Ecological interactions of the cadmium- and zinc-hyperaccumulating plant, Thlaspi caerulescens, and their implications for phytoremediation

The success of invasive species can be attributed to a combination of abiotic factors, such as abundant resources and favorable climate, and biotic factors, such as low levels of competition and predation or herbivory, at the introduced location. While studies have demonstrated the effects of these factors on known invasive species, the degree to which these factors affect a non-native species can be used to predict its likelihood of becoming invasive. The metal-hyperaccumulating plant Thlaspi caerulescens (Brassicaceae) is potentially useful for remediating soils that are moderately contaminated with Cd and Zn, and has been experimentally introduced to contaminated sites outside of its native range for phytoremediation. To assess the ecological risks involved in introducing metal-hyperaccumulating plants for phytoremediation, including their potential invasiveness, I have performed three studies to examine the abiotic and biotic factors that could influence the establishment of T. caerulescens at three contaminated sites near the Rocky Mountain Biological Laboratory in Gothic, Colorado. In the first two studies, I test the effects of soil metal concentrations and interspecific competition on plant performance, and in the third study I examine the strength of herbivore pressure on this plant. Results from these studies show that the growth rate of T. caerulescens in field conditions is generally low, but higher where there are high concentrations of soil Zn and low concentrations of soil Cu. Interspecific competition between T. caerulescens and a native congener is weak overall, and herbivory pressure from a native Lepidopteran herbivore is also low. Therefore, abiotic conditions are more limiting to T. caerulescens than biotic interactions, and would likely prevent T. caerulescens from becoming invasive or spreading outside of contaminated soils at these sites. In the fourth chapter, I use a long-term dataset to describe the demography of Frasera speciosa (Gentianaceae), a long-lived monocarpic plant. Results show that the population is stable, and despite the low elasticity values for the reproductive stages, masting events must be observed to describe accurately the population dynamics of this species

A standard protocol to report discrete stage-structured demographic information

Stage-based demographic methods, such as matrix population models (MPMs), are powerful tools used to address a broad range of fundamental questions in ecology, evolutionary biology and conservation science. Accordingly, MPMs now exist for over 3000 species worldwide. These data are being digitised as an ongoing process and periodically released into two large open-access online repositories: the COMPADRE Plant Matrix Database and the COMADRE Animal Matrix Database. During the last decade, data archiving and curation of COMPADRE and COMADRE, and subsequent comparative research, have revealed pronounced variation in how MPMs are parameterized and reported. Here, we summarise current issues related to the parameterisation and reporting of MPMs that arise most frequently and outline how they affect MPM construction, analysis, and interpretation. To quantify variation in how MPMs are reported, we present results from a survey identifying key aspects of MPMs that are frequently unreported in manuscripts. We then screen COMPADRE and COMADRE to quantify how often key pieces of information are omitted from manuscripts using MPMs. Over 80% of surveyed researchers (n = 60) state a clear benefit to adopting more standardised methodologies for reporting MPMs. Furthermore, over 85% of the 300 MPMs assessed from COMPADRE and COMADRE omitted one or more elements that are key to their accurate interpretation. Based on these insights, we identify fundamental issues that can arise from MPM construction and communication and provide suggestions to improve clarity, reproducibility and future research utilising MPMs and their required metadata. To fortify reproducibility and empower researchers to take full advantage of their demographic data, we introduce a standardised protocol to present MPMs in publications. This standard is linked to www.compa dre-db.org, so that authors wishing to archive their MPMs can do so prior to submission of publications, following examples from other open-access repositories such as DRYAD, Figshare and Zenodo. Combining and standardising MPMs parameterized from populations around the globe and across the tree of life opens up powerful research opportunities in evolutionary biology, ecology and conservation research. However, this potential can only be fully realised by adopting standardised methods to ensure reproducibility

A standard protocol to report discrete stage-structured demographic information

Stage-based demographic methods, such as matrix population models (MPMs), are powerful tools used to address a broad range of fundamental questions in ecology, evolutionary biology and conservation science. Accordingly, MPMs now exist for over 3000 species worldwide. These data are being digitised as an ongoing process and periodically released into two large open-access online repositories: the COMPADRE Plant Matrix Database and the COMADRE Animal Matrix Database. During the last decade, data archiving and curation of COMPADRE and COMADRE, and subsequent comparative research, have revealed pronounced variation in how MPMs are parameterized and reported. Here, we summarise current issues related to the parameterisation and reporting of MPMs that arise most frequently and outline how they affect MPM construction, analysis, and interpretation. To quantify variation in how MPMs are reported, we present results from a survey identifying key aspects of MPMs that are frequently unreported in manuscripts. We then screen COMPADRE and COMADRE to quantify how often key pieces of information are omitted from manuscripts using MPMs. Over 80% of surveyed researchers (n = 60) state a clear benefit to adopting more standardised methodologies for reporting MPMs. Furthermore, over 85% of the 300 MPMs assessed from COMPADRE and COMADRE omitted one or more elements that are key to their accurate interpretation. Based on these insights, we identify fundamental issues that can arise from MPM construction and communication and provide suggestions to improve clarity, reproducibility and future research utilising MPMs and their required metadata. To fortify reproducibility and empower researchers to take full advantage of their demographic data, we introduce a standardised protocol to present MPMs in publications. This standard is linked to www.compadre-db.org, so that authors wishing to archive their MPMs can do so prior to submission of publications, following examples from other open-access repositories such as DRYAD, Figshare and Zenodo. Combining and standardising MPMs parameterized from populations around the globe and across the tree of life opens up powerful research opportunities in evolutionary biology, ecology and conservation research. However, this potential can only be fully realised by adopting standardised methods to ensure reproducibility

Testing surrogacy assumptions: can threatened and endangered plants be grouped by biological similarity and abundances?

There is renewed interest in implementing surrogate species approaches in conservation planning due to the large number of species in need of management but limited resources and data. One type of surrogate approach involves selection of one or a few species to represent a larger group of species requiring similar management actions, so that protection and persistence of the selected species would result in conservation of the group of species. However, among the criticisms of surrogate approaches is the need to test underlying assumptions, which remain rarely examined. In this study, we tested one of the fundamental assumptions underlying use of surrogate species in recovery planning: that there exist groups of threatened and endangered species that are sufficiently similar to warrant similar management or recovery criteria. Using a comprehensive database of all plant species listed under the U.S. Endangered Species Act and tree-based random forest analysis, we found no evidence of species groups based on a set of distributional and biological traits or by abundances and patterns of decline. Our results suggested that application of surrogate approaches for endangered species recovery would be unjustified. Thus, conservation planning focused on individual species and their patterns of decline will likely be required to recover listed species

Summary of results from unsupervised random forest analyses examining whether threatened and endangered plant species can be grouped by distributional and biological traits, previous abundances, or a combination of traits and abundances.

<p>Check mark indicates the variable was included in an analysis, and asterisk indicates the variable was identified as an important grouping variable.</p

Summary of abundance variables included in our analyses.

<p>Summary of abundance variables included in our analyses.</p

Traits variable importance values.

<p>Variable importance for the distributional and biological traits from the random forest analysis examining whether listed plant species can be grouped by traits only (n = 213). Variable importance is measured as the mean decrease in model classification accuracy when values for that variable are randomly permuted. Abbreviations: duration = life history duration, max.ht. = maximum plant height, max.flower = maximum flower size, range, reprod.mode = reproductive mode, reprod.repetition = reproductive repetition, physiogdiv = physiographic division.</p

Abundance variable importance values.

<p>Variable importance for the previous abundance variables from the random forest analysis examining whether listed plant species can be grouped by previous abundances only, including both population-based and individual-based abundances (n = 197). Variable importance is measured as the mean decrease in model classification accuracy when values for that variable are randomly permuted. Abbreviations: Pop.Historical = Number of historical populations, Pop.Listing = Number of populations at time of ESA listing, Pop.Writing = Number of populations at time of recovery plan writing, Pop.Listing/Hist. = Proportion of historical populations remaining at time of listing, Pop.Writing/Hist. = Proportion of historical populations remaining at time of plan writing, Ind.Listing = Number of individuals at time of listing, Ind.Writing = Number of individuals at time of plan writing, Ind.Writing/List. = Number of individuals at time of plan writing remaining at time of listing.</p

The myriad of complex demographic responses of terrestrial mammals to climate change and gaps of knowledge: A global analysis

Approximately 25% of mammals are currently threatened with extinction, a risk that is amplified under climate change. Species persistence under climate change is determined by the combined effects of climatic factors on multiple demographic rates (survival, development and reproduction), and hence, population dynamics. Thus, to quantify which species and regions on Earth are most vulnerable to climate-driven extinction, a global understanding of how different demographic rates respond to climate is urgently needed. Here, we perform a systematic review of literature on demographic responses to climate, focusing on terrestrial mammals, for which extensive demographic data are available.\ud To assess the full spectrum of responses, we synthesize information from studies that quantitatively link climate to multiple demographic rates. We find only 106 such studies, corresponding to 87 mammal species. These 87 species constitute <1% of all terrestrial mammals. Our synthesis reveals a strong mismatch between the locations of demographic studies and the regions and taxa currently recognized as most vulnerable to climate change. Surprisingly, for most mammals and regions sensitive to climate change, holistic demographic responses to climate remain unknown. At the same time, we reveal that filling this knowledge gap is critical as the effects of climate change will operate via complex demographic mechanisms: a vast majority of mammal populations display projected increases in some demographic rates but declines in others, often depending on the specific environmental context, complicating simple projections of population fates. Assessments of population viability under climate change are in critical need to gather data that account for multiple demographic responses, and coordinated actions to assess demography holistically should be prioritized for mammals and other taxa