James A. Fordyce

Bio: James A. Fordyce is an academic researcher from University of Tennessee. The author has contributed to research in topics: Population & Lycaeides. The author has an hindex of 41, co-authored 126 publications receiving 9036 citations. Previous affiliations of James A. Fordyce include University of California & National Institute for Mathematical and Biological Synthesis.

The Ecology of Individuals: Incidence and Implications of Individual Specialization

Abstract: Most empirical and theoretical studies of resource use and population dynamics treat conspecific individuals as ecologically equivalent. This simplification is only justified if interindividual niche variation is rare, weak, or has a trivial effect on ecological processes. This article reviews the incidence, degree, causes, and implications of individual-level niche variation to challenge these simplifications. Evidence for individual specialization is available for 93 species dis- tributed across a broad range of taxonomic groups. Although few studies have quantified the degree to which individuals are specialized relative to their population, between-individual variation can some- times comprise the majority of the population's niche width. The degree of individual specialization varies widely among species and among populations, reflecting a diverse array of physiological, be- havioral, and ecological mechanisms that can generate intrapopu- lation variation. Finally, individual specialization has potentially im- portant ecological, evolutionary, and conservation implications. Theory suggests that niche variation facilitates frequency-dependent interactions that can profoundly affect the population's stability, the amount of intraspecific competition, fitness-function shapes, and the population's capacity to diversify and speciate rapidly. Our collection of case studies suggests that individual specialization is a widespread but underappreciated phenomenon that poses many important but unanswered questions.

Plant genotypic diversity predicts community structure and governs an ecosystem process.

Abstract: Theory predicts, and recent empirical studies have shown, that the diversity of plant species determines the diversity of associated herbivores and mediates ecosystem processes, such as aboveground net primary productivity (ANPP). However, an often-overlooked component of plant diversity, namely population genotypic diversity, may also have wide-ranging effects on community structure and ecosystem processes. We showed experimentally that increasing population genotypic diversity in a dominant old-field plant species, Solidago altissima, determined arthropod diversity and community structure and increased ANPP. The effects of genotypic diversity on arthropod diversity and ANPP were comparable to the effects of plant species diversity measured in other studies.

Supporting Online Material for Plant Genotypic Diversity Predicts Community Structure and Governs an Ecosystem Process

Abstract: Theory predicts, and recent empirical studies have shown, that the diversity of plant species determines the diversity of associated herbivores and mediates ecosystem processes, such as aboveground net primary productivity (ANPP). However, an often-overlooked component of plant diversity, namely population genotypic diversity, may also have wide-ranging effects on community structure and ecosystem processes. We showed experimentally that increasing population genotypic diversity in a dominant old-field plant species, Solidago altissima, determined arthropod diversity and community structure and increased ANPP. The effects of genotypic diversity on arthropod diversity and ANPP were comparable to the effects of plant species diversity measured in other studies.

Measuring individual-level resource specialization

Abstract: Many apparently generalized species are in fact composed of individual specialists that use a small subset of the population's resource distribution. Niche variation is usually established by testing the null hypothesis that individuals draw from a common resource distribution. This approach encourages a publication bias in which negative results are rarely reported, and obscures variation in the degree of individual specialization, limiting our ability to carry out comparative studies of the causes or consequences of niche variation. To facilitate studies of the degree of individual specialization, this paper outlines four quantitative indices of intrapopulation variation in resource use. Traditionally, such variation has been measured by partitioning the population's total niche width into within- and between-individual, sex, or phenotype components. We suggest two alternative measures that quantify the mean resource overlap between an individual and its population, and we discuss the advantages and disadvantages of all four measures. The utility of all indices depends on the quality of the empirical data. If resources are measured in a coarse-grained manner, individuals may falsely appear generalized. Alternatively, specialization may be overestimated by cross-sectional sampling schemes where diet variation can reflect a patchy environment. Isotope ratios, parasites, or diet-morphology correlations can complement cross-sectional data to establish temporal consistency of individual specialization.

Compounded effects of climate change and habitat alteration shift patterns of butterfly diversity

Abstract: Climate change and habitat destruction have been linked to global declines in vertebrate biodiversity, including mammals, amphibians, birds, and fishes. However, invertebrates make up the vast majority of global species richness, and the combined effects of climate change and land use on invertebrates remain poorly understood. Here we present 35 years of data on 159 species of butterflies from 10 sites along an elevational gradient spanning 0–2,775 m in a biodiversity hotspot, the Sierra Nevada Mountains of Northern California. Species richness has declined at half of the sites, with the most severe reductions at the lowest elevations, where habitat destruction is greatest. At higher elevations, we observed clear upward shifts in the elevational ranges of species, consistent with the influence of global warming. Taken together, these long-term data reveal the interacting negative effects of human-induced changes on both the climate and habitat available to butterfly species in California. Furthermore, the decline of ruderal, disturbance-associated species indicates that the traditional focus of conservation efforts on more specialized and less dispersive species should be broadened to include entire faunas when estimating and predicting the effects of pervasive stressors.

疟原虫var基因转换速率变化导致抗原变异[英]／Paul H, Robert P, Christodoulou Z, et al//Proc Natl Acad Sci U S A

Abstract: 抗原变异可使得多种致病微生物易于逃避宿主免疫应答。表达在感染红细胞表面的恶性疟原虫红细胞表面蛋白1（PfPMP1）与感染红细胞、内皮细胞、树突状细胞以及胎盘的单个或多个受体作用，在黏附及免疫逃避中起关键的作用。每个单倍体基因组var基因家族编码约60种成员，通过启动转录不同的var基因变异体为抗原变异提供了分子基础。

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Stacks: an analysis tool set for population genomics

Abstract: Massively parallel short-read sequencing technologies, coupled with powerful software platforms, are enabling investigators to analyse tens of thousands of genetic markers. This wealth of data is rapidly expanding and allowing biological questions to be addressed with unprecedented scope and precision. The sizes of the data sets are now posing significant data processing and analysis challenges. Here we describe an extension of the Stacks software package to efficiently use genotype-by-sequencing data for studies of populations of organisms. Stacks now produces core population genomic summary statistics and SNP-by-SNP statistical tests. These statistics can be analysed across a reference genome using a smoothed sliding window. Stacks also now provides several output formats for several commonly used downstream analysis packages. The expanded population genomics functions in Stacks will make it a useful tool to harness the newest generation of massively parallel genotyping data for ecological and evolutionary genetics.

Behavioral syndromes: an ecological and evolutionary overview.

Abstract: Recent studies suggest that populations and species often exhibit behavioral syndromes; that is, suites of correlated behaviors across situations. An example is an aggression syndrome where some individuals are more aggressive, whereas others are less aggressive across a range of situations and contexts. The existence of behavioral syndromes focuses the attention of behavioral ecologists on limited (less than optimal) behavioral plasticity and behavioral carryovers across situations, rather than on optimal plasticity in each isolated situation. Behavioral syndromes can explain behaviors that appear strikingly non-adaptive in an isolated context (e.g. inappropriately high activity when predators are present, or excessive sexual cannibalism). Behavioral syndromes can also help to explain the maintenance of individual variation in behavioral types, a phenomenon that is ubiquitous, but often ignored. Recent studies suggest that the behavioral type of an individual, population or species can have important ecological and evolutionary implications, including major effects on species distributions, on the relative tendencies of species to be invasive or to respond well to environmental change, and on speciation rates. Although most studies of behavioral syndromes to date have focused on a few organisms, mainly in the laboratory, further work on other species, particularly in the field, should yield numerous new insights.