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Peer Community Journal
Number of Followers: 3  Open Access journalISSN (Online) 2804-3871 Published by Peer Community in (PCI)  [1 journal]
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- Circovirus+canine)+variants+circulate+at+high+prevalence+in+grey+wolves+(
(Circovirus canine) variants circulate at high prevalence in grey wolves
(Canis lupus) from the Northwest Territories, Canada
Abstract: Canine circoviruses (CanineCV) have a worldwide distribution in dogs and are occasionally detected in wild carnivorans, indicating their ability for cross-species transmission. However, fox circovirus, a lineage of CanineCV, has been identified exclusively in wild canids. We analyzed spleen samples from 159 grey wolves from the Northwest Territories, Canada, to investigate the molecular epidemiology of CanineCV and formulate hypotheses about virus ecology and evolution. Overall, 72 out of 159 (45.3%) animals tested positive. Virus prevalence was similar between males and females, adults and juveniles, and across the investigated years and locations. CanineCV infection was not associated with a poor body condition. While the percentage of co-infections with canine parvoviruses, investigated in a previous study, was high (63/72, 87.5%), the rate of parvovirus infection in CanineCV-negative animals was significantly lower (42/87, 48.3%, χ2 = 27.03, p < 0.001), and CanineCV infection was associated with a 7.5- and 2.4-fold increase in the risk of acquiring canine parvovirus 2 or canine bufavirus infections, respectively (odds ratios: 3.5-16.9 and 1.3-5.8). Although common risk factors cannot be ruled out, this suggests that CanineCV may facilitate parvoviral super-infections. Sequencing revealed high CanineCV genetic diversity, further exacerbated by recombination. Of the 69 sequenced strains, 87.5% were fox circoviruses, five were related to a fox circovirus-like recombinant strain, and one belonged to a distant lineage. In the phylogenetic analysis, the virus sequences were distributed according to sampling locations, with some viruses being geographically restricted. Different clades of viruses were identified in the same areas and over multiple years (2007-2019), indicating the co-existence of multiple endemic lineages in the investigated area. Phylogenetic analysis of all available complete fox circovirus genomes (32 from foxes and 15 from wolves from North America and Europe) demonstrated four lineages, each including sequences from this study. Within each lineage, strains segregated geographically and not by host. This implies that, although multiple lineages co-exist, viruses do not frequently move between locations. Finally, viruses from Europe and North America were mixed, indicating that the origin of the four lineages might predate the segregation of European and American wolf and fox populations. Given the high prevalence and diversity of fox circoviruses in wolves, these animals should be considered reservoir hosts for these viruses. Although we cannot exclude a lower susceptibility of dogs, the lack of fox circovirus in dogs could be due to environmental circumstances that prevented its spread to dogs. Given the high diversity and wild host specificity, we presume a long-lasting association between fox circovirus and canine hosts and hypothesize a higher likelihood of transmission from dogs to wild animals than vice versa. Further studies should investigate other sympatric wild species and additional locations to explore the possible existence of additional maintenance hosts and the reasons behind the marked difference in cross-species transmission dynamics among CanineCV lineages.
PubDate: Thu, 08 Aug 2024 05:59:05 +000
- Coccomyxa+viridis+SAG+216-4&rft.title=Peer+Community+Journal&rft.issn=2804-3871&rft.date=2024&rft.volume=">Kraege, Anton; Chavarro-Carrero, Edgar A. et al. - High quality genome
assembly and annotation (v1) of the eukaryotic terrestrial microalga
Coccomyxa viridis SAG 216-4
Abstract: Unicellular green algae of the genus Coccomyxa are recognized for their worldwide distribution and ecological versatility. Most species described to date live in close association with various host species, such as in lichen associations. However, little is known about the molecular mechanisms that drive such symbiotic lifestyles. We generated a high-quality genome assembly for the lichen photobiont Coccomyxa viridis SAG 216-4 (formerly C. mucigena). Using long-read PacBio HiFi and Oxford Nanopore Technologies in combination with chromatin conformation capture (Hi-C) sequencing, we assembled the genome into 21 scaffolds with a total length of 50.9 Mb, an N50 of 2.7 Mb and a BUSCO score of 98.6%. While 19 scaffolds represent full-length nuclear chromosomes, two additional scaffolds represent the mitochondrial and plastid genomes. Transcriptome-guided gene annotation resulted in the identification of 13,557 protein-coding genes, of which 68% have annotated PFAM domains and 962 are predicted to be secreted.
PubDate: Thu, 08 Aug 2024 05:59:02 +000
- Caligo+martia eyespot+may+reduce+fatal+attacks+by+birds:+a+case+study+supports+the+deflection+hypothesis+in+nature&rft.title=Peer+Community+Journal&rft.issn=2804-3871&rft.date=2024&rft.volume=">Iserhard, Cristiano Agra; Malta, Shimene et al. - The large and
central Caligo martia eyespot may reduce fatal attacks by birds: a case
study supports the deflection hypothesis in nature
Abstract: Many animals have colorations that resemble eyes, but the functions of such eyespots are debated. Caligo martia (Godart, 1824) butterflies have large ventral hind wing eyespots, and we aimed to test whether these eyespots act to deflect or to thwart bird attacks through intimidation in a natural community in a Restinga Forest in austral South America. We used four types of paper facsimiles: unmanipulated C. martia (with eyespots, WE), facsimiles with UV enhanced eyespots (UV), camouflaged facsimiles lacking eyespots (CM), and light-coloured facsimiles that were not camouflaged and lacked eyespots (NC). Two experiments were performed: Experiment 1 used facsimiles in a natural resting position, and in Experiment 2 facsimiles were positioned with the wings open, with ventral wing surfaces and body exposed to viewers. In both experiments facsimiles were placed in two forest sites, organized in 50 blocks with four facsimiles each, and checked for predator attacks every 24 h for five consecutive days. While WE and UV facsimiles were mostly attacked in non-vital areas (wings), most bird attacks on CM were directed at vital body areas. Notably, CM facsimiles had lower attack probability than WE, UV and NC. Our results indicate that C. martia eyespots appear to have a deflection function. Eyespots did not appear to reduce attack rates, suggesting that local bird species were not intimidated. Both eyespots and camouflage can be considered efficient functional traits in defence against predation in forest environments, and experiments focusing on local predators and prey are key to our understanding of wing pattern evolution in Lepidoptera.
PubDate: Tue, 06 Aug 2024 12:36:24 +000
- Carabus+giant+ground+beetles+shows+an+Oligocene+origin+and+
ground beetles shows an Oligocene origin and in situ alpine
diversification
Abstract: The development of museomics represents a major paradigm shift in the use of natural history collection specimens for systematics and evolutionary biology. New approaches in this field allow the sequencing of hundreds to thousands of loci from across the genome using historical DNA. HyRAD-X, a recently introduced capture method using bench-top designed probes, has proved very efficient for recovering genomic-scale datasets using natural history collection specimens. Using this technique at both the intra- and interspecific levels, we infer the most robust phylogeny to date for Arcifera, an ecologically and morphologically diverse clade of Carabus giant ground beetles. We successfully generated a genomic dataset of up to 1965 HyRAD-X loci for all described species, permitting inference of a robust dated phylogenomic tree for this clade. Our species delimitation and population genomic analyses suggest that the current classification for Arcifera is in line with its evolutionary history. Our results suggest an origin of Arcifera in the late Oligocene followed by speciation events during the warm mid-Miocene unlinked to Pleistocene glaciations. The dynamic paleogeographic history of the Palearctic region likely contributed to the diversification of this lineage with a relatively ancient colonization of the proto-Alps followed by in situ speciation where most species of Arcifera are currently found sometimes syntopically likely as a result of post-glaciations secondary contacts.
PubDate: Mon, 05 Aug 2024 11:15:37 +000
- Beck, Miriam; Billoir, Elise et al. - Effects of water nutrient
concentrations on stream macroinvertebrate community stoichiometry: a
large-scale study
Abstract: Basal resources generally mirror environmental nutrient concentrations in the elemental composition of their tissue, meaning that nutrient alterations can directly reach consumer level. An increased nutrient content (e.g. phosphorus) in primary and detrital resources under nutrient enriched conditions should favour taxa with a high demand for this nutrient. With the nutrient demand of a taxon being correlated to the elemental composition of its body tissue (e.g. phosphorus content), such above described species shifts likely alter the overall community stoichiometry. However, studies addressing stoichiometry at community level are rare and most often restricted to lacustrine planktonic systems, single streams or limited experimental setups. Relying on a stoichiometric database for >200 taxa and >1300 standardized sampling events of macroinvertebrate assemblages from the French national monitoring programme, we investigated the effect of water phosphorus and nitrogen load on stream macroinvertebrate community stoichiometry. Community stoichiometry was significantly affected by water phosphorus concentration and the effect was strongest at low levels of nitrogen. While we could not confirm our hypothesis of increasing community %P (and decreasing C:P, N:P) with increasing water phosphorus concentrations for the overall community, it clearly followed this pattern for both Insecta and Malacostraca. General differences in the elemental composition among major taxonomic groups and a shift among these groups over the nutrient gradient probably explain the response of community stoichiometry. Our results show that assumptions from Ecological Stoichiometry Theory also hold at the community level, at least for two dominant taxa, and on a large spatial scale, with likely consequences for nutrient cycling and ecosystem function.
PubDate: Tue, 30 Jul 2024 12:00:38 +000
- Rogers, Alan R. - Genetic Evidence for Geographic Structure within
the Neanderthal Population
Abstract: PSMC estimates of Neanderthal effective population size (Ne) exhibit a roughly 5-fold decline across the most recent 20~ky before the death of each fossil. To explain this pattern, this article develops new theory relating genetic variation to geographic population structure and local extinction. It argues that the observed pattern results from subdivision and gene flow. If two haploid genomes are sampled from the same subpopulation, their recent ancestors are likely to be geographic neighbors and therefore coalesce rapidly. By contrast, remote ancestors are likely to be far apart, and their coalescent rate is lower. Consequently, Ne is larger in the distant past than in the recent past. New theoretical results show that modest rates of extinction cause substantial reductions in heterozygosity, Wright's FST, and Ne.
PubDate: Tue, 30 Jul 2024 05:08:30 +000
- Cheutin, Marie-Charlotte; Boucicot, Manon et al. - Microbiome turnover
during offspring development varies with maternal care, but not moult, in
a hemimetabolous insect
Abstract: The ecological success of insects often depends on their association with beneficial microbes. However, insect development involves repeated moults, which can have dramatic effects on their microbial communities. Here, we investigated whether and how moulting affects the microbiome of a hemimetabolous insect, and whether maternal care can modulate these effects. We reared European earwig juveniles with or without mothers and used 16S rRNA metabarcoding to analyse the prokaryotic fraction of the core microbiome of eggs, recently and old moulted individuals at four developmental stages and the resulting adults. The 218 samples obtained showed that the microbiome diversity changed non-linearly during development and that these changes were associated with bacterial biomarkers. Surprisingly, these changes did not occur during moulting, but rather between the beginning and end of certain developmental stages. We also found that access to maternal care affected the microbiome of both juveniles and adults, even when the last contact with mothers was two months before adulthood. Overall, these results provide new insights into our understanding of the (in)stability of the prokaryotic microbiome in hemimetabolous insects and its independence from moult. More generally, they question the role of microbiome acquisition through maternal care in maintaining family life in species where this behaviour is facultative.
PubDate: Mon, 29 Jul 2024 09:41:32 +000
- Daphnia+magna:+insights+from+elemental+behavior+and+speciation+in+a+standardized+test+medium&rft.title=Peer+Community+Journal&rft.issn=2804-3871&rft.date=2024&rft.volume=">Vignati, Davide A.L.; Martin, Loïc A. et al. - Ecotoxicity of lanthanides
to Daphnia magna: insights from elemental behavior and speciation in a
standardized test medium
Abstract: Lanthanides (LNs) are a group of 15 elements with steadily increasing economical importance due to their multiple uses in technologies essential for sustainable ecological, digital and energetic transitions. Although knowledge on LN ecotoxicology has greatly improved over the last decade, uncertainty persists with regard to their actual hazard and risk in freshwater environments. In particular, only limited information is available on i) the actual relationships between LN speciation vs. ecotoxicological responses in standardized laboratory tests and ii) the existence of regular and predictable patterns in LN ecotoxicity (expressed as e.g., EC50) along the LN series. The present paper provides the first report on the ecotoxicity of all lanthanides (except Pm) for the freshwater crustacean Daphnia magna along with an unprecedented level of detail on LN speciation in the exposure medium. Experimental data show that exposure concentrations can decrease by up to 95 % over the test duration, with the percentage decrease being inversely related with LN atomic mass. Thermodynamic speciation calculations confirm the possible formation of insoluble species, mainly LN carbonates. However, the corresponding theoretical solubility limits do not fully agree with measured concentrations at the end of the tests. Experimental verification of exposure concentrations (as a minimum at the beginning and end of laboratory tests) remains therefore mandatory to reach proper conclusions as to the ecotoxicity of each LN. A decreasing trend in ecotoxicity can actually be observed along the LN series when temporal changes in the exposure concentrations are properly accounted for. However, this trend remains dependent on exposure time and selected exposure metrics. This and other caveats must be considered in future research to reach a community-based consensus for the proper hazard and risk assessment of LN towards daphnids and other aquatic organisms.
PubDate: Fri, 19 Jul 2024 07:59:30 +000
- Bactrocera+dorsalis+population+growth+in+Senegalese+orchards&rft.title=Peer+Community+Journal&rft.issn=2804-3871&rft.date=2024&rft.volume=">Caumette, Cécile; Diatta, Paterne et al. - Hierarchizing multi-scale
environmental effects on agricultural pest population dynamics: a case
study on the annual onset of Bactrocera dorsalis population growth in
Senegalese orchards
Abstract: Implementing integrated pest management programs to limit agricultural pest damage requires an understanding of the interactions between the environmental variability and population demographic processes. However, identifying key environmental drivers of spatio-temporal pest population dynamics remains challenging as numerous candidate factors can operate at a range of scales, from the field (e.g. agricultural practices) to the regional scale (e.g. weather variability). In such a context, data-driven approaches applied to pre-existing data may allow identifying patterns, correlations, and trends that may not be apparent through more restricted hypothesis-driven studies. The resulting insights can lead to the generation of novel hypotheses and inform future experimental work focusing on a limited and relevant set of environmental predictors. In this study, we developed an ecoinformatics approach to unravel the multi-scale environmental conditions that lead to the early re-infestation of mango orchards by a major pest in Senegal, the oriental fruit fly Bactrocera dorsalis (BD). We gathered abundance data from a three-year monitoring conducted in 69 mango orchards as well as environmental data (i.e. orchard management, landscape structure and weather variability) across a range of spatial scales. We then developed a flexible analysis pipeline centred on a recent machine learning algorithm, which allows the combination of gradient boosting and grouped random effects models or Gaussian processes, to hierarchize the effects of multi-scale environmental variables on the onset of annual BD population growth in orchards. We found that physical factors (humidity, temperature), and to some extent landscape variables, were the main drivers of the spatio-temporal variability of the onset of population growth in orchards. These results suggest that favourable microclimate conditions could provide refuges for small BD populations that could survive, with little or no reproduction, during the mango off-season and, then, recolonize neighbouring orchards at the beginning of the next mango season. Confirmation of such a hypothesis could help to prioritize surveillance and preventive control actions in refuge areas.
PubDate: Thu, 18 Jul 2024 05:12:58 +000
- Godinho, Diogo Prino; Fragata, Inês et al. - Spider mites collectively
avoid plants with cadmium irrespective of their frequency or the presence
of competitors
Abstract: Accumulation of heavy metals by plants can serve as a defence against herbivory. Herbivores, in turn, may avoid feeding on contaminated tissues. Such avoidance, however, may hinge upon the specific conditions faced by herbivores. Here, we tested whether the spider mite Tetranychus urticae avoids tomato plants contaminated with cadmium in presence of conspecifics or heterospecifics and depending on the frequency of contaminated plants. We show that individual spider mite females do not preferentially move to leaf tissues with or without cadmium, despite clear costs on their performance. However, in a set-up where 200 mites were simultaneously given the choice between four plants with or without cadmium, they collectively avoided plants with cadmium, irrespective of the proportion of plants with cadmium. In addition, T. urticae did not discriminate between plants infested with its competitor T. evansi and other uncontaminated plants but they preferred plants with competitors when the other plants contained cadmium. Our results show that aggregation may facilitate avoidance of contaminated plants. They also indicate that cadmium accumulation in plants is a stronger selective pressure than interspecific competition with T. evansi. Therefore, collective avoidance of metal-accumulating plants by herbivores is robust to environmental conditions and may have important consequences for species distribution and interactions in metal contaminated sites.
PubDate: Thu, 11 Jul 2024 14:40:18 +000
- Billaud, Maud; Theodorou, Ilias et al. - T7 DNA polymerase treatment
improves quantitative sequencing of both double-stranded and
single-stranded DNA viruses
Abstract: Bulk microbiome, as well as virome-enriched shotgun sequencing only reveals the double-stranded DNA (dsDNA) content of a given sample, unless specific treatments are applied. However, genomes of viruses often consist of a circular single-stranded DNA (ssDNA) molecule. Pre-treatment and amplification of DNA using the multiple displacement amplification (MDA) method enables conversion of ssDNA to dsDNA, but this process can lead to over-representation of these circular ssDNA genomes. A more recent alternative permits to bypass the amplification step, as library adapters are ligated to sheared and denatured DNA, after an end-modification step (xGen kit). However, the sonication step might shear ssDNA more efficiently than dsDNA, therefore introducing another bias in virome sequencing. These limitations prompted us to explore an alternative method of DNA preparation for sequencing mixed ssDNA and dsDNA viromes. Using a synthetic mix of viral particles, we made use of the T7 DNA polymerase (T7pol) to convert viral circular ssDNA molecules to dsDNA, while preventing over-replication of such molecules, as is the case with the Phi29 DNA polymerase. Our findings indicate that using T7pol and a mix of degenerated primers to convert ssDNA to dsDNA prior library preparation is a good alternative to the currently used methods. It better represents the original synthetic mixtures compared to MDA or direct application of the xGen kit. Furthermore, when applied to two complex virome samples, the T7pol treatment improved both the richness and abundance in the Microviridae fraction. We conclude that T7pol pretreatment is preferable to MDA for the shotgun sequencing of viromes, which is easy to implement and inexpensive.
PubDate: Thu, 11 Jul 2024 14:39:57 +000
- Milvus+milvus)&rft.title=Peer+Community+Journal&rft.issn=2804-3871&rft.date=2024&rft.volume=">Sollmann, Rahel; Adenot, Nathalie et al. - Accounting for observation
biases associated with counts of young when estimating fecundity: case
study on the arboreal-nesting red kite (Milvus milvus)
Abstract: Counting the number of young in a brood from a distance is common practice, for example in tree-nesting birds. These counts can, however, suffer from over and undercounting, which can lead to biased estimates of fecundity (average number of nestlings per brood). Statistical model development to account for observation bias has focused on false negatives (undercounts), yet it has been shown that these models are sensitive to the presence of false positives (overcounts) when they are not accounted for. Here, we develop a model that estimates fecundity while accounting for both false positives and false negatives in brood counts. Its parameters can be estimated using a calibration approach that combines uncertain counts with certain ones, which can be obtained by accessing the brood, for example during ringing. The model uses multinomial distributions to estimate the probabilities of observing y young conditional on the true state of a brood z (i.e., true number of young) from paired uncertain and certain counts. These classification probabilities are then used to estimate the true state of broods for which only uncertain counts are available. We use a simulation study to investigate bias and precision of the model and parameterize the simulation with empirical data from 26 red kite nests visited with ground and nest-based counts during 2021 and 2022 in central Europe. In these data, bias in counts was at most 1 in either direction, more common in larger broods, and undercounting was more common than overcounting. This led to an overall 5% negative bias in fecundity in uncertain counts. The model produced essentially unbiased estimates (relative bias < 2%) of fecundity across a range of sample sizes. This held true whether or not fecundity was the same for nests with paired counts and those with uncertain-only counts. But the model could not estimate parameters when true states were missing from the paired data, which happened frequently in small sample sizes (n = 10 or 25). Further, we projected populations 50 years into the future using fecundity estimates corrected for observation biases from the multinomial model, and based on “raw” uncertain observations. We found that ignoring observation bias led to strong negative bias in projected population size for growing populations, but only minor negative bias in declining populations. Accounting for apparently minor biases associated with ground counts is important for ensuring accurate estimates of abundance and population dynamics especially for increasing populations. This could be particularly important for informing conservation decisions in projects aimed at recovering depleted populations.
PubDate: Tue, 09 Jul 2024 09:27:50 +000
- Gammarus+fossarum&rft.title=Peer+Community+Journal&rft.issn=2804-3871&rft.date=2024&rft.volume=">Bauer, Alexandre; Develay Nguyen, Lucie et al. - Differences in
specificity, development time and virulence between two acanthocephalan
parasites, infecting two cryptic species of Gammarus fossarum
Abstract: Multi-host parasites can exploit various host species that differ in abundance and susceptibility to infection, which will contribute unequally to their transmission and fitness. Several species of acanthocephalan manipulative parasites (among which Pomphorhynchus laevis and P. tereticollis) use various amphipod species of the genus Gammarus as intermediate hosts. Many Gammarus pulex and G. fossarum cryptic lineages are living in sympatry in European rivers, questioning the spectrum of intermediate hosts that acanthocephalans can use, and their relative contribution to their life cycles. In this work, the respective roles of parasites species (P. laevis and, for the first time, P. tereticollis) and sympatric host cryptic species (the G. fossarum species complex) were studied experimentally on two traits: host susceptibility to infection and parasite virulence. Differences were found, both in terms of infectivity and virulence, between the cryptic hosts and between the two parasite species. We confirm that these acanthocephalans, previously considered as generalists, show specificities among their sympatric hosts. Differences in field prevalence and susceptibility after experimental exposures were more pronounced between cryptic G. fossarum species for P. tereticollis than for P. laevis. The mortality of infected individuals increased significantly after several weeks of development of both parasite species. P. tereticollis was less virulent than P. laevis, perhaps due to differences in host exploitation, since we evidenced that P. tereticollis had a much slower growth rate.
PubDate: Mon, 08 Jul 2024 06:58:33 +000
- Yacine, Youssef; Loeuille, Nicolas - Attracting pollinators vs escaping
herbivores: eco-evolutionary dynamics of plants confronted with an
ecological trade-off
Abstract: Many plant traits are subject to an ecological trade-off between attracting pollinators and escaping herbivores. The interplay of both plant-animal interaction types determines their evolution. As most studies focus on either pollination or herbivory, how they jointly affect the eco-evolutionary dynamics of plant-animal communities is often left unknown. Within a plant-pollinator-herbivore community where interaction strengths depend on trait matching, we consider the evolution of a plant trait involved in both plant-animal interactions. Using adaptive dynamics, we uncover when stabilizing, runaway (i.e. directional) or disruptive selection emerges and its consequences for multispecies coexistence. We find that strong pollination relative to herbivory favors stabilizing selection and coexistence. Strong herbivory relative to pollination fosters runaway selection and threatens coexistence. Importantly, given balanced interactions, joint effects may lead to disruptive selection, allowing the emergence of plant dimorphism. The strength of the ecological trade-off largely explains the occurrence of these contrasting eco-evolutionary dynamics. In particular, plant diversification requires strong trade-offs, with the strongest trade-offs allowing long-term polymorphism. We discuss how our results relate to various empirical cases where the interplay of pollination and herbivory maintains plant polymorphism. Beyond maintenance, our work suggests that it might also have fueled the diversification process itself.
PubDate: Wed, 03 Jul 2024 13:43:15 +000
- Galaxea+fascicularis&rft.title=Peer+Community+Journal&rft.issn=2804-3871&rft.date=2024&rft.volume=">Puntin, Giulia; Wong, Jane C. Y. et al. - The bacterial microbiome of
symbiotic and menthol-bleached polyps of long-term aquarium-reared Galaxea
fascicularis
Abstract: Coral reefs support the livelihood of half a billion people but are at high risk of collapse due to the vulnerability of corals to climate change and local anthropogenic stressors. While understanding coral functioning is essential to guide conservation efforts, research is challenged by the complex nature of corals. They exist as metaorganisms (holobionts), constituted by the association between the (coral) animal host, its obligate endosymbiotic algae (Symbiodiniaceae), and other microorganisms comprising bacteria, viruses, archaea, fungi and other protists. Researchers therefore increasingly turn to model organisms to unravel holobiont complexity, dynamics, and how these determine the health and fitness of corals. The coral Galaxea fascicularis is an emerging model organism for coral symbiosis research with demonstrated suitability to aquarium rearing and reproduction, and to manipulation of the host-Symbiodiniaceae symbiosis. However, little is known about the response of the G. fascicularis microbiome to menthol bleaching—the experimental removal of the Symbiodiniaceae which represents the first step in coral-algal symbiosis manipulation. For this, we characterized the bacterial microbiome of symbiotic and menthol-bleached G. fascicularis originating from the Red Sea and South China Sea (Hong Kong) that were long-term aquarium-reared in separate facilities. We found that the coral-associated microbiomes were composed of relatively few bacterial taxa (10-78 ASVs). Symbiotic polyps (clonal replicates) from the same colony had similar microbiomes, which were distinct from those of other colonies despite co-culturing in shared aquaria. A pattern of seemingly differential response of the bacterial microbiome to menthol bleaching between the two facilities emerged, warranting further investigation into the role of rearing conditions. Nevertheless, the changes in community composition overall appeared to be stochastic suggesting a dysbiotic state. Considering the importance of bleaching treatment of captive corals for symbiosis research, our results—although preliminary—contribute fundamental knowledge for the development of the Galaxea model for coral symbiosis research.
PubDate: Thu, 27 Jun 2024 07:43:44 +000
- Gaucherel, Cedric; Fayolle, Stolian et al. - Diagnosis of planktonic
trophic network dynamics with sharp qualitative changes
Abstract: Trophic interaction networks are notoriously difficult to understand and to diagnose (i.e., to identify contrasted network functioning regimes). Such ecological networks have many direct and indirect connections between species, and these connections are not static but often vary over time. These topological changes, as opposed to a dynamic on a static (frozen) network, can be triggered by natural forcings (e.g., seasons) and/or by human influences (e.g., nutrient or pollution inputs). Aquatic trophic networks are especially dynamic and versatile, thus suggesting new approaches for identifying network structures and functioning in a comprehensive manner.In this study, a qualitative model was devised for this purpose. Applying discrete-event models from theoretical computer science, a mechanistic and qualitative model was developed that allowed computation of the exhaustive dynamics of a given trophic network and its environment. Once the model definition is assumed, it provides all possible trajectories of the network from a chosen initial state. In a rigorous and analytical approach, for the first time, we validated the model on one theoretical and two observed trajectories recorded at freshwater stations in the La Rochelle region (Western France). The model appears to be easy to build and intuitive, and it provides additional relevant trajectories to the expert community. We hope this formal approach will open a new avenue in identifying and predicting trophic (and non-trophic) ecological networks.
PubDate: Wed, 26 Jun 2024 07:49:49 +000
- Amin, Bawan; Fishman, Ruth et al. - Sex differences in the relationship
between maternal and foetal glucocorticoids in a free-ranging large mammal
Abstract: Maternal phenotypes can have long-term effects on offspring phenotypes. These maternal effects may begin during gestation, when maternal glucocorticoid (GC) levels may affect foetal GC levels, thereby having an organizational effect on the offspring phenotype. Recent studies have showed that maternal effects may be different between the sexes. However, how maternal GC levels relate to foetal levels is still not completely understood. Here we related, for the first time in a free-ranging large mammal, the fallow deer (Dama dama), maternal GC levels with foetal in utero GC levels. We did this in a non-invasive way by quantifying cortisol metabolites from faecal samples collected from pregnant does during late gestation, as proxy for maternal GC level. These were then related to GC levels from hair of their neonate offspring (n = 40). We have shown that maternal GC levels were positively associated with foetal GC levels, but only in female offspring. These findings highlight sex differences, which may have evolved to optimize male growth at the cost of survival.
PubDate: Thu, 20 Jun 2024 13:53:29 +000
- Kra, Arsène Kouassi; Fotso, Arlette Simo et al. - HIV self-testing
positivity rate and linkage to confirmatory testing and care: a telephone
survey in Côte d’Ivoire, Mali, and Senegal
Abstract: HIV self-testing (HIVST) empowers individuals to decide when and where to test and with whom to share their results. From 2019 to 2022, the ATLAS program distributed ∼ 400 000 HIVST kits in Côte d’Ivoire, Mali, and Senegal. It prioritised key populations, including female sex workers and men who have sex with men, and encouraged secondary distribution of HIVST to their partners, peers and clients.To preserve the confidential nature of HIVST, use of kits and their results were not systematically tracked. Instead, an anonymous phone survey was carried out in two phases during 2021 to estimate HIVST positivity rates (phase 1) and linkage to confirmatory testing (phase 2). Initially, participants were recruited via leaflets from March to June and completed a sociobehavioural questionnaire. In the second phase (September-October), participants who had reported two lines or who reported a reactive result were recontacted to complete another questionnaire. Of the 2 615 initial participants, 89.7% reported a consistent response between the number of lines on the HIVST and their interpretation of the result (i.e., ‘non-reactive’ for 1 line, ‘reactive’ for 2 lines).Overall positivity rate based on self-interpreted HIVST results was 2.5% considering complete responses, and could have ranged from 2.4% to 9.1% depending on the interpretation of incomplete responses. Using the reported number of lines, this rate was estimated at 4.5% (ranging from 4.4% to 7.2%). Positivity rates were significantly lower only among respondents with higher education. No significant difference was observed by age, key population profile, country or history of HIV testing.The second phase saw 78 out of 126 eligible participants complete the questionnaire. Of the 27 who reported a consistent reactive response in the first phase, 15 (56%, 95%CI: 36 to 74%) underwent confirmatory HIV testing, with 12 (80%) confirmed as HIV-positive, all of whom began antiretroviral treatment.The confirmation rate of HIVST results was fast, with 53% doing so within a week and 91% within three months of self-testing. Two-thirds (65%) went to a general public facility, and one-third to a facility dedicated to key populations.The ATLAS HIVST distribution strategy reached people living with HIV in West Africa. Linkage to confirmatory testing following a reactive HIVST remained relatively low in these first years of HIVST implementation. However, if confirmed HIV-positive, almost all initiated treatment. HIVST constitutes a relevant complementary tool to existing screening services.
PubDate: Thu, 13 Jun 2024 13:54:56 +000
- Blackwell, Samantha E M; Pasquier, Laura et al. - Relationship between
weapon size and six key behavioural and physiological traits in males of
the European earwig
Abstract: In many animals, male weapons are large and extravagant morphological structures that typically enhance fighting ability and reproductive success. It is generally assumed that growing and carrying large weapons is costly, thus only males in the best condition can afford it. In the European earwig, males carry weapons in the form of forceps-like cerci, which can vary widely in size within populations. While long forceps appear to increase male’s access to females, it is unknown whether it also correlates with other important male life-history traits. This information is important, however, in determining the potential reliability of forceps length as an indicator of male quality and the stability of this signalling system. Here, we tested whether forceps length is associated with six important behavioural and physiological traits in males of the European earwig. We sampled hundreds of males from two populations, selected 60 males with the longest and shortest forceps from each population, and then measured locomotor performance, boldness, aggregation behaviour, survival under harsh conditions, sperm storage, and survival after pathogen exposure. Contrary to our predictions, we detected no main association between forceps length and the traits measured. This lack of association was consistent between the two populations, although there were population-specific levels of boldness, aggregation and survival in harsh conditions (for long-forceps males only). Overall, these results challenge our current understanding of the function and quality signal of forceps length in this species and raise questions about the evolutionary drivers that could explain the maintenance of weapon size diversity within and between populations.
PubDate: Thu, 13 Jun 2024 13:54:07 +000
- van Iersel, Leo; Jones, Mark et al. - When Three Trees Go to War
Abstract: How many reticulations are needed for a phylogenetic network to display a given set of k phylogenetic trees on n leaves' For k = 2, Baroni et al. [Ann. Comb. 8, 391-408 (2005)] showed that the answer is n − 2. Here, we show that, for k ≥ 3 the answer is at least (3 /2 − ε)n. Concretely, we prove that, for each ε > 0, there is some n ∈ N such that three n-leaf caterpillar trees can be constructed in such a way that any network displaying these caterpillars contains at least (3 /2 − ε)n reticulations. The case of three trees is interesting since it is the easiest case that cannot be equivalently formulated in terms of agreement forests. Instead, we base the result on a surprising lower bound for multilabelled trees (MUL-trees) displaying the caterpillars. Indeed, we show that one cannot do (more than an ε) better than the trivial MUL-tree resulting from a simple concatenation of the given caterpillars. The results are relevant for the development of methods for the Hybridization Number problem on more than two trees. This fundamental problem asks to construct a binary phylogenetic network with a minimum number of reticulations displaying a given set of phylogenetic trees.
PubDate: Tue, 04 Jun 2024 07:22:46 +000
