Richard P. Shefferson

The University of Tokyo | Todai · Organization for Programs on Environmental Science

4 synthesis: The hypothesis that plants escape senescence generally assumes that plants can continue to grow larger and increase reproduction as they get older. The results here show that size and reproduction decline with age and the rates of these declines toward death are lifespan- and age-dependent. Further research is needed to delineate the...

1. I present an evolutionary ecology interpretation of vegetative dormancy in mature herbaceous perennials. This kind of vegetative dormancy has been noted for at least 40 years, but has only recently become a topic of study. 2. Vegetative dormancy may be considered in a life-history context. Both vegetative dormancy and mortality typically decreas...

Host breadth is often assumed to have no evolutionary significance in broad interactions because of the lack of cophylogenetic patterns between interacting species. Nonetheless, the breadth and suite of hosts utilized by one species may have adaptive value, particularly if it underlies a common ecological niche among hosts. Here, we present a preli...

Citation: Bashirzadeh, M.; Abedi, M.; Shefferson, R.P.; Farzam, M. Post-Fire Recovery of Plant Biodiversity Changes Depending on Time Intervals since Last Fire in Semiarid Shrublands. Fire 2023, 6, 103. Abstract: Fire is a key disturbance affecting plant biodiversity patterns and evolution. Although a wide range of studies have shown important impa...

Estimating effective population size (Ne) is important for theoretical and practical applications in evolutionary biology and conservation. Nevertheless, estimates of Ne in organisms with complex life‐history traits remain scarce because of the challenges associated with estimation methods. Partially clonal plants capable of both vegetative (clonal...

Introduction and technical manual for CRAN package lefko3

Restoration of degraded environments is essential to mitigate adverse impacts of human activities on ecosystems. Plant-plant interactions may provide effective means for restoring degraded arid lands, but little is understood about these impacts. In this regard, we analyzed the effects of two dominant nurse plants (i.e., Artemisia sieberi and Stipa...

Urbanization transforms environments in ways that alter biological evolution. We examined whether urban environmental change drives parallel evolution by sampling 110,019 white clover plants from 6169 populations in 160 cities globally. Plants were assayed for a Mendelian antiherbivore defense that also affects tolerance to abiotic stressors. Urban...

Urbanization transforms environments in ways that alter biological evolution. We examined whether urban environmental change drives parallel evolution by sampling 110,019 white clover plants from 6169 populations in 160 cities globally. Plants were assayed for a Mendelian antiherbivore defense that also affects tolerance to abiotic stressors. Urban...

Estimating effective population size (Ne) is essential for theoretical and practical applications in evolutionary biology and conservation. Nevertheless, estimates of Ne in organisms with complex life-history traits remain scarce because of the challenges associated with estimation methods. Partially clonal plants capable of vegetative (clonal) gro...

Survival analyses are a key tool for demographers, ecologists, and evolutionary biologists. This chapter presents the most common methods and illustrates their use for species across the Tree of Life. It discusses the challenges associated with various types of survival data, how to model species with a complex life cycle, and includes the impact o...

The histories of individuals impact the dynamics of their populations. Matrix projection models (MPMs) are used to analyse population dynamics, but are not structured to incorporate these influences. Historical MPMs (hMPM) were developed to incorporate these impacts, but their complexity has left them little used. We developed r package lefko3 to p...

The reintroduction of disease‐resistant hybrids is a commonly proposed solution to the introduction of pathogens and pests that weaken or eliminate native plant species. Plant interactions with soil biota result in plant–soil feedbacks (PSFs), which have consequences for individual plant growth and survival as well as broader community‐level proces...

Aim Latitudinal clines of species diversity are widely documented in terrestrial and marine ecosystems. However, the processes governing species diversity gradients in riverine ecosystems have not been well‐studied. We addressed this issue by comparing species diversity between riverine aquatic and terrestrial earthworm groups (genus Sparganophilus...

Terrestrial orchid life-cycles are complex and dependent on pollinators and mycorrhizal associates. Worldwide, orchid populations are declining because of urbanization, atmospheric nitrogen deposition and climate change. To advance understanding of the factors determining orchid population viability, we review knowledge about orchid demography, lif...

The study of local and regional mechanisms driving spatial patterns in beta diversity is essential to the understanding of biodiversity. We aimed to predict the roles of multiple mechanisms operating at regional to fine spatial scales in structuring the beta diversity in a mountainous semi-arid rangeland of the Khorassan-Kopet Dagh floristic provin...

Evolutionary history has profound influences on ecological systems. Such influence is generally observed as phylogenetic signal, in which trait similarity is a function of evolutionary relationships, or phylogenetic niche conservatism, in which clades of species exhibit a single trait value. These patterns are observed so often in ecological resear...

It don't make no difference 'cos I ain't gonna be, easy, easy, the only time I'm gonna be easy's when I'm Killed by death-Motörhead, Killed By Death (1984) Short Summary We humans have long wondered about the seemingly inevitable physiological decline that happens after our maturity. This phenomenon, known as 'senescence', is recognised as the phys...

Most species engage in broad interactions, in which they interact with multiple partner species. The evolutionary processes that generate such generalized interactions remain unknown, partly due to the difficulty in comparing their breadth. We argue that the interaction specificity of species involved in broad interactions evolves in three ways: a)...

Molecular phylogenies are increasingly used to understand how biotic interactions and environment shape phylogenetic community structure (PCS). However, we do not understand the effects of plant–plant interactions and environment on PCS and phylogenetic diversity across spatial scales, particularly in rangelands. Here, we ask: (1) do plant–plant in...

Terrestrial orchids do not always sprout every growing season and a significant proportion of the population may remain underground. Such vegetative dormancy may lead to absolute demographic costs or, alternatively, demographic benefits for dormant plants, as well as relative costs or benefits compared to the performance of plants that did emerge d...

The mechanisms determining community phylogenetic structure range from local ecological mechanisms to broad biogeographical processes. How these community assembly processes determine phylogenetic structure and patterns in rangeland communities across multiple spatial scales is still poorly understood. We sought to determine whether the structure o...

Fitness can be calculated using demographic parameters such as survival and fecundity, which are normally used to examine population dynamics in ecology. This concept is at the heart of Darwin's thinking on natural selection. Natural selection optimizes survival and fertility schedules through differential fitness, and these optimal schedules drive...

A central goal of evolutionary ecology is to understand the factors that select for particular life history strategies, such as delaying reproduction. For example, environmental variation and reproductive costs to survival and growth often select for reproductive delays in semelparous and iteroparous species. In this study, we examine how variation...

Vegetative dormancy, that is the temporary absence of aboveground growth for ≥ 1 year, is paradoxical, because plants cannot photosynthesise or flower during dormant periods. We test ecological and evolutionary hypotheses for its widespread persistence. We show that dormancy has evolved numerous times. Most species displaying dormancy exhibit life‐...

Conservation management for environmental sustainability is now ubiquitous. The ecological effects of these actions are well-intentioned and well-known. Although conservation biologists and managers increasingly incorporate evolutionary considerations into management plans, the evolutionary consequences of management strategies have remained relati...

Premise of the study: The slipper orchids (Cypripedioideae) are a morphologically distinct subfamily of Orchidaceae. They also have some of the largest genomes in the orchids, which may be due to polyploidy or some other mechanism of genome evolution. We generated 10 transcriptomes and incorporated existing RNA-seq data to infer a multilocus nucle...

Deadwood is an important legacy structure in managed forests, providing continuity in shelter and resource availability for many organisms and acting as a vehicle by which nutrients can be passed from one stand to the next following a harvest. Despite existing at the interface between below- and above-ground systems, however, much remains unknown a...

Evidence suggests that most, if not all, organisms are symbiotic to some degree. Symbioses strongly affect the fitness of their constituent organisms, particularly via their impacts on physiological processes related to nutrient acquisition, growth, survival and reproduction. In this chapter we use the mycorrhiza as a case study to argue that since...

The existing theories on the evolution of senescence assume that senescence is inevitable in all organisms. However, recent studies have shown that this is not necessarily true. A better understanding of senescence and its underlying mechanisms could have far-reaching consequences for conservation and eco-evolutionary research. This book is the fir...

Although many ecological properties of species respond to climate change, their evolutionary responses are poorly understood. Here, we use data from long-term demographic studies to predict evolutionary responses of three herbaceous perennial orchid species, Cypripedium parviflorum, C. candidum and Ophrys sphegodes, to predicted climate changes in...

The red list has become a ubiquitous tool in the conservation of species. We analyzed contemporary trends in the threat levels of European orchids, in total 166 species characterized in 27 national red lists, in relation to their reproductive biology and growth form, distribution area, and land cover where they occur. We found that species in centr...

Evolutionary losses of photosynthesis in terrestrial plants all originate in photosynthetic ancestors. The adaptive context under which this transition happens has remained elusive because of the rarity of plants in which both photosynthetic and nonphotosynthetic forms exist as a polymorphism. Here, we report on demographic patterns in photosynthet...

Evolution can happen rapidly and frequently. This realization has motivated a rethinking of ecological and evolutionary time-scales and their overlap, and stimulated research on processes at their interface. This premise lays at the heart of eco-evolutionary dynamics, a relatively recent field redeveloping how we conceive of ecological and evolutio...

Why some herbaceous plant species refrain from sprouting in some years is a longstanding puzzle in plant ecology. When vegetatively ‘dormant’, the plant lives as a rootstock, but does not produce or maintain photosynthetic tissue. During this time, energy may be remobilized from resource reserves or acquired from mycorrhizal fungi, although the mec...

Populations of many species are isolated within narrow elevation bands of Neotropical mountain habitat, and how well dispersal maintains genetic connectivity is unknown. We asked whether genetic structure of an epiphytic orchid, Epidendrum firmum, corresponds to gaps between Costa Rican mountain ranges, and how these gaps influence pollen and seed...

Populations of many species are isolated within narrow elevation bands of Neotropical mountain habitat, and how well dispersal maintains genetic connectivity is unknown. We asked whether genetic structure of an epiphytic orchid, Epidendrum firmum, corresponds to gaps between Costa Rican mountain ranges, and how these gaps influence pollen and seed...

Summary The distribution of rare plants may be limited by environmental or density-dependent factors that reduce population growth and persistence. The relative importance of environmental limitations vs. the degree to which conspecifics influence recruitment may determine optimal management strategies for plants of conservation concern. We sowed s...

Mycorrhizal associations are required for the germination of orchids in nature. Recent studies reveal that distributions of arbuscular mycorrhizal and ectomycorrhizal fungal species are influenced by soil nutrient availability. However, it is unclear how soil nutrient availability influences mycorrhizal and root endophytic fungal association in orc...

Symbiotic interactions are common in nature. In dynamic or degraded environments, the ability to associate with multiple partners (i.e. broad specificity) may enable species to persist through fluctuations in the availability of any particular partner. Understanding how species-interactions vary across landscapes is necessary to anticipate direct a...

Throughout the industrialized world, wetland species face the greatest risk of extinction from altered environmental conditions and loss of habitat. Manmade wetlands are often the only feasible strategy to provide habitat for these species. Wetland orchids are particularly susceptible to environmental degradation due to potentially limited availabi...

1. Senescence, the physiological decline that results in decreasing survival and/or reproduction with age, remains one of the most perplexing topics in biology. Most theories explaining the evolution of senescence (i.e. antagonistic pleiotropy, accumulation of mutations, disposable soma) were developed decades ago. Even though these theories have i...

Background/Question/Methods Historical biogeography, habitat suitability, the distribution of essential mycorrhizal fungi, and the dispersal of pollen and seeds across a landscape all contribute to spatial genetic structure of rare orchid species. We investigated spatial genetic structure of the Neotropical epiphytic orchid Epidendrum firmum in m...

Background/Question/Methods Ecological interactions are a ubiquitous force behind much of the diversification of life. Understanding the factors that promote or limit species interactions is of fundamental importance for any efforts to predict ecological responses to changing global and local environments. Of particular concern given the extremel...

Background/Question/Methods Most plant species exhibit annual patterns in reproduction, survival, and size transitions, with seed production and growth occurring during favorable months and death or dormancy during harsher months. In the Neotropics, seasonal changes in precipitation, light penetration, pollinator activity, herbivory, and other fa...

The theory of evolution via natural selection predicts that the genetic composition of wild populations changes over time in response to the environment. Different genotypes should exhibit different demographic patterns, but genetic variation in demography is often impossible to separate from environmental variation. Here, we asked if genetic varia...

2012. Linking vegetative dormancy to fitness in two long-lived herbaceous perennials. Ecosphere 3(2): Abstract. Vegetative dormancy occurs in many plant families, but its evolutionary context remains a mystery. We asked whether vegetative dormancy is an adaptive response to environmental stress and environmental stochasticity in certain long-lived...

Myco-heterotrophs are non-photosynthetic plants that parasitize mycorrhizal fungi for their nutritional requirements, especially carbon. Because green plants sprout both to photosynthesize and to reproduce, the lack of photosynthesis in myco-heterotrophs suggests that these plants need only to sprout to reproduce. Further, they may be long-lived, w...

Long-lived plants experience periods of acute stress during their lifetime that impact their demography and fitness. We induced stress (defoliation and heavy shading) on a natural population of the threatened lady-slipper orchid Cypripedium calceolus. We then utilized integral projection models (IPM's) to assess the effects of environmental stress...

Background/Question/Methods Symbiotic mycorrhizal fungi are ubiquitous in plant communities. Understanding the composition of mycorrhizal communities could advance the conservation of rare or exploited plants. All orchid species have obligate symbioses with mycorrhizal fungi because orchid seeds cannot germinate without associating with an approp...

Background/Question/Methods The mining and burning of oil shale results in massive quantities of tailings and ash which is heaped in large hills in northeastern Estonia. The ash hills are a novel, harsh environment with alkaline soils containing high levels of heavy metals, phenols, and oil residue. Microbial colonization precedes and in harsh en...

Background/Question/Methods The mycorrhiza is a requirement for the germination and establishment of orchids in nature. Most conservation efforts ignore mycorrhizal host specialization when designing management and rehabilitation strategies for rare orchids. Without an adequate understanding of how variability in host selection and the evolutiona...

Herbivores can have strong deleterious effects on plant growth, reproduction, and even survival. Because these effects might be strongly interrelated, the direct consumptive effects of herbivores and a variety of indirect effects are difficult to untangle. Reductions in growth, for example, may strongly impact the flowering behaviour of plant speci...

Background/Question/Methods The burning of oil shale provides electricity for the people of Estonia. The resulting ash hills are desolate, environmentally toxic, and prohibitive to potential plant colonizers. Eventually, these sites undergo primary succession, and among the first colonizers are rare terrestrial orchids from the Orchis, Dactylorhi...

Background/Question/Methods Population projections are often used to assess life history evolution and population viability, but assume that past and future environmental variation stays within levels observed in the study and that the genetic composition of a population is either unchanging or inconsequential to population dynamics. Here, we asses...