A Constraint-based model of Dynamic Island Biogeography: environmental history and species traits predict hysteresis in populations and communities

A Constraint-based model of Dynamic Island Biogeography: environmental history and species traits predict hysteresis in populations and communities We present a conceptual model that shows how hysteresis can emerge in dynamic island systems given simple constraints on trait-mediated processes. Over time, many islands cycle between phases of increasing and decreasing size and connectivity to a mainland species pool. As these phases alternate, the dominant process driving species composition switches between colonization and extinction. Both processes are mediated by interactions between organismal traits and environmental constraints: colonization probability is affected by a species’ ability to cross the intervening matrix between a population source and the island; population persistence (or extinction) is driven by the minimum spatial requirements for sustaining an isolated population. Because different suites of traits often mediate these two processes, similar environmental conditions can lead to differences in species compositions at two points of time. Thus, the Constraint-based model of Dynamic Island Biogeography (C-DIB) illustrates the possible role of hysteresis—the dependency of outcomes not only on the current system state but also the system’s history of environmental change—in affecting populations and communities in insular systems. The model provides a framework upon which additional considerations of lag times, biotic interactions, evolution, and other processes can be incorporated. Importantly, it provides a testable framework to study the physical and biological constraints on populations and communities across diverse taxa, scales, and systems

Metabolic heat production and thermal conductance are mass-independent adaptations to thermal environment in birds and mammals

How different kinds of organisms adapt to environmental temperature is central to understanding how they respond to past, present, and future climate change. We applied the Scholander–Irving model of thermoregulation to data on hundreds of species of birds and mammals to assess the contributions of three avenues of adaptation to environmental temperature: body size, basal metabolic rate (BMR), and thermal conductance. Adaptation via body size is limited; the entire ranges of body sizes of birds and mammals occur in nearly all climatic regimes. Using physiological and environmental data for 211 bird and 178 mammal species, we demonstrate that birds and mammals have adapted to geographic variation in environmental temperature regimes by concerted changes in both BMR and thermal conductance

Exploring the influence of ancient and historic megaherbivore extirpations on the global methane budget

Globally, large-bodied wild mammals are in peril. Because “megamammals” have a disproportionate influence on vegetation, trophic interactions, and ecosystem function, declining populations are of considerable conservation concern. However, this is not new; trophic downgrading occurred in the past, including the African rinderpest epizootic of the 1890s, the massive Great Plains bison kill-off in the 1860s, and the terminal Pleistocene extinction of megafauna. Examining the consequences of these earlier events yields insights into contemporary ecosystem function. Here, we focus on changes inmethane emissions, produced as a byproduct of enteric fermentation by herbivores. Although methane is ∼200 times less abundant than carbon dioxide in the atmosphere, the greater efficiency of methane in trapping radiation leads to a significant role in radiative forcing of climate. Using global datasets of late Quaternary mammals, domestic livestock, and human population from the United Nations as well as literature sources, we develop a series of allometric regressions relating mammal body mass to population density and CH4 production, which allows estimation of methane production by wild and domestic herbivores for each historic or ancient time period. We find the extirpation ofmegaherbivores reduced global enteric emissions between 2.2–69.6 Tg CH4 y−1 during the various time periods, representing a decrease of 0.8–34.8% of the overall inputs to tropospheric input. Our analyses suggest that large-bodied mammals have a greater influence on methane emissions than previously appreciated and, further, that changes in the source pool from herbivores can influence global biogeochemical cycles and, potentially, climate

Late quaternary biotic homogenization of North American mammalian faunas

Biotic homogenization-increasing similarity of species composition among ecological communities-has been linked to anthropogenic processes operating over the last century. Fossil evidence, however, suggests that humans have had impacts on ecosystems for millennia. We quantify biotic homogenization of North American mammalian assemblages during the late Pleistocene through Holocene (similar to 30,000 ybp to recent), a timespan encompassing increased evidence of humans on the landscape (similar to 20,000-14,000 ybp). From similar to 10,000 ybp to recent, assemblages became significantly more homogenous (>100% increase in Jaccard similarity), a pattern that cannot be explained by changes in fossil record sampling. Homogenization was most pronounced among mammals larger than 1 kg and occurred in two phases. The first followed the megafaunal extinction at similar to 10,000 ybp. The second, more rapid phase began during human population growth and early agricultural intensification (similar to 2,000-1,000 ybp). We show that North American ecosystems were homogenizing for millennia, extending human impacts back similar to 10,000 years.Peer reviewe

Investigating Biotic Interactions in Deep Time

Recent renewed interest in using fossil data to understand how biotic interactions have shaped the evolution of life is challenging the widely held assumption that long-term climate changes are the primary drivers of biodiversity change. New approaches go beyond traditional richness and co-occurrence studies to explicitly model biotic interactions using data on fossil and modern biodiversity. Important developments in three primary areas of research include analysis of (i) macroevolutionary rates, (ii) the impacts of and recovery from extinction events, and (iii) how humans (Homo sapiens) affected interactions among non-human species. We present multiple lines of evidence for an important and measurable role of biotic interactions in shaping the evolution of communities and lineages on long timescales.Peer reviewe

Late quaternary biotic homogenization of North American mammalian faunas

Biotic homogenization-increasing similarity of species composition among ecological communities-has been linked to anthropogenic processes operating over the last century. Fossil evidence, however, suggests that humans have had impacts on ecosystems for millennia. We quantify biotic homogenization of North American mammalian assemblages during the late Pleistocene through Holocene (similar to 30,000 ybp to recent), a timespan encompassing increased evidence of humans on the landscape (similar to 20,000-14,000 ybp). From similar to 10,000 ybp to recent, assemblages became significantly more homogenous (>100% increase in Jaccard similarity), a pattern that cannot be explained by changes in fossil record sampling. Homogenization was most pronounced among mammals larger than 1 kg and occurred in two phases. The first followed the megafaunal extinction at similar to 10,000 ybp. The second, more rapid phase began during human population growth and early agricultural intensification (similar to 2,000-1,000 ybp). We show that North American ecosystems were homogenizing for millennia, extending human impacts back similar to 10,000 years.Peer reviewe

Open Science principles for accelerating trait-based science across the Tree of Life.

Synthesizing trait observations and knowledge across the Tree of Life remains a grand challenge for biodiversity science. Species traits are widely used in ecological and evolutionary science, and new data and methods have proliferated rapidly. Yet accessing and integrating disparate data sources remains a considerable challenge, slowing progress toward a global synthesis to integrate trait data across organisms. Trait science needs a vision for achieving global integration across all organisms. Here, we outline how the adoption of key Open Science principles-open data, open source and open methods-is transforming trait science, increasing transparency, democratizing access and accelerating global synthesis. To enhance widespread adoption of these principles, we introduce the Open Traits Network (OTN), a global, decentralized community welcoming all researchers and institutions pursuing the collaborative goal of standardizing and integrating trait data across organisms. We demonstrate how adherence to Open Science principles is key to the OTN community and outline five activities that can accelerate the synthesis of trait data across the Tree of Life, thereby facilitating rapid advances to address scientific inquiries and environmental issues. Lessons learned along the path to a global synthesis of trait data will provide a framework for addressing similarly complex data science and informatics challenges

The Ontology of Biological Attributes (OBA)-computational traits for the life sciences.

Existing phenotype ontologies were originally developed to represent phenotypes that manifest as a character state in relation to a wild-type or other reference. However, these do not include the phenotypic trait or attribute categories required for the annotation of genome-wide association studies (GWAS), Quantitative Trait Loci (QTL) mappings or any population-focussed measurable trait data. The integration of trait and biological attribute information with an ever increasing body of chemical, environmental and biological data greatly facilitates computational analyses and it is also highly relevant to biomedical and clinical applications. The Ontology of Biological Attributes (OBA) is a formalised, species-independent collection of interoperable phenotypic trait categories that is intended to fulfil a data integration role. OBA is a standardised representational framework for observable attributes that are characteristics of biological entities, organisms, or parts of organisms. OBA has a modular design which provides several benefits for users and data integrators, including an automated and meaningful classification of trait terms computed on the basis of logical inferences drawn from domain-specific ontologies for cells, anatomical and other relevant entities. The logical axioms in OBA also provide a previously missing bridge that can computationally link Mendelian phenotypes with GWAS and quantitative traits. The term components in OBA provide semantic links and enable knowledge and data integration across specialised research community boundaries, thereby breaking silos

Data from: Body-size trends of the extinct giant shark Carcharocles megalodon: a deep-time perspective on marine apex predators

The extinct shark Carcharocles megalodon is one of the largest marine apex predators ever to exist. Nonetheless, little is known about its body-size variations through time and space. Here, we studied the body-size trends of C. megalodon through its temporal and geographic range to better understand its ecology and evolution. Given that this species was the last of the megatooth lineage, a group of species that shows a purported size increase through time, we hypothesized that C. megalodon also displayed this trend, increasing in size over time and reaching its largest size prior to extinction. We found that C. megalodon body-size distribution was left-skewed (suggesting a long-term selective pressure favoring larger individuals), and presented significant geographic variation (possibly as a result of the heterogeneous ecological constraints of this cosmopolitan species) over geologic time. Finally, we found that stasis was the general mode of size evolution of C. megalodon (i.e., no net changes over time), contrasting with the trends of the megatooth lineage and our hypothesis. Given that C. megalodon is a relatively long-lived species with a widely distributed fossil record, we further used this study system to provide a deep-time perspective to the understanding of the body-size trends of marine apex predators. For instance, our results suggest that (1) a selective pressure in predatory sharks for consuming a broader range of prey may favor larger individuals and produce left-skewed distributions on a geologic time scale; (2) body-size variations in cosmopolitan apex marine predators may depend on their interactions with geographically discrete communities; and (3) the inherent characteristics of shark species can produce stable sizes over geologic time, regardless of the size trends of their lineages