Regarding Jennifer's criticism of the \independence" ass... more Regarding Jennifer's criticism of the \independence" assumption in expression (2) of the paper, we agree that this is surely not true though it may be roughly true. However, the \correlation" calculation in (2) is a bit more complicated than it initially appears in that the calculation is with respect to a uniform distribution over say, the locations in unit i.
Supplementary Data and R Markdown workflows for Slingsby et al. "Intensifying post-fire weat... more Supplementary Data and R Markdown workflows for Slingsby et al. "Intensifying post-fire weather and biological invasion drive species loss in a Mediterranean-type biodiversity hotspot"<br>All data and repeatable R code workflows (R Markdown) used in the study are available here or as SI Datasets. Code and data are provided under the MIT license, but where possible we would appreciate users acknowledging "the South African Environmental Observation Network (SAEON) and partners" and citing this paper and/or the original data source outlined in the paper. We would also see it as a courtesy to inform the lead author of your intended use of the data. Co-authorship is not a prerequisite, but we would like to minimize duplication of effort and/or warn users where their plans for the data do not seem appropriate.
Forecasting ecological responses to climate change, invasion, and their interaction must rely on ... more Forecasting ecological responses to climate change, invasion, and their interaction must rely on understanding underlying mechanisms. However, such forecasts require extrapolation into new locations and environments. We linked demography and environment using experimental biogeography to forecast invasive and native species’ potential ranges under present and future climate in New England, United States to overcome issues of extrapolation in novel environments. We studied two potentially nonequilibrium invasive plants’ distributions, Alliaria petiolata (garlic mustard) and Berberis thunbergii (Japanese barberry), each paired with their native ecological analogs to better understand demographic drivers of invasions. Our models predict that climate change will considerably reduce establishment of a currently prolific invader (A. petiolata) throughout New England driven by poor demographic performance in warmer climates. In contrast, invasion of B. thunbergii will be facilitated becaus...
Proceedings of the National Academy of Sciences of the United States of America, May 17, 2017
Prolonged periods of extreme heat or drought in the first year after fire affect the resilience a... more Prolonged periods of extreme heat or drought in the first year after fire affect the resilience and diversity of fire-dependent ecosystems by inhibiting seed germination or increasing mortality of seedlings and resprouting individuals. This interaction between weather and fire is of growing concern as climate changes, particularly in systems subject to stand-replacing crown fires, such as most Mediterranean-type ecosystems. We examined the longest running set of permanent vegetation plots in the Fynbos of South Africa (44 y), finding a significant decline in the diversity of plots driven by increasingly severe postfire summer weather events (number of consecutive days with high temperatures and no rain) and legacy effects of historical woody alien plant densities 30 y after clearing. Species that resprout after fire and/or have graminoid or herb growth forms were particularly affected by postfire weather, whereas all species were sensitive to invasive plants. Observed differences in...
ABSTRACT Background/Question/Methods Maxent is one of the most popular species distribution model... more ABSTRACT Background/Question/Methods Maxent is one of the most popular species distribution modeling methods, with over 400 published applications in the just the last six years. Maxent users are confronted with a wide variety of options when fitting their models, from the multiple options and settings available in the software to which input datasets to choose. However, the default settings are often chosen as a consequence of unfamiliarity with maximum entropy models, even though alternatives may often be more appropriate when connected to specific ecological questions. To explore Maxent’s assumptions, we demonstrate the variability in model output that can result from altering model settings and offer suggestions for choosing these settings. Results/Conclusions Maxent models are capable of predicting the relative probability of occurrence, but not the absolute probability of occurrence. Considering this, and the quality of opportunistically collected occurrence data and coarse resolution, remotely sensed environmental data, predictions must be interpreted cautiously when creating range maps and using them to answer complex ecological or evolutionary questions. In many cases, Maxent is best suited for hypothesis generation and asking better questions, not answering them. To date, variable selection methods explored for Maxent derive almost exclusively from machine learning perspectives, which focus more on complex pattern recognition than on producing easily interpreted models. We outline a more general approach, based on constructing simpler models motivated by specific ecological questions. In Maxent, different prior assumptions (null models) are reflected by methods of background sample selection and accounting for sampling bias. We relate these subtle cases of prior specification to the more general case, where ‘ecological’ priors can be used to incorporate different ecological assumptions or output from other models. Ecological priors are used to improve predictions of models for invasive ranges using native range data and models accounting for dispersal limitation. When ecological priors are applied to understand the spread Celastrus orbiculatus, an invasive liana, across New England (USA) over the last century, we find that greater spread is predicted in northern New England than models using default settings.
. To take advantage of the high spectral resolution of Landsat TM images and the high spatial res... more . To take advantage of the high spectral resolution of Landsat TM images and the high spatial resolution of SPOT panchromatic images (SPOT PAN), we present a wavelet transform method to merge the two data types. In a pyramidal fashion, each TM reflective band or SPOT ...
Phenotypic plasticity may be an important contributor to the success of many invasive plant speci... more Phenotypic plasticity may be an important contributor to the success of many invasive plant species. Shifts in genotype induced by the recipient environment can also lead to a range of phenotypic expression not seen in the native range. Selection for these novel genotypes could lead to local adaptation in the introduced environment. To investigate plasticity and local adaptation in an invaded region, we established three reciprocal transplant gardens using clonal replicates from two common invasive species in New England, Berberis ...
ABSTRACT Background/Question/Methods As part of a multi-scale project to predict invasive plant s... more ABSTRACT Background/Question/Methods As part of a multi-scale project to predict invasive plant spread in response to climate and land-use change, we used experimental biogeography to evaluate a suite of environmental conditions, mitigated by demography, which may facilitate the establishment of three invasive alien species (IAS). Species distribution models have highlighted areas of northern New England, currently lacking IAS, as places where these species may potentially thrive. However, as these IAS move northward, they will encounter novel conditions affecting establishment and growth. How species’ population dynamics respond to these novel conditions will influence their further spread and potential impact across the region. We established regional transplant experiments to test species distribution model results and to estimate the colonization potential for representative IAS, Berberis thunbergii and Alliaria petiolata, compared to two native analogues, Lindera benzoin and Arabis glabra. We investigated the response of each species’ vital rates to the environmental gradients using linear regression models. We then built demographic Integral Projection Models (IPMs) for our study species from these regressions to assimilate demographic information and make population-level predictions. Results/Conclusions Results indicate that the invasive species tolerate a broad climate gradient across New England. The invasives were able to germinate, survive, grow and, in some cases, reproduce in northern New England outside of their current known distributions, validating the results of previous model predictions. Across the species pairs, the invasives had a much higher rate of germination in the field than their native analogs. Of those that germinated, the invasives had a greater rate of survival to seedling regardless of environment. At later demographic stages, the invasives overall also had greater rates of survival and growth. The resulting population growth rates varied by environment, in some cases drastically. These results highlight the necessity in taking microsite variation into account when calculating population dynamics. The observed responses for each vital rate enable us to make predictions about survival, reproduction, and population growth rate and assess how IAS may respond to a changing environment.
There is much spatial and temporal variation for reproductive output in white clover (Trifolium r... more There is much spatial and temporal variation for reproductive output in white clover (Trifolium repens L.), yet little is known about the control of this variation or whether there exist tradeoffs among components of seed yield. To examine these issues, seed yield components and vegetative biomass were measured on replicates of seven white clover genotypes planted in a common garden plot. Significant genetic differences among clones were found for biomass and for five of seven reproductive characters, including number of inflorescences, number of florets per inflorescence, number of fruits per infructescence, number of (late-maturing) seed per fruit, and seed weight in early-maturing fruits. Thus, there is considerable potential for natural or artificial selection to act on vegetative and reproductive characters in white clover. In addition to these genetic effects, we observed temporal variation for number of florets per inflorescence, number of fruits per infructescence, and seed weight in late-maturing fruits. Finally, analyses of phenotypic, genetic, and microenvironmental correlation coefficients revealed few pairs of traits with significant negative correlations. This suggests that few tradeoffs in resource allocation patterns existed for the phenotypic characters examined. Key words: Trifolium repens, genetic variation, seed yield components, tradeoffs, phenotypic correlation, genetic correlation.
Tuesday, August 4, 2009 - 8:00 AM Genetic variance of invasiveness in woody ornamental plants: Th... more Tuesday, August 4, 2009 - 8:00 AM Genetic variance of invasiveness in woody ornamental plants: The role of genotype differences versus phenotypic plasticity. Sarah A. Treanor 1 , Jenica M. Allen 1 , Matthew A. Kaproth 2 , Nancy ...
ABSTRACT Background/Question/Methods Phenology has proven to be an effective metric for assessing... more ABSTRACT Background/Question/Methods Phenology has proven to be an effective metric for assessing how climate change is impacting organisms around the world. In response to warmer temperatures and altered precipitation, plants and animals have adjusted their phenologies to various degrees. Here, we investigated how a suite of insect species from throughout Japan has responded to changes in climate both spatially and temporally. Forty years of data on emergence dates of 14 insect species from 102 observatories of the Japan Meteorological Agency (JMA) were used for this research along with basic natural history traits. The results of analysis of this insect dataset were then compared to datasets of plant and bird phenology to evaluate how the phenologies of organisms at different trophic levels are changing. If, for example, organisms at each trophic level are responding differently to changes in climate, then there is the potential for ecological mismatches. In such a scenario, the phenologies of associated organisms are no longer synchronous and the success of future populations may be put in danger. Extensive datasets exist on the phenology of plants, insects, and birds in Massachusetts and these were analyzed with additional data from the JMA to address this larger question. Results/Conclusions The emergence dates of insects in Japan are closely correlated with temperature, with individuals of most species emerging earlier in warmer years. Surprisingly however, insects are emerging later over time in a country that is growing progressively warmer. This apparent disparity may be due to extreme declines in populations due to factors outside of climate, such as land use change or urbanization. Insects in Massachusetts are also responding to temperature, with some showing a temporal response and others not. Looking across trophic levels, plant flowering and leaf-out have the strongest response to temperature as well as the greatest amount of variation explained by temperature. Bird migration phenology exhibits the weakest pattern of change with temperature, along with the weakest explanatory power. Insects fall in the middle and generally have a strong response to temperature, yet weak explanatory power. Although the animals in these studies are often generalist feeders, the fact that each trophic level is impacted differently by climate change is cause for concern. The finding that organisms at a given trophic level are responding similarly in different parts of the world gives additional weight to this study as altered relationships among species are not geographically confined.
Proceedings of the National Academy of Sciences of the United States of America, Jan 19, 2015
Changes in spring and autumn phenology of temperate plants in recent decades have become iconic b... more Changes in spring and autumn phenology of temperate plants in recent decades have become iconic bio-indicators of rapid climate change. These changes have substantial ecological and economic impacts. However, autumn phenology remains surprisingly little studied. Although the effects of unfavorable environmental conditions (e.g., frost, heat, wetness, and drought) on autumn phenology have been observed for over 60 y, how these factors interact to influence autumn phenological events remain poorly understood. Using remotely sensed phenology data from 2001 to 2012, this study identified and quantified significant effects of a suite of environmental factors on the timing of fall dormancy of deciduous forest communities in New England, United States. Cold, frost, and wet conditions, and high heat-stress tended to induce earlier dormancy of deciduous forests, whereas moderate heat- and drought-stress delayed dormancy. Deciduous forests in two eco-regions showed contrasting, nonlinear resp...
Regarding Jennifer&amp;amp;amp;#39;s criticism of the \independence&amp;amp;amp;quot; ass... more Regarding Jennifer&amp;amp;amp;#39;s criticism of the \independence&amp;amp;amp;quot; assumption in expression (2) of the paper, we agree that this is surely not true though it may be roughly true. However, the \correlation&amp;amp;amp;quot; calculation in (2) is a bit more complicated than it initially appears in that the calculation is with respect to a uniform distribution over say, the locations in unit i.
Supplementary Data and R Markdown workflows for Slingsby et al. "Intensifying post-fire weat... more Supplementary Data and R Markdown workflows for Slingsby et al. "Intensifying post-fire weather and biological invasion drive species loss in a Mediterranean-type biodiversity hotspot"<br>All data and repeatable R code workflows (R Markdown) used in the study are available here or as SI Datasets. Code and data are provided under the MIT license, but where possible we would appreciate users acknowledging "the South African Environmental Observation Network (SAEON) and partners" and citing this paper and/or the original data source outlined in the paper. We would also see it as a courtesy to inform the lead author of your intended use of the data. Co-authorship is not a prerequisite, but we would like to minimize duplication of effort and/or warn users where their plans for the data do not seem appropriate.
Forecasting ecological responses to climate change, invasion, and their interaction must rely on ... more Forecasting ecological responses to climate change, invasion, and their interaction must rely on understanding underlying mechanisms. However, such forecasts require extrapolation into new locations and environments. We linked demography and environment using experimental biogeography to forecast invasive and native species’ potential ranges under present and future climate in New England, United States to overcome issues of extrapolation in novel environments. We studied two potentially nonequilibrium invasive plants’ distributions, Alliaria petiolata (garlic mustard) and Berberis thunbergii (Japanese barberry), each paired with their native ecological analogs to better understand demographic drivers of invasions. Our models predict that climate change will considerably reduce establishment of a currently prolific invader (A. petiolata) throughout New England driven by poor demographic performance in warmer climates. In contrast, invasion of B. thunbergii will be facilitated becaus...
Proceedings of the National Academy of Sciences of the United States of America, May 17, 2017
Prolonged periods of extreme heat or drought in the first year after fire affect the resilience a... more Prolonged periods of extreme heat or drought in the first year after fire affect the resilience and diversity of fire-dependent ecosystems by inhibiting seed germination or increasing mortality of seedlings and resprouting individuals. This interaction between weather and fire is of growing concern as climate changes, particularly in systems subject to stand-replacing crown fires, such as most Mediterranean-type ecosystems. We examined the longest running set of permanent vegetation plots in the Fynbos of South Africa (44 y), finding a significant decline in the diversity of plots driven by increasingly severe postfire summer weather events (number of consecutive days with high temperatures and no rain) and legacy effects of historical woody alien plant densities 30 y after clearing. Species that resprout after fire and/or have graminoid or herb growth forms were particularly affected by postfire weather, whereas all species were sensitive to invasive plants. Observed differences in...
ABSTRACT Background/Question/Methods Maxent is one of the most popular species distribution model... more ABSTRACT Background/Question/Methods Maxent is one of the most popular species distribution modeling methods, with over 400 published applications in the just the last six years. Maxent users are confronted with a wide variety of options when fitting their models, from the multiple options and settings available in the software to which input datasets to choose. However, the default settings are often chosen as a consequence of unfamiliarity with maximum entropy models, even though alternatives may often be more appropriate when connected to specific ecological questions. To explore Maxent’s assumptions, we demonstrate the variability in model output that can result from altering model settings and offer suggestions for choosing these settings. Results/Conclusions Maxent models are capable of predicting the relative probability of occurrence, but not the absolute probability of occurrence. Considering this, and the quality of opportunistically collected occurrence data and coarse resolution, remotely sensed environmental data, predictions must be interpreted cautiously when creating range maps and using them to answer complex ecological or evolutionary questions. In many cases, Maxent is best suited for hypothesis generation and asking better questions, not answering them. To date, variable selection methods explored for Maxent derive almost exclusively from machine learning perspectives, which focus more on complex pattern recognition than on producing easily interpreted models. We outline a more general approach, based on constructing simpler models motivated by specific ecological questions. In Maxent, different prior assumptions (null models) are reflected by methods of background sample selection and accounting for sampling bias. We relate these subtle cases of prior specification to the more general case, where ‘ecological’ priors can be used to incorporate different ecological assumptions or output from other models. Ecological priors are used to improve predictions of models for invasive ranges using native range data and models accounting for dispersal limitation. When ecological priors are applied to understand the spread Celastrus orbiculatus, an invasive liana, across New England (USA) over the last century, we find that greater spread is predicted in northern New England than models using default settings.
. To take advantage of the high spectral resolution of Landsat TM images and the high spatial res... more . To take advantage of the high spectral resolution of Landsat TM images and the high spatial resolution of SPOT panchromatic images (SPOT PAN), we present a wavelet transform method to merge the two data types. In a pyramidal fashion, each TM reflective band or SPOT ...
Phenotypic plasticity may be an important contributor to the success of many invasive plant speci... more Phenotypic plasticity may be an important contributor to the success of many invasive plant species. Shifts in genotype induced by the recipient environment can also lead to a range of phenotypic expression not seen in the native range. Selection for these novel genotypes could lead to local adaptation in the introduced environment. To investigate plasticity and local adaptation in an invaded region, we established three reciprocal transplant gardens using clonal replicates from two common invasive species in New England, Berberis ...
ABSTRACT Background/Question/Methods As part of a multi-scale project to predict invasive plant s... more ABSTRACT Background/Question/Methods As part of a multi-scale project to predict invasive plant spread in response to climate and land-use change, we used experimental biogeography to evaluate a suite of environmental conditions, mitigated by demography, which may facilitate the establishment of three invasive alien species (IAS). Species distribution models have highlighted areas of northern New England, currently lacking IAS, as places where these species may potentially thrive. However, as these IAS move northward, they will encounter novel conditions affecting establishment and growth. How species’ population dynamics respond to these novel conditions will influence their further spread and potential impact across the region. We established regional transplant experiments to test species distribution model results and to estimate the colonization potential for representative IAS, Berberis thunbergii and Alliaria petiolata, compared to two native analogues, Lindera benzoin and Arabis glabra. We investigated the response of each species’ vital rates to the environmental gradients using linear regression models. We then built demographic Integral Projection Models (IPMs) for our study species from these regressions to assimilate demographic information and make population-level predictions. Results/Conclusions Results indicate that the invasive species tolerate a broad climate gradient across New England. The invasives were able to germinate, survive, grow and, in some cases, reproduce in northern New England outside of their current known distributions, validating the results of previous model predictions. Across the species pairs, the invasives had a much higher rate of germination in the field than their native analogs. Of those that germinated, the invasives had a greater rate of survival to seedling regardless of environment. At later demographic stages, the invasives overall also had greater rates of survival and growth. The resulting population growth rates varied by environment, in some cases drastically. These results highlight the necessity in taking microsite variation into account when calculating population dynamics. The observed responses for each vital rate enable us to make predictions about survival, reproduction, and population growth rate and assess how IAS may respond to a changing environment.
There is much spatial and temporal variation for reproductive output in white clover (Trifolium r... more There is much spatial and temporal variation for reproductive output in white clover (Trifolium repens L.), yet little is known about the control of this variation or whether there exist tradeoffs among components of seed yield. To examine these issues, seed yield components and vegetative biomass were measured on replicates of seven white clover genotypes planted in a common garden plot. Significant genetic differences among clones were found for biomass and for five of seven reproductive characters, including number of inflorescences, number of florets per inflorescence, number of fruits per infructescence, number of (late-maturing) seed per fruit, and seed weight in early-maturing fruits. Thus, there is considerable potential for natural or artificial selection to act on vegetative and reproductive characters in white clover. In addition to these genetic effects, we observed temporal variation for number of florets per inflorescence, number of fruits per infructescence, and seed weight in late-maturing fruits. Finally, analyses of phenotypic, genetic, and microenvironmental correlation coefficients revealed few pairs of traits with significant negative correlations. This suggests that few tradeoffs in resource allocation patterns existed for the phenotypic characters examined. Key words: Trifolium repens, genetic variation, seed yield components, tradeoffs, phenotypic correlation, genetic correlation.
Tuesday, August 4, 2009 - 8:00 AM Genetic variance of invasiveness in woody ornamental plants: Th... more Tuesday, August 4, 2009 - 8:00 AM Genetic variance of invasiveness in woody ornamental plants: The role of genotype differences versus phenotypic plasticity. Sarah A. Treanor 1 , Jenica M. Allen 1 , Matthew A. Kaproth 2 , Nancy ...
ABSTRACT Background/Question/Methods Phenology has proven to be an effective metric for assessing... more ABSTRACT Background/Question/Methods Phenology has proven to be an effective metric for assessing how climate change is impacting organisms around the world. In response to warmer temperatures and altered precipitation, plants and animals have adjusted their phenologies to various degrees. Here, we investigated how a suite of insect species from throughout Japan has responded to changes in climate both spatially and temporally. Forty years of data on emergence dates of 14 insect species from 102 observatories of the Japan Meteorological Agency (JMA) were used for this research along with basic natural history traits. The results of analysis of this insect dataset were then compared to datasets of plant and bird phenology to evaluate how the phenologies of organisms at different trophic levels are changing. If, for example, organisms at each trophic level are responding differently to changes in climate, then there is the potential for ecological mismatches. In such a scenario, the phenologies of associated organisms are no longer synchronous and the success of future populations may be put in danger. Extensive datasets exist on the phenology of plants, insects, and birds in Massachusetts and these were analyzed with additional data from the JMA to address this larger question. Results/Conclusions The emergence dates of insects in Japan are closely correlated with temperature, with individuals of most species emerging earlier in warmer years. Surprisingly however, insects are emerging later over time in a country that is growing progressively warmer. This apparent disparity may be due to extreme declines in populations due to factors outside of climate, such as land use change or urbanization. Insects in Massachusetts are also responding to temperature, with some showing a temporal response and others not. Looking across trophic levels, plant flowering and leaf-out have the strongest response to temperature as well as the greatest amount of variation explained by temperature. Bird migration phenology exhibits the weakest pattern of change with temperature, along with the weakest explanatory power. Insects fall in the middle and generally have a strong response to temperature, yet weak explanatory power. Although the animals in these studies are often generalist feeders, the fact that each trophic level is impacted differently by climate change is cause for concern. The finding that organisms at a given trophic level are responding similarly in different parts of the world gives additional weight to this study as altered relationships among species are not geographically confined.
Proceedings of the National Academy of Sciences of the United States of America, Jan 19, 2015
Changes in spring and autumn phenology of temperate plants in recent decades have become iconic b... more Changes in spring and autumn phenology of temperate plants in recent decades have become iconic bio-indicators of rapid climate change. These changes have substantial ecological and economic impacts. However, autumn phenology remains surprisingly little studied. Although the effects of unfavorable environmental conditions (e.g., frost, heat, wetness, and drought) on autumn phenology have been observed for over 60 y, how these factors interact to influence autumn phenological events remain poorly understood. Using remotely sensed phenology data from 2001 to 2012, this study identified and quantified significant effects of a suite of environmental factors on the timing of fall dormancy of deciduous forest communities in New England, United States. Cold, frost, and wet conditions, and high heat-stress tended to induce earlier dormancy of deciduous forests, whereas moderate heat- and drought-stress delayed dormancy. Deciduous forests in two eco-regions showed contrasting, nonlinear resp...
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