Elizabeth A Hadly

Elizabeth A Hadly
Stanford University | SU · Department of Biology

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122
Publications
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Publications

Publications (122)
Preprint
The big cats (genus Panthera ) represent some of the most popular and charismatic species on the planet. Although some reference genomes are available for this clade, few are at the chromosome level, inhibiting high-resolution genomic studies. Here, we assemble genomes from three members of the genus, the tiger ( Panthera tigris ), the snow leopard...
Article
Full-text available
Elephants are essential ecological engineers, creating and maintaining landscape structure and ecosystem function. The recently distinguished and critically endangered forest elephant is currently classified as a selective, non‐destructive frugivorous browser that maintains forest diversity, while the savanna elephant is a mixed feeder, often pushi...
Article
Full-text available
While trends in tropical deforestation are alarming, conservation biologists are increasingly recognizing the potential for species survival in human-modified landscapes. Identifying the factors underlying such persistence, however, requires basic ecological knowledge of a species' resource use. Here, we generate such data to guide conservation of...
Article
Understanding how raptors select prey is important to determine taphonomic biases both in modern and paleo pellet assemblages. We tested whether pellets more closely represent raptor dietary specialization or local small mammal diversity by sampling pellets from seven raptor species across four study sites in Yellowstone National Park, Wyoming, USA...
Article
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Wetlands worldwide are under threat from anthropogenic impacts. In large protected North American areas such as Yellowstone and Wood Buffalo National Parks, aquatic habitats are disappearing and wetland-dependent fauna are in decline1–3. Here we investigate population dynamics of an indicator species in Canada’s Peace-Athabasca Delta (“the delta”),...
Article
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Global biodiversity is threatened by the anthropogenic restructuring of animal communities, rewiring species interaction networks in real-time as individuals are extirpated or introduced. Conservation science and adaptive ecosystem management demand more rapid, quantitative, and non-invasive technologies for robustly capturing changing biodiversity...
Article
Full-text available
Acclimation to environmental changes driven by alterations in gene expression will serve as an important response for some species facing rapid Anthropogenic climate change. Pikas, genus Ochotona, are particularly vulnerable to climate change and current trends suggest that only the highest, coldest elevations within their ranges may remain suitabl...
Article
Full-text available
Before environmental DNA (eDNA) can establish itself as a robust tool for biodiversity monitoring, comparison with existing approaches is necessary, yet is lacking for terrestrial mammals. Moreover, much is unknown regarding the nature, spread and persistence of DNA shed by animals into terrestrial environments, or the optimal experimental design f...
Data
Bayesian phylogenetic hypothesis based on 664bp of MT-CYB. Posterior probability of each node is indicated. Scale bar represents substitutions per nucleotide site. (TIF)
Data
Detection of SNPs under selection using Bayescan. Each point corresponds to a SNP in our dataset. Fst is plotted against the q-value, where the q-value is the minimum False Discovery Rate at which the SNP would become significant. (TIF)
Data
Venn diagram of shared versus private SNPs for each sampling location. The number of total SNPs found in each site is given next to the site elevation. The number of SNPs in each section is indicated in bold. The percentage of the total SNPs for each site that a section makes up is indicated. The 5,000 m site is shown in light blue, the 4,000 m sit...
Data
Results of differential expression analysis of hemoglobin transcripts between the 5,000 m site and the lower-elevation sites. (DOCX)
Article
Full-text available
As humans move and alter habitats, they change the disease risk for themselves, their commensal animals and wildlife. Bartonella bacteria are prevalent in mammals and cause numerous human infections. Understanding how this genus has evolved and switched hosts in the past can reveal how current patterns were established and identify potential mechan...
Data
Maximum clade credibility phylogeny based on 540 bp fragment of gltA with estimated branch timing. The numbers in brackets indicate the lower and upper bounds of the 95% highest posterior density of the height of that branch, an estimate of the age of divergence of the node that the branch leads to. The width of the circle at each node is proportio...
Data
Metadata for all gltA sequences. (XLSX)
Data
Metadata for all 16s sequences. (XLSX)
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Final 16s maximum clade credibility phylogenetic hypothesis. (TREES)
Data
Model summaries for evolution of Bartonella geography (Continent). (DOCX)
Data
Summary of observed host and geographic transfers. This file lists every inferred host transfer or finding of a genotype or monophyletic clade on more than one continent. A legend for interpreting each category appears on the second sheet of the file. (XLSX)
Data
Reservoirs, phylogenetic context and geographic regions of Bartonella genotypes found in humans. Reservoir and geographic data are derived from gltA metadata, Breitschwerdt [32] and cited references. Phylogenetic context refers to placement in both the 277bp and 540bp MCC trees. (DOCX)
Data
Groups of identical sequences in 277 bp gltA analysis. Only one representative per group is included in the phylogeny and S2 Fig even though identical genotypes may have been found in other hosts or geographic regions. This file lists all Genbank accession numbers for sequences found in more than one individual in the study. A legend for all catego...
Data
540 bp gltA alignment. (NEX)
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R code for evolutionary model fits on the 277bp tree. (R)
Data
Model summaries for evolution of Bartonella host order. (DOCX)
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Model summaries for evolution of Bartonella geography (Old World versus New World). (DOCX)
Data
Maximum clade credibility phylogeny based on 277 bp fragment of gltA illustrating the order of the host and geographic region from which Bartonella genotypes were isolated. The color of the tip label indicates the order of the host from which the genotype was derived (ectoparasites are colored according to their host). Highlighted tips indicate tha...
Data
Inferred divergence times of host switches based on 540bp tree. This file lists every well-supported host switching event captured in our 540bp phylogenetic hypothesis. A legend for interpreting each column appears on the second sheet of the file. (XLSX)
Data
277 bp gltA alignment. (NEX)
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259 bp 16s alignment. (NEX)
Data
Final 277bp gltA maximum clade credibility phylogenetic hypothesis. (TREES)
Data
Final 540bp gltA maximum clade credibility phylogenetic hypothesis. (TREES)
Article
The genus Ochotona (pikas) is a clade of cold‐tolerant lagomorphs that includes many high‐elevation species. Pikas offer a unique opportunity to study adaptations and potential limitations of an ecologically important mammal to high‐elevation hypoxia. We analyzed the evolution of three mitochondrial genes encoding the catalytic core of cytochrome c...
Preprint
As humans alter habitats and move themselves and their commensal animals around the globe they change the disease risk for themselves, their commensal animals and wildlife. Bartonella bacteria are prevalent in many mammalian taxa, responsible for numerous human infections and presumed to be an important emerging group of zoonoses. Understanding how...
Article
Full-text available
Marked reductions in population size can trigger corresponding declines in genetic variation. Understanding the precise genetic consequences of such reductions, however, is often challenging due to the absence of robust pre- and post-reduction datasets. Here, we use heterochronous genomic data from samples obtained before and immediately after the...
Article
Bats have been observed to shift the frequency of their echolocation calls in the presence of other echolocating bats, ostensibly as a way to reduce acoustic interference. Few studies, however, have examined the theoretical efficacy of such jamming avoidance responses. The present study uses the wideband ambiguity function to analyze the effects of...
Article
Full-text available
If species’ evolutionary pasts predetermine their responses to evolutionarily novel stressors, then phylogeny could predict species survival in an increasingly human-dominated world. To understand the role of phylogenetic relatedness in structuring responses to rapid environmental change, we focused on assemblages of Neotropical bats, an ecological...
Article
Full-text available
Catastrophic natural events can have profound impacts on patterns of genetic diversity. Due to the typically unpredictable nature of such phenomena, however, few studies have been able to directly compare patterns of diversity before and after natural catastrophic events. Here, we examine the impacts of a recent volcanic eruption in southern Chile...
Article
Full-text available
BACKGROUND: The pace and magnitude of human-caused global change has accelerated dramatically over the past 50 years, overwhelming the capacity of many ecosystems and species to maintain themselves as they have under the more stable conditions that prevailed for at least 11,000 years. The next few decades threaten even more rapid transformations be...
Article
Question: Are there general traits that will foster the persistence of terrestrial vertebrates (Superclass Tetrapoda) through the challenges of the Anthropocene? Methods: We identified five primary anthropogenic threats to terrestrial biodiversity: habitat change, direct interaction/exploitation, invasive species, climate change, and pollution. We...
Article
Full-text available
Background High morphological diversity can occur in closely related animals when selection favors morphologies that are subject to intrinsic biological constraints. A good example is subterranean rodents of the genus Thomomys, one of the most taxonomically and morphologically diverse mammalian genera. Highly procumbent, tooth-digging rodent skull...
Article
Land-use change and climate change are driving a global biodiversity crisis. Yet, how species' responses to climate change are correlated with their responses to land-use change is poorly understood. Here, we assess the linkages between climate and land-use change on birds in Neotropical forest and agriculture. Across > 300 species, we show that af...
Data
Appendix S3. Data on bat captures, bat and bat fly identities and tree cover at each site.
Data
Figure S1. Assemblage change across sites in the study years is similar to assemblage change across sites in a 5 year capture dataset. Figure S2. Bat species accumulation curves show adequate sampling of most species. Figure S3. Correlation of bat and bat fly communities with tree cover at different spatial scales. Table S1. Bat and bat fly summ...
Article
Full-text available
Abstract We maintain that humanity’s grand challenge is solving the intertwined problems of human population growth and overconsumption, climate change, pollution, ecosystem destruction, disease spillovers, and extinction, in order to avoid environmental tipping points that would make human life more difficult and would irrevocably damage planetary...
Article
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Loss of megafauna, an aspect of defaunation, can precipitate many ecological changes over short time scales. We examine whether megafauna loss can also explain features of lasting ecological state shifts that occurred as the Pleistocene gave way to the Holocene. We compare ecological impacts of late-Quaternary megafauna extinction in five American...
Article
Full-text available
Habitat conversion is a major driver of the biodiversity crisis, yet why some species undergo local extinction while others thrive under novel conditions remains unclear. We suggest that focusing on species' niches, rather than traits, may provide the predictive power needed to forecast biodiversity change. We first examine two Neotropical frog con...
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Biodiversity loss will likely have surprising and dramatic consequences for human wellbeing. Identifying species that benefit society represents a critical first step towards predicting the consequences of biodiversity loss. Though natural predators prevent billions of dollars in agricultural pest damage annually, characterizing which predators con...
Article
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Habitat conversion is the primary driver of biodiversity loss, yet little is known about how it is restructuring the tree of life by favoring some lineages over others. We combined a complete avian phylogeny with 12 years of Costa Rican bird surveys (118,127 detections across 487 species) sampled in three land uses: forest reserves, diversified agr...
Article
Although scientists typically regard their work as finished with publication in an academic journal, in fact that is just the beginning if the goal is to help society solve problems. This is particularly true for the environmental sciences, in which a generation of scientists has documented that five interacting human impacts are causing undesirabl...
Article
Full-text available
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 pra...
Article
Full-text available
The Anthropocene is recognized (though not yet formally defined) as the time when human impacts are widespread on Earth. While some of the impacts are essential to supporting large human populations and can be sustainable in the long run, others can irretrievably damage the life support systems upon which the global society has come to depend, or s...
Article
Despite the technological advances that characterize the Anthropocene, it will be necessary to address and solve some key environmental problems in order to mitigate societal risks and avoid undesirable impacts. Success will require more effective interactions between scientists, policy makers, the business community, technological innovators, thou...
Article
Full-text available
Tigers (Panthera tigris), like many large carnivores, are threatened by anthropogenic impacts, primarily habitat loss and poaching. Current conservation plans for tigers focus on population expansion, with the goal of doubling census size in the next 10 years. Previous studies have shown that because the demographic decline was recent, tiger popula...
Article
With ever-increasing human pressure on ecosystems, it is critically important to predict how ecosystem functions will respond to such human-induced perturbations. We define perturbations as either changes to abiotic environment (e.g. eutrophication, climate change) that indirectly affects biota, or direct changes to biota (e.g. species introduction...
Article
Full-text available
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 coffee's most damaging insect pest,...
Article
Full-text available
Species ranges are mediated by physiology, environmental factors, and competition with other organisms. The allopatric distribution of five species of northern Californian pocket gophers (Thomomys spp.) is hypothesized to result from competitive exclusion. The five species in this environmentally heterogeneous region separate into two subgenera, Th...
Data
Similar to Table 4 but reporting the 6.5 km grid dataset. Soil bin Chi-squared values (in regular font) compare the expected and observed values for one subgenus in one soil bin. Values above 3.50 reflect a significant portion of the 5.99 critical value (CV) required for significance in the subgenus Chi square test. The subgenus Chi-squared tests (...
Data
Impact of validation on pocket gopher locality georeferences. Old localities (dark red circles) were designated using only the brief locality description as per the MaNIS protocol. New localities (blue and pink circles) were designated by AEM using the collector's original field notes. Our validation targeted localities that had red flags for coord...
Data
The much smaller 6.5 km grid dataset shows similar Chi square results as the full dataset. Compare to Figure 5. The null hypothesis for the Chi square tests: random distribution across the study area for the 6.5 km grid dataset (n = 200). Expected values are proportional to the percent study area in each soil bin. For bulk density, percent clay, an...
Article
Full-text available
Earth is rapidly approaching a tipping point. Human impacts are causing alarming levels of harm to our planet. As scientists who study the interaction of people with the rest of the biosphere using a wide range of approaches, we agree that the evidence that humans are damaging their ecological life-support systems is overwhelming. We further agree...
Conference Paper
Background/Question/Methods Human domination has dramatically altered the ecological and evolutionary dynamics of life on Earth. While many species are ill equipped to survive human impacts, others persist and even thrive amidst anthropogenic change. Clearly the current ecologies of these two species groups differ, but how did attributes that tod...
Article
Full-text available
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 pla...
Article
Full-text available
Recent data indicates that blotched tiger salamanders (Ambystoma tigrinum melanostictum) in northern regions of Yellowstone National Park are declining due to climate-related habitat changes. In this study, we used ancient and modern mitochondrial haplotype diversity to model the effective size of this amphibian population through recent geological...
Article
Full-text available
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 pla...
Article
Full-text available
The latitudinal gradient of species diversity is one of the oldest recognized patterns in biology. While the cause of the pattern remains debated, the global signal of greater diversity toward the tropics is widely established. Whether the pattern holds for genetic diversity within species, however, has received much less attention. We examine lati...
Article
An understanding of how ecological traits influence past species response to environmental change can aid our future predictions of species persistence. We used ancient DNA and serial coalescent modelling in a hypothesis-testing framework to reveal differences in temporal genetic variation over 10,000 years for two species of subterranean rodents t...
Article
Forecasting how species will respond to climatic change requires knowledge of past community dynamics. Here we use time-series data from the small-mammal fossil records of two caves in the Great Basin of the American West to evaluate how contrasting and variable local paleoclimates have shaped small-mammal abundance dynamics over the last $ 7500 ye...