Pub Date : 2019-01-21DOI: 10.3897/RETHINKINGECOLOGY.4.30890
L. Winder, C. J. Alexander, G. Griffiths, J. Holland, C. Woolley, J. Perry
SADIE (Spatial Analysis by Distance Indices) is designed specifically to quantify patterns in spatially-referenced count-based data. It was developed for dealing with data that can be considered ‘patchy’. Such distributions are commonly found, for example, in insect populations where discrete patches of individuals are often evident. The distributions of such populations have ‘hard edges’, with patches and gaps occurring spatially. In these cases variance of abundance does not vary smoothly, but discontinuously. In this paper we outline the use of SADIE and provide free access to the SADIE software suite, establishing Rethinking Ecology as its permanent home. Finally, we review the use of SADIE and demonstrate its use in a wide variety of sub-disciplines within the general field of ecology.
{"title":"Twenty years and counting with SADIE: Spatial Analysis by Distance Indices software and review of its adoption and use","authors":"L. Winder, C. J. Alexander, G. Griffiths, J. Holland, C. Woolley, J. Perry","doi":"10.3897/RETHINKINGECOLOGY.4.30890","DOIUrl":"https://doi.org/10.3897/RETHINKINGECOLOGY.4.30890","url":null,"abstract":"SADIE (Spatial Analysis by Distance Indices) is designed specifically to quantify patterns in spatially-referenced count-based data. It was developed for dealing with data that can be considered ‘patchy’. Such distributions are commonly found, for example, in insect populations where discrete patches of individuals are often evident. The distributions of such populations have ‘hard edges’, with patches and gaps occurring spatially. In these cases variance of abundance does not vary smoothly, but discontinuously. In this paper we outline the use of SADIE and provide free access to the SADIE software suite, establishing Rethinking Ecology as its permanent home. Finally, we review the use of SADIE and demonstrate its use in a wide variety of sub-disciplines within the general field of ecology.","PeriodicalId":36503,"journal":{"name":"Rethinking Ecology","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2019-01-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"47160886","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 : 2019-01-07DOI: 10.3897/RETHINKINGECOLOGY.4.33014
Piotr Bajdek
Biogeographic distribution of infected plants and the continental drift theory allow a tentative time calibration of the phylogenetic tree of Pospiviroidae. Hypothetically, viroids evolved in the late Early Cretaceous shortly after the appearance of angiosperms, which constitute their only known hosts. No decline in the estimated divergence rates of Pospiviroidae is observed during the Late Cretaceous but it appears that they abruptly decreased at the Cretaceous-Paleogene boundary. However, an adaptive radiation of Pospiviroidae which occurred in the late Paleocene may reflect a recovery from the Cretaceous-Paleogene (K–Pg) mass extinction. It seems that the evolutionary history of viroids has been in part shaped by radiation and extinction events of angiosperms. Herein, for the first time I show the probable impact of a mass extinction event on the divergence rates of subviral pathogens, which are the simplest known “lifeforms”.
{"title":"Divergence rates of subviral pathogens of angiosperms abruptly decreased at the Cretaceous-Paleogene boundary","authors":"Piotr Bajdek","doi":"10.3897/RETHINKINGECOLOGY.4.33014","DOIUrl":"https://doi.org/10.3897/RETHINKINGECOLOGY.4.33014","url":null,"abstract":"Biogeographic distribution of infected plants and the continental drift theory allow a tentative time calibration of the phylogenetic tree of Pospiviroidae. Hypothetically, viroids evolved in the late Early Cretaceous shortly after the appearance of angiosperms, which constitute their only known hosts. No decline in the estimated divergence rates of Pospiviroidae is observed during the Late Cretaceous but it appears that they abruptly decreased at the Cretaceous-Paleogene boundary. However, an adaptive radiation of Pospiviroidae which occurred in the late Paleocene may reflect a recovery from the Cretaceous-Paleogene (K–Pg) mass extinction. It seems that the evolutionary history of viroids has been in part shaped by radiation and extinction events of angiosperms. Herein, for the first time I show the probable impact of a mass extinction event on the divergence rates of subviral pathogens, which are the simplest known “lifeforms”.","PeriodicalId":36503,"journal":{"name":"Rethinking Ecology","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2019-01-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"47937440","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 : 2018-11-12DOI: 10.3897/RETHINKINGECOLOGY.3.28516
Marie-Anne Wycke, Romaric Perrocheau, E. Darrouzet
Vespavelutinanigrithorax, an invasive species, a direct result of increased trade and climate change, is spreading rapidly in Europe and endangering entomofauna in general and more alarmingly honeybee (Apismellifera) populations, and therefore their pollination services. All traps used now, to try to control this species, seem to be not efficient enough and non-selective. However, in the current context of massive disappearance of insects in general, it is urgent to find means of protection for the entomofauna. While no selective trapping is still occurring, we performed a pilot study to test a carnivorous plant as a potential biocontrol tool to trap V.velutina. In our study, we analyzed the hornet-capturing ability of two Sarracenia hybrids (S.juthatipsoper and S.evendine) on a 2-years period (2015 and 2016). Our results show that these plants trapped more dipterans than other taxa, and they do not attract many hornets. In such condition, both Sarracenia hybrids cannot therefore be used in a mass trapping system, because they are not selective, and too few hornets are trapped. To maximize captures of V.velutina while minimizing captures of non-target species, other systems need to be thus developed, as traps using hornet pheromone-based baiting.
{"title":"Sarracenia carnivorous plants cannot serve as efficient biological control of the invasive hornet Vespa velutina nigrithorax in Europe","authors":"Marie-Anne Wycke, Romaric Perrocheau, E. Darrouzet","doi":"10.3897/RETHINKINGECOLOGY.3.28516","DOIUrl":"https://doi.org/10.3897/RETHINKINGECOLOGY.3.28516","url":null,"abstract":"Vespavelutinanigrithorax, an invasive species, a direct result of increased trade and climate change, is spreading rapidly in Europe and endangering entomofauna in general and more alarmingly honeybee (Apismellifera) populations, and therefore their pollination services. All traps used now, to try to control this species, seem to be not efficient enough and non-selective. However, in the current context of massive disappearance of insects in general, it is urgent to find means of protection for the entomofauna. While no selective trapping is still occurring, we performed a pilot study to test a carnivorous plant as a potential biocontrol tool to trap V.velutina. In our study, we analyzed the hornet-capturing ability of two Sarracenia hybrids (S.juthatipsoper and S.evendine) on a 2-years period (2015 and 2016). Our results show that these plants trapped more dipterans than other taxa, and they do not attract many hornets. In such condition, both Sarracenia hybrids cannot therefore be used in a mass trapping system, because they are not selective, and too few hornets are trapped. To maximize captures of V.velutina while minimizing captures of non-target species, other systems need to be thus developed, as traps using hornet pheromone-based baiting.","PeriodicalId":36503,"journal":{"name":"Rethinking Ecology","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2018-11-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"49426431","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 : 2018-05-21DOI: 10.3897/RETHINKINGECOLOGY.3.29573
M. Charpentier, P. Kappeler
This preprint has been reviewed and recommended by Peer Community In Ecology (https://dx.doi.org/10.24072/pci.ecology.100001). In a recent article, Bicca-Marques and Calegaro-Marques [Bicca-Marques JC, Calegaro-Marques C (2016) Ranging behavior drives parasite richness: A more parsimonious hypothesis. American Journal of Primatology 78: 923–927.] discussed the putative assumptions related to an interpretation we provided regarding an observed positive relationship between weekly averaged parasite richness of a group of mandrills (Mandrillussphinx) and their daily path lengths (DPL), published earlier in the same journal [Brockmeyer T, Kappeler PM, Willaume E, Benoit L, Mboumba S, Charpentier MJE (2015) Social organization and space use of a wild mandrill (Mandrillussphinx) group. American Journal of Primatology 77: 1036–1048.]. In our article, we proposed, inter alia, that “the daily travels of mandrills could be seen as a way to escape contaminated habitats on a local scale”. In their article, Bicca-Marques and Calegaro-Marques proposed an alternative mechanism that they considered to be more parsimonious. In their view, increased DPL also increases exposure to novel parasites from the environment. In other words, while we proposed that elevated DPL may be a consequence of elevated parasite richness, they viewed it as a cause. We are happy to see that our study attracted so much interest that it evoked a public comment. We are also grateful to Bicca-Marques and Calegaro-Marques for pointing out an obvious alternative scenario that we failed to discuss and for laying out several key factors and assumptions that should be addressed by future studies examining the links between parasite risk and group ranging. We use this opportunity to advance this discourse by responding to some of the criticisms raised in their discussion of our article. In this reply, we briefly contextualize the main object of criticism. We then discuss the putative parsimony of the two competing scenarios.
{"title":"A reply to “Ranging Behavior Drives Parasite Richness: A More Parsimonious Hypothesis”","authors":"M. Charpentier, P. Kappeler","doi":"10.3897/RETHINKINGECOLOGY.3.29573","DOIUrl":"https://doi.org/10.3897/RETHINKINGECOLOGY.3.29573","url":null,"abstract":"This preprint has been reviewed and recommended by Peer Community In Ecology (https://dx.doi.org/10.24072/pci.ecology.100001).\u0000 In a recent article, Bicca-Marques and Calegaro-Marques [Bicca-Marques JC, Calegaro-Marques C (2016) Ranging behavior drives parasite richness: A more parsimonious hypothesis. American Journal of Primatology 78: 923–927.] discussed the putative assumptions related to an interpretation we provided regarding an observed positive relationship between weekly averaged parasite richness of a group of mandrills (Mandrillussphinx) and their daily path lengths (DPL), published earlier in the same journal [Brockmeyer T, Kappeler PM, Willaume E, Benoit L, Mboumba S, Charpentier MJE (2015) Social organization and space use of a wild mandrill (Mandrillussphinx) group. American Journal of Primatology 77: 1036–1048.]. In our article, we proposed, inter alia, that “the daily travels of mandrills could be seen as a way to escape contaminated habitats on a local scale”. In their article, Bicca-Marques and Calegaro-Marques proposed an alternative mechanism that they considered to be more parsimonious. In their view, increased DPL also increases exposure to novel parasites from the environment. In other words, while we proposed that elevated DPL may be a consequence of elevated parasite richness, they viewed it as a cause. We are happy to see that our study attracted so much interest that it evoked a public comment. We are also grateful to Bicca-Marques and Calegaro-Marques for pointing out an obvious alternative scenario that we failed to discuss and for laying out several key factors and assumptions that should be addressed by future studies examining the links between parasite risk and group ranging. We use this opportunity to advance this discourse by responding to some of the criticisms raised in their discussion of our article. In this reply, we briefly contextualize the main object of criticism. We then discuss the putative parsimony of the two competing scenarios.","PeriodicalId":36503,"journal":{"name":"Rethinking Ecology","volume":"1 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2018-05-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"42197362","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 : 2018-03-10DOI: 10.3897/RETHINKINGECOLOGY.3.29338
Nathalie Winiger, P. Korner, R. Arlettaz, A. Jacot
Woodland ecosystems of Europe have undergone major transitions in the last centuries. Changes in land use and the loss of natural forest dynamics have often led to structurally poor, uniform and dense stands. Not surprisingly, open forest species relying on a heterogeneous stand structure have suffered dramatic population declines. The European Nightjar Caprimulguseuropaeus, a nocturnal insectivorous bird, has undergone such a decline in its main Swiss stronghold in Valais. Despite the species’ potential to colonize new sites and habitat restoration measures implemented since 2001, recolonisation of restored sites has not taken place, suggesting problems with the current habitat restoration strategy. In order to refine management recommendations, we compared habitat structure and moth abundance, a key Nightjar food source, at sites that are still occupied and at sites that had been abandoned but have recently been restored. Vegetation structure was more heterogeneous and moth abundance greater at occupied than at abandoned sites. More specifically, occupied sites harboured a greater coverage of bare ground, while abandoned sites exhibited a higher amount of regeneration and intermediate shrub layer. The occurrence of natural perches was also higher in occupied sites. Abandoned sites are thus characterised by lower prey abundance and denser vegetation cover, the combination of which is likely to lead to lower prey availability for hunting Nightjars. Restoration action would benefit from maintaining snags and dead branches and by targeting unproductive habitats characterised by mineral soils, thereby slowing down regeneration and shrub regrowth. For future successful management of Nightjar habitats, it seems thereby essential trying to find the balance between actions that allow opening the lower and mid-strata of the forest while sustaining high moth populations.
{"title":"Vegetation structure and decreased moth abundance limit the recolonisation of restored habitat by the European Nightjar","authors":"Nathalie Winiger, P. Korner, R. Arlettaz, A. Jacot","doi":"10.3897/RETHINKINGECOLOGY.3.29338","DOIUrl":"https://doi.org/10.3897/RETHINKINGECOLOGY.3.29338","url":null,"abstract":"Woodland ecosystems of Europe have undergone major transitions in the last centuries. Changes in land use and the loss of natural forest dynamics have often led to structurally poor, uniform and dense stands. Not surprisingly, open forest species relying on a heterogeneous stand structure have suffered dramatic population declines. The European Nightjar Caprimulguseuropaeus, a nocturnal insectivorous bird, has undergone such a decline in its main Swiss stronghold in Valais. Despite the species’ potential to colonize new sites and habitat restoration measures implemented since 2001, recolonisation of restored sites has not taken place, suggesting problems with the current habitat restoration strategy. In order to refine management recommendations, we compared habitat structure and moth abundance, a key Nightjar food source, at sites that are still occupied and at sites that had been abandoned but have recently been restored. Vegetation structure was more heterogeneous and moth abundance greater at occupied than at abandoned sites. More specifically, occupied sites harboured a greater coverage of bare ground, while abandoned sites exhibited a higher amount of regeneration and intermediate shrub layer. The occurrence of natural perches was also higher in occupied sites. Abandoned sites are thus characterised by lower prey abundance and denser vegetation cover, the combination of which is likely to lead to lower prey availability for hunting Nightjars. Restoration action would benefit from maintaining snags and dead branches and by targeting unproductive habitats characterised by mineral soils, thereby slowing down regeneration and shrub regrowth. For future successful management of Nightjar habitats, it seems thereby essential trying to find the balance between actions that allow opening the lower and mid-strata of the forest while sustaining high moth populations.","PeriodicalId":36503,"journal":{"name":"Rethinking Ecology","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2018-03-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"43291459","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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