Samuel M. Charberet, Annick Maria, David Siaussat, Isabelle Gounand, Jérôme Mathieu
Isotopes are widely used in ecology to study food webs and physiology. The fractionation observed between trophic levels in nitrogen and carbon isotopes, explained by isotopic biochemical selectivity, is subject to important within-trophic level variations, leading to imprecision in trophic level estimation. Understanding the drivers of these variations is thus important to improve the study of food webs. In this study, we characterized this variation by submitting Spodoptera littoralis larvae to a gradient of starvation levels, a factor that we hypothesized would change the trophic fractionation between individuals. The various growth rates that were induced from these starvation levels resulted in a ∼ 1-1.5‰ within-trophic level variation of the trophic fractionation in both carbon and nitrogen, which is substantial compared to the 3-4‰ classically associated with between-trophic levels variations. Hence starved animals sampled in natura may be ranked at a higher trophic level than they really are. We were able to gain an understanding of the effect of growth rate on isotopes fluxes between three easy-to-measure biological materials, food, the organism and its wastes (frass), giving insight into physiological processes at play but also conveying helpful information to the sampling framework of field studies.
{"title":"Feeding and growth variations affect δ13C and δ15N budgets during ontogeny in a lepidopteran larva","authors":"Samuel M. Charberet, Annick Maria, David Siaussat, Isabelle Gounand, Jérôme Mathieu","doi":"10.24072/pcjournal.265","DOIUrl":"https://doi.org/10.24072/pcjournal.265","url":null,"abstract":"Isotopes are widely used in ecology to study food webs and physiology. The fractionation observed between trophic levels in nitrogen and carbon isotopes, explained by isotopic biochemical selectivity, is subject to important within-trophic level variations, leading to imprecision in trophic level estimation. Understanding the drivers of these variations is thus important to improve the study of food webs. In this study, we characterized this variation by submitting Spodoptera littoralis larvae to a gradient of starvation levels, a factor that we hypothesized would change the trophic fractionation between individuals. The various growth rates that were induced from these starvation levels resulted in a ∼ 1-1.5‰ within-trophic level variation of the trophic fractionation in both carbon and nitrogen, which is substantial compared to the 3-4‰ classically associated with between-trophic levels variations. Hence starved animals sampled in natura may be ranked at a higher trophic level than they really are. We were able to gain an understanding of the effect of growth rate on isotopes fluxes between three easy-to-measure biological materials, food, the organism and its wastes (frass), giving insight into physiological processes at play but also conveying helpful information to the sampling framework of field studies.","PeriodicalId":74413,"journal":{"name":"Peer community journal","volume":"44 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-04-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"136022204","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}
Studying human-animal interactions in domestic species and how they affect the establishment of a positive Human-Animal Relationship (HAR) may help us improve animal welfare and better understand the evolution of interspecific interactions associated with the domestication process. Understanding and describing the quality of an HAR requires information on several aspects of the animal biology and emotional states (social, spatial and postural behaviours, physiological and cognitive states). Growing evidence shows that acoustic features of animal vocalisations may be indicators of emotional states. Here, we tested the hypothesis that vocal structure may indicate the quality of HAR. At weaning, 30 piglets were positively handled by an experimenter who talked to and physically interacted with them three times a day, while 30 other piglets only received the contact necessary for proper husbandry. After two weeks, we recorded the behaviours and vocalisations produced in the presence of the static experimenter for 5 min. We repeated this test two weeks later, after a conditioning period during which human presence with additional positive contacts was used as a reward for all piglets. We hypothesized this conditioning period would lead to a positive human-piglet relationship for all piglets. As expected, piglets that were positively handled at weaning expressed a higher attraction toward the experimenter, and, after the conditioning, piglets that were not positively handled at weaning expressed a similar level of attraction than the positively handled ones. Piglets positively handled at weaning produced shorter grunts than the other ones, regardless of the context of recording, which may indicate a more positive affect. During reunions with the static experimenter, a more positive HAR was associated with a decrease in vocal reactivity to human proximity. However, during reunions with the experimenter providing additional positive contacts and over the conditioning, spatial proximity to the human systematically triggered shorter and higher pitched grunts, which may indicate a more positive emotional state. Results first show that changes in vocal structure are consistent with indicators of positive states in the presence of a human. Second, these changes are stronger when the human positively interact with the piglets, supposedly emphasizing a higher positive arousal state during these interactions. We show that vocalisation structure may be a promising indicator of the quality of human-pig relationship.
{"title":"The use of pigs vocalisation structure to assess the quality of human-pig relationship","authors":"Avelyne S Villain, Carole Guérin, Céline Tallet","doi":"10.24072/pcjournal.260","DOIUrl":"https://doi.org/10.24072/pcjournal.260","url":null,"abstract":"Studying human-animal interactions in domestic species and how they affect the establishment of a positive Human-Animal Relationship (HAR) may help us improve animal welfare and better understand the evolution of interspecific interactions associated with the domestication process. Understanding and describing the quality of an HAR requires information on several aspects of the animal biology and emotional states (social, spatial and postural behaviours, physiological and cognitive states). Growing evidence shows that acoustic features of animal vocalisations may be indicators of emotional states. Here, we tested the hypothesis that vocal structure may indicate the quality of HAR. At weaning, 30 piglets were positively handled by an experimenter who talked to and physically interacted with them three times a day, while 30 other piglets only received the contact necessary for proper husbandry. After two weeks, we recorded the behaviours and vocalisations produced in the presence of the static experimenter for 5 min. We repeated this test two weeks later, after a conditioning period during which human presence with additional positive contacts was used as a reward for all piglets. We hypothesized this conditioning period would lead to a positive human-piglet relationship for all piglets. As expected, piglets that were positively handled at weaning expressed a higher attraction toward the experimenter, and, after the conditioning, piglets that were not positively handled at weaning expressed a similar level of attraction than the positively handled ones. Piglets positively handled at weaning produced shorter grunts than the other ones, regardless of the context of recording, which may indicate a more positive affect. During reunions with the static experimenter, a more positive HAR was associated with a decrease in vocal reactivity to human proximity. However, during reunions with the experimenter providing additional positive contacts and over the conditioning, spatial proximity to the human systematically triggered shorter and higher pitched grunts, which may indicate a more positive emotional state. Results first show that changes in vocal structure are consistent with indicators of positive states in the presence of a human. Second, these changes are stronger when the human positively interact with the piglets, supposedly emphasizing a higher positive arousal state during these interactions. We show that vocalisation structure may be a promising indicator of the quality of human-pig relationship.","PeriodicalId":74413,"journal":{"name":"Peer community journal","volume":"64 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-04-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135290258","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}
S Nakagawa, M. Lagisz, R. Francis, Jessica Tam, Xun Li, Andrew Elphinstone, N. Jordan, J. O’Brien, B. Pitcher, M. van Sluys, A. Sowmya, R. Kingsford
Machine (especially deep) learning algorithms are changing the way wildlife imagery is processed. They dramatically speed up the time to detect, count, and classify animals and their behaviours. Yet, we currently have very few systematic literature surveys on its use in wildlife imagery. Through a literature survey (a ‘rapid’ review) and bibliometric mapping, we explored its use across: 1) species (vertebrates), 2) image types (e.g., camera traps, or drones), 3) study locations, 4) alternative machine learning algorithms, 5) outcomes (e.g., recognition, classifi-cation, or tracking), 6) reporting quality and openness, 7) author affiliation, and 8) publication journal types. We found that an increasing number of studies used convolutional neural networks (i.e., deep learning). Typically, studies have focused on large charismatic or iconic mammalian species. An increasing number of studies have been published in ecology-specific journals indicating the uptake of deep learning to transform the detection, classification and tracking of wildlife. Sharing of code was limited, with only 20% of studies providing links to analysis code. Much of the published research and focus on animals came from India, China, Australia, or the USA. There were relatively few collaborations across countries. Given the power of machine learning, we recommend increasing collaboration and sharing approaches to utilise increasing amounts of wildlife imagery more rapidly and transform and improve understanding of wildlife behaviour and conservation. Our survey, augmented with bibliometric analyses, provides valuable signposts for future studies to resolve and address shortcomings, gaps, and biases.
{"title":"Rapid literature mapping on the recent use of machine learning for wildlife imagery","authors":"S Nakagawa, M. Lagisz, R. Francis, Jessica Tam, Xun Li, Andrew Elphinstone, N. Jordan, J. O’Brien, B. Pitcher, M. van Sluys, A. Sowmya, R. Kingsford","doi":"10.24072/pcjournal.261","DOIUrl":"https://doi.org/10.24072/pcjournal.261","url":null,"abstract":"Machine (especially deep) learning algorithms are changing the way wildlife imagery is processed. They dramatically speed up the time to detect, count, and classify animals and their behaviours. Yet, we currently have very few systematic literature surveys on its use in wildlife imagery. Through a literature survey (a ‘rapid’ review) and bibliometric mapping, we explored its use across: 1) species (vertebrates), 2) image types (e.g., camera traps, or drones), 3) study locations, 4) alternative machine learning algorithms, 5) outcomes (e.g., recognition, classifi-cation, or tracking), 6) reporting quality and openness, 7) author affiliation, and 8) publication journal types. We found that an increasing number of studies used convolutional neural networks (i.e., deep learning). Typically, studies have focused on large charismatic or iconic mammalian species. An increasing number of studies have been published in ecology-specific journals indicating the uptake of deep learning to transform the detection, classification and tracking of wildlife. Sharing of code was limited, with only 20% of studies providing links to analysis code. Much of the published research and focus on animals came from India, China, Australia, or the USA. There were relatively few collaborations across countries. Given the power of machine learning, we recommend increasing collaboration and sharing approaches to utilise increasing amounts of wildlife imagery more rapidly and transform and improve understanding of wildlife behaviour and conservation. Our survey, augmented with bibliometric analyses, provides valuable signposts for future studies to resolve and address shortcomings, gaps, and biases.","PeriodicalId":74413,"journal":{"name":"Peer community journal","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-04-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"45783394","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}
Species distribution models (SDM) are widely used to describe and explain how species relate to their environment and predict their spatial distributions. As such, they are the cornerstone of most of spatial planning efforts worldwide. SDM can be implemented with a wide array of data types (presence-only, presence-absence, count...), which can either be point- or areal-based, and use a wide array of environmental conditions as predictor variables. The choice of the sampling type as well as the resolution of environmental conditions to be used are recognized as of crucial importance, yet we lack any quantification of the effects these decisions may have on SDM reliability. In the present work, we fill this gap with an unprecedented simulation procedure. We simulated 100 possible distributions of two different virtual species in two different regions. Species distribution were modelled using either segment- or areal-based sampling and five different spatial resolutions of environmental conditions. The SDM performances were inspected by statistical metrics, model composition, shapes of relationships and prediction quality. We provided clear evidence of stochasticity in the modelling process (particularly in the shapes of relationships): two dataset from the same survey, species and region could yield different results. Sampling type had stronger effects than spatial resolution on the final model relevance. The effect of coarsening the resolution was directly related to the resistance of the spatial features to changes of scale: SDM failed to adequately identify spatial distributions when the spatial features targeted by the species were diluted by resolution coarsening. These results have important implications for the SDM community, backing up some commonly accepted choices, but also by highlighting some up-to-now unexpected features of SDM (stochasticity). As a whole, this work calls for carefully weighted decisions in implementing models, and for caution in interpreting results.
{"title":"Data stochasticity and model parametrisation impact the performance of species distribution models: insights from a simulation study","authors":"Charlotte Lambert, Auriane Virgili","doi":"10.24072/pcjournal.263","DOIUrl":"https://doi.org/10.24072/pcjournal.263","url":null,"abstract":"Species distribution models (SDM) are widely used to describe and explain how species relate to their environment and predict their spatial distributions. As such, they are the cornerstone of most of spatial planning efforts worldwide. SDM can be implemented with a wide array of data types (presence-only, presence-absence, count...), which can either be point- or areal-based, and use a wide array of environmental conditions as predictor variables. The choice of the sampling type as well as the resolution of environmental conditions to be used are recognized as of crucial importance, yet we lack any quantification of the effects these decisions may have on SDM reliability. In the present work, we fill this gap with an unprecedented simulation procedure. We simulated 100 possible distributions of two different virtual species in two different regions. Species distribution were modelled using either segment- or areal-based sampling and five different spatial resolutions of environmental conditions. The SDM performances were inspected by statistical metrics, model composition, shapes of relationships and prediction quality. We provided clear evidence of stochasticity in the modelling process (particularly in the shapes of relationships): two dataset from the same survey, species and region could yield different results. Sampling type had stronger effects than spatial resolution on the final model relevance. The effect of coarsening the resolution was directly related to the resistance of the spatial features to changes of scale: SDM failed to adequately identify spatial distributions when the spatial features targeted by the species were diluted by resolution coarsening. These results have important implications for the SDM community, backing up some commonly accepted choices, but also by highlighting some up-to-now unexpected features of SDM (stochasticity). As a whole, this work calls for carefully weighted decisions in implementing models, and for caution in interpreting results.","PeriodicalId":74413,"journal":{"name":"Peer community journal","volume":"16 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-04-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135742564","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}
Coastal lagoons are an important habitat for endemic and threatened species in California that have suffered impacts from urbanization and increased drought. Environmental DNA has been promoted as a way to aid in the monitoring of biological communities, but much remains to be understood on the biases introduced by different protocols meant to overcome challenges presented by unique systems under study. Turbid water is one methodologic challenge to eDNA recovery in these systems as it quickly clogs filters, preventing timely processing of samples. We investigated biases in community composition produced by two solutions to overcome slow filtration due to turbidity: freezing of water prior to filtration (for storage purposes and long-term processing), and use of sediment (as opposed to water samples). Bias assessments of community composition in downstream eDNA analysis was conducted for two sets of primers, 12S (fish) and 16S (bacteria and archaea). Our results show that freezing water prior to filtration had different effects on community composition for each primer, especially for the 16S, when using a filter of larger pore size (3 μm). Nevertheless, pre-freezing water samples can still be a viable alternative for storage and processing of turbid water samples when focusing on fish communities (12S). The use of sediment samples as an alternative to processing water samples should be done with caution, and at minimum the number of biological replicates and/or volume sampled should be increased.
{"title":"Different approaches to processing environmental DNA samples in turbid waters have distinct effects for fish, bacterial and archaea communities","authors":"Rachel Turba, Glory H. Thai, David K. Jacobs","doi":"10.24072/pcjournal.256","DOIUrl":"https://doi.org/10.24072/pcjournal.256","url":null,"abstract":"Coastal lagoons are an important habitat for endemic and threatened species in California that have suffered impacts from urbanization and increased drought. Environmental DNA has been promoted as a way to aid in the monitoring of biological communities, but much remains to be understood on the biases introduced by different protocols meant to overcome challenges presented by unique systems under study. Turbid water is one methodologic challenge to eDNA recovery in these systems as it quickly clogs filters, preventing timely processing of samples. We investigated biases in community composition produced by two solutions to overcome slow filtration due to turbidity: freezing of water prior to filtration (for storage purposes and long-term processing), and use of sediment (as opposed to water samples). Bias assessments of community composition in downstream eDNA analysis was conducted for two sets of primers, 12S (fish) and 16S (bacteria and archaea). Our results show that freezing water prior to filtration had different effects on community composition for each primer, especially for the 16S, when using a filter of larger pore size (3 μm). Nevertheless, pre-freezing water samples can still be a viable alternative for storage and processing of turbid water samples when focusing on fish communities (12S). The use of sediment samples as an alternative to processing water samples should be done with caution, and at minimum the number of biological replicates and/or volume sampled should be increased.","PeriodicalId":74413,"journal":{"name":"Peer community journal","volume":"22 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-04-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135904763","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}
An intriguing aspect of vector-transmission of plant viruses is the frequent involvement of a helper component (HC). HCs are virus-encoded non-structural proteins produced in infected plant cells that are mandatory for the transmission success. Over five decades, all data collected on HCs from unrelated viral species transmitted by distinct vector species were consistent with a unique mode of action designated “the bridge hypothesis”: the HC has two functional domains, one binding the virus particle and the other binding a putative receptor in the vector, creating a reversible molecular bridge be-tween the two. This hypothesis appeared fully satisfactory as HCs were reported solely in viruses transmitted non-circulatively – i.e. the virus particle binds externally to the mouthpart of its vector, and can later be released therefrom and inoculated. Recently, however, HCs have also been reported in viruses transmitted circulatively, where the virus particles are internalized in gut cells and cycle
{"title":"The helper strategy in vector-transmission of plant viruses","authors":"Jérémy Di Mattia, J. Zeddam, M. Uzest, S. Blanc","doi":"10.24072/pcjournal.258","DOIUrl":"https://doi.org/10.24072/pcjournal.258","url":null,"abstract":"An intriguing aspect of vector-transmission of plant viruses is the frequent involvement of a helper component (HC). HCs are virus-encoded non-structural proteins produced in infected plant cells that are mandatory for the transmission success. Over five decades, all data collected on HCs from unrelated viral species transmitted by distinct vector species were consistent with a unique mode of action designated “the bridge hypothesis”: the HC has two functional domains, one binding the virus particle and the other binding a putative receptor in the vector, creating a reversible molecular bridge be-tween the two. This hypothesis appeared fully satisfactory as HCs were reported solely in viruses transmitted non-circulatively – i.e. the virus particle binds externally to the mouthpart of its vector, and can later be released therefrom and inoculated. Recently, however, HCs have also been reported in viruses transmitted circulatively, where the virus particles are internalized in gut cells and cycle","PeriodicalId":74413,"journal":{"name":"Peer community journal","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-03-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"47696871","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}
S. Ravel, Mahamat Hisséne Mahamat, A. Ségard, R. Argilés-Herrero, J. Bouyer, J. Rayaissé, P. Solano, Brahim Guihini Mollo, M. Peka, Justin Darnas, A. Bélem, Wilfrid Yoni, C. Noûs, T. de Meeûs
In Subsaharan Africa, tsetse flies (genus Glossina ) are vectors of trypanosomes causing Human African Trypanosomiasis (HAT) and Animal African Trypanosomosis (AAT). Some foci of HAT persist in Southern Chad, where a program of tsetse control was started against
{"title":"Population genetics of Glossina fuscipes fuscipes from southern Chad","authors":"S. Ravel, Mahamat Hisséne Mahamat, A. Ségard, R. Argilés-Herrero, J. Bouyer, J. Rayaissé, P. Solano, Brahim Guihini Mollo, M. Peka, Justin Darnas, A. Bélem, Wilfrid Yoni, C. Noûs, T. de Meeûs","doi":"10.24072/pcjournal.257","DOIUrl":"https://doi.org/10.24072/pcjournal.257","url":null,"abstract":"In Subsaharan Africa, tsetse flies (genus Glossina ) are vectors of trypanosomes causing Human African Trypanosomiasis (HAT) and Animal African Trypanosomosis (AAT). Some foci of HAT persist in Southern Chad, where a program of tsetse control was started against","PeriodicalId":74413,"journal":{"name":"Peer community journal","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-03-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"47550212","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}
Bertrand Néron, Rémi Denise, Charles Coluzzi, Marie Touchon, Eduardo P.C. Rocha, Sophie S. Abby
Complex cellular functions are usually encoded by a set of genes in one or a few organized genetic loci in microbial genomes. Macromolecular System Finder (MacSyFinder) is a program that uses these properties to model and then annotate cellular functions in microbial genomes. This is done by integrating the identification of each individual gene at the level of the molecular system. We hereby present a major release of MacSyFinder (version 2) coded in Python 3. The code was improved and rationalized to facilitate future maintainability. Several new features were added to allow more flexible modelling of the systems. We introduce a more intuitive and comprehensive search engine to identify all the best candidate systems and sub-optimal ones that respect the models’ constraints. We also introduce the novel macsydata companion tool that enables the easy installation and broad distribution of the models developed for MacSyFinder (macsy-models) from GitHub repositories. Finally, we have updated and improved MacSyFinder popular models: TXSScan to identify protein secretion systems, TFFscan to identify type IV filaments, CONJscan to identify conjugative systems, and CasFinder to identify CRISPR associated proteins. MacSyFinder and the updated models are available at: https://github.com/gem-pasteur/macsyfinder and https://github.com/macsy-models.
复杂的细胞功能通常是由微生物基因组中一个或几个有组织的遗传位点中的一组基因编码的。Macromolecular System Finder (MacSyFinder)是一个利用这些特性对微生物基因组中的细胞功能进行建模和注释的程序。这是通过在分子系统水平上整合每个个体基因的识别来完成的。我们在此发布MacSyFinder (version 2)的主要版本，使用Python 3编码。代码得到了改进和合理化，以促进未来的可维护性。增加了几个新功能，以允许更灵活的系统建模。我们引入了一个更直观和全面的搜索引擎来识别所有的最佳候选系统和次优的系统，这些系统尊重模型的约束。我们还介绍了新的macsydata配套工具，它可以从GitHub存储库中轻松安装和广泛分发为MacSyFinder开发的模型(macsy-models)。最后，我们更新和改进了MacSyFinder流行的模型:TXSScan用于鉴定蛋白质分泌系统，TFFscan用于鉴定IV型纤维，CONJscan用于鉴定共轭系统，CasFinder用于鉴定CRISPR相关蛋白。MacSyFinder和更新后的型号可在https://github.com/gem-pasteur/macsyfinder和https://github.com/macsy-models获得。
{"title":"MacSyFinder v2: Improved modelling and search engine to identify molecular systems in genomes","authors":"Bertrand Néron, Rémi Denise, Charles Coluzzi, Marie Touchon, Eduardo P.C. Rocha, Sophie S. Abby","doi":"10.24072/pcjournal.250","DOIUrl":"https://doi.org/10.24072/pcjournal.250","url":null,"abstract":"Complex cellular functions are usually encoded by a set of genes in one or a few organized genetic loci in microbial genomes. Macromolecular System Finder (MacSyFinder) is a program that uses these properties to model and then annotate cellular functions in microbial genomes. This is done by integrating the identification of each individual gene at the level of the molecular system. We hereby present a major release of MacSyFinder (version 2) coded in Python 3. The code was improved and rationalized to facilitate future maintainability. Several new features were added to allow more flexible modelling of the systems. We introduce a more intuitive and comprehensive search engine to identify all the best candidate systems and sub-optimal ones that respect the models’ constraints. We also introduce the novel macsydata companion tool that enables the easy installation and broad distribution of the models developed for MacSyFinder (macsy-models) from GitHub repositories. Finally, we have updated and improved MacSyFinder popular models: TXSScan to identify protein secretion systems, TFFscan to identify type IV filaments, CONJscan to identify conjugative systems, and CasFinder to identify CRISPR associated proteins. MacSyFinder and the updated models are available at: https://github.com/gem-pasteur/macsyfinder and https://github.com/macsy-models.","PeriodicalId":74413,"journal":{"name":"Peer community journal","volume":"60 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-03-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"136046489","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 de Vries, Matthias Galipaud, Hanna Kokko
Do environments or species traits that lower the mortality of individuals create selection for delaying senescence? Reading the literature creates an impression that mathematically oriented biologists cannot agree on the validity of George Williams' prediction (who claimed 'yes'). The abundance of models and opinions may bewilder those that are new to the field. Here we provide heuristics as well as simple models that outline when the Williams prediction holds, why there is a ‘null model’ where extrinsic mortality does not change the evolution of senescence at all, and why it is also possible to expect the opposite of William’s prediction, where increased extrinsic mortality favours slower senescence. We hope to offer intuition by quantifying how much delaying the ‘placement’ of an offspring into the population reduces its expected contribution to the gene pool of the future. Our first example shows why sometimes increased extrinsic mortality has no effect (the null result), and why density dependence can change that. Thereafter, a model with ten different choices for population regulation shows that high extrinsic mortality favours fast life histories (Williams) if increasing density harms the production of juveniles or their chances to recruit into the population. If instead increasing density harms the survival of older individuals in a population, then high extrinsic mortality favours slow life histories (anti-Williams). We discuss the possibility that empirically found Williams-like patterns provide indirect evidence for population regulation operating via harming the production or fitness prospects of juveniles, as opposed to the survival of established breeders.
{"title":"Extrinsic mortality and senescence: a guide for the perplexed","authors":"Charlotte de Vries, Matthias Galipaud, Hanna Kokko","doi":"10.24072/pcjournal.253","DOIUrl":"https://doi.org/10.24072/pcjournal.253","url":null,"abstract":"Do environments or species traits that lower the mortality of individuals create selection for delaying senescence? Reading the literature creates an impression that mathematically oriented biologists cannot agree on the validity of George Williams' prediction (who claimed 'yes'). The abundance of models and opinions may bewilder those that are new to the field. Here we provide heuristics as well as simple models that outline when the Williams prediction holds, why there is a ‘null model’ where extrinsic mortality does not change the evolution of senescence at all, and why it is also possible to expect the opposite of William’s prediction, where increased extrinsic mortality favours slower senescence. We hope to offer intuition by quantifying how much delaying the ‘placement’ of an offspring into the population reduces its expected contribution to the gene pool of the future. Our first example shows why sometimes increased extrinsic mortality has no effect (the null result), and why density dependence can change that. Thereafter, a model with ten different choices for population regulation shows that high extrinsic mortality favours fast life histories (Williams) if increasing density harms the production of juveniles or their chances to recruit into the population. If instead increasing density harms the survival of older individuals in a population, then high extrinsic mortality favours slow life histories (anti-Williams). We discuss the possibility that empirically found Williams-like patterns provide indirect evidence for population regulation operating via harming the production or fitness prospects of juveniles, as opposed to the survival of established breeders.","PeriodicalId":74413,"journal":{"name":"Peer community journal","volume":"19 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-03-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"136046492","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}
Marie Raynaud, Pierre-Alexandre Gagnaire, Nicolas Galtier
Knowledge of recombination rate variation along the genome provides important insights into genome and phenotypic evolution. Population genomic approaches offer an attractive way to infer the population-scaled recombination rate ρ=4Ner using the linkage disequilibrium information contained in DNA sequence polymorphism data. Such methods have been used in a broad range of plant and animal species to build genome-wide recombination maps. However, the reliability of these inferences has only been assessed under a restrictive set of conditions. Here, we evaluate the ability of one of the most widely used coalescent-based programs, LDhelmet, to infer a genomic landscape of recombination with the biological characteristics of a human-like landscape including hotspots. Using simulations, we specifically assessed the impact of methodological (sample size, phasing errors, block penalty) and evolutionary parameters (effective population size (Ne), demographic history, mutation to recombination rate ratio) on inferred map quality. We report reasonably good correlations between simulated and inferred landscapes, but point to limitations when it comes to detecting recombination hotspots. False positive and false negative hotspots considerably confound fine-scale patterns of inferred recombination under a wide range of conditions, particularly when Ne is small and the mutation/recombination rate ratio is low, to the extent that maps inferred from populations sharing the same recombination landscape appear uncorrelated. We thus address a message of caution for the users of these approaches, at least for genomes with complex recombination landscapes such as in humans.
{"title":"Performance and limitations of linkage-disequilibrium-based methods for inferring the genomic landscape of recombination and detecting hotspots: a simulation study","authors":"Marie Raynaud, Pierre-Alexandre Gagnaire, Nicolas Galtier","doi":"10.24072/pcjournal.254","DOIUrl":"https://doi.org/10.24072/pcjournal.254","url":null,"abstract":"Knowledge of recombination rate variation along the genome provides important insights into genome and phenotypic evolution. Population genomic approaches offer an attractive way to infer the population-scaled recombination rate ρ=4Ner using the linkage disequilibrium information contained in DNA sequence polymorphism data. Such methods have been used in a broad range of plant and animal species to build genome-wide recombination maps. However, the reliability of these inferences has only been assessed under a restrictive set of conditions. Here, we evaluate the ability of one of the most widely used coalescent-based programs, LDhelmet, to infer a genomic landscape of recombination with the biological characteristics of a human-like landscape including hotspots. Using simulations, we specifically assessed the impact of methodological (sample size, phasing errors, block penalty) and evolutionary parameters (effective population size (Ne), demographic history, mutation to recombination rate ratio) on inferred map quality. We report reasonably good correlations between simulated and inferred landscapes, but point to limitations when it comes to detecting recombination hotspots. False positive and false negative hotspots considerably confound fine-scale patterns of inferred recombination under a wide range of conditions, particularly when Ne is small and the mutation/recombination rate ratio is low, to the extent that maps inferred from populations sharing the same recombination landscape appear uncorrelated. We thus address a message of caution for the users of these approaches, at least for genomes with complex recombination landscapes such as in humans.","PeriodicalId":74413,"journal":{"name":"Peer community journal","volume":"133 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-03-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"136195782","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}
京公网安备 11010802042870号
京ICP备2023020795号-1
扫码关注我们
求助内容：
应助结果提醒方式：