G. Evelyn Hutchinson more than a half century ago proposed that one could characterize the ecological niche of a species as an abstract mapping of population dynamics onto an environmental space, the ...axes of which are abiotic and biotic factors that influence birth and death rates. If a habitat has conditions within a species' niche, a population should persist without immigration from external sources, whereas if conditions are outside the niche, it faces extinction. Analyses of species' niches are essential to understanding controls on species' geographical range limits and how these limits might shift in our rapidly changing world. Recent developments in ecology and evolutionary biology suggest it is time to revisit and refine Hutchinson's niche concept. After reviewing techniques for quantifying niches, I examine subtleties that arise because of impacts species have on their own environments, the density-dependent modulation of how individuals experience environments, and the interplay of dispersal and temporal heterogeneity in determining population persistence. Moreover, the evolutionary record over all time scales reveals a spectrum of rates of change in species' niches, from rapid niche evolution to profound niche conservatism. Substantial challenges revolving around the evolutionary dimension of the Hutchinsonian niche include quantifying the magnitude of evolved intraspecific and clade-level variation in niches and understanding the factors that govern where along the spectrum of potential evolutionary rates any given lineage lies. A growing body of theory provides elements of a conceptual framework for understanding niche conservatism and evolution, paving the way for an evolutionary theory of the niche.
Apparent Competition Holt, Robert D; Bonsall, Michael B
Annual review of ecology, evolution, and systematics,
11/2017, Letnik:
48, Številka:
1
Journal Article
Recenzirano
Most species have one or more natural enemies, e.g., predators, parasites, pathogens, and herbivores, among others. These species in turn typically attack multiple victim species. This leads to the ...possibility of indirect interactions among those victims, both positive and negative. The term apparent competition commonly denotes negative indirect interactions between victim species that arise because they share a natural enemy. This indirect interaction, which in principle can be reflected in many facets of the distribution and abundance of individual species and more broadly govern the structure of ecological communities in time and space, pervades many natural ecosystems. It also is a central theme in many applied ecological problems, including the control of agricultural pests, harvesting, the conservation of endangered species, and the dynamics of emerging diseases. At one end of the scale of life, apparent competition characterizes intriguing aspects of dynamics within individual organisms-for example, the immune system is akin in many ways to a predator that can induce negative indirect interactions among different pathogens. At intermediate scales of biological organization, the existence and strength of apparent competition depend upon many contingent details of individual behavior and life history, as well as the community and spatial context within which indirect interactions play out. At the broadest scale of macroecology and macroevolution, apparent competition may play a major, if poorly understood, role in the evolution of species' geographical ranges and adaptive radiations.
There is increasing awareness of the many different ways host-microbe interactions relate to cancer initiation and progression. Vaccines designed to drive immune responses against key tumor-promoting ...mechanisms of oncomicrobes like F. nucleatum may provide novel and effective interventions against colorectal cancer and other diseases.
There is increasing awareness of the many different ways host-microbe interactions relate to cancer initiation and progression. Vaccines designed to drive immune responses against key tumor-promoting mechanisms of oncomicrobes like F. nucleatum may provide novel and effective interventions against colorectal cancer and other diseases.
Environmental factors control spatial distributions and local abundances in distinct – but overlapping – ways. Osorio‐Olivera et al. examine when environments near the geometric center of a species' ...ecological niche – which they assume to be optimal for growth when rare – also harbor the greatest number of individuals on average at equilibrium, and when not. Transient dynamics, Allee effects and metapopulation dynamics can cloud this relationship. In this brief piece I sketch a number of further ways in which this relationship can break down, including asymmetry in the shape of the niche, spatial variation in density dependence, and nonlinear feedbacks with the environment.
Due to advances in sequencing technology, somatically mutated cancer antigens, or neoantigens, are now readily identifiable and have become compelling targets for immunotherapy. In particular, ...neoantigen-targeted vaccines have shown promise in several pre-clinical and clinical studies. However, to date, neoantigen-targeted vaccine studies have involved tumors with exceptionally high mutation burdens. It remains unclear whether neoantigen-targeted vaccines will be broadly applicable to cancers with intermediate to low mutation burdens, such as ovarian cancer. To address this, we assessed whether a derivative of the murine ovarian tumor model ID8 could be targeted with neoantigen vaccines. We performed whole exome and transcriptome sequencing on ID8-G7 cells. We identified 92 somatic mutations, 39 of which were transcribed, missense mutations. For the 17 top predicted MHC class I binding mutations, we immunized mice subcutaneously with synthetic long peptide vaccines encoding the relevant mutation. Seven of 17 vaccines induced robust mutation-specific CD4 and/or CD8 T cell responses. However, none of the vaccines prolonged survival of tumor-bearing mice in either the prophylactic or therapeutic setting. Moreover, none of the neoantigen-specific T cell lines recognized ID8-G7 tumor cells in vitro, indicating that the corresponding mutations did not give rise to bonafide MHC-presented epitopes. Additionally, bioinformatic analysis of The Cancer Genome Atlas data revealed that only 12% (26/220) of HGSC cases had a ≥90% likelihood of harboring at least one authentic, naturally processed and presented neoantigen versus 51% (80/158) of lung cancers. Our findings highlight the limitations of applying neoantigen-targeted vaccines to tumor types with intermediate/low mutation burdens.
Integrating Biogeography with Contemporary Niche Theory Godsoe, William; Jankowski, Jill; Holt, Robert D. ...
Trends in ecology & evolution (Amsterdam),
July 2017, 2017-Jul, 2017-07-00, 20170701, Letnik:
32, Številka:
7
Journal Article
Recenzirano
There is no consensus on when biotic interactions impact the range limits of species. Starting from MacArthur’s use of invasibility to understand how biotic interactions influence coexistence, here ...we examine how biotic interactions shape species distributions. Range limits emerge from how birth, death, and movement rates vary with the environment. We clarify some basic issues revolving around niche definitions, illustrated with simple resource–consumer theory. We then highlight two different avenues for linking community theory and range theory; the first based on calculating the effects of biotic interactions on range limits across scales and landscape configurations, and the second based on aggregate measures of diffuse interactions and network strength. We conclude with suggestions for a future research agenda.
We show how analyses of species coexistence can be used determine when biotic interactions shape range limits.
Coexistence theory predicts that range limits occur when the intrinsic growth rate of a species balances the effect of biotic interactions on population growth.
To study this empirically, the growth rate of a species should be measured when it is rare, with and without biotic interactions.
These insights generalize across spatial scales.
Predicting the impacts of climate change on species is one of the biggest challenges that ecologists face. Predictions routinely focus on the direct effects of climate change on individual species, ...yet interactions between species can strongly influence how climate change affects organisms at every scale by altering their individual fitness, geographic ranges and the structure and dynamics of their community. Failure to incorporate these interactions limits the ability to predict responses of species to climate change. We propose a framework based on ideas from global-change biology, community ecology, and invasion biology that uses community modules to assess how species interactions shape responses to climate change.
Although generations of researchers have studied the factors that limit the distributions of species, we still do not seem to understand this phenomenon comprehensively. Traditionally, species' ...ranges have been seen as the consequence of abiotic conditions and local adaptation to the environment. However, during the last years it has become more and more evident that biotic factors – such as intra- and interspecific interactions or the dispersal capacity of species – and even rapidly occurring evolutionary processes can strongly influence the range of a species and its potential to spread to new habitats. Relevant eco-evolutionary forces can be found at all hierarchical levels: from landscapes to communities via populations, individuals and genes. We here use the metapopulation concept to develop a framework that allows us to synthesize this broad spectrum of different factors. Since species' ranges are the result of a dynamic equilibrium of colonization and local extinction events, the importance of dispersal is immediately clear. We highlight the complex interrelations and feedbacks between ecological and evolutionary forces that shape dispersal and result in non-trivial and partially counter-intuitive range dynamics. Our concept synthesizes current knowledge on range biology and the eco-evolutionary dynamics of dispersal.
Metapopulation capacity provides an analytic tool to quantify the impact of landscape configuration on metapopulation persistence, which has proven powerful in biological conservation. Yet ...surprisingly few efforts have been made to apply this approach to multispecies systems. Here, we extend metapopulation capacity theory to predict the persistence of trophically interacting species. Our results demonstrate that metapopulation capacity could be used to predict the persistence of trophic systems such as prey-predator pairs and food chains in fragmented landscapes. In particular, we derive explicit predictions for food chain length as a function of metapopulation capacity, top-down control, and population dynamical parameters. Under certain assumptions, we show that the fraction of empty patches for the basal species provides a useful indicator to predict the length of food chains that a fragmented landscape can support and confirm this prediction for a host-parasitoid interaction. We further show that the impact of habitat changes on biodiversity can be predicted from changes in metapopulation capacity or approximately by changes in the fraction of empty patches. Our study provides an important step toward a spatially explicit theory of trophic metacommunities and a useful tool for predicting their responses to habitat changes.
Toward ecoevolutionary dynamics Sigmund, Karl; Holt, Robert D
Proceedings of the National Academy of Sciences - PNAS,
03/2021, Letnik:
118, Številka:
9
Journal Article
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