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A. Townsend Peterson

Bio: A. Townsend Peterson is an academic researcher from University of Kansas. The author has contributed to research in topics: Environmental niche modelling & Ecological niche. The author has an hindex of 91, co-authored 521 publications receiving 51524 citations. Previous affiliations of A. Townsend Peterson include California Academy of Sciences & University of Chicago.


Papers
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Journal ArticleDOI
TL;DR: This commentary calls for greater rigor in application of molecular clocks – clocks should only be used when clocklike behavior has been tested and confirmed, and when appropriate calibrations are available.
Abstract: Molecular clocks have seen many applications in ornithology, but many applications are uncritical. In this commentary, I point out logical inconsistencies in many uses of clocks in avian molecular systematics. I call for greater rigor in application of molecular clocks – clocks should only be used when clocklike behavior has been tested and confirmed, and when appropriate calibrations are available. Authors and reviewers should insist on such rigor to assure that systematics is indeed scientific, and not just storytelling.

32 citations

Journal ArticleDOI
TL;DR: The utility of ENM was explored to investigate potential distributions of chirodropid box-jellyfishes, a group of highly toxic invertebrates whose biogeography is poorly understood, and it was demonstrated that geographic over-prediction in ENM can be desirable when concerned with predictions beyond current knowledge of species' distribu- tions.
Abstract: Geographic distributions of many marine species are poorly documented or understood, which is particularly true for marine invertebrates. Ecological niche modeling (ENM) offers a means to address this issue, but to date most studies using ENM have focused on terrestrial taxa. In general, ENM relates environmental information to species' occurrence data to estimate the ecological niche of a species, rather than just interpolating a geographic distribution. This process leads to predictions of suitable habitat that generally exceed the range actually inhabited by a single species: such areas of geographic over-prediction (commission) may be inhabited by closely related species, and the model thus offers the inferential power to predict the potential distributions of these species as well. We explored the utility of ENM to investigate potential distributions of chirodropid box-jellyfishes (Cnidaria: Cubozoa), a group of highly toxic invertebrates whose biogeography is poorly understood. We were able to predict reported occurrences of box-jellyfishes throughout the Indo-Pacific from data of closely related species. By doing so, we demonstrate that geographic over-prediction in ENM can be desirable when concerned with predictions beyond current knowledge of species' distribu- tions. Several methods are used for ENM; here, we compared the 2 most commonly used methods, the Genetic Algorithm for Rule-Set Predictions (GARP) and a maximum entropy approach (Maxent). Our comparison shows that Maxent may be more prone to overfitting, whereas GARP tends to pro- duce broader predictions. Transforming continuous Maxent predictions into binary predictions reme- dies problems of overfitting, and allows for effective extrapolation into unsampled geographic space.

32 citations

Journal ArticleDOI
TL;DR: In this paper, a procedure for developing such biodiversity scenarios using available data on species distribution derived from primary biodiversity data and habitat conditions, and analytical software, which allows estimation of species distributions, and forecasting of likely effects of various agents of change on the distribution and status of the same species.
Abstract: A thorough understanding of biodiversity status and trends through time is necessary for decision-making at regional, national, and subnational levels. Information readily available in databases allows for development of scenarios of species distribution in relation to habitat changes. Existing species occurrence data are biased towards some taxonomic groups (especially vertebrates), and are more complete for Europe and North America than for the rest of the world. We outline a procedure for development of such biodiversity scenarios using available data on species distribution derived from primary biodiversity data and habitat conditions, and analytical software, which allows estimation of species’ distributions, and forecasting of likely effects of various agents of change on the distribution and status of the same species. Such approaches can translate into improved knowledge for countries regarding the 2010 Biodiversity Target of reducing significantly the rate of biodiversity loss—indeed, using methodologies such as those illustrated herein, many countries should be capable of analyzing trends of change for at least part of their biodiversity. Sources of errors that are present in primary biodiversity data and that can affect projections are discussed.

32 citations

Journal ArticleDOI
TL;DR: In this article, the authors used a simulation approach to test two propositions: (1) strong geographic patterns of variation in realized niche breadth can arise in the absence of variance in the size of fundamental niches, and (2) realized niche breadths can show latitudinal patterns as a consequence of spatio-temporal climate change.
Abstract: Aim. Tropical species are thought to experience and be adapted to narrow ranges of abiotic conditions. This idea has been invoked to explain a broad array of biological phenomena, including the latitudinal diversity gradient and differential rates of speciation and extinction. However, debate continues regarding the broad-scale applicability of this pattern and potential processes responsible. Here, we use a simulation approach to test two propositions: (1) strong geographic patterns of variation in realized niche breadth can arise in the absence of variance in the size of fundamental niches, and (2) realized niche breadths can show latitudinal patterns as a consequence of spatio-temporal climate change, even when fundamental niche breadths are unrelated to latitude, and dispersal abilities are held constant. Location. Global. Time period. Simulations were conducted using climate models from over the last 120 Ka, with trait dynamics captured at 95 Ka and present-day. Major taxa studied. We used virtual species with traits based loosely on plants. Methods. We simulated latitudinal trends of niche breadth and range size for virtual species using a cellular automaton algorithm that linked a gridded geographic domain with a three-dimensional environmental landscape. Results. In all simulations, strong spatial patterns in realized niches were obtained in the absence of niche evolution, and realized niches showed geographic patterns deriving only from real-world spatiotemporal variation in climate. We noted contrasting patterns of niche breadth in different environmental dimensions, with temperature breadth increasing with latitude, but precipitation breadth decreasing with latitude. Overall, simulation outcomes mimicked real-world pattern of latitudinal range extent covarying with amount of land area. Main conclusions. Tropical species can have narrower niche breadths for maximum and minimum temperature ranges compared to temperate species solely as the result of the spatial arrangement of environments. We therefore suggest that the complex spatiotemporal distribution of global abiotic environments has strong potential for structuring observed latitudinal gradients of niche breadths.

31 citations

Journal ArticleDOI
TL;DR: The Museums and Emerging Pathogens in the Americas (MEPA) as mentioned in this paper is a virtual network aimed at fostering communication, coordination, and collaborative problem-solving among pathogen researchers, public health officials, and biorepositories.
Abstract: The Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) pandemic reveals a major gap in global biosecurity infrastructure: a lack of publicly available biological samples representative across space, time, and taxonomic diversity. The shortfall, in this case for vertebrates, prevents accurate and rapid identification and monitoring of emerging pathogens and their reservoir host(s) and precludes extended investigation of ecological, evolutionary, and environmental associations that lead to human infection or spillover. Natural history museum biorepositories form the backbone of a critically needed, decentralized, global network for zoonotic pathogen surveillance, yet this infrastructure remains marginally developed, underutilized, underfunded, and disconnected from public health initiatives. Proactive detection and mitigation for emerging infectious diseases (EIDs) requires expanded biodiversity infrastructure and training (particularly in biodiverse and lower income countries) and new communication pipelines that connect biorepositories and biomedical communities. To this end, we highlight a novel adaptation of Project ECHO's virtual community of practice model: Museums and Emerging Pathogens in the Americas (MEPA). MEPA is a virtual network aimed at fostering communication, coordination, and collaborative problem-solving among pathogen researchers, public health officials, and biorepositories in the Americas. MEPA now acts as a model of effective international, interdisciplinary collaboration that can and should be replicated in other biodiversity hotspots. We encourage deposition of wildlife specimens and associated data with public biorepositories, regardless of original collection purpose, and urge biorepositories to embrace new specimen sources, types, and uses to maximize strategic growth and utility for EID research. Taxonomically, geographically, and temporally deep biorepository archives serve as the foundation of a proactive and increasingly predictive approach to zoonotic spillover, risk assessment, and threat mitigation.

31 citations


Cited by
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Journal ArticleDOI
TL;DR: Preface to the Princeton Landmarks in Biology Edition vii Preface xi Symbols used xiii 1.
Abstract: Preface to the Princeton Landmarks in Biology Edition vii Preface xi Symbols Used xiii 1. The Importance of Islands 3 2. Area and Number of Speicies 8 3. Further Explanations of the Area-Diversity Pattern 19 4. The Strategy of Colonization 68 5. Invasibility and the Variable Niche 94 6. Stepping Stones and Biotic Exchange 123 7. Evolutionary Changes Following Colonization 145 8. Prospect 181 Glossary 185 References 193 Index 201

14,171 citations

Journal ArticleDOI
TL;DR: In this paper, the use of the maximum entropy method (Maxent) for modeling species geographic distributions with presence-only data was introduced, which is a general-purpose machine learning method with a simple and precise mathematical formulation.

13,120 citations

Journal Article
Fumio Tajima1
30 Oct 1989-Genomics
TL;DR: It is suggested that the natural selection against large insertion/deletion is so weak that a large amount of variation is maintained in a population.

11,521 citations

Journal ArticleDOI
TL;DR: The Bayesian Evolutionary Analysis by Sampling Trees (BEAST) software package version 1.7 is presented, which implements a family of Markov chain Monte Carlo algorithms for Bayesian phylogenetic inference, divergence time dating, coalescent analysis, phylogeography and related molecular evolutionary analyses.
Abstract: Computational evolutionary biology, statistical phylogenetics and coalescent-based population genetics are becoming increasingly central to the analysis and understanding of molecular sequence data. We present the Bayesian Evolutionary Analysis by Sampling Trees (BEAST) software package version 1.7, which implements a family of Markov chain Monte Carlo (MCMC) algorithms for Bayesian phylogenetic inference, divergence time dating, coalescent analysis, phylogeography and related molecular evolutionary analyses. This package includes an enhanced graphical user interface program called Bayesian Evolutionary Analysis Utility (BEAUti) that enables access to advanced models for molecular sequence and phenotypic trait evolution that were previously available to developers only. The package also provides new tools for visualizing and summarizing multispecies coalescent and phylogeographic analyses. BEAUti and BEAST 1.7 are open source under the GNU lesser general public license and available at http://beast-mcmc.googlecode.com and http://beast.bio.ed.ac.uk

9,055 citations

Journal ArticleDOI
TL;DR: Range-restricted species, particularly polar and mountaintop species, show severe range contractions and have been the first groups in which entire species have gone extinct due to recent climate change.
Abstract: Ecological changes in the phenology and distribution of plants and animals are occurring in all well-studied marine, freshwater, and terrestrial groups These observed changes are heavily biased in the directions predicted from global warming and have been linked to local or regional climate change through correlations between climate and biological variation, field and laboratory experiments, and physiological research Range-restricted species, particularly polar and mountaintop species, show severe range contractions and have been the first groups in which entire species have gone extinct due to recent climate change Tropical coral reefs and amphibians have been most negatively affected Predator-prey and plant-insect interactions have been disrupted when interacting species have responded differently to warming Evolutionary adaptations to warmer conditions have occurred in the interiors of species’ ranges, and resource use and dispersal have evolved rapidly at expanding range margins Observed genetic shifts modulate local effects of climate change, but there is little evidence that they will mitigate negative effects at the species level

7,657 citations