Balkan Peninsula. Methods Phylogenetic analysis of studied populations and their mitochondrial diversity were studied using COI and 16S sequences and population genetic structure was described using 15 microsatellite loci. Results Phylogeographic analysis revealed new divergent mitochondrial haplotypes for the populations in the westernmost part of the Balkan Peninsula in the tributaries of the Sava and Drava rivers. Microsatellite data indicated that these populations harbour an important component of genetic diversity within A. astacus. The results suggest that the western part of the Balkans played an important role as microrefugia during the Pleistocene climate fluctuations, allowing the long term persistence of A. astacus populations in this region. These results will also be important to supporting conservation decision making and planning.

The signal crayfish Pacifastacus leniusculus, native to northwestern North America, has become the most widespread invasive crayfish species in Europe. It has been introduced repeatedly since 1959, and altogether >60,000 individuals were imported. Secondary introductions across the continent followed, resulting in its current presence in ≥26 European countries. Recent studies indicate that multiple highly divergent lineages of signal crayfish exist in its North American range, and previous investigators have suggested that >1 signal crayfish subspecies are present in Europe. We investigated its genetic variation by sequencing a fragment of the mitochondrial gene for cytochrome c oxidase subunit I (COI) to clarify the diversity of this invasive species in its European range. We analyzed 348 signal crayfish from 68 European populations and compared the resulting patterns with reference sequences from North America. All European individuals studied fell within 1 clade of P. leniusculus, but we observ...

Austropotamobius pallipes is an endangered decapod attracting much attention in freshwater conservation programmes. In some cases population transfers or reintroductions are carried out in lentic ecosystems such as ponds or quarries. Such conservation actions require rapid, low cost and powerful tools to census suitable habitat. Some species of the Characeae family (Chara spp.), share ecological needs with A. pallipes and are proposed as bioindicators of suitable habitat. Chara species were tested, among other plants, as bioindicators, and to see whether Chara species are a stronger indicator than water chemistry. The Pinail Nature Reserve, with 3000 permanent ponds, is inhabited by white-clawed crayfish probably introduced historically into ponds used for fish production. This allows a replicated study of suitable habitats where plant communities are bioindicators of crayfish presence. Crayfish presence is associated with Chara species (such as Chara aspera, Chara virgata, Chara fragifera, Chara polyacantha and Chara vulgaris). Austropotamobius pallipes is present in ponds with Chara spp. (N = 10/10) while other ponds without crayfish are lacking charophytes (N = 1/23). Algae of the genus Chara are thus a simple and low-cost additional tool for determining suitable habitat for crayfish introductions within enclosed waters protected from exotic invasive species and disease. Cladium mariscus also appears to be another useful bioindicator for crayfish habitat.

This study gives an overview of status and distribution of signal crayfish (Pacifastacus leniusculus), the first NICS in Estonia and its influence on native noble crayfish (Astacus astacus) populations. The first specimen of signal crayfish was caught during the monitoring of noble crayfish in North Estonia in 2008. The signal crayfish has since been found in three additional sites. Test fishing has indicated that the abundance of signal crayfish has been fluctuating between years and among localities. It has had strong negative impact on abundance of one noble crayfish population. The disconnected distribution of signal crayfish strongly suggests that these populations are the result of human-assisted introductions. Real-time PCR analyses proved that signal crayfish carry the causative agent of the crayfish plague, an oomycete Aphanomyces astaci, thus contributing to its spread. Mortalities in noble crayfish populations had been caused by A. astaci strains from A, B and E genotype group.

Background The recently published complete mitogenome of the European lobster (Homarus gammarus) that was generated using long-range PCR exhibits unusual gene composition (missing nad2) and gene rearrangements among decapod crustaceans with strong implications in crustacean phylogenetics. Such atypical mitochondrial features will benefit greatly from validation with emerging long read sequencing technologies such as Oxford Nanopore that can more accurately identify structural variation. Results We re-sequenced the H. gammarus mitogenome on an Oxford Nanopore Minion flowcell and performed a long-read only assembly, generating a complete mitogenome assembly for H. gammarus. In contrast to previous reporting, we found an intact mitochondrial nad2 gene in the H. gammarus mitogenome and showed that its gene organization is broadly similar to that of the American lobster (H. americanus) except for the presence of a large tandemly duplicated region with evidence of pseudogenization in one of each duplicated protein-coding genes. Conclusions Using the European lobster as an example, we demonstrate the value of Oxford Nanopore long read technology in resolving problematic mitogenome assemblies. The increasing accessibility of Oxford Nanopore technology will make it an attractive and useful tool for evolutionary biologists to verify new and existing unusual mitochondrial gene rearrangements recovered using first and second generation sequencing technologies, particularly those used to make phylogenetic inferences of evolutionary scenarios. Electronic supplementary material The online version of this article (10.1186/s12864-019-5704-3) contains supplementary material, which is available to authorized users.

International audience; Biological invasions have reached an unprecedented level and the number of introduced species is still increasing worldwide. Despite major advances in invasion science, the determinants of success of introduced species, the magnitude and dimensions of their impact, and the mechanisms sustaining successful invasions are still debated. Empirical studies show divergent impacts of nonnativepopulations on ecosystems and contrasting effects of biotic and abiotic factors on the dynamics of non-native populations; this is hindering the emergence of a unified theory of biological invasions. We propose a synthesis that merges perspectives from population, community, and ecosystem levels. Along a timeline of ecosystem transformation driven by nonnative species, from historical to human-modified ecosystems, we order invasion concepts and theories to clarify their chaining and relevance during each step of the invasion process. This temporal sorting of invasion concepts shows that each concept is relevant at a specific stage of theinvasion. Concepts and empirical findings on non-native species may appear contradictory. However, we suggest that, when mapped onto an invasion timeline, they may be combined in a complementary way. An overall scheme is proposed to summarise the theoretical dynamics of ecosystems subjected to invasions. For any given case study, this framework provides a guide through the maze of theories and should help choose the appropriate concepts according to the stage of invasion.

The Lesser Antilles, in the Eastern Caribbean, were long considered to have only two species in the genus Iguana Laurenti 1768: the Lesser Antillean iguana Iguana delicatissima, which is endemic to parts of the Lesser Antilles, and the Common green iguana Iguana iguana, which also occurs throughout Central and South America. No subspecies are currently recognised. However, herpetologists and reptile collectors have pointed out strong physical differences between some of the island populations of Iguana iguana and those from the continent. Drawing on both morphological and genetic data, this paper describes two subspecies of the Common green iguana Iguana iguana from the southern Lesser Antilles, specifically the countries of Saint Lucia Iguana iguana sanctaluciae and Iguana iguana insularis from St Vincent & the Grenadines, and Grenada. The form on the island of Saint Vincent has not been identified. The new subspecies are described based on the following unique combination of characters: Presence of high median and medium to small lateral horns on the snout; Small subtympanic plate not exceeding 20% of the eardrum size; Two or three scales of decreasing size anterior to the subtympanic plate; Fewer than ten small to medium triangular gular spikes; Medium sized dewlap; Low number of small to medium dispersed nuchal tubercles; Dark brown iris, with the white of the eye visible; Oval, prominent nostril; Short and relatively flat head; High dorsal spines; No swelling of the jowls in reproductively active males. Iguana iguana sanctaluciae has in adults vertical black stripes on body and tail and a black dewlap whereas Iguana iguana insularis is pale grey or creamy white in adults. Both subspecies are globally threatened by unsustainable hunting (including the pet trade) and by invasive alien species, including hybridization from invasive iguanas from South and Central America (I. iguana iguana and I. rhinolopha, considered here as full species) that have become established in all three countries. The authors call for stronger measures to conserve the remaining purebred Iguana i. insularis and Iguana i. sanctaluciae ssp. nov. throughout their ranges and for further research to identify other cryptic species and subspecies of Iguana in the Lesser Antilles.

International audience; The Oomycete Aphanomyces astaci is an obligate crayfish parasite that co-evolved with American crayfish species, and they therefore generally live in a balanced relationship. On the contrary, European native crayfish are highly susceptible to A. astaci, and infestation with it causes development of the lethal disease termed crayfish plague. Until now, 5 A. astacistrains have been described from the freshwater crayfish present in Europe. In this study we aimed to investigate the occurrence of the pathogen A. astaci in Croatian native and non-native crayfish populations, as well as to genotype established strains using microsatellite markers and obtain information on the pathogens epidemiology. Our results showed that the pathogen is widespread in both native and non-native crayfish populations. Agent level, when positive, in non-native crayfish was generally low; in native species it was higher. Genotyping from microsatellites proved the presence of the B (Ps) strain in non-native species (Pacifastacus leniusculus), while the A (As) strain was detected from viable native species (Astacus astacus and Austropotamobius torrentium) that are distributed in areas lacking non-native crayfish. The genotype from A. torrentium differed from a typical A (As) by 1 allele. Strain B (Ps) was identified in native Astacus leptodactylus from the population that co-occurs with P. leniuscuslus. Interestingly, in 1 A. leptodactylus population both A (As) and B (Ps) strains were present.

The Lesser Antilles, in the Eastern Caribbean, were long considered to have only two species in the genusIguanaLaurenti 1768: the Lesser Antillean iguanaIguana delicatissima, which is endemic to parts of the Lesser Antilles, and the common green iguanaIguana iguana, which also occurs throughout Central and South America. However, herpetologists and reptile collectors have pointed out strong physical differences between some of the island populations ofIguana iguanaand those from the continent. Drawing on both morphological and genetic data, this paper describes a third speciesIguana insularissp. nov. from the southern Lesser Antilles, specifically the countries of Saint Lucia, St Vincent & the Grenadines, and Grenada. The new species is described based on the following unique combination of characters: Presence of high median and medium to small lateral horns on the snout; Small subtympanic plate not exceeding 20% of the eardrum size; Two or three scales of decreasing size anterior to the subtympanic plate; Fewer than ten small to medium triangular gular spikes; Medium sized dewlap; Low number of small to medium dispersed nuchal tubercles; Dark brown iris, with the white of the eye visible; Oval, prominent nostril; Short and relatively flat head; High dorsal spines; No swelling of the jowls in reproductively active males; Colour of head, body and tail changing from green to pale grey or creamy white in old adults; Vertical black stripes on body and tail, fading with age in some populations. This paper furthermore distinguishes two subspecies:Iguana insularis insularisfrom the Grenada Bank (comprising Grenada and the Grenadine islands), andIguana insularis sanctaluciaefrom Saint Lucia. The form on the island of Saint Vincent has not been identified. Both subspecies are globally threatened by unsustainable hunting (including the pet trade) and by invasive alien species, including hybridization from invasive iguanas from South and Central America (I. iguanaandI. rhinolopha, considered here as full species) that have become established in all three countries. The authors call for stronger measures to conserve the remaining purebredIguana insularissp. nov. throughout its range and for further research to identify other cryptic species and subspecies ofIguanain the Lesser Antilles.

The infraorder Anomura consists of a morphologically and ecologically heterogeneous group of decapod crustaceans, and has attracted interest from taxonomists for decades attempting to find some order out of the seemingly chaotic diversity within the group. Species-level diversity within the Anomura runs the gamut from the “hairy” spindly-legged yeti crab found in deep-sea hydrothermal vent environments to the largest known terrestrial invertebrate, the robust coconut or robber crab. Owing to a well-developed capacity for parallel evolution, as evidenced by the occurrence of multiple independent carcinization events, Anomura has long tested the patience and skill of both taxonomists attempting to find order, and phylogeneticists trying to establish stable hypotheses of evolutionary inter-relationships. In this study, we performed genome skimming to recover the mitogenome sequences of 12 anomuran species including the world’s largest extant invertebrate, the robber crab (Birgus latro), thereby over doubling these resources for this group, together with 8 new brachyuran mitogenomes. Maximum-likelihood (ML) and Bayesian-inferred (BI) phylogenetic reconstructions based on amino acid sequences from mitogenome protein-coding genes provided strong support for the monophyly of the Anomura and Brachyura and their sister relationship, consistent with previous studies. The majority of relationships within families were supported and were largely consistent with current taxonomic classifications, whereas many relationships at higher taxonomic levels were unresolved. Nevertheless, we have strong support for a polyphyletic Paguroidea and recovered a well-supported clade of a subset of paguroids (Diogenidae + Coenobitidae) basal to all other anomurans, though this requires further testing with greater taxonomic sampling. We also introduce a new feature to the MitoPhAST bioinformatics pipeline ( https://github.com/mht85/MitoPhAST ) that enables the extraction of mitochondrial gene order (MGO) information directly from GenBank files and clusters groups based on common MGOs. Using this tool, we compared MGOs across the Anomura and Brachyura, identifying Anomura as a taxonomic “hot spot” with high variability in MGOs among congeneric species from multiple families while noting the broad association of highly-rearranged MGOs with several anomuran lineages inhabiting extreme niches. We also demonstrate the value of MGOs as a source of novel synapomorphies for independently reinforcing tree-based relationships and for shedding light on relationships among challenging groups such as the Aegloidea and Lomisoidea that were unresolved in phylogenetic reconstructions. Overall, this study contributes a substantial amount of new genetic material for Anomura and attempts to further resolve anomuran evolutionary relationships where possible based on a combination of sequence and MGO information. The new feature in MitoPhAST adds to the relatively limited number of bioinformatics tools available for MGO analyses, which can be utilized widely across animal groups.

10 pages; International audience; Carbon dioxide released in the atmosphere and dissolved in water leads to acidification. Relatively few studies have focused on fresh waters, where biocalcifying species are more readily impacted by changes in pH. Sensitivity to pH of an endangered calcium-demanding organism, the crayfish Austropotamobius pallipes, was investigated in the Pinail nature reserve, a natural system with 3000 permanent ponds, some inhabited by the crayfish and others not, originally due to human introduction. From the 14 chemical parameters measured in this study, the main limiting factor preventing crayfish establishment appears to be water acidity (pH < 6.8), which affects calcification, molting, growth and reproduction. We predict that 20% of the Pinail populations will disappear by 2060 due to freshwater acidification with the present level of fossil fuel consumption. Ongoing and future restoration projects for conservation of this heritage crustacean must select hard water with the highest water pH (> 7).