Peer Community Journal

The Miocene sands of the Swiss Jura Mountains, long exploited in quarries for the construction industry, have yielded abundant fossil remains of large mammals. Among Deinotheriidae (Proboscidea), two species, Prodeinotherium bavaricum and Deinotherium giganteum, had previously been identified in the Delemont valley, but never described. A third species, Deinotherium levius, from the locality of Charmoille in Ajoie, is reported herein for the first time in Switzerland. These occurrences are dated from the middle to the late Miocene, correlating to the European Mammal biozones MN5 to MN9. The study is completed by a discussion on the palaeobiogeography of deinotheres at the European scale.

The common European grove snail, Cepaea nemoralis (Helicidae), has been a model species in genetics and evolutionary biology for over a century thanks largely to its genetic shell colour polymorphism. Although most aspects of its shell colour variation are known to be purely genetic, with little or no phenotypic plasticity involved, the width of the spiral bands has been suspected to display a certain amount of plasticity. To test this, we conducted a transplantation experiment, in which 548 growing banded snails were marked and transplanted, either within the same habitat (open or closed vegetation, displaying 19% and 61% band fusion, respectively) or between habitat types. The numbers recaptured were low: 8%, 5% after removal of individuals that had not grown. Based on these samples, we did not find any substantial influence of transplantation on band width.

Mosasauroids are primarily known as aquatic squamates that diversified in the marine realm during the Late Cretaceous. While most species had paddles, elongated skull, body, and a laterally compressed tail, and lived in the open sea, some early species, with limbs similar to those of terrestrial animals and a varanoid-like body, lived in marine coastal shallow waters. Recently, mosasauroid remains have been discovered in freshwater environments in several continental deposits of the Santonian-Campanian of Europe. This study describes new cranial and postcranial mosasauroid remains from Santonian continental deposits in Provence, southeastern France, and attributes them to a new tethysaurine: Garamaudo bauciensis nov. gen., nov. sp. This mosasauroid, approximately 2.5 m long, with terrestrial-like limbs and a sacrum, and with osteosclerosis in its vertebrae and humerus (at least), was probably hovering at shallow depth in freshwater ecosystems. This new discovery raises the fact that, according to current knowledge, it is only within the Tethysaurinae that freshwater forms evolved, pointing to a possible niche partitioning, associated with of the maintain of the plesiopedal / plesiopelvic condition, in parallel with the invasion of open waters by most other hydropedal and hydropelvic mosasauroids. This therefore suggests for mosasauroids a richer evolutionary history than currently assumed.

The Japanese knotweed (Fallopia japonica) is considered as highly invasive in Europe and is largely widespread in France, without any established predator. This short study first characterized the herbivory of Fallopia by the black vine weevil (Otiorhynchus sulcatus), a commonly encountered coleopteran in France. Through an experimental design of leaf choices, between Fragaria spp. and Fallopia spp., our results show that the insects prefer Fallopia, even if it is presented for the first time. Even if this simple observation may appear as trivial, it highlights a novel plant-insect interaction and may start new insight in plant control or invasion management.

The fear of being predated can influence many decisions taken by preys and this may have important consequences for the ecosystems. Preys can respond to the risk of being predated in three ways: habitat selection, diel activity modifications and adoption of behaviors to detect predators before they constitute a danger. However, rarely these strategies have been analyzed simultaneously within an entire community. Through a camera trapping study conducted in the Julian Prealps Natural Park and surrounding territories (North-East of Italy), we analyze these three antipredator responses to understand which strategy is adopted by target species. Results show how, for the majority of species, the main antipredator response is the selection of time intervals when corresponding predators are inactive. On the opposite, habitat selection seems to be more influenced by environmental characteristics of the area. Similar, behavioral traits do not result related to presence probability of predators. Therefore, in the area analyzed, we demonstrated the existence of a landscape of fear that influences species choices regarding mainly diel activities. The study underlines also the importance of simultaneous consideration of antipredator responses for a more accurate understanding of how fear structures communities and ecosystems.

Biological invasions are a major component of global change and biodiversity loss. Rumina decollata, a Mediterranean land snail, has been introduced beyond its native range through human-mediated dispersal and is now widely distributed across much of Argentina. Here, we investigated the origin of Argentine populations using mitochondrial COI sequences from Argentine populations spanning a broad latitudinal and environmental gradient. All analysed populations clustered within the mitochondrial lineage previously identified as invasive worldwide. A single haplotype identical to sequences from Spain and Portugal dominated most Argentine populations, while two additional haplotypes matched lineages from Portugal and southern France, indicating multiple introduction events followed by extensive secondary spread. Despite low mitochondrial diversity, R. decollata has successfully colonised diverse environments, suggesting that reproductive traits such as self-fertilisation may have contributed to population persistence following introduction. In addition, body and sole colouration was variable and did not reliably diagnose the invasive clade. Our results highlight how repeated introductions and life-history traits interact to facilitate establishment and spread, even under strong demographic constraints.

O_LITrait-based community assembly studies have mostly been addressed along spatial gradients, and do not consider explicitly a fundamental dimension governing community assembly, the time. Nevertheless, such consideration seems particularly necessary in systems in which organisms have to face regular disturbances and rapid changes in vegetation phenology, such as in intensively managed farmlands. C_LIO_LIIn this study, we aimed at understanding how the functional diversity of carabid beetle communities varied across the growing season in response to crop type. We tested three alternative hypotheses on mechanisms underlying the community assembly. C_LIO_LIWe used data from a long-term monitoring conducted over nine years in an intensively-managed farmland in central western France, in a total of 625 fields. First, we measured morphological traits related to body size, dispersal mode, and resource acquisition on the 13 dominant carabid species (> 85 % of all trapped individuals) and identified three independent dimensions of functional specialization within our species pool along axes of a PCA and highlighted key traits for community assembly. Second, we evaluated the community assembly temporal dynamics and the impact of habitat filtering and niche differentiation in the different crop types with time, using linear mixed-effects models. C_LIO_LIWe showed that functional species assembly of carabid beetle communities occurring in crop fields varies importantly intra-annually, with strong variations in these dynamics depending on crop type and crop phenology. Each crop acted as a filter on carabid communities for body size and resource-acquisition traits, and functional differentiation between crops increased with time. We did not find any evidence of habitat filtering on traits related to dispersal mode. C_LIO_LIOur results emphasize the major role of crop phenology but also disturbances involved by agricultural practices such as crop harvesting on changes in community assembly, likely due to seasonal and inter-annual redistributions of species in agricultural landscapes in response to such changes. The temporal dimension cannot be ignored to understand the assembly of local carabid communities in farmlands. C_LI

Rodent population cycles are observed in highly seasonal environments. As most rodents are herbivorous, the availability and the quality of their food resources varies greatly across seasons. Furthermore, it is well documented that herbivore densities have a measurable effect on vegetation and conversely. So, many studies investigated whether rodent population cycles could be induced by bottom-up regulation. A recent review summarized several sub-hypotheses leading to rodent population cycles: cycles may be due to inherent inter-annual variations of plant quantity, to overshoot of carrying capacity by overgrazing (i.e. lack of quantity), to changes in quality of food (decrease of quality of preferred food or switch towards less quality food) in response to rodent grazing (e.g. plant defences). If some sub-hypothesis seems to be more important than others, there is currently a prerequisite to construct scientific consensus: dietary description is still overlooked in many systems and should be more investigated. This study focuses on fossorial water vole. It shows contrasted population dynamics depending on its geographical locations. It is known to be able to exhibit large outbreaks in grasslands in highly seasonal climate. It is thus a good model species to investigate plant hypotheses, first beginning by diet description. The diet of water vole was investigated in and out of the outbreak area with a combination of approaches in the field, in different sampling sites and considering seasonality. We demonstrated that voles have a very large fundamental trophic niche, but strong behavioural selection, inducing a narrower realised niche, especially during winter. We created an experimental device based on camera trap and cafeteria tests. We observed a strong preference for dandelion (Taraxacum officinale) in wild water voles, that results in exclusive selection during winter for food stores. These preferences were constant across seasons, altitudes and grassland productivity gradients, despite the scarcity of this species in some experimental sites. First, we conclude on the importance of using different methods to fully describe the diet of rodents Second, we assess that dandelion is a winter key resource for water vole. It thus might be interesting to investigate the role of dandelion in vole population dynamics.

Worldwide the 16 species of lyssaviruses all exhibit a similar pathology in most mammals, including man; with successful infections usually ending with death. Recently it has been demonstrated that European bat lyssaviruses (EBLV) are not invariably fatal in their wild reservoir host bat species, however the mechanisms and epidemiological consequences of this resistance are interesting and unexplored and the fundamental pathology in bats is still unclear. Here we modelled alternative pathological pathways to explore which appear most plausible, with respect to our limited knowledge of bat-rabies epidemiology and also host population dynamics. Two models were created, one based on a standard progression of disease (classic SEIR model) and the other modified to allow for animals to become either rabid or immune (flexible model). Of these our flexible model was found to be more plausible, demonstrating a much lower sensitivity to epidemiological parameters and by inference the more likely to represent the real-life process occurring in wild European bat populations, with a comparative state space ratio of 1:47. This result implies that it is highly probable survival and post-infection immunity is a widespread epidemiological phenomenon rather than an infrequent consequence of an aborted infection in few individuals. These results can be used to inform laboratory studies on bat immunology and future bat modelling work.

In their paper A refined proposal for the origin of dogs: the case study of Gnirshohle, a Magdalenian cave site, Baumann and colleagues[1] claim that their data support the hypothesis that the Hegau Jura was a potential center of early European wolf domestication, and that such a scenario becomes plausible considering a close proximity of canids and humans thereby introducing a controlled, or at least a restrictive diet. The study focusses on fossil remains of large canids from the Gnirshohle cave site in SW Germany. Morphometric data on only one specimen, GN-999, as well as collagen {delta}15N and {delta}13C isotopic data and mitochondrial DNA analyses on the Gnirshohle specimens and a comparative sample were used to conclude that the Gnirshohle specimens shed light on the origin of dogs as purported by the title of the paper. Here we argue that the paper is fundamentally flawed and excluded available relevant data.

When a gene is horizontally transferred (HGT), under the "replacement" model where the transferred gene replaces its homolog in the recipient genome, the corresponding gene phylogeny departs from the species phylogeny by a Subtree Prune and Regraft (SPR) operation: the "recipient branch" is moved from its initial position to attach to the "donor branch". Based on this observation, various methods have used SPRs to infer HGTs. We examine this apparent equivalence in the light of ghost lineages, i.e. related species absent from the phylogeny because they are extinct, unknown or have not been sampled. In this case an SPR is not directly interpretable by an HGT from the donor branch, because HGTs can have ghost lineages as donors. A possible and frequent interpretation - that we call "induced HGT" - is that the transferred gene leaves the sampled phylogeny for a ghost lineage at the donor branch, and is transferred back from a ghost lineage at the recipient branch. We show by simulations that this interpretation is misleading in a significant number of cases. For instance if the studied phylogeny represents 1% of all the species susceptible to exchange genetic material with the 100 sampled species, and 11 transfers occurred, then SPRs do not correspond to induced HGTs in around 50% of the cases. This leaves the question of a coherent interpretation of SPR in the presence of ghosts open, and applies to a certain extent to other phylogenetic simulation or inference methods of HGT, like reconciliation, or phylogenetic networks.

The Moorish gecko Tarentola mauritanica is currently expanding around the Mediterranean basin as a result of natural dispersal and anthropogenic spread. The species is observed at several sites in sympatry with other gecko species. To date, no impact has been observed on the native species and T. mauritanica is not considered invasive. We present an eight-year survey in southern France, where it lives in sympatry with the European leaf-toed gecko Euleptes europaea. The survey started when the Moorish gecko was rare which enabled us to observe an important increase in abundance. This increase was strongly correlated with a notable decline of E. europaea, explaining 49% of transect-specific temporal variation in abundance. We suspect that the increase in T. mauritanica density is causally related to this decline and recommend intensive monitoring of the species throughout the Mediterranean Basin to determine whether or not the species should be classified as invasive.

Common probabilistic models of substitutions of bases (Jukes-Cantor, Kimura 2-parameter, Tamura-Nei, F84, HKY, and the 6-parameter models used in linear invariants methods) must be rejected, at least for mitochondrial genomes of animals. They are rejected by a new test that is simple and lenient.

The Rock Bunting (Emberiza cia) occurs from the Iberian Peninsula to mountainous regions in Central Asia. In Europe, its centre of distribution lays in the Mediterranean region. A small subpopulation is found in Germany in rocky habitats (often with vineyards) along the rivers Middle Rhine, Nahe, Main, Moselle and Ahr. In this study, the German population of the Rock Bunting was monitored for more than 15 years and a continuous decline was observed. Buntings were mist netted and colour ringed; furthermore, blood samples were collected for a DNA analysis. For 122 samples the variability of nucleotide sequences of the mitochondrial cytochrome b gene and the allele distribution of 12 polymorphic microsatellite markers were investigated. Both mtDNA and nuclear DNA show genetical variability, but no geographic clustering, indicating a connectivity and gene flow between the German subpopulations.

Inferring the dispersal processes of vector-borne plant pathogens is a great challenge because the plausible epidemiological scenarios often involve complex spread patterns at multiple scales. European stone fruit yellows (ESFY), a disease caused by Candidatus Phytoplasma prunorum and disseminated via planting material and vectors belonging to the species Cacopsylla pruni, is a major threat for stone fruit production throughout Europe. The spatial genetic structure of the pathogen was investigated at multiple scales by the application of a combination of statistical approaches to a large dataset obtained through the intensive sampling of the three ecological compartments hosting the pathogen (psyllids, wild and cultivated Prunus) in three Prunus-growing regions in France. This work revealed new haplotypes of Ca. P. prunorum, and showed that the prevalence of the different haplotypes of this pathogen is highly uneven between all regions, and within two of them. In addition, we identified a significant clustering of similar haplotypes within a radius of at most 50 km, but not between nearby wild and cultivated Prunus. We also provide evidence that the two species of the C. pruni complex are unevenly distributed but can spread the pathogen, and that infected plants are transferred between production areas. Altogether, this work supports a main epidemiological scenario where Ca. P. prunorum is endemic in, and mostly acquired from, wild Prunus by immature C. pruni (of both species) who then migrate to \"shelter plants\" that epidemiologically connect sites less than 50 km apart by later providing infectious mature C. pruni to their \"migration basins\", which differ in their haplotypic composition. We argue that such multiscale studies would be very useful for other pathosystems.

Withdrawal StatementThe authors have withdrawn this manuscript as we carry out reanalysis and reinterpretation of our results. Therefore, the authors do not wish this work to be cited as reference for the project. If you have any questions, please contact the corresponding author.

Pathogens should evolve to avirulence. However, while baculoviruses can be transmitted through direct contact, their main route of infection goes through the death and liquefaction of their caterpillar hosts and highly virulent strains still seem to be advantaged through infection cycles. Furthermore, one of them, Autographa californica multiple nucleopolyhedrovirus, is so generalist that it can infect more than 100 different hosts.\n\nTo understand and characterize the evolutionary potential of this virus and how it is maintained while killing some of its hosts in less than a week, we performed an experimental evolution starting from an almost natural isolate of AcMNPV, known for its generalist infection capacity. We made it evolve on 4 hosts of different susceptibilities for 10 cycles and followed hosts survival each day. We finally evaluated whether the generalist capacity was maintained after evolving on one specific host species and tested an epidemiological model through simulations to understand how.\n\nFinally, on very highly susceptible hosts, transmission-virulence trade-offs seem to disappear and the virus can maximize transmission and virulence. When less adapted to its host, the pathogens virulence has not been modified along cycles but the yield was increased, apparently through an increased transmission probability and an increased latent period between exposition and infection.

Global urbanization is rapidly increasing, transforming ecosystems and favoring generalist species that adapt to human-modified environments. The wild boar, a highly adaptable species, is expanding its range and increasingly observed in urban and peri-urban areas, where it can cause accidents, damage, and health concerns. To mitigate their presence, non-lethal control strategies such as vegetation clearing in peri-urban parks and wastelands are being implemented to reduce the number of suitable resting sites. However, the ecological consequences of such habitat modifications on other wildlife species remain poorly understood. This knowledge gap limits the development of effective urban wildlife management strategies that seeks to balance ecological, social and economic considerations without harming wild boar populations and urban ecosystems. In this context, we used camera trapping to study the covariation between wild boars and other mammal species in a peri-urban area, with the aim of guiding targeted and effective management strategies. Here, we show a widespread presence of wild boars but no spatial or temporal covariation between the wild boars and the other species. In contrast, we found strong spatial structuring in mammal communities, primarily driven by small carnivores (mustelids, genets, cats, foxes) and a minimal influence of temporal variation, confirming that spatial factors, rather than seasonal changes, largely shaped species distributions. The study of the temporal variation across months indicated minimal seasonal structuring but revealed substantial within-site variability in month-to-month species abundance, with a general abundance gradient driven by common species like wild boar, cat, and fox. In conclusion, our results show that the lack of spatial covariation between wild boar and other species prevents reliable predictions, supporting a targeted rather than general approach to vegetation management.

Among the hundreds of collected Devonian vertebrate macrofossils in the Holy Cross Mountains, placoderms dominate and provide data on their morphology, distribution and taphonomy. So far 17 out of more than 500 studied specimens have revealed bones with surfaces covered by sediment-filled trace fossils. The traces have been made on the vertebrate remains before their final burial. The borings, oval in cross-section, include dendroidal networks of shallow tunnels or short, straight or curved individual scratches and grooves, which frequently create groups on the both sides of the bones. ?Karethraichnus isp. from Kowala and ?Osteocallis isp. from Wietrznia are the oldest record of these ichnogenera. Sedimentological clues indicate a shallow water environment, probably from the slope below the storm wave base.

The Permian (Cisuralian) Irati Formation, from the Brazilian southeastern Parana Basin bears, at some levels, Chondrichthyes, besides other vertebrates. Outcrops of this unit are frequent at the state of Sao Paulo eastern belt. Two members of the Irati are recognized at this state, Assistencia, the upper, and Taquaral. A sandy facies, mostly at the base of the Taquaral, is noteworthy by the richness of the Chondrichthyes, mainly Holocephali. The Petalodontiformes are the Chondrichthyes most abundant, so far referred to Itapyrodus punctatus. Recent studies of several specimens revealed that some morphotypes must belong to different species of the genus Itapyrodus. Others are akin to this genus, justifying a proposition of an endemic family Itapyrodidae. The presence of this endemic family is an argument, among others, for a proposed isolation of two Brazilan Basins northeast Parnaiba and southeast Parana, during the time of deposition of the Irati, inasmuch as Itapyrodidae are present in both basins.