Showing papers by "A. Townsend Peterson published in 2012"

Uses and misuses of bioclimatic envelope modeling

Abstract: Bioclimatic envelope models use associations between aspects of climate and species' occurrences to estimate the conditions that are suitable to maintain viable populations. Once bioclimatic envelopes are characterized, they can be applied to a variety of questions in ecology, evolution, and conservation. However, some have questioned the usefulness of these models, because they may be based on implausible assumptions or may be contradicted by empirical evidence. We review these areas of contention, and suggest that criticism has often been misplaced, resulting from confusion between what the models actually deliver and what users wish that they would express. Although improvements in data and methods will have some effect, the usefulness of these models is contingent on their appropriate use, and they will improve mainly via better awareness of their conceptual basis, strengths, and limitations.

Species Distribution Modeling and Ecological Niche Modeling: Getting the Concepts Right

Abstract: We provide an overview of conceptual considerations in terminology related to ecological niche modeling and species distribution modeling, two near-synonymous (but not quite), relatively new tools in macroecology and biogeography. We show that a large majority of published studies taking advantage of these tools use terminology inappropriate to the biogeographic and ecological basis on which their application is founded. We suggest that only via rigorous and appropriate terminology will these tools achieve their fullest potential.

Constraints on Interpretation of Ecological Niche Models by Limited Environmental Ranges on Calibration Areas: Software Script Appendix

Abstract: Software for 1-dimensional plots of species' responses to environment, and for MOP calculations.

Geographic distribution of chagas disease vectors in Brazil based on ecological niche modeling.

Abstract: Although Brazil was declared free from Chagas disease transmission by the domestic vector Triatoma infestans, human acute cases are still being registered based on transmission by native triatomine species. For a better understanding of transmission risk, the geographic distribution of Brazilian triatomines was analyzed. Sixteen out of 62 Brazilian species that both occur in >20 municipalities and present synanthropic tendencies were modeled based on their ecological niches. Panstrongylus geniculatus and P. megistus showed broad ecological ranges, but most of the species sort out by the biome in which they are distributed: Rhodnius pictipes and R. robustus in the Amazon; R. neglectus, Triatoma sordida, and T. costalimai in the Cerrado; R. nasutus, P. lutzi, T. brasiliensis, T. pseudomaculata, T. melanocephala, and T. petrocchiae in the Caatinga; T. rubrovaria in the southern pampas; T. tibiamaculata and T. vitticeps in the Atlantic Forest. Although most occurrences were recorded in open areas (Cerrado and Caatinga), our results show that all environmental conditions in the country are favorable to one or more of the species analyzed, such that almost nowhere is Chagas transmission risk negligible.

Ecological connectivity of Trypanosoma cruzi reservoirs and Triatoma pallidipennis hosts in an anthropogenic landscape with endemic Chagas disease.

Abstract: Traditional methods for Chagas disease prevention are targeted at domestic vector reduction, as well as control of transfusion and maternal-fetal transmission. Population connectivity of Trypanosoma cruzi-infected vectors and hosts, among sylvatic, ecotone and domestic habitats could jeopardize targeted efforts to reduce human exposure. This connectivity was evaluated in a Mexican community with reports of high vector infestation, human infection, and Chagas disease, surrounded by agricultural and natural areas. We surveyed bats, rodents, and triatomines in dry and rainy seasons in three adjacent habitats (domestic, ecotone, sylvatic), and measured T. cruzi prevalence, and host feeding sources of triatomines. Of 12 bat and 7 rodent species, no bat tested positive for T. cruzi, but all rodent species tested positive in at least one season or habitat. Highest T. cruzi infection prevalence was found in the rodents, Baiomys musculus and Neotoma mexicana. In general, parasite prevalence was not related to habitat or season, although the sylvatic habitat had higher infection prevalence than by chance, during the dry season. Wild and domestic mammals were identified as bloodmeals of T. pallidipennis, with 9% of individuals having mixed human (4.8% single human) and other mammal species in bloodmeals, especially in the dry season; these vectors tested >50% positive for T. cruzi. Overall, ecological connectivity is broad across this matrix, based on high rodent community similarity, vector and T. cruzi presence. Cost-effective T. cruzi, vector control strategies and Chagas disease transmission prevention will need to consider continuous potential for parasite movement over the entire landscape. This study provides clear evidence that these strategies will need to include reservoir/host species in at least ecotones, in addition to domestic habitats.

Ecology and geography of human monkeypox case occurrences across Africa.

Abstract: As ecologic niche modeling (ENM) evolves as a tool in spatial epidemiology and public health, selection of the most appropriate and informative environmental data sets becomes increasingly important. Here, we build on a previous ENM analysis of the potential distribution of human monkeypox in Africa by refining georeferencing criteria and using more-diverse environmental data to identify environmental parameters contributing to monkeypox distributional ecology. Significant environmental variables include annual precipitation, several temperature-related variables, primary productivity, evapotranspiration, soil moisture, and pH. The potential distribution identified with this set of variables was broader than that identified in previous analyses but does not include areas recently found to hold monkeypox in southern Sudan. Our results emphasize the importance of selecting the most appropriate and informative environmental data sets for ENM analyses in pathogen transmission mapping.

Spatial and temporal dynamics of Aedes aegypti larval sites in Bello, Colombia

Abstract: Counts of immature stages of the mosquito Aedes aegypti have been used to calculate several entomological indices of dengue vector abundance. Some studies have concluded that these indices can be used as indicators of dengue epidemic risk, while other studies have failed to find a predictive relationship. Ecological niche models have been able to predict distributional patterns in space and time, not only of vectors, but also of the diseases that they transmit. In this study, we used Landsat 7 ETM+ images and two niche-modeling algorithms to estimate the local-landscape ecological niche and the dynamics of Ae. aegypti larval habitats in Bello, Colombia, and to evaluate their potential spatial and temporal distribution. Our models showed low omission error with high confidence levels: about 13.4% of the area presents conditions consistently suitable for breeding across the entire study period (2002–2008). The proportion of neighborhoods predicted to be suitable showed a positive association with ...

Ecological niche modeling as a tool for understanding distributions and interactions of vectors, hosts, and etiologic agents of Chagas disease.

Abstract: Chagas disease, or American Trypanosomiasis, is a tropical parasitic disease caused by the flagellate protozoan Trypanosoma cruzi, which is in turn transmitted by blood-sucking insects of the subfamily Triatominae (family Reduviidae). Because no drugs or vaccines are available to cure Chagas disease in its chronic phase, vectorial control (i.e., insecticide spraying) constitutes the principal means by which to impair Chagas disease transmission. Environmental and social factors have caused changes in the epidemiology of this disease—it was originally restricted to Latin America, but is now becoming a global heath concern in non-endemic areas as a consequence of human migrations. In Brazil, despite the fact that the most effective vector has been controlled, other triatomine species infest and colonize domiciliary habitats and can transmit the pathogen. As a consequence, Chagas disease transmission continues: the prevalence of the disease remains at ∼12 million people, with ∼200,000 new cases per year in 15 countries of Latin America, making control actions still necessary. Understanding the environmental requirements and geographic distributions of vectors is key to guiding control measures, and understanding better epidemiologic aspects of the disease. Ecologic niche modeling is a relatively new tool that permits such insights—as a consequence, here, we present an overview of insights gained using this approach in understanding of Chagas disease.

Niche Modeling: Model Evaluation

Abstract: Ecological niche modeling has become a very popular tool in ecological and biogeographic studies across broad extents. The tool is used in hundreds of publications each year now, but some fundamental aspects of the approach have seen a fair amount of carelessness. Among these aspects is that of model evaluation or validation. This unit provides a simple introduction to the basic concepts that are important in model validation, using some very simple examples. The focus is on two solutions to the challenge of model evaluation: a simple cumulative binomial approach that can be used with binary model outputs, and partial ROC analysis, which can be used with continuous model outputs.

Effects of georeferencing effort on mapping monkeypox case distributions and transmission risk

Abstract: Background: Maps of disease occurrences and GIS-based models of disease transmission risk are increasingly common, and both rely on georeferenced diseases data. Automated methods for georeferencing disease data have been widely studied for developed countries with rich sources of geographic referenced data. However, the transferability of these methods to countries without comparable geographic reference data, particularly when working with historical disease data, has not been as widely studied. Historically, precise geographic information about where individual cases occur has been collected and stored verbally, identifying specific locations using place names. Georeferencing historic data is challenging however, because it is difficult to find appropriate geographic reference data to match the place names to. Here, we assess the degree of care and research invested in converting textual descriptions of disease occurrence locations to numerical grid coordinates (latitude and longitude). Specifically, we develop three datasets from the same, original monkeypox disease occurrence data, with varying levels of care and effort: the first based on an automated web-service, the second improving on the first by reference to additional maps and digital gazetteers, and the third improving still more based on extensive consultation of legacy surveillance records that provided considerable additional information about each case. To illustrate the implications of these seemingly subtle improvements in data quality, we develop ecological niche models and predictive maps of monkeypox transmission risk based on each of the three occurrence data sets. Results: We found macrogeographic variations in ecological niche models depending on the type of georeferencing method used. Less-careful georeferencing identified much smaller areas as having potential for monkeypox transmission in the Sahel region, as well as around the rim of the Congo Basin. These results have implications for mapping efforts, as each higher level of georeferencing precision required considerably greater time investment. Conclusions: The importance of careful georeferencing cannot be overlooked, despite it being a time- and labor-intensive process. Investment in archival storage of primary disease-occurrence data is merited, and improved digital gazetteers are needed to support public health mapping activities, particularly in developing countries, where maps and geographic information may be sparse.

Microspatial Distributional Patterns of Vectors of Cutaneous Leishmaniasis in Pernambuco, Northeastern Brazil

Abstract: The purpose of this study is to analyze the spatial distribution and population trends through time of Lutzomyia species in a long-term focus of cutaneous leishmaniasis transmission in an Atlantic Forest area, northeastern Brazil. Sand fly populations of different ecological niches were monitored spatiotemporally in 2009. To summarize vegetation characteristics and phenology, we calculated the Normalized Difference Vegetation Index from Landsat images. Using niche modeling approaches, we assessed suites of environmental factors to identify areas of transmission risk. Although 12 species were detected, L. whitmani was the most abundant and broadly distributed across the area, particularly in peridomiciliary locations, and associated negatively with denser vegetation areas. On the other hand, L. complexa, L. sordelli, and L. tupynambai were found almost exclusively in forested areas (P < 0.05), and associated positively with denser vegetation. Lutzomyia species' occurrences are related to specific environmental combinations (with contrast among species) in the region.

Climate-change and mass mortality events in overwintering monarch butterflies

Abstract: Monarch butterflies (Danaus plexippus) have a unique yearly life cycle, in which successive generations breed and move northward from the southern USA in spring to the northern US and southern Canada by late summer; they overwinter in extremely restricted areas in central Mexico and along the California coast. Mexican overwintering populations have experienced significant mortality events recently, which have been hypothesized as increasing in frequency owing to climate change. Here, we test the hypothesis of climate-change causation of these mortality events, at least in part, finding significant local weather trends toward conditions lethal for monarch survival. We use ecological niche estimates and future climate projections to estimate future overwintering distributions; results anticipate dramatic reductions in suitability of present overwintering areas, and serious implications for local human economies.

Predicting suitable environments and potential occurrences for coelacanths (Latimeria spp.)

Abstract: Extant coelacanths (Latimeria chalumnae) were first discovered in the western Indian Ocean in 1938; in 1998, a second species of coelacanth, Latimeria menadoensis, was discovered off the north coast of Sulawesi, Indonesia, expanding the known distribution of the genus across the Indian Ocean Basin. This study uses ecological niche modeling techniques to estimate dimensions of realized niches of coelacanths and generate hypotheses for additional sites where they might be found. Coelacanth occurrence information was integrated with environmental and oceanographic data using the Genetic Algorithm for Rule-set Production (GARP) and a maximum entropy algorithm (Maxent). Resulting models were visualized as maps of relative suitability of sites for coelacanths throughout the Indian Ocean, as well as scatterplots of ecological variables. Our findings suggest that the range of coelacanths could extend beyond their presently known distribution and suggests alternative mechanisms for currently observed distributions. Further investigation into these hypotheses could aid in forming a more complete picture of the distributions and populations of members of genus Latimeria, which in turn could aid in developing conservation strategies, particularly in the case of L. menadoensis.

Assessing Migratory Double Breeding Through Complementary Specimen Densities and Breeding Records

Abstract: . We re-evaluate the plausibility that five species of birds that breed in late summer in northwestern Mexico are migratory double breeders that first bred earlier in the same season to the north. We use data aggregated from scientific collections to generate abundance indices that adjust counts of specimens in collections by collecting effort, which we measure as the number of passerines collected in the same region and time period as the species of interest. Our abundance indices generally show displaced phenologies, such that presumed double breeders arrive and breed early in the north, then later in northwestern Mexico. We also compare breeding records for these regions, but these records could not be corrected for effort. Our phenologies suggest that the breeding populations of the Yellow-billed Cuckoo (Coccyzus americanus) from the western U.S. and northwestern Mexico may be derived from birds that bred earlier in eastern North America. Similarly, Orchard Orioles (Icterus spurius) breeding i...

Species’ Geographic Distributions Through Time: Playing Catch-up with Changing Climates

Abstract: Species’ ranges are often treated as a fixed characteristic, rather than a fluid, ever-changing manifestation of their ecological requirements and dispersal abilities. Paleontologists generally have had a better appreciation of the changeable nature of species’ ranges than neontologists, but each perspective can improve by appreciating the other. Here, we provide an overview of paleontological and neontological perspectives on species’ geographic distributions, focusing on what can be learned about historical variations in distributions. In particular, we focus on enriching the field of phylogeography with a more explicit view of geography, taking into account variation through time in the geographic distribution of different environments, effectively integrating information from the fossil record, molecular genetics, and paleoclimatology. The cross-disciplinary view that would result offers novel perspectives on biogeography and macroevolution.

Phylogenetic assessment of filoviruses: how many lineages of Marburg virus?

Abstract: Filoviruses have to date been considered as consisting of one diverse genus (Ebola viruses) and one undifferentiated genus (Marburg virus). We reconsider this idea by means of detailed phylogenetic analyses of sequence data available for the Filoviridae: using coalescent simulations, we ascertain that two Marburg isolates (termed the “RAVN” strain) represent a quite-distinct lineage that should be considered in studies of biogeography and host associations, and may merit recognition at the level of species. In contrast, filovirus isolates recently obtained from bat tissues are not distinct from previously known strains, and should be considered as drawn from the same population. Implications for understanding the transmission geography and host associations of these viruses are discussed.

Avian influenza infections in nonmigrant land birds in andean peru

Abstract: As part of ongoing surveillance for avian influenza viruses (AIV) in Peruvian birds, in June 2008, we sampled 600 land birds of 177 species, using real-time reverse-transcription PCR. We addressed the assumption that AIV prevalence is low or nil among land birds, a hypothesis that was not supported by the results—rather, we found AIV infections at relatively high prevalences in birds of the orders Apodiformes (hummingbirds) and Passeriformes (songbirds). Surveillance programs for monitoring spread and identification of AIV should thus not focus solely on water birds.

New phylogenetic information suggests both an increase and at least one loss of cooperative breeding during the evolutionary history of Aphelocoma jays

Abstract: Efforts to identify ecological and life history factors associated with cooperative breeding have been largely unsuccessful, and interest is growing in the role of phylogenetic history in determining the distribution of this social system among lineages. In birds, cooperative breeding is distributed non-randomly among lineages, suggesting that phylogenetic inertia may play an important role in determining its distribution. The bird genus Aphelocoma has been particularly well studied because, although it is a relatively small genus, it shows broad among-lineage variation in level of cooperation. Previous analyses described an unusual unidirectional pattern of evolutionary loss of cooperation in Aphelocoma. Here, historical reconstructions based on new phylogenetic data suggest that evolutionary changes in cooperation have been bidirectional, with at least one gain and at least one loss over relatively recent timescales. This result emphasizes that, although history plays an important role in determining the incidence of cooperative breeding, cooperative behavior can switch relatively quickly in evolutionary time and may be influenced by the ecological context within which particular populations are distributed.

Rhododendron Species in the Indian Eastern Himalayas: New Approaches to Understanding Rare Plant Species Distributions

Abstract: Rhododendron species serve an impor-tant ecological and economic role in the mountains of the Eastern Himalayas. Re-cent changes in this once-pristine land-scape have resulted in the classification of many Rhododendron species as threatened or endangered. This study used field sur-veys and ecological niche modeling to ex-pand existing knowledge about Rhododen-dron species’ distributions in the region, with a view to helping develop strategies for conservation action and possible rein-troductions. Introduction Keystone species play a crucial role in maintaining the organization and diversity of their ecological communities. Rhodo-dendrons (Figure 1) act as keystone species in the high-elevation portions of the East-ern Himalayas. The subalpine-to-alpine transition zone that includes timberline is the most fragile ecosystem in this part of the Himalayas. Rhododendron is the only group of plants that extends broadly across this ecotone. Unfortunately, however, increasing anthropogenic demands and technological development have rendered the region no longer immune to large-scale land-use change (Menon

perspective: Phylogeography is not enough: The need for multiple lines of evidence

Abstract: perspectives ISSN 1948-6596 Phylogeography is not enough: The need for multiple lines of evidence A. Townsend Peterson Biodiversity Research Center, The University of Kansas, Lawrence, Kan- sas 66045 USA e-mail: town@ku.edu; http://specify5.specifysoftware.org/Informatics/ bios/biostownpeterson/ Figure 1. Temperature and precipitation fluctuations over the past 135,000 yr: shown are annual mean temperature profiles (all on the same scale) for the present day, Last Glacial Maximum (21,000 yr ago; CCSM scenario), and Last Interglacial (135,000 yr ago; Otto-Bliesner et al. 2006). The 10 shading classes cover equal intervals between -50° and +31.5°C. Last Glacial Maximum Present day date translated into detailed analyses of key events structuring biogeographic patterns in many phylogeographic analyses. In particular, the Pleistocene was character- ized by a complex series of warm periods (similar to present-day climates) and cold periods (“ice ages”), with impressively short transitions in be- tween (Figure 2; Dansgaard et al. 1993). Although considerable attention has focused on the last of the glacial maxima (~21,000 yr before present), in reality, all of these alternating periods of warm and cold climates probably had some influence on present patterns of diversity and distribution of biodiversity (Svenning and Skov 2004). The pur- pose of this commentary is to reflect on likely ef- fects of such repeated and dramatic global climate fluctuations in shaping patterns of distribution of species, and to emphasize the need for broader Last Interglacial The concepts of equilibrium and stability in bio- geography are perhaps much more fleeting than has generally been appreciated, and disequilib- rium may actually rule the situation in most cases (Manning et al. 2009). That is, although research- ers may discuss current distributional patterns as fixed, those patterns may have been in place only for a relatively short period of time (~10 4 yr), per- haps since the last major global cool period at the end of the Pleistocene (Figure 1). Although Pleis- tocene climatic fluctuations have been considered a major force in biogeography, and some have argued that they may have produced much of cur- rent species diversity (Mengel 1970, Haffer 1997), the validity of the Pleistocene speciation paradigm has been debated hotly recently—see, e.g., Klicka and Zink (1997) versus Weir and Schluter (2004). “The Pleistocene” is often cited as a bio- geographic force, but too often uncritically and without full consideration of the complexity of world climates over the past million years. That is, molecular systematists frequently use molecular “clocks” that date splitting events imprecisely, usually with confidence intervals so broad as to inspire concern (Peterson 2007); these studies often refer to Pleistocene climatic fluctuations, but with no specifics, although the ability to date splitting events may improve with broader use of population-genetic approaches to the challenge (Arbogast et al. 2002). This general appreciation of the role of Pleistocene climatic fluctuations as im- portant biogeographically nonetheless has not to frontiers of biogeography 1.1, 2009 — © 2009 the authors; journal compilation © 2009 The International Biogeography Society

Datasets: Phylogenetic assessment of filoviruses: how many lineages of Marburg virus?

Abstract: These are datasets that accompany the following article: Peterson AT, Holder MT. 2012. Phylogenetic assessment of filoviruses: How many lineages of Marburgvirus? Ecology and Evolution.

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