A critical comparison of integral projection and matrix projection models for demographic analysis

Structured demographic models are among the most common and useful tools in population biology. However, the introduction of integral projection models (IPMs) has caused a profound shift in the way many demographic models are conceptualized. Some researchers have argued that IPMs, by explicitly representing demographic processes as continuous functions of state variables such as size, are more statistically efficient, biologically realistic, and accurate than classic matrix projection models, calling into question the usefulness of the many studies based on matrix models. Here, we evaluate how IPMs and matrix models differ, as well as the extent to which these differences matter for estimation of key model outputs, including population growth rates, sensitivity patterns, and life spans. First, we detail the steps in constructing and using each type of model. Second, we present a review of published demographic models, concentrating on size-based studies, which shows significant overlap in the way IPMs and matrix models are constructed and analyzed. Third, to assess the impact of various modeling decisions on demographic predictions, we ran a series of simulations based on size-based demographic data sets for five biologically diverse species. We found little evidence that discrete vital rate estimation is less accurate than continuous functions across a wide range of sample sizes or size classes (equivalently bin numbers or mesh points). Most model outputs quickly converged with modest class numbers (≥10), regardless of most other modeling decisions. Another surprising result was that the most commonly used method to discretize growth rates for IPM analyses can introduce substantial error into model outputs. Finally, we show that empirical sample sizes generally matter more than modeling approach for the accuracy of demographic outputs. Based on these results, we provide specific recommendations to those constructing and evaluating structured population models. Both our literature review and simulations question the treatment of IPMs as a clearly distinct modeling approach or one that is inherently more accurate than classic matrix models. Importantly, this suggests that matrix models, representing the vast majority of past demographic analyses available for comparative and conservation work, continue to be useful and important sources of demographic information.Support for this work was provided by NSF awards 1146489, 1242558, 1242355, 1353781, 1340024, 1753980, and 1753954, 1144807, 0841423, and 1144083. Support also came from USDA NIFA Postdoctoral Fellowship (award no. 2019-67012-29726/project accession no. 1019364) for R. K. Shriver; the Swiss Polar Institute of Food and Agriculture for N. I. Chardon; the ICREA under the ICREA Academia Programme for C. Linares; and SERDP contract RC-2512 and USDA National Institute of Food and Agriculture, Hatch project 1016746 for A .M. Louthan. This is Contribution no. 21-177-J from the Kansas Agricultural Experiment Station

A critical comparison of integral projection and matrix projection models for demographic analysis: Reply

We thank Ellner et al. (2022; henceforth E22) for taking an interest in our recent paper on demographic modeling methods (Doak et al., 2021, henceforth referred to as D21). While the tone of E22's comment might imply otherwise, most of their comment emphasizes points with which we agree and made ourselves in D21, and, as we repeatedly acknowledged in D21, are similar to past advice and critiques of demographic modeling by these authors and by others. There are, however, some areas of disagreement or differences in emphasis, and we welcome this opportunity to engage in a constructive dialogue on these points. Overall, however, E22 and D21 offer differing advice on fairly few substantial points about how to build demographic models. This is good news for ecologists and conservation managers who wish to use these tools to model population processes, estimate the vulnerability of target species, and provide effective management guidelines. Below, we outline our thoughts on E22's main points.Peer reviewe

Natural Resources Condition Assessment, Agate Fossil Beds National Monument (February 2020 Revision)

Executive Summary In collaboration with the National Park Service, the University of Wyoming Ruckelshaus Institute of Environment and Natural Resources and the Wyoming Natural Diversity Database completed the Natural Resource Condition Assessment (NRCA) for Agate Fossil Beds National Monument (NM). The purpose of the NRCA is to provide park leaders and resource managers with information on resource conditions to support near-term planning and management, long-term strategic planning, and effective science communication to decision-makers and the public. Agate Fossil Beds NM was authorized in 1965 and established in 1997. The purposes of the park include protecting the paleontological resources on the site and providing a center for paleontological research and fossil display; protecting, curating, and exhibiting the James H. Cook Red Cloud Native American collection; protecting and revealing the intersection between culture, landscape, and science; and preserving the short-grass prairie and Niobrara riparian ecosystems. The assessment for Agate Fossil Beds NM began in 2015 with a facilitated discussion among park leadership and natural resource managers to identify high-priority natural resources and existing data with which to assess condition of those resources. Data were synthesized to evaluate each resource according to condition, trend in the condition, and confidence in the assessment. Natural resource conditions were the basis for a discussion with park leadership and natural resource managers, who then identified critical data gaps and management issues specific to Agate Fossil Beds NM. Resource experts, park staff, and network personnel reviewed this assessment. Priority natural resources were grouped into three categories: Landscape Condition Context, Supporting Environment, and Biological Integrity. The resources categorized as Landscape Condition Context included viewshed, night sky, and soundscape. At the time of this assessment, these resources were all in good condition. Supporting Environment—or physical environment—resources included air quality, surface water quality, geology, and paleontological resources. Air quality, surface water quality, and geology were of moderate concern; the condition of paleontological resources was not available due to a lack of data on poaching and vandalism of fossils. The natural resources that composed the Biological Integrity category included vegetation, birds, fish, and pollinators. Vegetation and pollinators resources were of moderate concern, fish condition had deteriorated substantially since the late 1980s and warranted significant concern. We were unable to assign a condition to birds in the absence of specific management goals. This assessment includes a general background on the NRCA process (Chapter 1), an introduction to Agate Fossil Beds NM and the natural resources included in the assessment (Chapter 2), a description of methods (Chapter 3), condition assessments for 11 natural resources (Chapter 4), and a summary of findings accompanied by management considerations (Chapter 5). Note: This report was first published in 2019, however, an error was noted in the report resulting in this revised version. The scope/nature of the revision includes: The sentence “In 2012, a request for assistance with northern pike removal and reintroduction of native fish was denied (Medley 2012)”—included on page 188 of the original report (section 4.10.1 Background and Importance)—has been removed

YermoDemoData

YermoDemoDat

NOAA_weather_1907_2015 Riverton WY

NOAA_weather_1907_2015 Riverton W

Dibner_etal_metadata

Dibner_etal_metadat

Data from: Multiple mechanisms confer stability to isolated populations of a rare endemic plant

The persistence of small populations remains a puzzle for ecology and conservation. Especially interesting is how naturally small, isolated populations are able to persist in the face of multiple environmental forces that create fluctuating conditions and should, theory predicts, lead to high probabilities of extirpation. We used a combination of long term census data and a five-year demographic study of a naturally rare, endemic plant, Yermo xanthocephalus, to evaluate the importance of several possible mechanisms for small population persistence: negative density dependence, vital rate buffering, demographic compensation, asynchrony in dynamics among sub-populations, and source-sink dynamics. These non-exclusive explanations for population persistence all have been shown to operate in some systems, but have rarely if ever been simultaneously examined for the same population or species. We hypothesized that asynchrony in dynamics and demographic compensation would be more powerful than the other three mechanisms. We found partial support for our hypothesis: density dependence, asynchrony among population segments, and source-sink patterns appear to be the most important mechanisms maintaining population viability in this species. Importantly, these processes all appear to operate strongly at very fine spatial scales for Yermo, allowing the only two, extremely small, populations to persist. We also found considerable differences in the results of our census and demographic analyses. In general, we estimated substantially greater chances of survival from the census data than from the shorter-term demographic studies. In part, this difference is due to drier than average climate conditions during the years of the demographic work. These results emphasize that while demographic information is necessary to understand various components of population dynamics, longer term studies, even if much less detailed, can be more powerful in uncovering some mechanisms that may be critical in stabilizing population numbers, especially in variable environments

Natural Resource Condition Assessment, Scotts Bluff National Monument

Executive Summary In collaboration with the National Park Service, the University of Wyoming Ruckelshaus Institute of Environment and Natural Resources and the Wyoming Natural Diversity Database completed the Natural Resource Condition Assessment (NRCA) for Scotts Bluff National Monument (NM). The purpose of the NRCA is to provide park leaders and resource managers with information on resource conditions to support near-term planning and management, long-term strategic planning, and effective science communication to decision-makers and the public. Scotts Bluff NM was established in 1919. The purposes of the park include protecting and preserving the Mitchell Pass portion of the Oregon Trail and the geologic features of the bluffs. The assessment for Scotts Bluff NM began in 2015 with a facilitated discussion among park leadership and natural resource managers to identify high-priority natural resources and existing data with which to assess condition of those resources. Data were synthesized to evaluate each resource according to condition, trend in the condition, and confidence in the assessment. Natural resource conditions were the basis for a discussion with park leadership and natural resource managers, who then identified critical data gaps and management issues specific to Scotts Bluff NM. Resource experts, park staff, and network personnel reviewed this assessment. Priority natural resources were grouped into three categories: Landscape Condition Context, Supporting Environment, and Biological Integrity. The resources categorized as Landscape Condition Context included viewshed, night sky, and soundscape. At the time of this assessment, viewshed condition was of moderate concern and condition of night sky and soundscape warranted significant concern. Supporting Environment—or physical environment—resources included air quality, surface water quality, geology, and paleontological resources. Air quality warranted moderate concern, and condition of surface water quality, geology, and paleontological resources warranted significant concern. The natural resources that composed the Biological Integrity category included vegetation, birds, prairie dogs, and pollinators. Vegetation, prairie dogs, and pollinators were of moderate concern; we were unable to assign a condition to birds in the absence of specific management goals. This assessment includes a general background on the NRCA process (Chapter 1), an introduction to Scotts Bluff NM and the natural resources included in the assessment (Chapter 2), a description of methods (Chapter 3), condition assessments for 11 natural resources (Chapter 4), and a summary of findings accompanied by management considerations (Chapter 5)

Data from: Multiple mechanisms confer stability to isolated populations of a rare endemic plant

The persistence of small populations remains a puzzle for ecology and conservation. Especially interesting is how naturally small, isolated populations are able to persist in the face of multiple environmental forces that create fluctuating conditions and should, theory predicts, lead to high probabilities of extirpation. We used a combination of long term census data and a five-year demographic study of a naturally rare, endemic plant, Yermo xanthocephalus, to evaluate the importance of several possible mechanisms for small population persistence: negative density dependence, vital rate buffering, demographic compensation, asynchrony in dynamics among sub-populations, and source-sink dynamics. These non-exclusive explanations for population persistence all have been shown to operate in some systems, but have rarely if ever been simultaneously examined for the same population or species. We hypothesized that asynchrony in dynamics and demographic compensation would be more powerful than the other three mechanisms. We found partial support for our hypothesis: density dependence, asynchrony among population segments, and source-sink patterns appear to be the most important mechanisms maintaining population viability in this species. Importantly, these processes all appear to operate strongly at very fine spatial scales for Yermo, allowing the only two, extremely small, populations to persist. We also found considerable differences in the results of our census and demographic analyses. In general, we estimated substantially greater chances of survival from the census data than from the shorter-term demographic studies. In part, this difference is due to drier than average climate conditions during the years of the demographic work. These results emphasize that while demographic information is necessary to understand various components of population dynamics, longer term studies, even if much less detailed, can be more powerful in uncovering some mechanisms that may be critical in stabilizing population numbers, especially in variable environments

Time outweighs the effect of host developmental stage on microbial community composition

Thousands of microbial taxa in the soil form symbioses with host plants, and due to their contribution to plant performance, these microbes are often considered an extension of the host genome. Given microbial effects on host performance, it is important to understand factors that govern microbial community assembly. Host developmental stage could affect rhizosphere microbial diversity while, alternatively, microbial assemblages could change simply as a consequence of time and the opportunity for microbial succession. Previous studies suggest that rhizosphere microbial assemblages shift across plant developmental stages, but time since germination is confounded with developmental stage. We asked how elapsed time and potential microbial succession relative to host development affected microbial diversity in the rhizosphere using monogenic flowering-time mutants of Arabidopsis thaliana. Under our experimental design, different developmental stages were present among host genotypes after the same amount of time following germination, e.g. at 76 days following germination some host genotypes were flowering while others were fruiting or senescing. We found that elapsed time was a strong predictor of microbial diversity whereas there were few differences among developmental stages. Our results support the idea that time and, likely, microbial succession more strongly affect microbial community assembly than host developmental stage