Pub Date : 2024-09-19DOI: 10.1101/2024.09.18.613661
Daniel Bonn
Adjuvants are often used to improve the efficiency of plant protection products. However, there is concern that these compounds themselves might result in ecotoxicological effects. To investigate this concern, we compare the toxicity of different agricultural tank-mix adjuvants for two standard test organisms, i.e. the water flea Daphnia magna and the honey bee Apis mellifera. Daphnia trials comprised tests at 1, 5 and 20 times the normal prescribed label dosage. It is found that at 48h, the novel polymer-based adjuvant Squall is significantly less harmful to D. magna compared to traditional surfactant or oil-based adjuvants. For A. mellifera, we tested topical exposure to label-rate, five and twenty times label-rate. After 96h exposure to polymerand oil based adjuvants no statistically significant harmful effects were observed. The trisiloxane-based adjuvants, however, did significantly increase bee mortality at higher dose rates, indicating a higher toxicity of these specific compounds.
{"title":"Eco-toxicity of different agricultural tank-mix adjuvants","authors":"Daniel Bonn","doi":"10.1101/2024.09.18.613661","DOIUrl":"https://doi.org/10.1101/2024.09.18.613661","url":null,"abstract":"Adjuvants are often used to improve the efficiency of plant protection products. However, there is concern that these compounds themselves might result in ecotoxicological effects. To investigate this concern, we compare the toxicity of different agricultural tank-mix adjuvants for two standard test organisms, i.e. the water flea Daphnia magna and the honey bee Apis mellifera. Daphnia trials comprised tests at 1, 5 and 20 times the normal prescribed label dosage. It is found that at 48h, the novel polymer-based adjuvant Squall is significantly less harmful to D. magna compared to traditional surfactant or oil-based adjuvants. For A. mellifera, we tested topical exposure to label-rate, five and twenty times label-rate. After 96h exposure to polymerand oil based adjuvants no statistically significant harmful effects were observed. The trisiloxane-based adjuvants, however, did significantly increase bee mortality at higher dose rates, indicating a higher toxicity of these specific compounds.","PeriodicalId":501320,"journal":{"name":"bioRxiv - Ecology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-09-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142260158","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}
Pub Date : 2024-09-19DOI: 10.1101/2024.09.18.613733
Vandana Gupta, Sarah Grosjean, Aloyse Moreau, David Carbonell, Alison B. Duncan
Coinfections where hosts harbour more than one parasite species are common in nature. Facilitation among parasites enabling them to better exploit host resources is widespread with direct consequences on their life-history. Plant viruses can facilitate their vectors to increase their transmission, but equivalent studies in virus- non vectors are lacking. Here we study facilitation of two (non-vector) species of Tetranychus spider mites, Tetranychus urticae and T. evansi, by a plant virus, tomato spotted wilt virus (TSWV), in coinfections on a host tomato plant, Solanum lycopersicum. We compared the effect of different strains of TSWV on life-history traits of Tetranychus mites on cut leaves and whole plants of different tomato varieties. TSWV facilitated both species of spider mite on two different tomato varieties on whole plants, with more offspring of both species becoming adults. In contrast, on cut leaves, facilitation of T. urticae was much more variable depending on the experiment, viral strain and tomato variety. We attribute this to the non-homogeneous spread of virus throughout the host plant. Virus is first transported to the top leaves, and not middle leaves which we had used for the experiment. Indeed, if facilitation is indirect via the host immune system or resource based via the release of free-amino acids then this may be less efficient on cut plant parts. These results highlight that facilitation among parasites may increase parasite fitness and at the same time levels of virulence experienced by the host.
{"title":"Tomato spotted wilt virus facilitates non-vector spider mite species (Tetranychus urticae and Tetranychus evansi) on whole tomato plants","authors":"Vandana Gupta, Sarah Grosjean, Aloyse Moreau, David Carbonell, Alison B. Duncan","doi":"10.1101/2024.09.18.613733","DOIUrl":"https://doi.org/10.1101/2024.09.18.613733","url":null,"abstract":"Coinfections where hosts harbour more than one parasite species are common in nature. Facilitation among parasites enabling them to better exploit host resources is widespread with direct consequences on their life-history. Plant viruses can facilitate their vectors to increase their transmission, but equivalent studies in virus- non vectors are lacking. Here we study facilitation of two (non-vector) species of Tetranychus spider mites, Tetranychus urticae and T. evansi, by a plant virus, tomato spotted wilt virus (TSWV), in coinfections on a host tomato plant, Solanum lycopersicum. We compared the effect of different strains of TSWV on life-history traits of Tetranychus mites on cut leaves and whole plants of different tomato varieties. TSWV facilitated both species of spider mite on two different tomato varieties on whole plants, with more offspring of both species becoming adults. In contrast, on cut leaves, facilitation of T. urticae was much more variable depending on the experiment, viral strain and tomato variety. We attribute this to the non-homogeneous spread of virus throughout the host plant. Virus is first transported to the top leaves, and not middle leaves which we had used for the experiment. Indeed, if facilitation is indirect via the host immune system or resource based via the release of free-amino acids then this may be less efficient on cut plant parts. These results highlight that facilitation among parasites may increase parasite fitness and at the same time levels of virulence experienced by the host.","PeriodicalId":501320,"journal":{"name":"bioRxiv - Ecology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-09-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142260155","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}
Pub Date : 2024-09-18DOI: 10.1101/2024.09.17.613458
Katrin Moeller, Annalena Ritter, Phillip Stobinsky, Kai Jensen, Ina C. Meier, Harihar Jaishree Subrahmaniam
The chemical complexity of root exudates has garnered significant attention in recent years, yet critical gaps remain in understanding the full scope of root exudate chemical variation across the plant kingdom. To address this, we conducted a systematic review of 57 studies, comprising 124 experiments, aimed at evaluating current methodologies and findings in untargeted root exudate chemical analysis. Our review revealed that hydroponic (44%) and soil-hydroponic hybrid (32%) sampling approaches, primarily utilising water as the collection medium, were the most common experimental setups. Liquid chromatography-mass spectrometry (LC-MS) was the predominant analytical technique used in 54% of the studies, followed by gas chromatography-mass spectrometry (GC-MS) in 31%. The average number of metabolites identified per analysis was 960, though the number of annotated metabolites varied considerably. Shikimates, phenylpropanoids, and carbohydrates were the most frequently identified classes, with their relative abundances varying widely. Several methodological challenges were highlighted, including inconsistencies in sampling techniques, underrepresentation of non-crop plants, and incomplete chemical annotation. To address these limitations, we propose a framework emphasising the need for representative exudate sampling, the use of multiple analytical approaches, the development of advanced bioinformatics tools, and the integration of these findings to enhance our understanding of root exudates and their ecological functions.
{"title":"Targeting the untargeted: Uncovering the chemical complexity of root exudates","authors":"Katrin Moeller, Annalena Ritter, Phillip Stobinsky, Kai Jensen, Ina C. Meier, Harihar Jaishree Subrahmaniam","doi":"10.1101/2024.09.17.613458","DOIUrl":"https://doi.org/10.1101/2024.09.17.613458","url":null,"abstract":"The chemical complexity of root exudates has garnered significant attention in recent years, yet critical gaps remain in understanding the full scope of root exudate chemical variation across the plant kingdom. To address this, we conducted a systematic review of 57 studies, comprising 124 experiments, aimed at evaluating current methodologies and findings in untargeted root exudate chemical analysis. Our review revealed that hydroponic (44%) and soil-hydroponic hybrid (32%) sampling approaches, primarily utilising water as the collection medium, were the most common experimental setups. Liquid chromatography-mass spectrometry (LC-MS) was the predominant analytical technique used in 54% of the studies, followed by gas chromatography-mass spectrometry (GC-MS) in 31%. The average number of metabolites identified per analysis was 960, though the number of annotated metabolites varied considerably. Shikimates, phenylpropanoids, and carbohydrates were the most frequently identified classes, with their relative abundances varying widely. Several methodological challenges were highlighted, including inconsistencies in sampling techniques, underrepresentation of non-crop plants, and incomplete chemical annotation. To address these limitations, we propose a framework emphasising the need for representative exudate sampling, the use of multiple analytical approaches, the development of advanced bioinformatics tools, and the integration of these findings to enhance our understanding of root exudates and their ecological functions.","PeriodicalId":501320,"journal":{"name":"bioRxiv - Ecology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142260159","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}
Pub Date : 2024-09-18DOI: 10.1101/2024.09.12.612793
Siobhan Schenk, Varoon P Supratya, Patrick T Martone, Laura W Parfrey
Historical baseline data are critical to measuring how communities shift in response to climate change and anthropogenic activity. Macroalgae are marine foundation species that are vulnerable to climate change, but there is a lack of baseline macroalgal biodiversity data for many areas of British Columbia, particularly at a high temporal resolution over years. This presents an obstacle for measuring how communities change in response to shifting average conditions as well as after extreme events, such as the 2021 heat dome. To increase baseline macroalgae biodiversity data in British Columbia, we established a monthly transect-based macroalgal survey in 2021 at an urban intertidal site with a survey protocol that is low cost and easy to replicate. Our datasets and our survey protocol are freely available. Over 35 months we have recorded 59 species of macroalgae, including the canopy forming kelp Nereocystis luetkeana and the non-native fucoid Sargassum muticum. Surveying throughout the year at regular intervals has revealed large-scale seasonal shifts in macroalgal community composition, timing of kelp recruitment, and a decrease in abundance of Fucus distichus in the upper intertidal zone over multiple years. Our publicly accessible data constitute the most comprehensive survey of intertidal macroalgal diversity in Burrard Inlet, illustrating how simple surveying methods can provide high resolution records of macroalgae biodiversity, particularly in easily accessible urban environments.
{"title":"Monthly macroalgal surveys reveal a diverse and dynamic community in an urban intertidal zone","authors":"Siobhan Schenk, Varoon P Supratya, Patrick T Martone, Laura W Parfrey","doi":"10.1101/2024.09.12.612793","DOIUrl":"https://doi.org/10.1101/2024.09.12.612793","url":null,"abstract":"Historical baseline data are critical to measuring how communities shift in response to climate change and anthropogenic activity. Macroalgae are marine foundation species that are vulnerable to climate change, but there is a lack of baseline macroalgal biodiversity data for many areas of British Columbia, particularly at a high temporal resolution over years. This presents an obstacle for measuring how communities change in response to shifting average conditions as well as after extreme events, such as the 2021 heat dome. To increase baseline macroalgae biodiversity data in British Columbia, we established a monthly transect-based macroalgal survey in 2021 at an urban intertidal site with a survey protocol that is low cost and easy to replicate. Our datasets and our survey protocol are freely available. Over 35 months we have recorded 59 species of macroalgae, including the canopy forming kelp Nereocystis luetkeana and the non-native fucoid Sargassum muticum. Surveying throughout the year at regular intervals has revealed large-scale seasonal shifts in macroalgal community composition, timing of kelp recruitment, and a decrease in abundance of Fucus distichus in the upper intertidal zone over multiple years. Our publicly accessible data constitute the most comprehensive survey of intertidal macroalgal diversity in Burrard Inlet, illustrating how simple surveying methods can provide high resolution records of macroalgae biodiversity, particularly in easily accessible urban environments.","PeriodicalId":501320,"journal":{"name":"bioRxiv - Ecology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142260157","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}
Pub Date : 2024-09-18DOI: 10.1101/2024.09.13.612829
Agnese Aguzzoni, Francesco Giammarchi, Ignacio A. Mundo, Giulio Voto, Giustino Tonon, Werner Tirler, Enrico Tomelleri
International timber trading is subject to rigorous certification schemes that require the disclosure of essential information, including the tree species and geographic origin of the timber in question. Regrettably, the lack of readily accessible forensic tools to verify compliance has facilitated the proliferation of illegal timber trading, with dramatic consequences for ecosystems and biodiversity. The objective of this study was to investigate the potential of a multichemical approach based on the multielement and strontium isotope (87Sr/86Sr) ratio analysis combined with chemometrics to test sample recognition according to their species and geographic origin. The sampling area covered a portion of the Eastern Alpine region, which is characterised by a significant economic reliance on wood. The study focused on three representative species from local forests: Norway spruce, European larch, and Swiss stone pine. Samples were characterised from stands grown on diverse bedrock types. Our findings revealed a strikingly consistent variation in the multielement profiles across different species, thereby enabling flawless sample recognition. Considering the geographic origin, the 87Sr/86Sr ratio proved to be a pivotal parameter, by virtue of its correlation with the geo-lithological composition of the growing area. Combining the chemical markers, an accurate sample classification based on multiple decision trees was attained, even comparing forest stands grown on the same bedrock type. These findings offer novel insights into the utilisation of chemical markers in provenancing and authenticity studies, thereby enhancing the adoption of integrated approaches to counteract illegal timber trade.
{"title":"Enhancing timber traceability via multielement and strontium isotope ratio: An example from the Eastern Alps","authors":"Agnese Aguzzoni, Francesco Giammarchi, Ignacio A. Mundo, Giulio Voto, Giustino Tonon, Werner Tirler, Enrico Tomelleri","doi":"10.1101/2024.09.13.612829","DOIUrl":"https://doi.org/10.1101/2024.09.13.612829","url":null,"abstract":"International timber trading is subject to rigorous certification schemes that require the disclosure of essential information, including the tree species and geographic origin of the timber in question. Regrettably, the lack of readily accessible forensic tools to verify compliance has facilitated the proliferation of illegal timber trading, with dramatic consequences for ecosystems and biodiversity. The objective of this study was to investigate the potential of a multichemical approach based on the multielement and strontium isotope (87Sr/86Sr) ratio analysis combined with chemometrics to test sample recognition according to their species and geographic origin. The sampling area covered a portion of the Eastern Alpine region, which is characterised by a significant economic reliance on wood. The study focused on three representative species from local forests: Norway spruce, European larch, and Swiss stone pine. Samples were characterised from stands grown on diverse bedrock types. Our findings revealed a strikingly consistent variation in the multielement profiles across different species, thereby enabling flawless sample recognition. Considering the geographic origin, the 87Sr/86Sr ratio proved to be a pivotal parameter, by virtue of its correlation with the geo-lithological composition of the growing area. Combining the chemical markers, an accurate sample classification based on multiple decision trees was attained, even comparing forest stands grown on the same bedrock type. These findings offer novel insights into the utilisation of chemical markers in provenancing and authenticity studies, thereby enhancing the adoption of integrated approaches to counteract illegal timber trade.","PeriodicalId":501320,"journal":{"name":"bioRxiv - Ecology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142260259","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}
Pub Date : 2024-09-18DOI: 10.1101/2024.09.13.612839
Lukas Adam, Kostas Papafitsoros, Claire Jean, Alan Rees
Animal Photo-identification (photo-ID) denotes the process of identifying individual animals based on their unique and stable morphological characteristics. It has been proven to be a particularly useful tool for a variety of studies on sea turtles increasing the knowledge of their ecology and informing conservation efforts. The photo-ID process in sea turtles is predominantly based on the geometric patterns of the scales of their two head sides which are unique to every individual, and also different from side to side. As such, both manual and automated photo-ID techniques are performed under a side-specific image retrieval setting. There, a query image showing a single profile of an unknown individual, either left or right, is only compared to images of previously identified individuals showing the same side. Here, by employing the recently introduced state-of-the-art deep feature extractor MegaDescriptor, we show for the first time an inherit deep visual similarity between left and right facial profiles of the same individuals in three sea turtle species. We show that the similarity between the left and right profiles of the same individual with respect to geometry, coloration and pigmentation, is on average higher than the similarity between profiles of different individuals. The similarity is detectable even when images are taken years apart and under diverse settings and conditions. We perform several image retrieval experiments under scenarios which mimic realistic sea turtle photo-ID matching processes, where we also allow comparisons of opposite sides in the matching process which have no spatial overlap. We show that the detection and exploitation of this similarity is translated to improved accuracies when compared to the traditional side-specific image retrieval setting. Notably this similarity cannot be detected and thus neither explored by the so-far state-of-the-art sea turtle photo-ID automated methods such as those based on SIFT. Our work leads to a change of paradigm for the sea turtle photo-ID workflows which will be further facilitated by the constant improvement of deep feature-based re-identification methods and paves the path for adopting similar workflows in other animal species as well.
{"title":"Exploiting facial side similarities to improve AI-driven sea turtle photo-identification systems","authors":"Lukas Adam, Kostas Papafitsoros, Claire Jean, Alan Rees","doi":"10.1101/2024.09.13.612839","DOIUrl":"https://doi.org/10.1101/2024.09.13.612839","url":null,"abstract":"Animal Photo-identification (photo-ID) denotes the process of identifying individual animals based on their unique and stable morphological characteristics. It has been proven to be a particularly useful tool for a variety of studies on sea turtles increasing the knowledge of their ecology and informing conservation efforts. The photo-ID process in sea turtles is predominantly based on the geometric patterns of the scales of their two head sides which are unique to every individual, and also different from side to side. As such, both manual and automated photo-ID techniques are performed under a side-specific image retrieval setting. There, a query image showing a single profile of an unknown individual, either left or right, is only compared to images of previously identified individuals showing the same side. Here, by employing the recently introduced state-of-the-art deep feature extractor MegaDescriptor, we show for the first time an inherit deep visual similarity between left and right facial profiles of the same individuals in three sea turtle species. We show that the similarity between the left and right profiles of the same individual with respect to geometry, coloration and pigmentation, is on average higher than the similarity between profiles of different individuals. The similarity is detectable even when images are taken years apart and under diverse settings and conditions. We perform several image retrieval experiments under scenarios which mimic realistic sea turtle photo-ID matching processes, where we also allow comparisons of opposite sides in the matching process which have no spatial overlap. We show that the detection and exploitation of this similarity is translated to improved accuracies when compared to the traditional side-specific image retrieval setting. Notably this similarity cannot be detected and thus neither explored by the so-far state-of-the-art sea turtle photo-ID automated methods such as those based on SIFT. Our work leads to a change of paradigm for the sea turtle photo-ID workflows which will be further facilitated by the constant improvement of deep feature-based re-identification methods and paves the path for adopting similar workflows in other animal species as well.","PeriodicalId":501320,"journal":{"name":"bioRxiv - Ecology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142260156","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}
Pub Date : 2024-09-18DOI: 10.1101/2024.09.12.612774
Ingrid C. Romero, Surangi W. Punyasena
The concept of niche conservatism describes the tendency of organisms to retain ecological traits through time and space. Reviewing this concept in different groups of angiosperms is critical to understanding what factors drove their expansion and geographic distribution, as well as assessing how, in taxonomic levels higher than species, ecological traits have remained relatively constant through time and space. Studying niche conservatism can also help us understand how the distribution of clades may be affected by climate change. Niche conservatism has been observed in many clades of legumes. Amherstieae, the largest tribe of the Detarioideae subfamily, has a geographic distribution, evolutionary history, and phylogeny that makes it a good candidate for evaluating patterns in niche conservatism. We analyzed the distribution of two Amherstieae suprageneric clades, the Berlinia and Brownea clades. The former is endemic to sub-Saharan Africa and the latter is restricted to the Neotropics. We used the geographic distributions of each clade to define their G-space (geographic space) and extracted 19 climatic variables to define the E-space (environmental space) of each clade. We used two tests to evaluate the similarity in the climatic niche of both clades, the niche overlap test (NOT) to estimate similarities between the occupied E-spaces (realized niche space) and the niche divergence test (NDT) to assess the similarity of the environmental niche relative to the accessible analogous E-space (potential niche space) of each biogeographic region. Our results suggest that the Brownea clade are descendants of a climatic subset of the Berlinia clade preferring less variable temperature and higher precipitation levels, and that the dry-adapted subset of Berlinia may represent a more recent evolutionary expansion.
生态位保守概念描述了生物在时间和空间上保持生态特征的趋势。在不同的被子植物类群中回顾这一概念，对于了解是什么因素推动了它们的扩张和地理分布，以及评估在比物种更高的分类级别中，生态特征是如何在时间和空间上保持相对不变的，都是至关重要的。研究生态位保守性还有助于我们了解支系的分布如何受到气候变化的影响。在豆科植物的许多支系中都观察到了生态位保守性。Amherstieae是豆科（Detarioideae）亚科中最大的一个支系，其地理分布、进化历史和系统发育使其成为评估生态位保守性模式的一个很好的候选支系。我们分析了两个Amherstieae超属支系的分布，即Berlinia和Brownea支系。前者是撒哈拉以南非洲的特有种，后者则局限于新热带地区。我们利用每个支系的地理分布来定义它们的 G 空间（地理空间），并提取 19 个气候变量来定义每个支系的 E 空间（环境空间）。我们使用了两种检验方法来评估两个支系气候生态位的相似性，即生态位重叠检验（NOT）和生态位分异检验（NDT），前者用于估算所占据的 E 空间（实现的生态位空间）之间的相似性，后者用于评估环境生态位相对于每个生物地理区域可获得的类似 E 空间（潜在的生态位空间）的相似性。我们的研究结果表明，Brownea 支系是喜好较低温度变化和较高降水量的柏林藻支系气候亚群的后裔，而适应干旱的柏林藻亚群可能代表了较新的进化扩展。
{"title":"Niche conservatism in the Legume Amherstieae tribe: Insights from the tropical Berlinia and Brownea clades","authors":"Ingrid C. Romero, Surangi W. Punyasena","doi":"10.1101/2024.09.12.612774","DOIUrl":"https://doi.org/10.1101/2024.09.12.612774","url":null,"abstract":"The concept of niche conservatism describes the tendency of organisms to retain ecological traits through time and space. Reviewing this concept in different groups of angiosperms is critical to understanding what factors drove their expansion and geographic distribution, as well as assessing how, in taxonomic levels higher than species, ecological traits have remained relatively constant through time and space. Studying niche conservatism can also help us understand how the distribution of clades may be affected by climate change. Niche conservatism has been observed in many clades of legumes. Amherstieae, the largest tribe of the Detarioideae subfamily, has a geographic distribution, evolutionary history, and phylogeny that makes it a good candidate for evaluating patterns in niche conservatism. We analyzed the distribution of two Amherstieae suprageneric clades, the Berlinia and Brownea clades. The former is endemic to sub-Saharan Africa and the latter is restricted to the Neotropics. We used the geographic distributions of each clade to define their G-space (geographic space) and extracted 19 climatic variables to define the E-space (environmental space) of each clade. We used two tests to evaluate the similarity in the climatic niche of both clades, the niche overlap test (NOT) to estimate similarities between the occupied E-spaces (realized niche space) and the niche divergence test (NDT) to assess the similarity of the environmental niche relative to the accessible analogous E-space (potential niche space) of each biogeographic region. Our results suggest that the Brownea clade are descendants of a climatic subset of the Berlinia clade preferring less variable temperature and higher precipitation levels, and that the dry-adapted subset of Berlinia may represent a more recent evolutionary expansion.","PeriodicalId":501320,"journal":{"name":"bioRxiv - Ecology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142260160","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}
Pub Date : 2024-09-18DOI: 10.1101/2024.09.15.613158
Kesia Louise Savill, Iain Parnum, Jennifer McIlwain, David Belton
Over the last decade, Structure-from-Motion (SfM) photogrammetry has successfully been used to survey marine benthic environments, including artificial reefs, shipwrecks, and coral reefs, for a wide range of applications. The method is likely to become one of the most common tools for surveying marine benthic environments. However, SfM photogrammetry has been developed in clear water environments, and its suitability in turbid, benthic environments is less certain. Turbid coral reefs are example of an important marine benthic environment, making up 12% of coral reefs globally. Corals in these environments have a tolerance for low-light and high sediment conditions. Such attributes mean these reefs may be important refuges from extreme light and temperatures. Therefore, assessment and optimisation of the photogrammetry methodology in these environments is needed. This study investigates the performance of SfM photogrammetry in turbid environments, by comparing two camera types, settings (automatic vs manual derived from local conditions), the height of image acquisition above the seafloor, and post-processing image enhancement. Three dimensional (3D) SfM photogrammetry meshes of an artificial reef structure using two cameras, an action camera and a compact camera, were compared with its known dimensions detailed in an engineering diagram. According to surface area calculations, the compact camera provided a better 3D mesh than the action camera, with surface area calculations providing an accuracy of 98.2% against the engineering model, compared to 93.2% for the action camera. Images taken at a height of 1 m above the seafloor provided 3D meshes that were more accurate than those using images taken at 2 m above the seafloor. Two image enhancement techniques, histogram equalisation and contrast limited adaptive histogram equalisation (CLAHE), were then applied to assess if this improved the SfM photogrammetry mesh. The 3D mesh from images using the action camera that had a histogram equalisation enhancement provided the most comparable surface area measurement to the engineering diagram, with 100.6% accuracy, indicating our mesh had accounted for growth of benthic organisms on the structure since its installation. In contrast, raw (not enhanced) images had most comparable surface area measurement (98.2% accuracy) using the compact camera. However, the higher apparent accuracy of surface area measurements with the action camera following image enhancement may also be an artefact of inaccurate visual representations from the 3D mesh. Given the comparable accuracy of both approaches, we suggest SfM photogrammetry in turbid benthic environments uses cameras with a larger sensor sizes and customisable settings. This will result in the most accurate 3D meshes from raw imagery, particularly with images taken at a close distance (e.g., ≤ 1 m above the seafloor) and at high intervals (0.5 sec) with percentage overlap (>70%) among images. As the artificia
{"title":"Influence of camera type, height and image enhancement on photogrammetry success in turbid marine environments.","authors":"Kesia Louise Savill, Iain Parnum, Jennifer McIlwain, David Belton","doi":"10.1101/2024.09.15.613158","DOIUrl":"https://doi.org/10.1101/2024.09.15.613158","url":null,"abstract":"Over the last decade, Structure-from-Motion (SfM) photogrammetry has successfully been used to survey marine benthic environments, including artificial reefs, shipwrecks, and coral reefs, for a wide range of applications. The method is likely to become one of the most common tools for surveying marine benthic environments. However, SfM photogrammetry has been developed in clear water environments, and its suitability in turbid, benthic environments is less certain. Turbid coral reefs are example of an important marine benthic environment, making up 12% of coral reefs globally. Corals in these environments have a tolerance for low-light and high sediment conditions. Such attributes mean these reefs may be important refuges from extreme light and temperatures. Therefore, assessment and optimisation of the photogrammetry methodology in these environments is needed. This study investigates the performance of SfM photogrammetry in turbid environments, by comparing two camera types, settings (automatic vs manual derived from local conditions), the height of image acquisition above the seafloor, and post-processing image enhancement. Three dimensional (3D) SfM photogrammetry meshes of an artificial reef structure using two cameras, an action camera and a compact camera, were compared with its known dimensions detailed in an engineering diagram. According to surface area calculations, the compact camera provided a better 3D mesh than the action camera, with surface area calculations providing an accuracy of 98.2% against the engineering model, compared to 93.2% for the action camera. Images taken at a height of 1 m above the seafloor provided 3D meshes that were more accurate than those using images taken at 2 m above the seafloor. Two image enhancement techniques, histogram equalisation and contrast limited adaptive histogram equalisation (CLAHE), were then applied to assess if this improved the SfM photogrammetry mesh. The 3D mesh from images using the action camera that had a histogram equalisation enhancement provided the most comparable surface area measurement to the engineering diagram, with 100.6% accuracy, indicating our mesh had accounted for growth of benthic organisms on the structure since its installation. In contrast, raw (not enhanced) images had most comparable surface area measurement (98.2% accuracy) using the compact camera. However, the higher apparent accuracy of surface area measurements with the action camera following image enhancement may also be an artefact of inaccurate visual representations from the 3D mesh. Given the comparable accuracy of both approaches, we suggest SfM photogrammetry in turbid benthic environments uses cameras with a larger sensor sizes and customisable settings. This will result in the most accurate 3D meshes from raw imagery, particularly with images taken at a close distance (e.g., ≤ 1 m above the seafloor) and at high intervals (0.5 sec) with percentage overlap (>70%) among images. As the artificia","PeriodicalId":501320,"journal":{"name":"bioRxiv - Ecology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142260197","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}
Pub Date : 2024-09-17DOI: 10.1101/2024.09.11.612499
Isabell Schmidt, Birgit Gehlen, Katja Winkler, Alvaro Arrizabalaga, Nico Arts, Nuno Bicho, Philippe Crombé, Berit Valentin Eriksen, Sonja B. Grimm, Katarina Kapustka, Mathieu Langlais, Ludovic Mevel, Nicolas Naudinot, Zdeňka Nerudová, Marcel Niekus, Marco Peresani, Felix Riede, Florian Sauer, Werner Schön, Iwona Sobkowiak-Tabaka, Hans Vandendriessche, Mara-Julia Weber, Annabell Zander, Andreas Zimmermann, Andreas Maier
The European Final Palaeolithic witnessed marked changes in almost all societal domains. Despite a rich body of evidence, our knowledge of palaeodemographic processes and regional population dynamics still needs to be improved. In this study, we present regionally differentiated estimates of absolute numbers and population densities for the Greenland Interstadial 1d-a (GI-1d-a; 14-12.7 ka BP) and the Greenland Stadial 1 (GS-1; 12.7-11.6 ka BP) for western and central Europe. The data were obtained by applying the Cologne Protocol, a geostatistical approach for estimating prehistoric population size and density, to a newly compiled dataset of Final Palaeolithic sites. On a large spatio-temporal scale, we observe a shift of the main areas of human occupation from the Franco-Cantabrian region, which was intensely occupied during most phases of the preceding Upper Palaeolithic, to regions north of the Alps. At smaller scales, we observe divergent regional trends in the Final Palaeolithic meta-population: during GI 1d-a, a decreasing population in southwestern Europe and an increasing population in north-eastern Central Europe. For the first time since the dispersal of anatomically modern humans into Europe, we see that Central Europe becomes the dominant demographic growth area. Subsequently, the climatic cooling of GS-1 coincides with a pronounced population decline in most parts of the study area. An apparent increase in population density occurs only in north-eastern Central Europe and north-eastern Italy. Our estimates suggest that the total population was reduced by half. Similar results, with a relationship between decreasing temperatures and decreasing populations, have already been observed for the late phase of the Gravettian, when populations were reduced to only one third of those estimated for the early phase. Yet, in contrast to the collapse of local populations during the late Gravettian, the increase in population densities in central Europe during GS-1 indicates population movements eastwards, possibly in response to deteriorating climatic conditions, particularly in western regions during the Younger Dryas.
欧洲最终旧石器时代见证了几乎所有社会领域的显著变化。尽管有丰富的证据，我们对古人口统计过程和区域人口动态的了解仍有待提高。在本研究中，我们提出了欧洲西部和中部格陵兰岛间期 1d-a（GI-1d-a；14-12.7 ka BP）和格陵兰岛期 1（GS-1；12.7-11.6 ka BP）的绝对数量和人口密度的地区差异估计值。这些数据是通过将科隆协议（一种估算史前人口规模和密度的地质统计方法）应用于新编制的旧石器时代晚期遗址数据集而获得的。在大的时空尺度上，我们观察到人类活动的主要地区从上旧石器时代大部分时期密集活动的弗朗哥-坎塔布里亚地区转移到了阿尔卑斯山以北地区。在较小的尺度上，我们观察到了最终旧石器时代元人群的不同地区趋势：在 GI 1d-a 期间，欧洲西南部的人群在减少，而中欧东北部的人群在增加。自解剖学意义上的现代人扩散到欧洲以来，我们首次看到中欧成为人口增长的主要地区。随后，GS-1 的气候变冷与研究区域大部分地区的人口明显减少相吻合。只有中欧东北部和意大利东北部的人口密度出现了明显的增加。我们的估计表明，总种群数量减少了一半。在格拉维蒂晚期也观察到了类似的结果，即温度下降与种群数量减少之间的关系，当时的种群数量仅为早期估计数量的三分之一。然而，与格拉维蒂晚期当地种群的崩溃相反，GS-1期间中欧种群密度的增加表明种群向东迁移，这可能是对气候条件恶化的反应，尤其是在幼年干旱期的西部地区。
{"title":"Demographic responses to climatic changes during the Final Palaeolithic in Europe","authors":"Isabell Schmidt, Birgit Gehlen, Katja Winkler, Alvaro Arrizabalaga, Nico Arts, Nuno Bicho, Philippe Crombé, Berit Valentin Eriksen, Sonja B. Grimm, Katarina Kapustka, Mathieu Langlais, Ludovic Mevel, Nicolas Naudinot, Zdeňka Nerudová, Marcel Niekus, Marco Peresani, Felix Riede, Florian Sauer, Werner Schön, Iwona Sobkowiak-Tabaka, Hans Vandendriessche, Mara-Julia Weber, Annabell Zander, Andreas Zimmermann, Andreas Maier","doi":"10.1101/2024.09.11.612499","DOIUrl":"https://doi.org/10.1101/2024.09.11.612499","url":null,"abstract":"The European Final Palaeolithic witnessed marked changes in almost all societal domains. Despite a rich body of evidence, our knowledge of palaeodemographic processes and regional population dynamics still needs to be improved. In this study, we present regionally differentiated estimates of absolute numbers and population densities for the Greenland Interstadial 1d-a (GI-1d-a; 14-12.7 ka BP) and the Greenland Stadial 1 (GS-1; 12.7-11.6 ka BP) for western and central Europe. The data were obtained by applying the Cologne Protocol, a geostatistical approach for estimating prehistoric population size and density, to a newly compiled dataset of Final Palaeolithic sites. On a large spatio-temporal scale, we observe a shift of the main areas of human occupation from the Franco-Cantabrian region, which was intensely occupied during most phases of the preceding Upper Palaeolithic, to regions north of the Alps. At smaller scales, we observe divergent regional trends in the Final Palaeolithic meta-population: during GI 1d-a, a decreasing population in southwestern Europe and an increasing population in north-eastern Central Europe. For the first time since the dispersal of anatomically modern humans into Europe, we see that Central Europe becomes the dominant demographic growth area. Subsequently, the climatic cooling of GS-1 coincides with a pronounced population decline in most parts of the study area. An apparent increase in population density occurs only in north-eastern Central Europe and north-eastern Italy. Our estimates suggest that the total population was reduced by half. Similar results, with a relationship between decreasing temperatures and decreasing populations, have already been observed for the late phase of the Gravettian, when populations were reduced to only one third of those estimated for the early phase. Yet, in contrast to the collapse of local populations during the late Gravettian, the increase in population densities in central Europe during GS-1 indicates population movements eastwards, possibly in response to deteriorating climatic conditions, particularly in western regions during the Younger Dryas.","PeriodicalId":501320,"journal":{"name":"bioRxiv - Ecology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142260199","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}
Pub Date : 2024-09-17DOI: 10.1101/2024.08.28.609837
Claire Guinat, Lisa Fourtune, Sebastien Lambert, Eva Martin, Guillaume Gerbier, Andrea Jimenez Pellicer, Jean-Luc Guerin, Timothee Vergne
The ongoing panzootic of highly pathogenic avian influenza (HPAI) H5 clade 2.3.4.4b has caused widespread poultry mortality and raised concerns about zoonotic pandemics and wildlife conservation. France recently adopted a preventive vaccination strategy, vaccinating domestic ducks with inactivated and mRNA vaccines. This study evaluates the impact of this campaign on reducing HPAI H5 outbreaks. Using predictive modeling based on previous outbreak data, the expected number of outbreaks in 2023-24 without vaccination was significantly higher than the observed cases, indicating a 95.9% reduction attributable to vaccination. These findings suggest that vaccination effectively mitigated the HPAI H5 outbreak in France.
{"title":"Promising effects of duck vaccination against highly pathogenic avian influenza, France 2023-24","authors":"Claire Guinat, Lisa Fourtune, Sebastien Lambert, Eva Martin, Guillaume Gerbier, Andrea Jimenez Pellicer, Jean-Luc Guerin, Timothee Vergne","doi":"10.1101/2024.08.28.609837","DOIUrl":"https://doi.org/10.1101/2024.08.28.609837","url":null,"abstract":"The ongoing panzootic of highly pathogenic avian influenza (HPAI) H5 clade 2.3.4.4b has caused widespread poultry mortality and raised concerns about zoonotic pandemics and wildlife conservation. France recently adopted a preventive vaccination strategy, vaccinating domestic ducks with inactivated and mRNA vaccines. This study evaluates the impact of this campaign on reducing HPAI H5 outbreaks. Using predictive modeling based on previous outbreak data, the expected number of outbreaks in 2023-24 without vaccination was significantly higher than the observed cases, indicating a 95.9% reduction attributable to vaccination. These findings suggest that vaccination effectively mitigated the HPAI H5 outbreak in France.","PeriodicalId":501320,"journal":{"name":"bioRxiv - Ecology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142269180","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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