Peer community journal最新文献

{"title":"Phylogeographic breaks and how to find them: An empirical attempt at separating vicariance from isolation by distance in a lizard with restricted dispersal","authors":"Loïs Rancilhac, Aurélien Miralles, Philippe Geniez, Daniel Mendez-Aranda, Menad Beddek, José Carlos Brito, Raphaël Leblois, Pierre-André Crochet","doi":"10.24072/pcjournal.301","DOIUrl":"https://doi.org/10.24072/pcjournal.301","url":null,"abstract":"Aim: Discontinuity in the distribution of genetic diversity (often based on mtDNA) is usually interpreted as evidence for phylogeographic breaks, underlying vicariant units. However, a misleading signal of phylogeographic break can arise in the absence of barrier to gene flow, under mechanisms of isolation by distance (IBD). How and under which conditions phylogeographic breaks can be reliably differentiated from populations evolving under IBD remain unclear. Here, we use multi-locus sequence data from a widely distributed lizard species to address these questions in an empirical setting. Location: Morocco. Taxon: Spiny-footed lizard (Acanthodactylus erythrurus), Squamata: Lacertidae. Methods: Using 325 samples from 40 localities, we identified genetic discontinuities within A. erythrurus based on a mitochondrial fragment and nine nuclear markers independently. Using the nuclear markers, we then applied linear regression models to investigate whether genetic divergence could be explained by geographical distances alone, or barriers to gene flow (real phylogeographic breaks). Results: A. erythrurus is characterized by an important mitochondrial diversity, with 11 strongly supported phylogeographic lineages with a crown age of 6 Mya. Nuclear markers, however, yielded weak phylogenetic support for these lineages. Using clustering methods based on genotypes at nine nuclear loci, we identified phylogeographic clusters that were partly discordant with the mtDNA lineages. Tests of IBD delimited at least four groups of populations separated by barriers to gene flow, but unambiguous separation of vicariance from IBD remained challenging in several cases. Main conclusions: The genetic diversity of A. erythrurus originates from a mix of IBD and vicariance, which were difficult to distinguish, and resulted in similar levels of mitochondrial differentiation. These results highlight that phylogeographic breaks inferred from mitochondrial data should be further investigated using multi-locus data and explicit testing to rule out alternative processes generating discontinuities in mitochondrial diversity, including IBD. We identified four groups of populations within A. erythrurus, separated by barriers to gene flow, but even using nine independent nuclear makers the power of our approach was limited, and further investigation using genome-wide data will be required to resolve the phylogeographic history of this species.","PeriodicalId":74413,"journal":{"name":"Peer community journal","volume":"173 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-08-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"136242994","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genomic data suggest parallel dental vestigialization within the xenarthran radiation","authors":"Christopher A Emerling, Gillian C Gibb, Marie-Ka Tilak, Jonathan J Hughes, Melanie Kuch, Ana T Duggan, Hendrik N Poinar, Michael W Nachman, Frédéric Delsuc","doi":"10.24072/pcjournal.303","DOIUrl":"https://doi.org/10.24072/pcjournal.303","url":null,"abstract":"The recent influx of genomic data has provided greater insights into the molecular basis for regressive evolution, or vestigialization, through gene loss and pseudogenization. As such, the analysis of gene degradation patterns has the potential to provide insights into the evolutionary history of regressed anatomical traits. We specifically applied these principles to the xenarthran radiation (anteaters, sloths, armadillos), which is characterized by taxa with a gradation in regressed dental phenotypes. Whether the pattern among extant xenarthrans is due to an ancient and gradual decay of dental morphology or occurred repeatedly in parallel is unknown. We tested these competing hypotheses by examining 11 core dental genes in most living species of Xenarthra, characterizing shared inactivating mutations and patterns of relaxed selection during their radiation. Here we report evidence of independent and distinct events of dental gene loss in the major xenarthran subclades. First, we found strong evidence of complete enamel loss in the common ancestor of sloths and anteaters, suggested by the inactivation of five enamel-associated genes (AMELX, AMTN, MMP20, ENAM, ACP4). Next, whereas dental regression appears to have halted in sloths, presumably a critical event that ultimately permitted adaptation to an herbivorous lifestyle, anteaters continued losing genes on the path towards complete tooth loss. Echoes of this event are recorded in the genomes of all living anteaters, being marked by a 2-bp deletion in a gene critical for dentinogenesis (DSPP) and a putative shared 1-bp insertion in a gene linked to tooth retention (ODAPH). By contrast, in the two major armadillo clades, genes pertaining to the dento-gingival junction and amelogenesis appear to have been independently inactivated prior to losing all or some enamel. These genomic data provide evidence for multiple pathways and rates of anatomical regression, and underscore the utility of using pseudogenes to reconstruct evolutionary history when fossils are sparse.","PeriodicalId":74413,"journal":{"name":"Peer community journal","volume":"142 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-08-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"136281078","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Ensuring ethical animal welfare research: Are more ethics review committees the solution?","authors":"B. Nielsen, H. Golledge, Jen-Yun Chou, I. Camerlink, P. Pongrácz, M. C. Ceballos, A. Whittaker, I. Olsson","doi":"10.24072/pcjournal.310","DOIUrl":"https://doi.org/10.24072/pcjournal.310","url":null,"abstract":"This article has no abstract] 1Universities Federation for Animal Welfare (UFAW), The Old School, Wheathampstead, United Kingdom, 2Pig Development Department, Animal & Grassland Research and Innovation Centre, Teagasc, Moorepark, Ireland, 3Institute of Animal Welfare Science, University of Veterinary Medicine, Vienna, Austria, 4Department of Animal Behaviour andWelfare, Institute of Genetics and Animal Biotechnology, Polish Academy of Sciences, Jastrzebiec, Poland, 5Department of Ethology, ELTE Eötvös Loránd University, Budapest, Hungary, 6Faculty of VeterinaryMedicine, University of Calgary, Calgary, Alberta, Canada, 7School of Animal and Veterinary Sciences, The University of Adelaide, Australia, 8I3S – Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal","PeriodicalId":74413,"journal":{"name":"Peer community journal","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-08-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"43538690","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Within-species variation in the gut microbiome of medaka (Oryzias latipes) is driven by the interaction of light intensity and genetic background","authors":"Charlotte Evangelista, Stefaniya Kamenova, Beatriz Diaz Pauli, Joakim Sandkjenn, Leif Asbjørn Vøllestad, Eric Edeline, Pål Trosvik, Eric Jacques de Muinck","doi":"10.24072/pcjournal.306","DOIUrl":"https://doi.org/10.24072/pcjournal.306","url":null,"abstract":"Unravelling evolution-by-environment interactions on the gut microbiome is particularly relevant considering the unprecedented level of human-driven disruption of the ecological and evolutionary trajectories of species. Here, we aimed to evaluate whether an evolutionary response to size-selective mortality influences the gut microbiome of medaka (Oryzias latipes), how environmental conditions interact with the genetic background of medaka on their microbiota, and the association between microbiome diversity and medaka growth-related traits. To do so, we studied two lineages of medaka with known divergence in foraging efficiency and life history raised under antagonistic size-selective regimes for 10 generations (i.e. the largest or the smallest breeders were removed to mimic fishing-like or natural mortality). In pond mesocosms, the two lineages were subjected to contrasting population density and light intensity (used as proxies of resource availability). We observed significant differences in the gut microbiome composition and richness between the two lines, and this effect was mediated by light intensity. The bacterial richness of fishing-like medaka (small-breeder line) was reduced by 34% under low-light conditions compared to high-light conditions, while it remained unchanged in natural mortality-selected medaka (large-breeder line). However, the observed changes in bacterial richness did not correlate with changes in adult growth-related traits. Given the growing evidence about the gut microbiomes importance to host health, more in-depth studies are required to fully understand the role of the microbiome in size-selected organisms and the possible ecosystem-level consequences.","PeriodicalId":74413,"journal":{"name":"Peer community journal","volume":"22 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-08-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135817981","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Sensitive windows for within- and trans-generational plasticity of anti-predator defences","authors":"Juliette Tariel-Adam, É. Luquet, S. Plénet","doi":"10.24072/pcjournal.304","DOIUrl":"https://doi.org/10.24072/pcjournal.304","url":null,"abstract":"Transgenerational plasticity could be an important mechanism for adaptation to variable environments in addition to within-generational plasticity. But its potential for adaptation may be restricted to specific developmental windows that are highly sensitive and responsive to environmental cues. Determining these sensitive windows is essential to understand the temporal dynamic of environmental cue detection, phenotype induction and selection. We examined the sensitive windows of both within-and trans-generational plasticity of anti-predator defences in the freshwater snail Physa acuta . Parental snails were exposed to olfactory cues of their cray-fish predator at different exposure windows: embryonic development, early, mid or late post-embryonic development. Behavioural and morphological defences were then assessed in adult parents and offspring. The sensitive window of within-generational plasticity was the embryonic development, the whole post-embryonic development, or a combination of early-life","PeriodicalId":74413,"journal":{"name":"Peer community journal","volume":"1 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-08-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41531535","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Behavioral flexibility is manipulable and it improves flexibility and innovativeness in a new context","authors":"C. Logan, D. Lukas, A. Blaisdell, Z. Johnson-Ulrich, M. MacPherson, Benjamin M. Seitz, A. Sevchik, Kelsey B. McCune","doi":"10.24072/pcjournal.284","DOIUrl":"https://doi.org/10.24072/pcjournal.284","url":null,"abstract":"Behavioral flexibility, the ability to adapt behavior to new circumstances, is thought to play an important role in a species’ ability to successfully adapt to new environments and expand its geographic range. However, flexibility is rarely directly tested in a way that would allow us to determine how flexibility works to predict a species’ ability to adapt their behavior to new environments. We use great-tailed grackles ( Quiscalus mexicanus ; a bird species) as a model to investigate this question because they have recently rapidly expanded their range into North America. We attempted to manipulate grackle flexibility using shaded (light and dark gray) tube reversal learning to determine whether flexibility","PeriodicalId":74413,"journal":{"name":"Peer community journal","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-08-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"48328334","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Being a tree crop increases the odds of experiencing yield declines irrespective of pollinator dependence","authors":"Marcelo A. Aizen, Gabriela Gleiser, Thomas A. Kitzberger, Ruben Milla","doi":"10.24072/pcjournal.305","DOIUrl":"https://doi.org/10.24072/pcjournal.305","url":null,"abstract":"Crop yields, i.e. harvestable production per unit of cropland area, are in decline for a number of crops and regions, but the drivers of this process are poorly known. Global decreases in pollinator abundance and diversity have been proposed as a major driver of yield declines in crops that depend on animals, mostly bees, to produce fruits and seeds. Alternatively, widespread tree mortality has been directly and indirectly related to global climate change, which could also explain yield decreases in tree crops. As tree crops are expected to be more dependent on pollinators than other crop types, disentangling the relative influence of growth form and pollinator dependence is relevant to identify the ultimate factors driving yield declines. Yield decline, defined here as a negative average annual yearly change in yield from 1961 to 2020, was measured in 4270 time series, involving 136 crops and 163 countries and territories. About one‑fourth of all time series showed declines in crop yield, a characteristic associated with both high pollinator dependence and a tree growth form. Because pollinator dependence and plant growth form were partially correlated, we disentangled the effect of each of these two predictors using a series of generalized linear mixed models that evaluated direct and indirect associations. Our analyses revealed a stronger association of yield decline with growth form than with pollinator dependence, a relationship that persisted after partialling out the effect of pollinator dependence. In particular, yield declines were more common among tree than herbaceous and shrub crops in all major regions but in Africa, a continent showing a high incidence of yield declines irrespective of growth form. These results suggest that pollinator decline is not the main reason behind crop productivity loss, but that other factors such as climate change could be already affecting crop yield.","PeriodicalId":74413,"journal":{"name":"Peer community journal","volume":"186 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-08-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"136392403","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Pollen contamination and mating structure in maritime pine (Pinus pinaster Ait.) clonal seed orchards revealed by SNP markers","authors":"Laurent Bouffier, Sandrine Debille, Pierre Alazard, Annie Raffin, Patrick Pastuszka, Jean-François Trontin","doi":"10.24072/pcjournal.302","DOIUrl":"https://doi.org/10.24072/pcjournal.302","url":null,"abstract":"Maritime pine (Pinus pinaster Ait.) is a major forest tree species in south-western Europe. In France, an advanced breeding program for this conifer species has been underway since the early 1960s. Open-pollinated seed orchards currently supply more than 90% of maritime pine seedlings for plantation forestry. However, pollen contamination and mating structure have been poorly studied in such seed orchards whereas they could impact genetic gains and diversity. We analyzed these features in three maritime pine clonal seed orchards. We addressed biological (tree genotype, age, flowering phenology) and environmental factors (vicinity with external pollen sources, orchard structure, soil type, climatic conditions) that are expected to determine the genetic composition of seed lots. Genetic analyses were based on an optimized set of 60 SNP markers and performed on 2,552 seedlings with Cervus software (likelihood inference methodology). Pollen contamination rates were highly variable between seed lots (from 20 to 96%), with a mean value of 50%. Interpretative factors included the distance between the seed orchard and external pollen sources, rain during the pollination period, seed orchard age, soil conditions and seed parent identity. All parental genotypes from the seed orchards contributed to the offspring as pollen parents, but differences in paternal reproductive success were detected. Finally, the overall self-fertilization rate was estimated at 5.4%, with considerable variability between genotypes (from 0% to 26%). These findings are useful to formulate recommendations for seed orchard management (seed orchard location, soil and climate optimal conditions, minimum age for commercial seed lots harvesting) and for identifying new research perspectives (exploring links between pollen contamination and climatic data, genetic control of flowering traits).","PeriodicalId":74413,"journal":{"name":"Peer community journal","volume":"12 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-08-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135442715","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Field margins as substitute habitat for the conservation of birds in agricultural wetlands","authors":"Pierre Mallet, Arnaud Bechet, Clelia Sirami, Francois Mesleard, Thomas Blanchon, Francois Calatayud, Thomas Dagonet, Elie Gaget, Carole Leray, Thomas Galewski","doi":"10.24072/pcjournal.299","DOIUrl":"https://doi.org/10.24072/pcjournal.299","url":null,"abstract":"Breeding birds in agricultural landscapes have declined considerably since the 1950s and the beginning of agricultural intensification in Europe. Given the increasing pressure on agricultural land, it is necessary to identify conservation measures that consume little productive land. We tested the compensation hypothesis which states that field margins may represent substitute habitats for bird species in agricultural wetlands. We monitored bird species in 86 crop fields in rice paddy landscapes of Camargue (southern France), a wetland of international importance for birds. We investigated whether the area of three types of field margins (reed strips, grass strips and hedgerows) within a 500 meter buffer around the centroid of each crop fields had an effect on the abundance of bird species from three groups defined based on their primary habitat (reedbeds, grasslands, and forest edge species). We controlled for the area of each type of semi-natural habitat (wetlands, grasslands, and woodlands), crop diversity (rice, wheat, alfalfa, rape, and market gardening) and mean crop field size. Results show partial support of the compensation hypothesis with species-dependent responses to primary and substitute habitat area. Some species within the reedbed and grassland bird guilds are favored by the area of their primary habitat as well as by the area of field margins, in line with the compensation hypothesis. Eurasian reed warbler is favored by the area of both wetlands and reed strips. Corn bunting is favored by grassland and grass strip areas. We could not confirm the compensation hypothesis for other species. However, this may be due to the fact that most of these species did not respond to their primary habitat. These results therefore suggest that field margins may represent substitute habitats for some species but further studies, in contexts where species are strongly associated with their primary habitat, would be needed to confirm the generality of this hypothesis. Our results also suggest that species response to increasing the area of a field margin type may vary among guilds and even within guilds. Therefore, it may be difficult to favor all species within a given landscape and management actions may need to be tailored to whichever species are locally associated with the highest conservation priority. To tackle this challenge, it may be necessary to design landscape management actions at different spatial scales.","PeriodicalId":74413,"journal":{"name":"Peer community journal","volume":"20 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135970811","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Balancing selection at a wing pattern locus is associated with major shifts in genome-wide patterns of diversity and gene flow","authors":"María Ángeles Rodríguez de Cara, Paul Jay, Quentin Rougemont, Mathieu Chouteau, Annabel Whibley, Barbara Huber, Florence Piron-Prunier, Renato Rogner Ramos, André V. L. Freitas, Camilo Salazar, Karina Lucas Silva-Brandão, Tatiana Teixeira Torres, Mathieu Joron","doi":"10.24072/pcjournal.298","DOIUrl":"https://doi.org/10.24072/pcjournal.298","url":null,"abstract":"Selection shapes genetic diversity around target mutations, yet little is known about how selection on specific loci affects the genetic trajectories of populations, including their genome-wide patterns of diversity and demographic responses. Here we study the patterns of genetic variation and geographic structure in a neotropical butterfly, Heliconius numata, and its closely related allies in the so-called melpomene-silvaniform clade. H. numata is known to have evolved an inversion supergene which controls variation in wing patterns involved in mimicry associations with distinct groups of co-mimics whereas it is associated to disassortative mate preferences and heterozygote advantage at this locus. We contrasted patterns of genetic diversity and structure 1) among extant polymorphic and monomorphic populations of H. numata, 2) between H. numata and its close relatives, and 3) between ancestral lineages. We show that H. numata populations which carry the inversions as a balanced polymorphism show markedly distinct patterns of diversity compared to all other taxa. They show the highest genetic diversity and effective population size estimates in the entire clade, as well as a low level of geographic structure and isolation by distance across the entire Amazon basin. By contrast, monomorphic populations of H. numata as well as its sister species and their ancestral lineages all show lower effective population sizes and genetic diversity, and higher levels of geographical structure across the continent. One hypothesis is that the large effective population size of polymorphic populations could be caused by the shift to a regime of balancing selection due to the genetic load and disassortative preferences associated with inversions. Testing this hypothesis with forward simulations supported the observation of increased diversity in populations with the supergene. Our results are consistent with the hypothesis that the formation of the supergene triggered a change in gene flow, causing a general increase in genetic diversity and the homogenisation of genomes at the continental scale.","PeriodicalId":74413,"journal":{"name":"Peer community journal","volume":"6 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-07-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135556690","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}