Elizabeth A. Hadly

Approaching a state shift in Earth’s biosphere

Localized ecological systems are known to shift abruptly and irreversibly from one state to another when they are forced across critical thresholds. Here we review evidence that the global ecosystem as a whole can react in the same way and is approaching a planetary-scale critical transition as a result of human influence. The plausibility of a planetary-scale ‘tipping point’ highlights the need to improve biological forecasting by detecting early warning signs of critical transitions on global as well as local scales, and by detecting feedbacks that promote such transitions. It is also necessary to address root causes of how humans are forcing biological changes.

Serial SimCoal: A population genetics model for data from multiple populations and points in time

UNLABELLED We present Serial SimCoal, a program that models population genetic data from multiple time points, as with ancient DNA data. An extension of SIMCOAL, it also allows simultaneous modeling of complex demographic histories, and migration between multiple populations. Further, we incorporate a statistical package to calculate relevant summary statistics, which, for the first time allows users to investigate the statistical power provided by, conduct hypothesis-testing with, and explore sample size limitations of ancient DNA data. AVAILABILITY Source code and Windows/Mac executables at http://www.stanford.edu/group/hadlylab/ssc.html CONTACT senka@stanford.edu.

Similarity of Mammalian Body Size across the Taxonomic Hierarchy and across Space and Time

Although it is commonly assumed that closely related animals are similar in body size, the degree of similarity has not been examined across the taxonomic hierarchy. Moreover, little is known about the variation or consistency of body size patterns across geographic space or evolutionary time. Here, we draw from a data set of terrestrial, nonvolant mammals to quantify and compare patterns across the body size spectrum, the taxonomic hierarchy, continental space, and evolutionary time. We employ a variety of statistical techniques including “sib‐sib” regression, phylogenetic autocorrelation, and nested ANOVA. We find an extremely high resemblance (heritability) of size among congeneric species for mammals over ∼18 g; the result is consistent across the size spectrum. However, there is no significant relationship among the body sizes of congeneric species for mammals under ∼18 g. We suspect that life‐history and ecological parameters are so tightly constrained by allometry at diminutive size that animals can only adapt to novel ecological conditions by modifying body size. The overall distributions of size for each continental fauna and for the most diverse orders are quantitatively similar for North America, South America, and Africa, despite virtually no overlap in species composition. Differences in ordinal composition appear to account for quantitative differences between continents. For most mammalian orders, body size is highly conserved, although there is extensive overlap at all levels of the taxonomic hierarchy. The body size distribution for terrestrial mammals apparently was established early in the Tertiary, and it has remained remarkably constant over the past 50 Ma and across the major continents. Lineages have diversified in size to exploit environmental opportunities but only within limits set by allometric, ecological, and evolutionary constraints.

Predicting biodiversity change and averting collapse in agricultural landscapes

The equilibrium theory of island biogeography is the basis for estimating extinction rates and a pillar of conservation science. The default strategy for conserving biodiversity is the designation of nature reserves, treated as islands in an inhospitable sea of human activity. Despite the profound influence of islands on conservation theory and practice, their mainland analogues, forest fragments in human-dominated landscapes, consistently defy expected biodiversity patterns based on island biogeography theory. Countryside biogeography is an alternative framework, which recognizes that the fate of the world’s wildlife will be decided largely by the hospitality of agricultural or countryside ecosystems. Here we directly test these biogeographic theories by comparing a Neotropical countryside ecosystem with a nearby island ecosystem, and show that each supports similar bat biodiversity in fundamentally different ways. The island ecosystem conforms to island biogeographic predictions of bat species loss, in which the water matrix is not habitat. In contrast, the countryside ecosystem has high species richness and evenness across forest reserves and smaller forest fragments. Relative to forest reserves and fragments, deforested countryside habitat supports a less species-rich, yet equally even, bat assemblage. Moreover, the bat assemblage associated with deforested habitat is compositionally novel because of predictable changes in abundances by many species using human-made habitat. Finally, we perform a global meta-analysis of bat biogeographic studies, spanning more than 700 species. It generalizes our findings, showing that separate biogeographic theories for countryside and island ecosystems are necessary. A theory of countryside biogeography is essential to conservation strategy in the agricultural ecosystems that comprise roughly half of the global land surface and are likely to increase even further.

Small mammal diversity loss in response to late-Pleistocene climatic change.

Communities have been shaped in numerous ways by past climatic change; this process continues today. At the end of the Pleistocene epoch about 11,700 years ago, North American communities were substantially altered by the interplay of two events. The climate shifted from the cold, arid Last Glacial Maximum to the warm, mesic Holocene interglacial, causing many mammal species to shift their geographic distributions substantially. Populations were further stressed as humans arrived on the continent. The resulting megafaunal extinction event, in which 70 of the roughly 220 largest mammals in North America (32%) became extinct, has received much attention. However, responses of small mammals to events at the end of the Pleistocene have been much less studied, despite the sensitivity of these animals to current and future environmental change. Here we examine community changes in small mammals in northern California during the last ‘natural’ global warming event at the Pleistocene–Holocene transition and show that even though no small mammals in the local community became extinct, species losses and gains, combined with changes in abundance, caused declines in both the evenness and richness of communities. Modern mammalian communities are thus depauperate not only as a result of megafaunal extinctions at the end of the Pleistocene but also because of diversity loss among small mammals. Our results suggest that across future landscapes there will be some unanticipated effects of global change on diversity: restructuring of small mammal communities, significant loss of richness, and perhaps the rising dominance of native ‘weedy’ species.

Genetic Response to Climatic Change: Insights from Ancient DNA and Phylochronology

Understanding how climatic change impacts biological diversity is critical to conservation. Yet despite demonstrated effects of climatic perturbation on geographic ranges and population persistence, surprisingly little is known of the genetic response of species. Even less is known over ecologically long time scales pertinent to understanding the interplay between microevolution and environmental change. Here, we present a study of population variation by directly tracking genetic change and population size in two geographically widespread mammal species (Microtus montanus and Thomomys talpoides) during late-Holocene climatic change. We use ancient DNA to compare two independent estimates of population size (ecological and genetic) and corroborate our results with gene diversity and serial coalescent simulations. Our data and analyses indicate that, with population size decreasing at times of climatic change, some species will exhibit declining gene diversity as expected from simple population genetic models, whereas others will not. While our results could be consistent with selection, independent lines of evidence implicate differences in gene flow, which depends on the life history strategy of species.

MAMMALIAN RESPONSE TO GLOBAL WARMING ON VARIED TEMPORAL SCALES

Abstract Paleontological information was used to evaluate and compare how Rocky Mountain mammalian communities changed during past global warming events characterized by different durations (350, ∼10,000–20,000, and 4 million years) and different per–100-year warming rates (1.0°C, 0.1°C, 0.06–0.08°C, 0.0002–0.0003°C per 100 years). Our goals were to determine whether biotic changes observed today are characteristic of or accelerated relative to what took place during past global warming events and to clarify the possible trajectory of mammalian faunal change that climate change may initiate. This determination is complicated because actual warming rates scale inversely with the time during which temperature is measured, and species with different life-history strategies respond (or do not) in different ways. Nevertheless, examination of past global warming episodes suggested that approximately concurrent with warming, a predictable sequence of biotic events occurs at the regional scale of the central and northern United States Rocky Mountains. First, phenotypic and density changes in populations are detectable within 100 years. Extinction of some species, noticeable changes in taxonomic composition of communities, and possibly reduction in species richness follow as warming extends to a few thousand years. Faunal turnover nears 100% and species diversity may increase when warm temperatures last hundreds of thousands to millions of years, because speciation takes place and faunal changes initiated by a variety of shorter-term processes accumulate. Climate-induced faunal changes reported for the current global warming episode probably do not yet exceed the normal background rate, but continued warming during the next few decades, especially combined with the many other pressures of humans on natural ecosystems, has a high probability of producing effects that have not been experienced often, if ever, in mammalian history.

Forest bolsters bird abundance, pest control and coffee yield

Efforts to maximise crop yields are fuelling agricultural intensification, exacerbating the biodiversity crisis. Low-intensity agricultural practices, however, may not sacrifice yields if they support biodiversity-driven ecosystem services. We quantified the value native predators provide to farmers by consuming coffees most damaging insect pest, the coffee berry borer beetle (Hypothenemus hampei). Our experiments in Costa Rica showed birds reduced infestation by ~ 50%, bats played a marginal role, and farmland forest cover increased pest removal. We identified borer-consuming bird species by assaying faeces for borer DNA and found higher borer-predator abundances on more forested plantations. Our coarse estimate is that forest patches doubled pest control over 230 km2 by providing habitat for ~ 55 000 borer-consuming birds. These pest-control services prevented US

Bayesian estimation of the timing and severity of a population bottleneck from ancient DNA.

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Using phylochronology to reveal cryptic population histories: review and synthesis of 29 ancient DNA studies

310 ha-year(-1) in damage, a benefit per plantation on par with the average annual income of a Costa Rican citizen. Retaining forest and accounting for pest control demonstrates a win-win for biodiversity and coffee farmers.