Donald M. Waller

University of Wisconsin–Madison | UW

In response to a petition filed in October, 2016, the U.S. FIsh and Wildlife Service recently decided not to list the Venus Flytrap as federally Threatened or Endangered. This essay responds to that decision by pointing out continuing threats to this species and its habitats.

Aim. Environmental conditions strongly affect the distribution and abundance of species via complex forces. Shifts in environmental conditions and differences in the speed and scale of these effects complicate our efforts to infer how species will respond to future environmental change. We test how 18 functional traits affect plant species response...

Inbreeding exposes deleterious recessive alleles in homozygotes, lowering fitness and generating inbreeding depression (ID). Both purging (via selection) and fixation (via drift) should reduce segregating deleterious mutations and ID in more inbred populations. These theoretical predictions are not well-tested in wild populations, which is concerni...

Classical models that ignore linkage predict that deleterious recessive mutations should purge or fix within inbred populations, yet inbred populations often retain moderate to high segregating load. True overdominance could generate balancing selection strong enough to sustain inbreeding depression even within inbred populations, but this is consi...

Ungulate populations are increasing across Europe with important implications for forest plant communities. Concurrently, atmospheric nitrogen (N) deposition continues to eutrophicate forests, threatening many rare, often more nutrient-efficient, plant species. These pressures may critically interact to shape biodiversity as in grassland and tundra...

Premise: Numerous processes influence plant distributions and co‐occurrence patterns, including ecological sorting, limiting similarity, and stochastic effects. To discriminate among these processes and determine the spatial scales at which they operate, we investigated how functional traits and phylogenetic relatedness influence the distribution o...

Premise Numerous processes influence plant distributions and co‐occurrence patterns, including ecological sorting, limiting similarity, and stochastic effects. To discriminate among these processes and determine the spatial scales at which they operate, we investigated how functional traits and phylogenetic relatedness influence the distribution of...

Historical approaches have always informed ecology but have gained great importance now as people struggle to understand the forces driving the many ecological changes occurring around them. This chapter first discusses difficulties in studying long‐term ecological change. Understanding these help people to explain why good long‐term studies are sc...

Ungulate herbivore populations are increasing across Europe with important implications for forest plant communities. Concurrently, atmospheric nitrogen (N) deposition continues to eutrophy forests, threatening many rare plant species. These pressures may critically interact to shape biodiversity as in grassland and tundra systems, yet any potentia...

Classical models ignoring linkage predict that deleterious recessive mutations purge or fix within inbred populations, yet these often retain moderate to high segregating load. True overdominance generates balancing selection that sustains inbreeding depression even in inbred populations but is rare. In contrast, arrays of mildly deleterious recess...

Premise of the study: Habitat fragmentation generates molecular genetic divergence among isolated populations but few studies have assessed phenotypic divergence and fitness in populations where the genetic consequences of habitat fragmentation are known. Phenotypic divergence could reflect plasticity, local adaptation, and/or genetic drift. Meth...

Assessing biodiversity status and trends in plant communities is critical for understanding, quantifying and predicting the effects of global change on ecosystems. Vegetation plots record the occurrence or abundance of all plant species co‐occurring within delimited local areas. This allows species absences to be inferred, information seldom provid...

Wisconsin’s plant communities are responding to shifting disturbance regimes, habitat fragmentation, aerial nitrogen deposition, exotic species invasions, ungulate herbivory, and successional processes. To better understand how plant functional traits mediate species’ responses to changing environmental conditions, we collected a large set of funct...

As climates change, species with locally adapted populations may be particularly vulnerable as specialization narrows the range of conditions under which populations can persist. Populations adapted to local climate as well as other site‐specific characteristics like soils present challenges for inferring how changing climates affect fitness, as cl...

Traits differentially adapt plant species to particular conditions generating compositional shifts along environmental gradients. As a result, community‐scale trait values show concomitant shifts, termed trait‒environment relationships. Trait‒environment relationships are often assessed by evaluating community‐weighted mean (CWM) traits observed al...

In this report Wisconsin’s Green Fire examines,  Chronic wasting disease (CWD) which is now found in 32 Wisconsin counties.  Widespread habitat deterioration caused by deer over-browsing.  An inability to control deer herd size in Wisconsin’s farmlands.  Long-term declines in the number of deer hunters which limits ability to manage herds throu...

The magnitude of inbreeding depression (ID) varies unpredictably among environments. ID often increases in stressful environments suggesting that these expose more deleterious alleles to selection or increase their effects. More simply, ID could increase under conditions that amplify phenotypic variation (CV²), e.g., by accentuating size hierarchie...

Forests in eastern North America are experiencing high densities of white-tailed deer (Odocoileus virginianus) and encroachment by invasive plants, both of which threaten native biodiversity. We review the literature on deer and invasive plant impacts focusing on studies that simultaneously evaluate the consequences of both. Deer have more frequent...

Fertilizers and manure applied to cropland to increase yields are often lost via surface erosion, soil leaching, and runoff, increasing nutrient loads in surface and sub-surface waters, degrading water quality, and worsening the 'dead zone' in the Gulf of Mexico. We leverage spatial and temporal variation in agricultural practices and precipitation...

Darwin spent years investigating the effects of self‐fertilization, concluding that “nature abhors perpetual self‐fertilisation.” Given that selection purges inbred populations of strongly deleterious mutations and drift fixes mild mutations, why does inbreeding depression persist in highly inbred taxa and why do no purely selfing taxa exist? Backg...

PREMISE: We tested 25 classic and novel hypotheses regarding trait–origin, trait–trait, and trait– environment relationships to account for flora-wide variation in life history, habit, and especially reproductive traits using a plastid DNA phylogeny of most native (96.6%, or 1494/1547 species) and introduced (87.5%, or 690/789 species) angiosperms...

Adaptive relationships between traits and the environment are often inferred from observational data by regressing community-weighted mean (CWM) traits on environmental gradients. However, trait‒environment relationships are better understood as the outcome of trait‒abundance and environment‒abundance relationships, and the interaction between trai...

Upon inbreeding, the architecture of the inbreeding load shifts as selection purges strongly deleterious recessive mutations and drift fixes many milder ones. Most small inbred populations show limited genetic variation while crosses between such populations commonly express pronounced heterosis, confirming fixation. In contrast, purging appears to...

Despite advances in community assembly theory, uncertainties remain regarding how ecological and evolutionary processes shape species distributions and communities. We analyzed patterns of occurrence for 139 herbaceous plant species across 257 forest stands in Wisconsin (USA) to test predictions from community assembly theory. Specifically, we appl...

Forest loss and fragmentation threaten the high diversity of tropical forests. Tropical epiphytes are a key component of plant diversity and significant for ecosystem functioning, and they are vulnerable to these forces. We explored the potential of shade trees in agroforestry systems to sustain and restore epiphyte communities where forest cover h...

Ecology and Recovery of Eastern Old-Growth Forests. Edited by Andrew M. Barton and William S. Keeton; Foreword by Thomas A. Spies. Washington (DC): Island Press. $40.00 (paper). xvi + 340 p. + 7 pl.; ill.; index. ISBN: 978-1-61091-890-9. 2018. Before European settlement, ancient old-growth forests stretched across vast areas of eastern North Amer...

Biodiversity time series reveal global losses and accelerated redistributions of species, but no net loss in local species richness. To better understand how these patterns are linked, we quantify how individual species trajectories scale up to diversity changes using data from 68 vegetation resurvey studies of seminatural forests in Europe. Herb-l...

When calls go out for “the best,” “credible,” “rigorous,” or “objective” science, the most appropriate response is virtually always an independent review of the work. If the science is found wanting, subsequent steps are usu- ally obvious as a result of the review. Although it is true that calls for review can delay action, there are ways to ensure...

Inbreeding (also referred to as “consanguinity”) occurs when mates are related to each other due to incest, assortative mating, small population size, or population sub-structuring. Inbreeding results in an excess of homozygotes and hence a deficiency of heterozygotes. This, in turn, exposes recessive genetic variation otherwise hidden by heterozyg...

Human‐driven species annihilations loom as a major crisis. However the recovery of deer and wolf populations in many parts of the northern hemisphere has resulted in conflicts and controversies rather than in relief. Both species interact in complex ways with their environment, each other, and humans. We review these interactions in the context of...

Aim The relative importance of stochastic and deterministic niche processes can affect the assembly of communities in response to land use context and change. In this study, we quantified the relative importance of dispersal‐ vs niche‐based processes in structuring forest plant metacommunities and sought to understand how these processes have chang...

Eastern hemlock (Tsuga canadensis (L.) Carrière) is a shade-tolerant, slow-growing tree once common in forests across the Great Lakes region. It was heavily exploited in the late 19th and early 20th centuries and now experiences limited regeneration across much of its range. This failure to regenerate has been ascribed to poor seedbed conditions, i...

Atmospheric nitrogen and sulfur pollution increased over much of the United States during the twentieth century from fossil fuel combustion and industrial agriculture. Despite recent declines, nitrogen and sulfur deposition continue to affect many plant communities in the United States, although which species are at risk remains uncertain. We used...

Landscape features often shape patterns of gene flow and genetic differentiation in plant species. Populations that are small and isolated enough also become subject to genetic drift. We examined patterns of gene flow and differentiation among 12 flood‐ plain populations of the selfing annual jewelweed (Impatiens capensis Meerb.) nested within four...

Landscape features often shape patterns of gene flow and genetic differentiation in plant species. Populations that are small and isolated enough also become subject to genetic drift. We examined patterns of gene flow and differentiation among 12 flood‐ plain populations of the selfing annual jewelweed (Impatiens capensis Meerb.) nested within four...

Landscape features often shape patterns of gene flow and genetic differentiation in plant species. Populations that are small and isolated enough also become subject to genetic drift. We examined patterns of gene flow and differentiation among 12 floodplain populations of the selfing annual jewelweed (Impatiens capensis Meerb.) nested within four r...

PREMISE OF THE STUDY: We used spatial phylogenetics to analyze the assembly of the Wisconsin flora, linking processes of dispersal and niche evolution to spatial patterns of floristic and phylogenetic diversity and testing whether phylogenetic niche conservatism can account for these patterns. METHODS: We used digitized records and a new molecular...

Aim Ecological communities are composed of both species and the biotic relationships (interactions or spatial associations) among them. Biotic homogenization in species composition (i.e., increased site‐to‐site similarity) is recognized as a common consequence of global change, but less is known about how the similarity of species relationships ch...

Aim: Ecological communities are comprised of both species and the biotic relationships among them. Biotic homogenization in species composition (i.e. increased site-to-site similarity) is recognized as a common consequence of global change. Far less is known about how patterns of species relationships (interactions and/or spatial associations) chan...

Understorey communities can dominate forest plant diversity and strongly affect forest ecosystem structure and function. Understoreys often respond sensitively but inconsistently to drivers of ecological change, including nitrogen (N) deposition. Nitrogen deposition effects, reflected in the concept of critical loads, vary greatly not only among sp...

Ecologists rely on field surveys to monitor long‐term ecological change but finite sampling and the prevalence of rare species mean that surveys inevitably miss some species present at a given location. These ‘phantom species’ produce pseudo‐turnover by inflating observed rates of local colonization and extinction in resurvey studies, especially am...

Our contribution provides a brief overview of key ideas associated with inbreeding, along with short sets of relevant annotated citations. We submitted this to the Oxford Bibliographies series for peer review and consideration for publication in April 2018.

Indigenous peoples manage forestlands and wildlife differently than public and private forestland managers. To evaluate ecological outcomes from these differences, we compared the structure, composition, and diversity of Ojibwe and Menominee tribal forests to nearby nontribal forestlands in northern Wisconsin. These indigenous peoples seek to manag...

American Indians have long managed forests and wildlife for different values than Euro-Americans. Does this result in measurable differences in forest and wildlife conditions? We examined forest and wildlife management on the Ojibwe and Menominee reservations in Wisconsin and compared ecological conditions on tribal vs. non-tribal lands. The longer...

Ecological communities are comprised of both species and the biotic relationships among them. Biotic homogenization in species composition (i.e. increased site-to-site similarity) is recognized a common consequence of global change, but less is known about how species relationships change over space and time. Does homogenization of species composit...

## METADATA for suf_phantom_species_data_12Feb2018jb.csv ## site: unique site identifier ## taxa: species name ## frequency_1950s: number of quadrats in which species was present during 1950s field survey ## frequency_2000s: number of quadrats in which species was present during 2000s field survey ## n.quadrats_1950s: number of quadrats sampled dur...

From Twig to Tree: Simple methods for teachers and students to track deer impacts Donald M. Waller Dept. of Botany University of Wisconsin - Madison Madison, WI 53706 USA dmwaller@wisc.edu Essay for the American J. Botany series: “On the Nature of Things” Vers. 7.3: 2/11/2018 Word count: 1755 + 24 references < no Abstract > Great trees arise vi...

Deer impacts on plant communities have increased making it important to find simple, effective ways to measure these. We assessed the time, effort, and power of the “oak sentinel” method for assessing deer impacts. We will compare these to similar data for two alternative methods based on seedling height and twig age. We planted one-year old seedli...

High densities of white-tailed deer restrict the regeneration of tree species, reduce understory cover and diversity , enhance invasions of exotic species, and facilitate the spread of human and deer diseases. Deer managers often base management decisions on estimated deer densities and carrying capacities, generating controversy. It may be simpler...

Detailed protocol. Accompanies the Forest Ecology and Management article of the same name.

[This corrects the article DOI: 10.1371/journal.pone.0115843.].

Now out: https://doi.org/10.1111/oik.05114 Ecologists rely on field surveys to monitor long-term ecological change but finite sampling and the prevalence of rare species mean that surveys inevitably miss some species present at a given location. These “phantom species” produce pseudo-turnover by inflating observed rates of local colonization and e...

High densities of white-tailed deer restrict the regeneration of tree species, reduce understory cover and diversity, enhance invasions of exotic earthworms and plants, and facilitate the spread of human and deer diseases. Deer managers often base management decisions on estimated deer densities and carrying capacities, generating controversy. It m...

Plant functional traits allow us to mechanistically link changes in species composition to changes in ecosystem functions. Understanding how and why changes occur in functional composition of plant communities can thus help us better conserve and restore biodiversity. We aim to examine long-term effects of fire exclusion and climate change on the f...

In forests of eastern North America, white‐tailed deer ( O docoileus virginianus ) can directly affect, via herbivory, the presence, abundance and reproductive success of many plant species. In addition, deer indirectly influence understorey communities by altering environmental conditions. To examine how deer indirectly influence understorey plant...

Phylogenetic and functional trait‐based analyses inform our understanding of community composition, yet methods for quantifying the overlap in information derived from functional traits and phylogenies remain underdeveloped. Does adding traits to analyses of community composition reduce the phylogenetic signal in the residual variation? If not, the...

More and more ecologists have started to resurvey communities sampled in earlier decades to determine long-term shifts in community composition and infer the likely drivers of the ecological changes observed. However, to assess the relative importance of and interactions among multiple drivers, joint analyses of resurvey data from many regions span...

Do invasive plant species act more as "passengers" or drivers of ecological change in native plant communities? Snapshot studies based on correlations at the site scale ignore longer-term dynamics and variation in how particular invaders affect particular native species. We analyzed patterns of co-occurrence between three invading species (Alliaria...

Metacommunity matrices contain data on species incidence or abundance across sites, compactly portraying community composition and how it varies over sites. We constructed models based on an initial metacommunity matrix of either species incidence or abundance to test whether such data suffice to predict subsequent changes in incidence or abundance...

Dams, levees, and water withdrawals disrupt hydrologic regimes and associated floodplain forests. Because these forests are also responding to changes in land use, species invasions, and climate change, the relative effects of these factors are hard to disentangle. Most studies of floodplain forests lack historic data, requiring us to rely on recen...

National parks of the United States seek to preserve the natural and cultural heritage of the United States, yet parks in the eastern and Midwestern United States were established after periods of human settlement and disturbance. In the Great Lakes region, fire and windfall originally dominated as disturbance agents, driving dynamics in prairies,...

The Venus Flytrap (Dionaea muscipula Ellis) is a rare and localized species in the family Droseraceae endemic to wet coastal plain and sandhills habitats in North and South Carolina. Its dramatic specialized aerial snap trap makes it the most widely recognized carnivorous plant in the world. Its trap is a unique evolutionary adaptation shared with...

Local, short- to medium-term studies make clear that white-tailed deer can greatly suppress tree growth and survival in palatable tree species. To assess how deer have broadly affected patterns of tree recruitment across northern Wisconsin, we analyzed recruitment success in 11 common trees species that vary in palatability across 13,105 USFS - FIA...

Can species shift their distributions fast enough to track changes in climate? We used abundance data from the 1950s and the 2000s in Wisconsin to measure shifts in the distribution and abundance of 78 forest-understory plant species over the last half-century and compare these shifts to changes in climate. We estimated temporal shifts in the geogr...

Local, short-to medium-term studies make clear that white-tailed deer can greatly suppress tree growth and survival in palatable tree species. To assess how deer have broadly affected patterns of tree recruitment across northern Wisconsin, we analyzed recruitment success in 11 common trees species that vary in palatability across 13,105 USFS - FIA...

Table S1. Sample sizes for each site. Sample sizes for each lineage (Group 1, Group 2, Group 3, and hybrids) within sites are given in parentheses. Table S2. Mutation‐scaled migration rate, M (= m/μ), with 95% confidence intervals for each Amphicarpatea bracteata genetic group. Table S3. High resolution melt (HRM) primers and alleles used to assi...

Metacommunity matrices contain data on species incidence or abundance across sites, compactly portraying community composition and how it varies over sites. We constructed models based on an initial metacommunity matrix of either species incidence or abundance to test whether such data suffice to predict subsequent changes in incidence or abundance...

The amphicarpic annual legume Amphicarpaea bracteata is unusual in producing aerial and subterranean cleistogamous flowers that always self-fertilize and, less commonly, aerial chasmogamous flowers that outcross. Although both morphologic and genetic variants are known in this highly selfing species, debate continues over whether this variation is...

Significance Human activities have elevated nitrogen (N) deposition and there is evidence that deposition impacts species diversity, but spatially extensive and context-specific estimates of N loads at which species losses begin remain elusive. Across a wide range of climates, soil conditions, and vegetation types in the United States, we found tha...

Patterns of biodiversity are changing rapidly. "Legacy studies" use historical data to document changes between past and present communities, revealing long-term trends that can often be linked to particular drivers of ecological change. However, a single pair of historical samples cannot ascertain whether rates of change are consistent or whether...

Plant species co-occur within communities in response to variation in environmental conditions, limited species dispersal and biotic interactions. We used surveys and resurveys of the same sites of three temperate forest plant communities to study patterns of association between co-occurring species pairs and to infer how these mechanisms contribut...

Understanding how ecological communities are organized and how they change through time is critical to predicting the effects of climate change. Recent work documenting the co-occurrence structure of modern communities found that most significant species pairs co-occur less frequently than would be expected by chance. However, little is known about...