Traditional analyses of projectile points often use visual identification, the presence or absence of discrete characteristics, or linear measurements and angles to classify points into distinct types. Geometric morphometrics provides additional tools for analyzing, visualizing
{"title":"Geometric morphometric analysis of projectile points from the Southwest United States","authors":"Robert J. Bischoff","doi":"10.24072/pcjournal.312","DOIUrl":"https://doi.org/10.24072/pcjournal.312","url":null,"abstract":"Traditional analyses of projectile points often use visual identification, the presence or absence of discrete characteristics, or linear measurements and angles to classify points into distinct types. Geometric morphometrics provides additional tools for analyzing, visualizing","PeriodicalId":74413,"journal":{"name":"Peer community journal","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-09-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"45251079","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}
Several studies have highlighted the presence of contaminated entries in public sequence repositories, calling for special attention to the associated metadata. Here, we propose and evaluate a fast and efficient k–mer-based approach to assess the degree of mislabeling or contamination. We applied it to high-throughput whole-genome raw sequence data for 236 Ind-Seq and 22 Pool-Seq samples of the invasive species Drosophila suzukii. We first used Clark software to build a dictionary of species-discriminating k–mers from the curated assemblies of 29 target drosophilid species (including D. melanogaster, D. simulans, D. subpulchrella, or D. biarmipes) and 12 common drosophila pathogens and commensals (including Wolbachia). Counting the number of k–mers composing each query sample sequence that matched a discriminating k–mer from the dictionary provided a simple criterion for assignment to target species and evaluation of the entire sample. Analyses of a wide range of samples, representative of both target and other drosophilid species, demonstrated very good performance of the proposed approach, both in terms of run time and accuracy of sequence assignment. Of the 236 D. suzukii individuals, five were reassigned to D. simulans and eleven to D. subpulchrella. Another four showed moderate to substantial microbial contamination. Similarly, among the 22 Pool-Seq samples analyzed, two from the native range were found to be contaminated with 1 and 7 D. subpulchrella individuals, respectively (out of 50), and one from Europe was found to be contaminated with 5 to 6 D. immigrans individuals (out of 100). Overall, the present analysis allowed the definition of a large curated dataset consisting of > 60 population samples representative of the worldwide genetic diversity, which may be valuable for further population genetics studies on D. suzukii. More generally, while we advocate careful sample identification and verification prior to sequencing, the proposed framework is simple and computationally efficient enough to be included as a routine post-hoc quality check prior to any data analysis and prior to data submission to public repositories.
{"title":"Efficient k-mer based curation of raw sequence data: application in Drosophila suzukii","authors":"Mathieu Gautier","doi":"10.24072/pcjournal.309","DOIUrl":"https://doi.org/10.24072/pcjournal.309","url":null,"abstract":"Several studies have highlighted the presence of contaminated entries in public sequence repositories, calling for special attention to the associated metadata. Here, we propose and evaluate a fast and efficient k–mer-based approach to assess the degree of mislabeling or contamination. We applied it to high-throughput whole-genome raw sequence data for 236 Ind-Seq and 22 Pool-Seq samples of the invasive species Drosophila suzukii. We first used Clark software to build a dictionary of species-discriminating k–mers from the curated assemblies of 29 target drosophilid species (including D. melanogaster, D. simulans, D. subpulchrella, or D. biarmipes) and 12 common drosophila pathogens and commensals (including Wolbachia). Counting the number of k–mers composing each query sample sequence that matched a discriminating k–mer from the dictionary provided a simple criterion for assignment to target species and evaluation of the entire sample. Analyses of a wide range of samples, representative of both target and other drosophilid species, demonstrated very good performance of the proposed approach, both in terms of run time and accuracy of sequence assignment. Of the 236 D. suzukii individuals, five were reassigned to D. simulans and eleven to D. subpulchrella. Another four showed moderate to substantial microbial contamination. Similarly, among the 22 Pool-Seq samples analyzed, two from the native range were found to be contaminated with 1 and 7 D. subpulchrella individuals, respectively (out of 50), and one from Europe was found to be contaminated with 5 to 6 D. immigrans individuals (out of 100). Overall, the present analysis allowed the definition of a large curated dataset consisting of > 60 population samples representative of the worldwide genetic diversity, which may be valuable for further population genetics studies on D. suzukii. More generally, while we advocate careful sample identification and verification prior to sequencing, the proposed framework is simple and computationally efficient enough to be included as a routine post-hoc quality check prior to any data analysis and prior to data submission to public repositories.","PeriodicalId":74413,"journal":{"name":"Peer community journal","volume":"41 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"136355055","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}
Arnoul Van Rooij, É. Badel, J. Barczi, Y. Caraglio, T. Alméras, J. Gril
9 This work aims to model the mechanical processes used by tree branches to control their posture despite 10 their increasing weight loading. The two known options for a branch to maintain its orientation are the 11 asymmetry of maturation stress, including reaction wood formation, and eccentric radial growth. Both 12 options can be observed in nature and influence the stress distribution developed in the branch each 13 year. This so-called "growth stress" reflects the mechanical state of the branch. In this work, a growth 14 stress model was developed at the cross-section level in order to quantify and study the bio-mechanical 15 impact of each process. For illustration, this model was applied to branches of two 50-year-old trees, 16 one softwood Pinus pinaster and one hardwood Prunus avium (wild cherry tree), both simulated with 17 the AmapSim discrete element software. For the wild cherry tree, the computed ouputs enlightened that 18 the eccentricity of radial growth seems to be as efficient as the formation of reaction wood to maintain 19 the postural control despite the increasing gravity. err The computed outputs enlightened that, for both 20 Prunus avium and Pinus pinaster , eccentric radial growth appears less efficient than the formation of 21 reaction wood to counter the increasing gravity stress applied to the branch. err For the pine tree, eccentric 22 radial growth appears to be less efficient than the formation of reaction wood err . But although eccentric 23 growth err it err does not necessarily act as a relevant lever for postural control, it greatly modifies the
{"title":"Modelling the growth stress in tree branches: eccentric growth vs. reaction wood","authors":"Arnoul Van Rooij, É. Badel, J. Barczi, Y. Caraglio, T. Alméras, J. Gril","doi":"10.24072/pcjournal.308","DOIUrl":"https://doi.org/10.24072/pcjournal.308","url":null,"abstract":"9 This work aims to model the mechanical processes used by tree branches to control their posture despite 10 their increasing weight loading. The two known options for a branch to maintain its orientation are the 11 asymmetry of maturation stress, including reaction wood formation, and eccentric radial growth. Both 12 options can be observed in nature and influence the stress distribution developed in the branch each 13 year. This so-called \"growth stress\" reflects the mechanical state of the branch. In this work, a growth 14 stress model was developed at the cross-section level in order to quantify and study the bio-mechanical 15 impact of each process. For illustration, this model was applied to branches of two 50-year-old trees, 16 one softwood Pinus pinaster and one hardwood Prunus avium (wild cherry tree), both simulated with 17 the AmapSim discrete element software. For the wild cherry tree, the computed ouputs enlightened that 18 the eccentricity of radial growth seems to be as efficient as the formation of reaction wood to maintain 19 the postural control despite the increasing gravity. err The computed outputs enlightened that, for both 20 Prunus avium and Pinus pinaster , eccentric radial growth appears less efficient than the formation of 21 reaction wood to counter the increasing gravity stress applied to the branch. err For the pine tree, eccentric 22 radial growth appears to be less efficient than the formation of reaction wood err . But although eccentric 23 growth err it err does not necessarily act as a relevant lever for postural control, it greatly modifies the","PeriodicalId":74413,"journal":{"name":"Peer community journal","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-08-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"44762174","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}
Katerina Newman, C. Forestier, B. Cheval, Zachary Zenko, Margaux de Chanaleilles, B. Gardner, A. Rebar
Evidence shows that people with strong physical activity habits tend to engage in more physical activity than those with weaker habits, but little is known about how habit influ-ences specific types of physical activity. This study aimed to test whether mean level of habit strength and magnitude of the habit strength – behaviour association differed as a function of physical activity modality. Participants (N = 120; M age = 25 years, 75% female) who reported engaging in organised sport separately reported their habit strength for organised sport and leisure time physical activity as well as the time they spent engaging in these physical activity behaviours. Means comparisons and multilevel modelling revealed that people
{"title":"Comparing habit-behaviour relationships for organised versus leisure time physical activity","authors":"Katerina Newman, C. Forestier, B. Cheval, Zachary Zenko, Margaux de Chanaleilles, B. Gardner, A. Rebar","doi":"10.24072/pcjournal.311","DOIUrl":"https://doi.org/10.24072/pcjournal.311","url":null,"abstract":"Evidence shows that people with strong physical activity habits tend to engage in more physical activity than those with weaker habits, but little is known about how habit influ-ences specific types of physical activity. This study aimed to test whether mean level of habit strength and magnitude of the habit strength – behaviour association differed as a function of physical activity modality. Participants (N = 120; M age = 25 years, 75% female) who reported engaging in organised sport separately reported their habit strength for organised sport and leisure time physical activity as well as the time they spent engaging in these physical activity behaviours. Means comparisons and multilevel modelling revealed that people","PeriodicalId":74413,"journal":{"name":"Peer community journal","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-08-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"45648624","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}
Background: Diphtheria, caused by Corynebacterium diphtheriae, reemerges in Europe since 2022. Genomic sequencing can inform on transmission routes and genotypes of concern, but currently, no standard approach exists to detect clinically important genomic features and to interpret emergence in the global C. diphtheriae population framework. Methods: We developed the bioinformatics pipeline diphtOscan (available at https://gitlab.pasteur.fr/BEBP/diphtoscan) to extract from genomes of Corynebacteria of the diphtheriae species complex, medically relevant features including tox gene presence and disruption. We analyzed 101 human C. diphtheriae isolates collected in 2022 in metropolitan and overseas France (France-2022). To define the population background of this emergence, we sequenced 379 additional isolates (mainly from France, 2018-2021) and collated 870 publicly-available genomes. Results: The France-2022 isolates comprised 45 tox-positive (44 toxigenic) isolates, mostly imported, belonging to 10 sublineages (<500 distinct core genes). The global dataset comprised 245 sublineages and 33.9% tox-positive genomes, with diphtOscan predicting non-toxigenicity in 16.0% of these. 12% of the global isolates, and 43.6% of France-2022 ones, were multidrug resistant. Convergence of toxigenicity with penicillin and erythromycin resistance was observed in 2 isolates from France-2022. Phylogenetic lineages Gravis and Mitis contrasted strikingly in their pathogenicity-associated genes. Conclusions: This work provides a bioinformatics tool and global population framework to analyze C. diphtheriae genomes, revealing important heterogeneities in virulence and resistance features. Emerging genotypes combining toxigenicity and first-line antimicrobial resistance represent novel threats. Genomic epidemiology studies of C. diphtheriae should be intensified globally to improve understanding of reemergence and spatial spread.
{"title":"A global Corynebacterium diphtheriae genomic framework sheds light on current diphtheria reemergence","authors":"Mélanie Hennart, Chiara Crestani, Sébastien Bridel, Nathalie Armatys, Sylvie Brémont, Annick Carmi-Leroy, Annie Landier, Virginie Passet, Laure Fonteneau, Sophie Vaux, Julie Toubiana, Edgar Badell, Sylvain Brisse","doi":"10.24072/pcjournal.307","DOIUrl":"https://doi.org/10.24072/pcjournal.307","url":null,"abstract":"Background: Diphtheria, caused by Corynebacterium diphtheriae, reemerges in Europe since 2022. Genomic sequencing can inform on transmission routes and genotypes of concern, but currently, no standard approach exists to detect clinically important genomic features and to interpret emergence in the global C. diphtheriae population framework. Methods: We developed the bioinformatics pipeline diphtOscan (available at https://gitlab.pasteur.fr/BEBP/diphtoscan) to extract from genomes of Corynebacteria of the diphtheriae species complex, medically relevant features including tox gene presence and disruption. We analyzed 101 human C. diphtheriae isolates collected in 2022 in metropolitan and overseas France (France-2022). To define the population background of this emergence, we sequenced 379 additional isolates (mainly from France, 2018-2021) and collated 870 publicly-available genomes. Results: The France-2022 isolates comprised 45 tox-positive (44 toxigenic) isolates, mostly imported, belonging to 10 sublineages (<500 distinct core genes). The global dataset comprised 245 sublineages and 33.9% tox-positive genomes, with diphtOscan predicting non-toxigenicity in 16.0% of these. 12% of the global isolates, and 43.6% of France-2022 ones, were multidrug resistant. Convergence of toxigenicity with penicillin and erythromycin resistance was observed in 2 isolates from France-2022. Phylogenetic lineages Gravis and Mitis contrasted strikingly in their pathogenicity-associated genes. Conclusions: This work provides a bioinformatics tool and global population framework to analyze C. diphtheriae genomes, revealing important heterogeneities in virulence and resistance features. Emerging genotypes combining toxigenicity and first-line antimicrobial resistance represent novel threats. Genomic epidemiology studies of C. diphtheriae should be intensified globally to improve understanding of reemergence and spatial spread.","PeriodicalId":74413,"journal":{"name":"Peer community journal","volume":"7 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-08-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135890669","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}
Loïs Rancilhac, Aurélien Miralles, Philippe Geniez, Daniel Mendez-Aranda, Menad Beddek, José Carlos Brito, Raphaël Leblois, Pierre-André Crochet
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.
{"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}
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
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.
{"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}
B. Nielsen, H. Golledge, Jen-Yun Chou, I. Camerlink, P. Pongrácz, M. C. Ceballos, A. Whittaker, I. Olsson
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
[摘要]1大学动物福利联合会(UFAW)， The Old School, Wheathampstead，英国;2动物与草原研究与创新中心，Teagasc, Moorepark，爱尔兰;3动物福利科学研究所，维也纳兽医大学，奥地利;4动物行为与福利系，波兰科学院，Jastrzebiec，波兰，遗传与动物生物技术研究所;ELTE Eötvös Loránd匈牙利布达佩斯大学，6加拿大阿尔伯塔省卡尔加里卡尔加里大学兽医学院，7澳大利亚阿德莱德大学动物与兽医科学学院，8I3S -葡萄牙波尔图波尔图大学动物与兽医研究所Saúde
{"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}
Charlotte Evangelista, Stefaniya Kamenova, Beatriz Diaz Pauli, Joakim Sandkjenn, Leif Asbjørn Vøllestad, Eric Edeline, Pål Trosvik, Eric Jacques de Muinck
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.
{"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}
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
{"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}
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