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.

The Importance of Biodiversity E-infrastructures for Megadiverse Countries

Abstract: Addressing the challenges of biodiversity conservation and sustainable development requires global cooperation, support structures, and new governance models to integrate diverse initiatives and achieve massive, open exchange of data, tools, and technology. The traditional paradigm of sharing scientific knowledge through publications is not sufficient to meet contemporary demands that require not only the results but also data, knowledge, and skills to analyze the data. E-infrastructures are key in facilitating access to data and providing the framework for collaboration. Here we discuss the importance of e-infrastructures of public interest and the lack of long-term funding policies. We present the example of Brazil’s speciesLink network, an e-infrastructure that provides free and open access to biodiversity primary data and associated tools. SpeciesLink currently integrates 382 datasets from 135 national institutions and 13 institutions from abroad, openly sharing ~7.4 million records, 94% of which are associated to voucher specimens. Just as important as the data is the network of data providers and users. In 2014, more than 95% of its users were from Brazil, demonstrating the importance of local e-infrastructures in enabling and promoting local use of biodiversity data and knowledge. From the outset, speciesLink has been sustained through project-based funding, normally public grants for 2–4-year periods. In between projects, there are short-term crises in trying to keep the system operational, a fact that has also been observed in global biodiversity portals, as well as in social and physical sciences platforms and even in computing services portals. In the last decade, the open access movement propelled the development of many web platforms for sharing data. Adequate policies unfortunately did not follow the same tempo, and now many initiatives may perish.

Current knowledge of Leishmania vectors in Mexico: how geographic distributions of species relate to transmission areas.

Abstract: . Leishmaniases are a group of vector-borne diseases with different clinical manifestations caused by parasites transmitted by sand fly vectors. In Mexico, the sand fly Lutzomyia olmeca olmeca is the only vector proven to transmit the parasite Leishmania mexicana to humans, which causes leishmaniasis. Other vector species with potential medical importance have been obtained, but their geographic distributions and relation to transmission areas have never been assessed. We modeled the ecological niches of nine sand fly species and projected niches to estimate potential distributions by using known occurrences, environmental coverages, and the algorithms GARP and Maxent. All vector species were distributed in areas with known recurrent transmission, except for Lu. diabolica, which appeared to be related only to areas of occasional transmission in northern Mexico. The distribution of Lu. o. olmeca does not overlap with all reported cutaneous leishmaniasis cases, suggesting that Lu. cruciata and Lu. shannoni are likely also involved as primary vectors in those areas. Our study provides useful information of potential risk areas of leishmaniasis transmission in Mexico.

Phylogeny and Rates of Molecular Evolution in the Aphelocoma Jays (Corvidae)

Abstract: -I examined hypotheses of Aphelocoma jay phylogeny derived from allozyme data. Results from various algorithms differ in details, but the overall patterns are consistent: Scrub Jays (A. coerulescens) and Unicolored Jays (A. unicolor) were derived independently from different populations of Gray-breasted Jays (A. ultramarina). Within Scrub Jays, the californica subspecies group was derived from the populations of interior North America (woodhouseii group). One Unicolored Jay population and two Scrub Jay populations, all strongly differentiated, are placed consistently at the base of the phylogeny, but phenotypic, biogeographic, and theoretical evidence suggests that these populations represent rapidly evolving populations derived from within populations of their respective species. Because analyses of rates of molecular evolution demonstrate significant rate heterogeneity, I suggest that the application of a molecular clock to date-splitting events in the Aphelocoma jays is not a valid approach. Received 18 February 1991, accepted 3 July 1991. THE THREE species of Aphelocoma jays range throughout western and southern North America and northern Central America (Fig. 1; Pitelka 1951). Scrub Jays (A. coerulescens) range from Oregon and Wyoming south to the Isthmus of Tehuantepec, with disjunct populations on Santa Cruz Island off the coast of southern California and in peninsular Florida. The 15 subspecies form five groups, each characterized by unique combinations of plumage, morphological, and behavioral characters (Fig. 1; Pitelka 1951, Peterson 1991a): (1) woodhouseii group (Wyoming and southeastern Oregon south through Great Basin and along both sides of Rocky Mountains, and then along interior slopes of Sierra Madre Oriental and Sierra Madre Occidental of northern Mexico to southern Chihuahuan Desert and vicinity of Mexico City); (2) californica group (western Oregon, California, and Baja California); (3) sumichrasti group (southern Mexico); (4) coerulescens group (peninsular Florida); and (5) insularis group (Santa Cruz Island). The Gray-breasted Jay (A. ultramarina) ranges throughout the mountains of northern and central Mexico and the southwestern United States. The seven subspecies fall into three groups characterized by unique combinations of morphological and behavioral characters (Fig. 1; Pitelka 1951): (1) potosina group (Sierra Madre Oriental); (2) wollweberi group (Si' Present address: Department of Zoology, Field Museum of Natural History, Roosevelt Road at Lake Shore Drive, Chicago, Illinois 60605, USA. erra Madre Occidental); and (3) ultramarina group (Transvolcanic Belt). Finally, the Unicolored Jay (A. unicolor) consists of five allopatric populations, each a separate subspecies, in southern Mexico and northern Central America (Pitelka 1951). The Aphelocoma jays have been the subject of numerous comparative studies. Evaluations of social systems in the genus have led to advances in understanding ecological factors important in the evolution of sociality (Woolfenden and Fitzpatrick 1984, Fitzpatrick and Woolfenden 1986, Brown 1987, Peterson and Burt, in press). Differential habitat use in Scrub Jays (Peterson and Vargas 1992) is correlated with geographic variation in beak shape, suggesting that beak shapes have responded to natural selection (Peterson, in prep.). Integration of phylogenetic information into such investigations will allow an important new dimension of understanding (Brooks and McLennan 1990). Hence, I have attempted to estimate the phylogeny of the differentiated forms in the genus. Rates of molecular evolution. -Since the publication of the influential paper of Zuckerkandl and Pauling (1962), the idea of a "molecular clock" has been controversial in molecular biology and systematics. The clock concept is based on the assumption of a uniform rate of molecular evolution in a group. If the uniform rate assumption were correct, the accumulation of genetic differentiation between sister taxa would be time-invariant, and divergence times could be estimated from genetic distances. The clock concept is an important feature of

Ecological niche modeling re-examined: A case study with the Darwin's fox.

Abstract: Many previous studies have attempted to assess ecological niche modeling performance using receiver operating characteristic (ROC) approaches, even though diverse problems with this metric have been pointed out in the literature. We explored different evaluation metrics based on independent testing data using the Darwin's Fox (Lycalopex fulvipes) as a detailed case in point. Six ecological niche models (ENMs; generalized linear models, boosted regression trees, Maxent, GARP, multivariable kernel density estimation, and NicheA) were explored and tested using six evaluation metrics (partial ROC, Akaike information criterion, omission rate, cumulative binomial probability), including two novel metrics to quantify model extrapolation versus interpolation (E-space index I) and extent of extrapolation versus Jaccard similarity (E-space index II). Different ENMs showed diverse and mixed performance, depending on the evaluation metric used. Because ENMs performed differently according to the evaluation metric employed, model selection should be based on the data available, assumptions necessary, and the particular research question. The typical ROC AUC evaluation approach should be discontinued when only presence data are available, and evaluations in environmental dimensions should be adopted as part of the toolkit of ENM researchers. Our results suggest that selecting Maxent ENM based solely on previous reports of its performance is a questionable practice. Instead, model comparisons, including diverse algorithms and parameterizations, should be the sine qua non for every study using ecological niche modeling. ENM evaluations should be developed using metrics that assess desired model characteristics instead of single measurement of fit between model and data. The metrics proposed herein that assess model performance in environmental space (i.e., E-space indices I and II) may complement current methods for ENM evaluation.

Adaptive Geographical Variation in Bill Shape of Scrub Jays (Aphelocoma coerulescens)

Abstract: The hypothesis of an adaptive basis to geographical variation in scrub jay bill shapes was tested using morphometric and phylogenetic approaches. Bill shapes of scrub jays include a short, hooked form and a long, pointed form, at least in females. The variation is closely associated with habitat use across the species' range: populations living in oak woodlands have short, hooked bills, whereas populations living in pinyon-juniper woodlands have long, pointed bills. The short, hooked form is apparently the primitive (pleisiomorphic) state in the species. The pointed form probably has been derived twice and lost once during the phylogenetic history of the species, each derivation being associated with invasion of pinyon-juniper woodlands and the loss with invasion of oak woodlands. Each bill form is most efficient at exploiting the foods present in the habitat with which it is associated, according to behavioral observations and functional arguments. Hence, the hypothesis that the variation is adaptive is ...

The Theory of Island Biogeography

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

Bayesian Phylogenetics with BEAUti and the BEAST 1.7

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

Ecological and Evolutionary Responses 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