Subjects -> PALEONTOLOGY (Total: 43 journals)
Showing 1 - 21 of 21 Journals sorted by number of followers
Journal of Quaternary Science     Hybrid Journal   (Followers: 36)
Quaternary Science Reviews     Hybrid Journal   (Followers: 29)
Quaternary Research     Full-text available via subscription   (Followers: 21)
Palaeontology     Hybrid Journal   (Followers: 19)
Boreas: An International Journal of Quaternary Research     Hybrid Journal   (Followers: 15)
Palaeogeography, Palaeoclimatology, Palaeoecology     Hybrid Journal   (Followers: 14)
Historical Biology: An International Journal of Paleobiology     Hybrid Journal   (Followers: 10)
Journal of Paleontology     Hybrid Journal   (Followers: 10)
Facies     Hybrid Journal   (Followers: 8)
Journal of Vertebrate Paleontology     Full-text available via subscription   (Followers: 8)
Geologica Saxonica     Open Access   (Followers: 8)
Paleobiology     Full-text available via subscription   (Followers: 7)
Alcheringa: An Australasian Journal of Palaeontology     Hybrid Journal   (Followers: 6)
European Journal of Protistology     Hybrid Journal   (Followers: 5)
Journal of Paleolimnology     Hybrid Journal   (Followers: 5)
Paleontological Journal     Full-text available via subscription   (Followers: 5)
Paläontologische Zeitschrift     Hybrid Journal   (Followers: 5)
Paleoceanography and Paleoclimatology     Full-text available via subscription   (Followers: 5)
Fossil Record     Open Access   (Followers: 5)
Peer Community Journal     Open Access   (Followers: 5)
Annales de Paléontologie     Full-text available via subscription   (Followers: 4)
Geobios     Full-text available via subscription   (Followers: 4)
Palaeoworld     Hybrid Journal   (Followers: 4)
EvoDevo     Open Access   (Followers: 4)
Swiss Journal of Palaeontology     Hybrid Journal   (Followers: 4)
Neues Jahrbuch für Geologie und Paläontologie - Abhandlungen     Full-text available via subscription   (Followers: 3)
Quaternaire     Open Access   (Followers: 3)
International Journal of Speleology     Open Access   (Followers: 3)
Zitteliana     Open Access   (Followers: 3)
Marine Micropaleontology     Hybrid Journal   (Followers: 2)
Open Quaternary     Open Access   (Followers: 2)
Palaeontographica A     Full-text available via subscription   (Followers: 2)
Review of Palaeobotany and Palynology     Hybrid Journal   (Followers: 1)
Annals of Carnegie Museum     Full-text available via subscription   (Followers: 1)
Palynology     Hybrid Journal   (Followers: 1)
PaleoBios     Open Access   (Followers: 1)
Rivista Italiana di Paleontologia e Stratigrafia (Research In Paleontology and Stratigraphy)     Open Access   (Followers: 1)
Novitates Paleoentomologicae     Open Access   (Followers: 1)
Vertebrate Anatomy Morphology Palaeontology     Open Access   (Followers: 1)
Papers in Palaeontology     Hybrid Journal   (Followers: 1)
Ameghiniana     Open Access  
Spanish Journal of Palaeontology     Open Access  
Ichnos: An International Journal for Plant and Animal Traces     Hybrid Journal  
Revue de Micropaleontologie     Full-text available via subscription  
Comptes Rendus Palevol     Open Access  
Similar Journals
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Peer Community Journal
Number of Followers: 5  

  This is an Open Access Journal Open Access journal
ISSN (Online) 2804-3871
Published by Peer Community in (PCI) Homepage  [1 journal]
  • Pigeault, Romain; Cozzarolo, Camille-Sophie et al. - Spring reproductive
           success influences autumnal malarial load in a passerine bird

    • Abstract: Although avian haemosporidian parasites are widely used as model organisms to study fundamental questions in evolutionary and behavorial ecology of host-parasite interactions, some of their basic characteristics, such as seasonal variations in within-host density, are still mostly unknown. In addition, their interplay with host reproductive success in the wild seems to depend on the interaction of many factors, starting with host and parasite species and the temporal scale under study. Here, we monitored the parasitemia of two haemosporidian parasites – Plasmodium relictum (lineage SGS1) and P. homonucleophilum (lineage SW2) – in two wild populations of great tits (Parus major) in Switzerland over three years, to characterize their dynamics. We also collected data on birds’ reproductive output – laying date, clutch size, fledging success – to determine whether they were associated with parasitemia before (winter), during (spring) and after (autumn) breeding season. Parasitemia of both species dramatically increased in spring, in a way that was correlated to parasitemia in winter. Parasitemia before and during breeding season did not explain reproductive success. However, the birds which fledged the more chicks had higher parasitemia in autumn, which was not associated with their parasitemia in previous spring. Our results tend to indicate that high haemosporidian parasite loads do not impair reproduction in great tits, but high resource allocation into reproduction can leave birds less able to maintain low parasitemia over the following months.
      PubDate: Wed, 21 Feb 2024 09:59:50 +000
       
  • Lenormand, Thomas; Roze, Denis - Can mechanistic constraints on
           recombination reestablishment explain the long-term maintenance of
           degenerate sex chromosomes'

    • Abstract: Y and W chromosomes often stop recombining and degenerate. Most work on recombination suppression has focused on the mechanisms favoring recombination arrest in the short term. Yet, the long-term maintenance of recombination suppression is critical to evolving degenerate sex chromosomes. This long-term maintenance has been little investigated. In the long term, recombination suppression may be maintained for selective reasons (e.g., involving the emergence of nascent dosage compensation), or due to mechanistic constraints preventing the reestablishment of recombination, for instance when complex chromosomal rearrangements evolve on the Y. In this paper, we investigate these ‘constraint’ theories. We show that they face a series of theoretical difficulties: they are not robust to extremely low rates of recombination restoration; they would rather cause population extinction than Y degeneration; they are less efficient at producing a non-recombining and degenerate Y than scenarios adding a selective pressure against recombination, whatever the rate of recombination restoration. Finally, whether such very high constraints exist is questionable. Very low rates of recombination reestablishment are sufficient to prevent Y degeneration, given the large fitness advantage to recover a non-degenerate Y or W for the heterogametic sex. The assumption of a lack of genetic variation to restore recombination seems also implausible given known mechanisms to restore a recombining pair of sex chromosomes.
      PubDate: Fri, 16 Feb 2024 15:21:14 +000
       
  • Drosophila-parasitoids+complex&rft.title=Peer+Community+Journal&rft.issn=2804-3871&rft.date=2024&rft.volume=">Varaldi, Julien; Lepetit, David et al. - Community structure of heritable
           viruses in a Drosophila-parasitoids complex

    • Abstract: The diversity and phenotypic impacts related to the presence of heritable bacteria in insects have been extensively studied in the last decades. On the contrary, heritable viruses have been overlooked for several reasons, including technical ones. This is regrettable because of the size of this gap knowledge and because case study indicate that viruses may have profound impact on the functionning of individuals and communities. Additionally, the factors that may shape viral communities are poorly known, except in some very specific viral-insect systems. Here we analyze the community structure of heritable viruses in a multi-hosts-multi-parasitoids community. Drosophilidae and their larval and pupal parasitoids were sampled in two locations, two years and two seasons. After two lab generations, putative DNA and RNA viruses were purified and sequenced. Our analysis revealed the presence of 53 viruses (including 37 new viruses), the great majority of which were RNA viruses. The "species" factor was by far the most significant one, explaining more than 50% of the variance in viral structure. Additionally, parasitoids had a higher number of heritable viruses compared to their hosts, suggesting that this lifestyle favours the association with viruses. Finally, our community-level survey challenged previous interpretation concerning the host range of some previously described viruses.  
      PubDate: Tue, 13 Feb 2024 14:58:56 +000
       
  • Perrot, Charlotte; Seranne, Léo et al. - Use of linear features by
           red-legged partridges in an intensive agricultural landscape: implications
           for landscape management in farmland

    • Abstract: Current agricultural practices and change are the major cause of biodiversity loss. An important change associated with the intensification of agriculture in the last 50 years is the spatial homogenization of the landscape with substantial loss of such biodiversity-rich elements as seminatural linear features (hedgerows, field margins, grassy strips, etc.). In Europe, some management prescriptions serve to increase heterogeneity by the creation of these seminatural linear features which are not being used primarily for agricultural production. However, these elements are not equal in their support for biodiversity according to their structure and composition. The aim of this study is to determine the importance of landscape heterogeneity and specifically linear features on the spatial distribution of red-legged partridges, a small game species in decline in Europe. Through GPS-monitoring of adult birds, we first assess home range size throughout the year and during the breeding season, in relation to breeding status and to linear features (seminatural linear vegetation and tracks-roads for human traffic) density. Then, we focus on habitat selection during the breeding period in relation to linear features. We found that linear elements shape the use of space by red-legged partridges according to their reproductive status. Traffic routes and seminatural features structured by both herbaceous and woody cover, negatively influenced home range size. Further, breeding birds select linear elements with herbaceous cover while non-breeders select linear elements with woody cover, underlining the different needs of birds according to their breeding status. All birds selected areas near tracks, but non-breeders seemed to avoid roads. This study shows the importance for this species of the linear components that structure the agricultural landscape. We propose recommendations to promote the presence of the red-legged partridge in this agricultural environment but also of the biodiversity in general.
      PubDate: Mon, 12 Feb 2024 08:35:00 +000
       
  • Abbate, Jessica L.; Galan, Maxime et al. - Pathogen community composition
           and co-infection patterns in a wild community of rodents

    • Abstract: Rodents are major reservoirs of pathogens that can cause disease in humans and livestock. It is therefore important to know what pathogens naturally circulate in rodent populations, and to understand the factors that may influence their distribution in the wild. Here, we describe the occurrence and distribution patterns of a range of endemic and zoonotic pathogens circulating among rodent communities in northern France. The community sample consisted of 713 rodents, including 11 host species from diverse habitats. Rodents were screened for virus exposure (hantaviruses, cowpox virus, Lymphocytic choriomeningitis virus, Tick-borne encephalitis virus) using antibody assays. Bacterial communities were characterized using 16S rRNA amplicon sequencing of splenic samples. Multiple correspondence (MCA), multiple regression and association screening (SCN) analyses were used to determine the degree to which extrinsic factors (study year and site; host habitat, species, sex and age class) contributed to pathogen community structure, and to identify patterns of associations between pathogens within hosts. We found a rich diversity of bacterial genera, with 36 known or suspected to be pathogenic. We revealed that host species is the most important determinant of pathogen community composition, and that hosts that share habitats can have very different pathogen communities. Pathogen diversity and co-infection rates also vary among host species. Aggregation of pathogens responsible for zoonotic diseases suggests that some rodent species may be more important for transmission risk than others. Moreover, we detected positive associations between several pathogens, including Bartonella, Mycoplasma species, Cowpox virus (CPXV) and hantaviruses, and these patterns were generally specific to particular host species. Altogether, our results suggest that host and pathogen specificity is the most important driver of pathogen community structure, and that interspecific pathogen-pathogen associations also depend on host species.
      PubDate: Wed, 07 Feb 2024 08:04:57 +000
       
  • Jacques, Alicia; Duclos, Delphine et al. - Assessing the potential of
           germplasm collections for the management of genetic diversity: the case of
           the French National Cryobank

    • Abstract: Through a combination of selective pressure and genetic drift, there has been a notable erosion of genetic diversity in domesticated animal populations. In response, many countries, including France, have developed gene banks in order to conserve reproductive genetic material. Cryopreserved resources can potentially be used to manage the genetic diversity of populations, but this opportunity is seldom exploited. As an initial step toward this goal, we describe here a methodology for the characterization of the genetic diversity of cryopreserved collections. Using the example of the French National Cryobank, this study employs newly proposed biodiversity metrics to conduct a detailed assessment of the status of collections for six livestock species: cattle, sheep, goat, horse, donkey, and pig. Both the amount of resources available and their characteristics varied among species and/or breeds. Overall, breeds with a large commercial distribution had more donors in the collection than local breeds, while the number of doses available was mainly determined by the physiology of the species. An adapted version of the Gini-Simpson equitability index revealed an unbalanced number of donors between breeds for some species. Similarly, estimates of effective donor numbers (De) highlighted the unequal distribution of donors within a breed. Finally, we developed a new index of diversity impact (IDI) to assess the potential of a collection to reintroduce genetic diversity in contemporary populations. The IDI was calculated on the basis of pedigree data for 17 breeds of three livestock species, pig, sheep, and cattle, which differed in both population size and management program. IDI values are negative when the use of cryoconserved sires would decrease the overall kinship of the current population and positive when it would increase it, enabling the most interesting donors to be chosen for immediate use. Negative (favorable) IDI values were found for both local breeds as well as for commercial populations. In general, older collections exhibited better IDI values but recently collected donors could also be useful for populations undergoing strong selection. Within a breed, IDI can be computed individually and thus be used to select the best sires for a given objective. In the absence of pedigree data, IDI values could also be calculated on the basis of marker genotypes. Overall, this study proposes a framework for the assessment of germplasm collections in the service of various objectives. Compared to FAO indicators motivated by breed reconstitution, the Gini-Simpson and De indices can help to plan sampling more efficiently, whereas IDI can guide donor selection in order to manage the diversity of existing populations. These indicators can be calculated at regular intervals to support the planning and management of collections at national and international levels and help population managers to exploit the resources currently available.
      PubDate: Thu, 01 Feb 2024 14:44:57 +000
       
  • Rous, Axel; Santa-Catalina, Gaëlle et al. - Comparison of enrichment
           methods for efficient nitrogen fixation on a biocathode

    • Abstract: The production of nitrogen fertilizers in modern agriculture is mostly based on the Haber-Bosch process, representing nearly 2% of the total energy consumed in the world. Low-energy bioelectrochemical fixation of N2 to microbial biomass was previously observed but the mechanisms of microbial interactions in N2-fixing electroactive biofilms are still poorly understood. The present study aims to develop a new method of enrichment of autotrophic and diazotrophic bacteria from soil samples with a better electron source availability than using H2 alone. The enrichment method was based on a multi-stage procedure. The first enrichment step was specifically designed for the selection of N2-fixing bacteria from soil samples with organic C as electron and carbon source. Then, a polarized cathode was used for the enrichment of autotrophic bacteria using H2 (hydrogenotrophic) or the cathode as electron source. This enrichment was compared with an enrichment culture of pure diazotrophic hydrogenotrophic bacteria without the use of a microbial electrochemical system. Interestingly, both methods showed comparable results for N2 fixation rates at day 340 of the enrichment with an estimated average of approximately 0.2 mgNfixed/L.d. Current densities up to -15 A/m² were observed in the polarized cathode enrichments and a significant increase of the microbial biomass on the cathode was shown between 132 and 214 days of enrichment.These results confirmed an enrichment in autotrophic and diazotrophic bacteria on the polarized cathode. It was hypothesied that autotrophic bacteria were able to use either the H2 produced at the cathode or directly the cathode through direct electron transfer (DET) as more biomass was produced than with H2 alone. Finally, the analysis of the enriched communities suggested that Desulforamulus ruminis mediated microbial interactions between autotrophic anaerobic and heterotrophic aerobic bacteria in polarized cathode enrichment. These interactions could play a key role in the development of biomass in these systems and on N2 fixation. Based on these findings, a conceptual model on the functioning of mixed cultures N2-fixing electroactive biofilms was proposed.
      PubDate: Thu, 01 Feb 2024 14:43:16 +000
       
  • Taconet, Paul; Soma, Dieudonné Diloma et al. - Physiological and
           behavioural resistance of malaria vectors in rural West-Africa: a data
           mining study to address their fine-scale spatiotemporal heterogeneity,
           drivers, and predictability

    • Abstract: Insecticide resistance and behavioural adaptation of malaria mosquitoes affect the efficacy of long-lasting insecticide nets - currently the main tool for malaria vector control. To develop and deploy complementary, efficient and cost-effective control interventions, a good understanding of the drivers of these physiological and behavioural traits is needed. In this data-mining exercise, we modelled a set of indicators of physiological resistance to insecticide (prevalence of three target-site mutations) and behavioural resistance phenotypes (early- and late-biting, exophagy) of anopheles mosquitoes in two rural areas of West-Africa, located in Burkina Faso and Cote d'Ivoire. To this aim, we used mosquito field collections along with heterogeneous, multi-source and multi-scale environmental data. The objectives were i) to assess the small-scale spatial and temporal heterogeneity of physiological resistance to insecticide and behavioural resistance phenotypes, ii) to better understand their drivers, and iii) to assess their spatio-temporal predictability, at scales that are consistent with operational action. The explanatory variables covered a wide range of potential environmental determinants of vector resistance to insecticide or behavioural resistance phenotypes: vector control, human availability and nocturnal behaviour, macro and micro-climatic conditions, landscape, etc. The resulting models revealed many statistically significant associations, although their predictive powers were overall weak. We interpreted and discussed these associations in light of several topics of interest, such as: respective contribution of public health and agriculture in the selection of physiological resistances, biological costs associated with physiological resistances, biological mechanisms underlying biting behaviour, and impact of micro-climatic conditions on the time or place of biting. To our knowledge, our work is the first modeling insecticide resistance and feeding behaviour of malaria vectors at such fine spatial scale with such a large dataset of both mosquito and environmental data.
      PubDate: Wed, 31 Jan 2024 10:14:13 +000
       
  • Mycobacterium+bovis+infection+in+three+French+badger+populations&rft.title=Peer+Community+Journal&rft.issn=2804-3871&rft.date=2024&rft.volume=">Calenge, Clément; Payne, Ariane et al. - Assessing the dynamics of 
           Mycobacterium bovis infection in three French badger populations

    • Abstract: The Sylvatub system is a national surveillance program established in 2011 in France to monitor infections caused by Mycobacterium bovis, the main etiologic agent of bovine tuberculosis, in wild species. This participatory program, involving both national and local stakeholders, allowed us to monitor the progression of the infection in three badger populations in clusters covering between 3222 km2 and 7698 km2 from 2013 to 2019. In each cluster, badgers were trapped and tested for M. bovis. Our first aim was to describe the dynamics of the infection in these clusters. We developed a Bayesian model of prevalence accounting for the spatial structure of the cases, the imperfect and variable sensitivity of the diagnostic tests, and the correlation of the infection status of badgers in the same commune caused by local factors (e.g., social structure and proximity to infected farms). This model revealed that the prevalence increased with time in one cluster (Dordogne/Charentes), decreased in the second cluster (Burgundy), and remained stable in the third cluster (Bearn). In all the clusters, the infection was strongly spatially structured, whereas the mean correlation between the infection status of the animals trapped in the same commune was negligible. Our second aim was to develop indicators for monitoring M. bovis infection by stakeholders of the program. We used the model to estimate, in each cluster, (i) the mean prevalence level at mid-period, and (ii) the proportion of the badger population that became infected in one year. We then derived two indicators of these two key quantities from a much simpler regression model, and we showed how these two indicators could be easily used to monitor the infection in the three clusters. We showed with simulations that these two simpler indicators were good approximations of these key quantities.
      PubDate: Tue, 30 Jan 2024 16:48:33 +000
       
  • Saubin, Méline; Coville, Jérome et al. - A mechanistic-statistical
           approach to infer dispersal and demography from invasion dynamics, applied
           to a plant pathogen

    • Abstract: Dispersal, and in particular the frequency of long-distance dispersal (LDD) events, has strong implications for population dynamics with possibly the acceleration of the colonisation front, and for evolution with possibly the conservation of genetic diversity along the colonised domain. However, accurately inferring LDD is challenging as it requires both large-scale data and a methodology that encompasses the redistribution of individuals in time and space. Here, we propose a mechanistic-statistical framework to estimate dispersal from one-dimensional invasions. The mechanistic model takes into account population growth and grasps the diversity in dispersal processes by using either diffusion, leading to a reaction-diffusion (R.D.) formalism, or kernels, leading to an integro-differential (I.D.) formalism. The latter considers different dispersal kernels (e.g. Gaussian, Exponential, and Exponential-power) differing in their frequency of LDD events. The statistical model relies on dedicated observation laws that describe two types of samples, clumped or not. As such, we take into account the variability in both habitat suitability and occupancy perception. We first check the identifiability of the parameters and the confidence in the selection of the dispersal process. We observed good identifiability for all parameters (correlation coefficient >0.9 between true and fitted values). The dispersal process that is the most confidently identified is Exponential-Power (i.e. fat-tailed) kernel. We then applied our framework to data describing an annual invasion of the poplar rust disease along the Durance River valley over nearly 200 km. This spatio-temporal survey consisted of 12 study sites examined at seven time points. We confidently estimated that the dispersal of poplar rust is best described by an Exponential-power kernel with a mean dispersal distance of 1.94 km and an exponent parameter of 0.24 characterising a fat-tailed kernel with frequent LDD events. By considering the whole range of possible dispersal processes our method forms a robust inference framework. It can be employed for a variety of organisms, provided they are monitored in time and space along a one-dimension invasion.
      PubDate: Tue, 30 Jan 2024 16:01:18 +000
       
  • Ludwigia+L.+section+Jussiaea+using+a+combination+of+molecular+cytogenetic,+morphological,+and+crossing+investigations&rft.title=Peer+Community+Journal&rft.issn=2804-3871&rft.date=2024&rft.volume=">Barloy, Dominique; Portillo-Lemus, Luis et al. - Genomic relationships
           among diploid and polyploid species of the genus Ludwigia L. section
           Jussiaea using a combination of molecular cytogenetic, morphological, and
           crossing investigations

    • Abstract: The genus Ludwigia L. section Jussiaea is composed of a polyploid species complex with 2x, 4x, 6x and 10x ploidy levels, suggesting possible hybrid origins. The aim of the present study is to understand the genomic relationships among diploid and polyploid species in the section Jussiaea. Morphological and cytogenetic observations, controlled crosses, genomic in situ hybridization (GISH), and flow cytometry were used to characterize species, ploidy levels, ploidy patterns, and genomic composition across taxa. Genome sizes obtained were in agreement with the diploid, tetraploid, hexaploid, and decaploid ploidy levels. Results of GISH showed that progenitors of Ludwigia stolonifera (4x) were Ludwigia peploides subsp. montevidensis (2x) and Ludwigia helminthorrhiza (2x), which also participated for one part (2x) to the Ludwigia ascendens genome (4x). Ludwigia grandiflora subsp. hexapetala (10x) resulted from the hybridization between L. stolonifera (4x) and Ludwigia grandiflora subsp. grandiflora (6x). One progenitor of L. grandiflora subsp. grandiflora was identified as L. peploides (2x). Our results suggest the existence of several processes of hybridization, leading to polyploidy, and possibly allopolyploidy, in the section Jussiaea due to the diversity of ploidy levels. The success of GISH opens up the potential for future studies to identify other missing progenitors in Ludwigia L. as well as other taxa.
      PubDate: Tue, 30 Jan 2024 10:49:25 +000
       
  • Monalonion+velezangeli+(Hemiptera:+Miridae)+revealed+by+high-throughput+16S-rRNA+sequencing&rft.title=Peer+Community+Journal&rft.issn=2804-3871&rft.date=2024&rft.volume=">Navarro-Escalante, Lucio; Benavides, Pablo et al. - Diversity of bacterial
           symbionts associated with the tropical plant bug Monalonion velezangeli
           (Hemiptera: Miridae) revealed by high-throughput 16S-rRNA sequencing

    • Abstract: Insects and microbes have developed complex symbiotic relationships that evolutionarily and ecologically play beneficial roles for both, the symbiont and the host. In most Hemiptera insects, bacterial symbionts offer mainly nutritional, defensive, and reproductive roles in addition to promoting the adaptive radiation of several hemipteran phytophagous lineages. The tropical plant bug Monalonion velezangeli (Hemiptera: Miridae) is a polyphagous herbivore considered an important insect pest for several economically relevant tropical crops, but information about the composition of its bacterial microbiota was missing. In this study, we describe the diversity and structure of the bacterial microbiota in the nymph and adult life stages of M. velezangeli using Illumina high-throughput sequencing of 16S ribosomal RNA gene amplicons (meta-barcoding). We found that both insect life stages share a similar microbiota in terms of bacterial diversity and community structure. The intracellular symbiont Wolbachia dominated the overall microbiome composition (~92%) in these life stages. Members of the core microbiota include Wolbachia, Romboutsia, Ignavibacterium, Clostridium, Allobaculum, Paracoccus, Methylobacterium, Faecalibacterium, Collinsella, Rothia, Sphingomonas and 4 other undetermined bacterial genera. Based on PCR screening and DNA sequencing of the wsp gene, Wolbachia infection was confirmed in almost 80% of samples, and represented by two different isolates or strains within the supergroup B. This data offers opportunities for studying the contribution of symbiotic bacteria in the biological performance of this insect pest, and provides a base to explore other insect control methods.
      PubDate: Mon, 29 Jan 2024 07:50:32 +000
       
  • Bourdon, Charlotte; Cachot, Jérôme et al. - Characterization of the
           bioaccumulation and toxicity of copper pyrithione, an antifouling
           compound, on juveniles of rainbow trout

    • Abstract: Since the global ban on tributyltin in antifouling paints in 2008 by the International Maritime Organization, new products have been developed and brought to the market. Among them, copper pyrithione (CuPT) is used, but its mechanisms of toxicity remain little known. This project aimed to identify and measure the impacts of aqueous exposure to CuPT, an organic compound, and compare it to ionic Cu2+ added in the form of its inorganic salt CuSO4, in equivalent Cu2+ molar concentrations, on rainbow trout (Oncorhynchus mykiss) juveniles under controlled laboratory conditions. A 24-hour acute exposure was performed with nominal concentrations of 50 and 100 µg/L Cu from either CuSO4 or CuPT (labelled CuSO4_50, CuSO4_100, CuPT_50 and CuPT_100, respectively). The CuPT_100 condition induced 85 % mortality in 15 hours and the CuPT_50 condition induced 5 % mortality in the same period. A chronic exposure was then performed with nominal concentrations of 1 and 10 µg/L Cu from CuPT and 10 µg/L Cu2+ from CuSO4 (labelled CuSO4_1, CuSO4_10, CuPT_1 and CuPT_10, respectively). Measured aqueous concentrations of Cu2+ were slightly higher than nominal concentrations for the lower concentrations, but lower for the CuPT_10 condition. The 8- and 16-day toxicokinetics showed a greater accumulation of copper in the gills of fish exposed to CuPT compared to fish exposed to Cu2+ from CuSO4. The CuPT_10 condition induced 35 and 38 % mortality after 8 and 16 days of exposure, while no mortality was observed in the CuSO4_10 condition. The growth of juveniles was not impacted during the 16 days of exposure for any condition. The activity of antioxidant enzymes (CAT, SOD, GPx) did not respond to exposure to either contaminant. The expression of genes involved in the antioxidant response (sod1, sod2, gpx), detoxification (cyp1a, mt1x, mt2x), Cu transport (ctr1, ctr2, slc11a2), energy metabolism (AcoAc, cox, 12S) and cell cycle regulation (bax) strongly decreased at Day 8 in the gills and at Day 16 in the liver of CuPT-exposed fish in comparison to controls at the same time point. This study clearly showed that the toxicity of Cu in the form of CuPT was much higher than that of ionic Cu from CuSO4and provides new information on the compound that will be useful to develop regulations concerning its use and release in the aquatic environment.
      PubDate: Wed, 24 Jan 2024 16:36:18 +000
       
  • Rueff, Bastien - Dealing with post-excavation data: the Omeka S TiMMA
           web-database

    • Abstract: This paper reports on the creation and use of a web database designed as part of the TiMMA project with the Content Management System Omeka S. Rather than resulting in a technical manual, its goal is to analyze the relevance of using Omeka S in the frame of a post-excavation project, gathering a wide team of researchers from several countries, working in their own language and having their own specialty. Designed to assist organizations and institutions in creating and managing digital collections, Omeka S offers a number of commodities from the perspective of both the administrator(s) and the users, the most significant being its efficiency in capitalizing on linked data standards for items description. Additionally, one of the successful achievements of this platform is to benefit the open-science tools more broadly, permitting for instance, as was done in this project, to import images with the iiiF API and bibliographical references with the Zotero module, thus avoiding the creation of new digital files and metadata. Designed with simplicity in mind, the graphic interface of Omeka S makes it a particularly appropriate tool for collective projects, permitting each user to perform a specific role and record data in their chosen language. This user-friendliness extends up to the data recording and publishing, as well as to the website designing which requires no specific skills in code. The TiMMA project also faces the limitations of Omeka S, such as the lack of efficiency of the search engine, which makes the use of web-semantic vocabularies difficult, a few bugs, and the absence of convenient functionalities in archaeological projects (e.g. the automatic creation of primary keys, a statistic dashboard, cells’ automatic filling). Despite these limitations, the TiMMA project contributes to showing that, without being a complete archaeological system recording, Omeka S is adapted to post-excavation projects.
      PubDate: Wed, 24 Jan 2024 13:31:32 +000
       
  • Lepeophtheirus+salmonis&rft.title=Peer+Community+Journal&rft.issn=2804-3871&rft.date=2024&rft.volume=">Folk, Alexius; Mennerat, Adèle - Methods for tagging an ectoparasite, the
           salmon louse Lepeophtheirus salmonis

    • Abstract: Monitoring individuals within populations is a cornerstone in evolutionary ecology, yet individual tracking of invertebrates and particularly parasitic organisms remains rare. To address this gap, we describe here a method for attaching radio frequency identification (RFID) tags to individual adult females of a marine ectoparasite, the salmon louse Lepeophtheirus salmonis. Comparing two alternative types of glue, we found that one of them (2-octyl cyanoacrylate, 2oc) gave a significantly higher tag retention rate than the other (ethyl 2-cyanoacrylate, e2c). This glue comparison test also resulted in a higher loss rate of adult ectoparasites from the population where tagging was done using 2oc, but this included males not tagged and thus could also suggest a mere tank effect. Corroborating this, a more extensive analysis using data collected over two years showed no significant difference in mortality after repeated exposure to the 2oc glue, nor did it show any significant effect of the tagging procedure on the reproduction of female salmon lice. The proportion of RFID-tagged individuals followed a negative exponential decline, with tag retention among the living female population generally high. The projected retention was found to be about 88% after 30 days or 80% after 60 days, although one of the four batches of glue used, purchased from a different supplier, appeared to give significantly lower tag retention and with greater initial loss (74% and 60% respectively). Overall, we find that RFID tagging is a simple and effective technology that enables documenting individual life histories for invertebrates of a suitable size, including marine and parasitic species, and that it can be used over long periods of study.
      PubDate: Wed, 24 Jan 2024 13:07:04 +000
       
  • Galtier, Nicolas - An approximate likelihood method reveals ancient gene
           flow between human, chimpanzee and gorilla

    • Abstract: Gene flow and incomplete lineage sorting are two distinct sources of phylogenetic conflict, i.e., gene trees that differ in topology from each other and from the species tree. Distinguishing between the two processes is a key objective of current evolutionary genomics. This is most often pursued via the so-called ABBA-BABA type of method, which relies on a prediction of symmetry of gene tree discordance made by the incomplete lineage sorting hypothesis. Gene flow, however, need not be asymmetric, and when it is not, ABBA-BABA approaches do not properly measure the prevalence of gene flow. I introduce Aphid, an approximate maximum-likelihood method aimed at quantifying the sources of phylogenetic conflict via topology and branch length analysis of three-species gene trees. Aphid draws information from the fact that gene trees affected by gene flow tend to have shorter branches, and gene trees affected by incomplete lineage sorting longer branches, than the average gene tree. Accounting for the among-loci variance in mutation rate and gene flow time, Aphid returns estimates of the speciation times and ancestral effective population size, and a posterior assessment of the contribution of gene flow and incomplete lineage sorting to the conflict. Simulations suggest that Aphid is reasonably robust to a wide range of conditions. Analysis of coding and non-coding data in primates illustrates the potential of the approach and reveals that a substantial fraction of the human/chimpanzee/gorilla phylogenetic conflict is due to ancient gene flow. Aphid also predicts older speciation times and a smaller estimated effective population size in this group, compared to existing analyses assuming no gene flow.
      PubDate: Mon, 22 Jan 2024 08:12:45 +000
       
  • Ixodes+ricinus+nymph+abundance+in+relation+to+climate&rft.title=Peer+Community+Journal&rft.issn=2804-3871&rft.date=2024&rft.volume=">Hoch, Thierry; Madouasse, Aurélien et al. - Seasonality of host-seeking
           Ixodes ricinus nymph abundance in relation to climate

    • Abstract: There is growing concern about climate change and its impact on human health. Specifically, global warming could increase the probability of emerging infectious diseases, notably because of changes in the geographical and seasonal distributions of disease vectors such as mosquitoes and ticks. For example, the range of Ixodes ricinus, the most common and widespread tick species in Europe, is currently expanding northward and at higher altitudes. However, little is known about the seasonal variation in tick abundance in different climates. Seasonality of I. ricinus is often based on expert opinions while field surveys are usually limited in time. Our objective was to describe seasonal variations in I. ricinus abundance under different climates. To this end, a seven-year longitudinal study, with monthly collections of I. ricinus host-seeking nymphs, was carried out in France, in six locations corresponding to different climates. Tick data were log-transformed and grouped between years so as to obtain seasonal variations for a typical year. Daily average temperature was measured during the study period. Seasonal patterns of nymph abundance were established for the six different locations using linear harmonic regression. Model parameters were estimated separately for each location. Seasonal patterns appeared different depending on the climate considered. Western temperate sites showed an early spring peak, a summer minimum and a moderate autumn and winter abundance. More continental sites showed a later peak in spring, and a minimum in winter. The peak occurred in summer for the mountainous site, with an absence of ticks in winter. In all cases except the mountainous site, the timing of the spring peak could be related to the sum of degree days since the beginning of the year. Winter abundance was positively correlated to the corresponding temperature. Our results highlight clear patterns in the different sites corresponding to different climates, which allow further forecast of tick seasonality under changing climate conditions.
      PubDate: Mon, 15 Jan 2024 16:25:09 +000
       
  • Sollmann, Rahel - Mt or not Mt: Temporal variation in detection
           probability in spatial capture-recapture and occupancy models

    • Abstract: State variables such as abundance and occurrence of species are central to many questions in ecology and conservation, but our ability to detect and enumerate species is imperfect and often varies across space and time. Accounting for imperfect and variable detection is important for obtaining unbiased estimates of state variables. Here, I investigate whether closed spatial capture-recapture (SCR) and single season occupancy models are robust to ignoring temporal variation in detection probability. Ignoring temporal variation allows collapsing detection data across repeated sampling occasions, speeding up computations, which can be important when analyzing large datasets with complex models. I simulated data under different scenarios of temporal and spatio-temporal variation in detection, analyzed data with the data-generating model and an alternative model ignoring temporal variation in detection, and compared estimates between these two models with respect to relative bias, coefficient of variation (CV) and relative root mean squared error (RMSE). SCR model estimates of abundance, the density-covariate coefficient β and the movement-related scale parameter of the detection function σ were robust to ignoring temporal variation in detection, with relative bias, CV and RMSE of the two models generally being within 4% of each other. An SCR case study for brown tree snakes showed identical estimates of density and σ under models accounting for or ignoring temporal variation in detection. Occupancy model estimates of the occupancy-covariate coefficient β and average occupancy were also largely robust to ignoring temporal variation in detection, and differences in occupancy predictions were mostly <<0.1. But there was a slight tendency for bias in β under the alternative model to increase when detection varied more strongly over time. Thus, when temporal variation in detection is extreme, it may be necessary to model that variation to avoid bias in parameter estimates in occupancy models. An occupancy case study for ten bird species with a more complex model structure showed considerable differences in occupancy parameter estimates under models accounting for or ignoring temporal variation in detection; but estimates and predictions from the latter were always within 95% confidence intervals of the former. There are cases where we cannot or may not want to ignore temporal variation in detection: a behavioral response to detection and certain SCR observation models do not allow collapsing data across sampling occasions; and temporal variation in detection may be informative of species phenology/behavior or for future study planning. But this study shows that it can be safely ignored under a range of conditions when analyzing SCR or occupancy data.
      PubDate: Mon, 08 Jan 2024 09:05:20 +000
       
  • Touzalin, Frédéric; Petit, Eric J. et al. - Mark loss can strongly bias
           estimates of demographic rates in multi-state models: a case study with
           simulated and empirical datasets

    • Abstract: 1. The development of methods for individual identification in wild species and the refinement of Capture-Mark-Recapture (CMR) models over the past few decades have greatly improved the assessment of population demographic rates to address ecological and conservation questions. In particular, multi-state models, which offer flexibility in analysing complex study systems, have gained popularity within the ecological community. In this study, we focus on the issue of mark loss and the associated recycling of remarked individuals, which requires further exploration given the increasing use of these models. 2. To fill this knowledge gap, we employed a wide range of simulation scenarios that reflect commonly encountered real case studies, drawing inspiration from the survival rates of 700 vertebrate species. Using a multi-state, Arnason-Schwartz (AS) modelling framework, we estimated the effects of mark loss and recycled individuals on parameter estimates. We assessed parameter bias by simulating a metapopulation system with varying capture and survival rates. Additionally, we demonstrated how mark loss can be easily estimated and accounted for using a 10-year empirical CMR dataset of bats. The bats were individually identified using Passive Integrated Transponder (PIT) tag technology as potentially lost marks and multi-locus genotypes as 'permanent marks'. 3. Our simulation results revealed that the occurrence of bias and the affected parameters were highly dependent on the study system, making it difficult to establish general rules to predict bias a priori. The model structure and the interdependency among parameters pose challenges in predicting the impact of bias on estimates. 4. Our findings underscore the importance of assessing the effect of mark loss when using AS models. Ignoring such violations of model assumptions can have significant implications for ecological inferences and conservation policies. In general, the use of permanent marks, such as genotypes, should always be preferred when modelling population dynamics. If that is not feasible, an alternative is to combine two independent types of temporary marks, such as PIT tags and bands. 5. Analysis of our empirical dataset on Myotis myotis bats revealed that tag loss is higher in juveniles than in adults during the first year after tagging. The use of surgical glue to close the injection hole reduces tag loss rate from 28% to 19% in juveniles, while it has no effect on the tag loss rate in adults (~10%). The main bias observed in our metapopulation system appears in the survival rate, with up to a 20% underestimation if tag loss is not accounted for.
      PubDate: Thu, 21 Dec 2023 08:18:46 +000
       
  • slendr:+a+framework+for+spatio-temporal+population+genomic+simulations+on+geographic+landscapes&rft.title=Peer+Community+Journal&rft.issn=2804-3871&rft.date=2023&rft.volume=">Petr, Martin; Haller, Benjamin C. et al. - slendr: a framework for
           spatio-temporal population genomic simulations on geographic landscapes

    • Abstract: One of the goals of population genetics is to understand how evolutionary forces shape patterns of genetic variation over time. However, because populations evolve across both time and space, most evolutionary processes also have an important spatial component, acting through phenomena such as isolation by distance, local mate choice, or uneven distribution of resources. This spatial dimension is often neglected, partly due to the lack of tools specifically designed for building and evaluating complex spatio-temporal population genetic models. To address this methodological gap, we present a new framework for simulating spatially-explicit genomic data, implemented in a new R package called slendr (www.slendr.net), which leverages a SLiM simulation back-end script bundled with the package. With this framework, the users can programmatically and visually encode spatial population ranges and their temporal dynamics (i.e., population displacements, expansions, and contractions) either on real Earth landscapes or on abstract custom maps, and schedule splits and gene-flow events between populations using a straightforward declarative language. Additionally, slendr can simulate data from traditional, non-spatial models, either with SLiM or using an alternative built-in coalescent msprime back end. Together with its R-idiomatic interface to the tskit library for tree-sequence processing and analysis, slendr opens up the possibility of performing efficient, reproducible simulations of spatio-temporal genomic data entirely within the R environment, leveraging its wealth of libraries for geospatial data analysis, statistics, and visualization. Here, we present the design of the slendr R package and demonstrate its features on several practical example workflows.
      PubDate: Fri, 15 Dec 2023 15:56:15 +000
       
 
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  Subjects -> PALEONTOLOGY (Total: 43 journals)
Showing 1 - 21 of 21 Journals sorted by number of followers
Journal of Quaternary Science     Hybrid Journal   (Followers: 36)
Quaternary Science Reviews     Hybrid Journal   (Followers: 29)
Quaternary Research     Full-text available via subscription   (Followers: 21)
Palaeontology     Hybrid Journal   (Followers: 19)
Boreas: An International Journal of Quaternary Research     Hybrid Journal   (Followers: 15)
Palaeogeography, Palaeoclimatology, Palaeoecology     Hybrid Journal   (Followers: 14)
Historical Biology: An International Journal of Paleobiology     Hybrid Journal   (Followers: 10)
Journal of Paleontology     Hybrid Journal   (Followers: 10)
Facies     Hybrid Journal   (Followers: 8)
Journal of Vertebrate Paleontology     Full-text available via subscription   (Followers: 8)
Geologica Saxonica     Open Access   (Followers: 8)
Paleobiology     Full-text available via subscription   (Followers: 7)
Alcheringa: An Australasian Journal of Palaeontology     Hybrid Journal   (Followers: 6)
European Journal of Protistology     Hybrid Journal   (Followers: 5)
Journal of Paleolimnology     Hybrid Journal   (Followers: 5)
Paleontological Journal     Full-text available via subscription   (Followers: 5)
Paläontologische Zeitschrift     Hybrid Journal   (Followers: 5)
Paleoceanography and Paleoclimatology     Full-text available via subscription   (Followers: 5)
Fossil Record     Open Access   (Followers: 5)
Peer Community Journal     Open Access   (Followers: 5)
Annales de Paléontologie     Full-text available via subscription   (Followers: 4)
Geobios     Full-text available via subscription   (Followers: 4)
Palaeoworld     Hybrid Journal   (Followers: 4)
EvoDevo     Open Access   (Followers: 4)
Swiss Journal of Palaeontology     Hybrid Journal   (Followers: 4)
Neues Jahrbuch für Geologie und Paläontologie - Abhandlungen     Full-text available via subscription   (Followers: 3)
Quaternaire     Open Access   (Followers: 3)
International Journal of Speleology     Open Access   (Followers: 3)
Zitteliana     Open Access   (Followers: 3)
Marine Micropaleontology     Hybrid Journal   (Followers: 2)
Open Quaternary     Open Access   (Followers: 2)
Palaeontographica A     Full-text available via subscription   (Followers: 2)
Review of Palaeobotany and Palynology     Hybrid Journal   (Followers: 1)
Annals of Carnegie Museum     Full-text available via subscription   (Followers: 1)
Palynology     Hybrid Journal   (Followers: 1)
PaleoBios     Open Access   (Followers: 1)
Rivista Italiana di Paleontologia e Stratigrafia (Research In Paleontology and Stratigraphy)     Open Access   (Followers: 1)
Novitates Paleoentomologicae     Open Access   (Followers: 1)
Vertebrate Anatomy Morphology Palaeontology     Open Access   (Followers: 1)
Papers in Palaeontology     Hybrid Journal   (Followers: 1)
Ameghiniana     Open Access  
Spanish Journal of Palaeontology     Open Access  
Ichnos: An International Journal for Plant and Animal Traces     Hybrid Journal  
Revue de Micropaleontologie     Full-text available via subscription  
Comptes Rendus Palevol     Open Access  
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