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Showing papers by "A. Townsend Peterson published in 2016"


Journal ArticleDOI
TL;DR: Niche Analyst (NicheA), a toolkit developed to generate virtual species following the Hutchinsonian approach of an n-multidimensional space occupied by the species, is presented.
Abstract: Robust methods by which to generate virtual species are needed urgently in the emerging field of distributional ecology to evaluate performance of techniques for modeling ecological niches and species distributions and to generate new questions in biogeography. Virtual species provide the opportunity to test hypotheses and methods based on known and unbiased distributions. We present Niche Analyst (NicheA), a toolkit developed to generate virtual species following the Hutchinsonian approach of an n-multidimensional space occupied by the species. Ecological niche models are generated, analyzed, and visualized in an environmental space, and then projected to the geographic space in the form of continuous or binary species distribution models. NicheA is implemented in a stable and user-friendly Java platform. The software, online manual, and user support are freely available at .

147 citations


Journal ArticleDOI
03 Oct 2016-PLOS ONE
TL;DR: The present potential distribution of C. quinquefasciatus showed high suitability across low-latitude parts of the world, reflecting the current distribution of the species, and model transfers to future conditions showed a potential distribution similar to that under present-day conditions, although with higher suitability in southern Australia.
Abstract: Rapid emergence of most vector-borne diseases (VBDs) may be associated with range expansion of vector populations. Culex quinquefasciatus Say 1823 is a potential vector of West Nile virus, Saint Louis encephalitis virus, and lymphatic filariasis. We estimated the potential distribution of Cx. quinquefasciatus under both current and future climate conditions. The present potential distribution of Cx. quinquefasciatus showed high suitability across low-latitude parts of the world, reflecting the current distribution of the species. Suitable conditions were identified also in narrow zones of North Africa and Western Europe. Model transfers to future conditions showed a potential distribution similar to that under present-day conditions, although with higher suitability in southern Australia. Highest stability with changing climate was between 30°S and 30°N. The areas present high agreement among diverse climate models as regards distributional potential in the future, but differed in anticipating potential for distribution in North and Central Africa, southern Asia, central USA, and southeastern Europe. Highest disparity in model predictions across representative concentration pathways (RCPs) was in Saudi Arabia and Europe. The model predictions allow anticipation of changing distributional potential of the species in coming decades.

138 citations


Journal ArticleDOI
TL;DR: A novel set of analyses using environmental characteristics, vector mosquito distributions, and socioeconomic risk factors to develop the first map to detail global ZIKV transmission risk in multiple dimensions based on ecological niche models.
Abstract: The Americas are presently experiencing the most serious known outbreak of Zika virus (ZIKV). Here, we present a novel set of analyses using environmental characteristics, vector mosquito distributions, and socioeconomic risk factors to develop the first map to detail global ZIKV transmission risk in multiple dimensions based on ecological niche models. Our model predictions were tested against independent evaluation data sets, and all models had predictive ability significantly better than random expectations. The study addresses urgent knowledge gaps regarding (1) the potential geographic scope of the current ZIKV epidemic, (2) the global potential for spread of ZIKV, and (3) drivers of ZIKV transmission. Our analysis of potential drivers of ZIKV distributions globally identified areas vulnerable in terms of some drivers, but not for others. The results of these analyses can guide regional education and preparedness efforts, such that medical personnel will be better prepared for diagnosis of potential ZIKV cases as they appear.

74 citations


Journal ArticleDOI
23 Nov 2016-Zootaxa
TL;DR: The question whether taxonomic descriptions naming new animal species without type specimen(s) deposited in collections should be accepted for publication by scientific journals and allowed by the Code has already been discussed in Zootaxa.
Abstract: The question whether taxonomic descriptions naming new animal species without type specimen(s) deposited in collections should be accepted for publication by scientific journals and allowed by the Code has already been discussed in Zootaxa (Dubois & Nemesio 2007; Donegan 2008, 2009; Nemesio 2009a–b; Dubois 2009; Gentile & Snell 2009; Minelli 2009; Cianferoni & Bartolozzi 2016; Amorim et al. 2016). This question was again raised in a letter supported by 35 signatories published in the journal Nature (Pape et al. 2016) on 15 September 2016. On 25 September 2016, the following rebuttal (strictly limited to 300 words as per the editorial rules of Nature) was submitted to Nature, which on 18 October 2016 refused to publish it. As we think this problem is a very important one for zoological taxonomy, this text is published here exactly as submitted to Nature, followed by the list of the 493 taxonomists and collection-based researchers who signed it in the short time span from 20 September to 6 October 2016.

59 citations


Journal ArticleDOI
TL;DR: In this article, the authors modeled current and future snakebite risk using ecological niche models (ENMs) of 90 venomous snake taxa and corroborated the current snake bite risk predictions by incidence data from eight regions/periods with different characteristics.
Abstract: Snakebite envenoming is an important public health concern worldwide. In the Americas, ~300,000 bites occur annually, leaving 84,110–140,981 envenomings and 652–3466 deaths. Here, we modeled current and future snakebite risk using ecological niche models (ENMs) of 90 venomous snake taxa. Current snakebite risk predictions were corroborated by incidence data from eight regions/periods with different characteristics. Detailed projections of potential future range shifts on distributions of the medically most relevant species indicated that North American species’ ranges are likely to increase in the future, but mixed results were obtained for Latin American snakes. A likely expansion of overall risk area and an increase of rural population at risk were observed from a consensus model among future scenarios. Our study highlights the capacity of ENMs to provide detailed information on current and future potential distributions of venomous snakes, as well as useful perspectives on snakebite risk, at least broad scales.

55 citations


Journal ArticleDOI
09 Mar 2016-PLOS ONE
TL;DR: A comprehensive occurrence data set is developed to map the current distribution, estimate the ecological niche, and explore the future potential distribution of BTV globally using ecological niche modeling and based on diverse future climate scenarios from general circulation models (GCMs) for four representative concentration pathways (RCPs).
Abstract: The geographic distribution of arboviruses has received considerable attention after several dramatic emergence events around the world. Bluetongue virus (BTV) is classified among category “A” diseases notifiable to the World Organization of Animal Health (OIE), and is transmitted among ruminants by biting midges of the genus Culicoides. Here, we developed a comprehensive occurrence data set to map the current distribution, estimate the ecological niche, and explore the future potential distribution of BTV globally using ecological niche modeling and based on diverse future climate scenarios from general circulation models (GCMs) for four representative concentration pathways (RCPs). The broad ecological niche and potential geographic distribution of BTV under present-day conditions reflected the disease’s current distribution across the world in tropical, subtropical, and temperate regions. All model predictions were significantly better than random expectations. As a further evaluation of model robustness, we compared our model predictions to 331 independent records from most recent outbreaks from the Food and Agriculture Organization Emergency Prevention System for Transboundary Animal and Plant Pests and Diseases Information System (EMPRES-i); all were successfully anticipated by the BTV model. Finally, we tested ecological niche similarity among possible vectors and BTV, and could not reject hypotheses of niche similarity. Under future-climate conditions, the potential distribution of BTV was predicted to broaden, especially in central Africa, United States, and western Russia.

55 citations


Journal ArticleDOI
TL;DR: The authors' simulations provide a bottom-up perspective on the generation and maintenance of diversity under climate change, offering a better understanding of potential interactions between species’ intrinsic macroecological characteristics and a dynamic extrinsic environment in the process of biological diversification.
Abstract: We describe a spatially explicit simulation experiment designed to assess relative impacts of macroecological traits on patterns of biological diversification under changing environmental conditions. Using a simulation framework, we assessed impacts of species’ niche breadth (i.e., the range of their abiotic tolerances) and dispersal ability on resulting patterns of speciation and extinction and evaluated how these traits, in conjunction with environmental change, shape biological diversification. Simulation results supported both niche breadth and dispersal ability as important drivers of diversification in the face of environmental change, and suggested that the rate of environmental change influences how species interact with the extrinsic environment to generate diversity. Niche breadth had greater effects on speciation and extinction than dispersal ability when climate changed rapidly, whereas dispersal ability effects were elevated when climate changed slowly. Our simulations provide a botto...

41 citations


Journal ArticleDOI
TL;DR: In this paper, the authors used ecological niche modeling techniques to understand the relationship between known filovirus occurrences and environmental characteristics, and derived a picture of the potential transmission geography of Ebola virus species and Marburg, paired with views of the spatial uncertainty associated with model-to-model variation in their predictions.

28 citations


Journal ArticleDOI
TL;DR: A simple model incorporating cases generated locally and cases imported from other countries, and forecasted transmission hotspots at the level of countries and at finer scales, in terms of ecological features generated descriptive and predictive information on spread of emerging diseases in the short-term under simple models based on open-access tools and data.
Abstract: Chikungunya virus (CHIKV) is endemic to Africa and Asia, but the Asian genotype invaded the Americas in 2013. The fast increase of human infections in the American epidemic emphasized the urgency of developing detailed predictions of case numbers and the potential geographic spread of this disease. We developed a simple model incorporating cases generated locally and cases imported from other countries, and forecasted transmission hotspots at the level of countries and at finer scales, in terms of ecological features. By late January 2015, >1.2 M CHIKV cases were reported from the Americas, with country-level prevalences between nil and more than 20 %. In the early stages of the epidemic, exponential growth in case numbers was common; later, however, poor and uneven reporting became more common, in a phenomenon we term "surveillance fatigue." Economic activity of countries was not associated with prevalence, but diverse social factors may be linked to surveillance effort and reporting. Our model predictions were initially quite inaccurate, but improved markedly as more data accumulated within the Americas. The data-driven methodology explored in this study provides an opportunity to generate descriptive and predictive information on spread of emerging diseases in the short-term under simple models based on open-access tools and data that can inform early-warning systems and public health intelligence.

20 citations


Journal ArticleDOI
TL;DR: In this paper, the authors map risk of ZCL infection based on occurrence records of Leishmania major, P. papatasi, and four potential animal reservoirs (Meriones libycus, Meriones shawi, Psammomys obesus, and Gerbillus gerbillus).
Abstract: Cutaneous leishmaniasis ranks among the tropical diseases least known and most neglected in Libya. World Health Organization reports recognized associations of Phlebotomus papatasi, Psammomys obesus, and Meriones spp., with transmission of zoonotic cutaneous leishmaniasis (ZCL; caused by Leishmania major) across Libya. Here, we map risk of ZCL infection based on occurrence records of L. major, P. papatasi, and four potential animal reservoirs (Meriones libycus, Meriones shawi, Psammomys obesus, and Gerbillus gerbillus). Ecological niche models identified limited risk areas for ZCL across the northern coast of the country; most species associated with ZCL transmission were confined to this same region, but some had ranges extending to central Libya. All ENM predictions were significant based on partial ROC tests. As a further evaluation of L. major ENM predictions, we compared predictions with 98 additional independent records provided by the Libyan National Centre for Disease Control (NCDC); all of these records fell inside the belt predicted as suitable for ZCL. We tested ecological niche similarity among vector, parasite, and reservoir species and could not reject any null hypotheses of niche similarity. Finally, we tested among possible combinations of vector and reservoir that could predict all recent human ZCL cases reported by NCDC; only three combinations could anticipate the distribution of human cases across the country.

20 citations


Journal ArticleDOI
TL;DR: In this article, the authors assessed inventory completeness and identified gaps in current Digital Accessible Knowledge (DAK) of the plants of Ghana, to prioritize areas for future surveys and inventories.
Abstract: Providing comprehensive, informative, primary, research-grade biodiversity information represents an important focus of biodiversity informatics initiatives. Recent efforts within Ghana have digitized >90% of primary biodiversity data records associated with specimen sheets in Ghanaian herbaria; additional herbarium data are available from other institutions via biodiversity informatics initiatives such as the Global Biodiversity Information Facility. However, data on the plants of Ghana have not as yet been integrated and assessed to establish how complete site inventories are, so that appropriate levels of confidence can be applied. In this study, we assessed inventory completeness and identified gaps in current Digital Accessible Knowledge (DAK) of the plants of Ghana, to prioritize areas for future surveys and inventories. We evaluated the completeness of inventories at ½° spatial resolution using statistics that summarize inventory completeness, and characterized gaps in coverage in terms of geographic distance and climatic difference from well-documented sites across the country. The southwestern and southeastern parts of the country held many well-known grid cells; the largest spatial gaps were found in central and northern parts of the country. Climatic difference showed contrasting patterns, with a dramatic gap in coverage in central-northern Ghana. This study provides a detailed case study of how to prioritize for new botanical surveys and inventories based on existing DAK.

Journal ArticleDOI
TL;DR: It is pointed out that climate varies rather dramatically with respect to elevation and latitude, such that a single elevational criterion will be a poor predictor of potential for transmission.
Abstract: INTRODUCTION Zika virus has appeared in the Americas in the form of a major outbreak, and is now known to cause birth defects when pregnant women are infected. As a result, the Centers for Disease Control and Prevention issued travel guidelines, in the form of an elevational risk definition: destinations below 2000m are considered as at-risk. METHODS We explored the distribution of known Zika virus vector mosquito species in relation to climatic conditions, elevation, latitude, and air traffic connections to the United States. RESULTS In view of the tropical and subtropical nature of the mosquito species that are the primary Zika virus vectors, we point out that climate varies rather dramatically with respect to elevation and latitude, such that a single elevational criterion will be a poor predictor of potential for transmission. DISCUSSION We suggest an initial adjustment would consider latitude in addition to elevation; a more definitive, quantitative analysis of risk would consider variables of ecology, climate, human condition, and connectivity of areas.

Journal ArticleDOI
TL;DR: Peterson et al. as mentioned in this paper, A. T. and Navarro-Siguenza, A. G. (2016), Bird conservation and biodiversity research in Mexico: status and priorities, which has been published in final form at doi:10.1111/jofo.12146.
Abstract: This is the peer reviewed version of the following article: Peterson, A. T. and Navarro-Siguenza, A. G. (2016), Bird conservation and biodiversity research in Mexico: status and priorities. J. Field Ornithol.. doi:10.1111/jofo.12146, which has been published in final form at doi:10.1111/jofo.12146. This article may be used for non-commercial purposes in accordance with Wiley Terms and Conditions for Self-Archiving.

Journal ArticleDOI
TL;DR: The documentation of Mexican bird diversity grew in each of these phases, but has now become a Mexican enterprise, thanks to the combined availability of information and funding from within the country and that “repatriated” from around the world.
Abstract: Mexican ornithology has seen a curious trajectory, beginning with remarkably well documented indigenous knowledge, progressing to colonial expeditions and intensive nineteenth-century exploration. The baton passed to collectors and scientists from the United States of America around the beginning of the twentieth century, and most recently to Mexican scientists. The documentation of Mexican bird diversity grew in each of these phases, but has now become a Mexican enterprise, thanks to the combined availability of information (both from within the country and that “repatriated” from around the world) and funding (provided in largest part by the Mexican government). This evolutionary process of a science community is perhaps general and global, but with different phases emphasized in different countries, and at diverse points in the process.

Journal ArticleDOI
07 Sep 2016-PeerJ
TL;DR: Development of repeated surveys for many sites across Mexico, and particularly for sites for which historical surveys document their avifaunas prior to major climate change processes, would pay rich rewards in information about distributional dynamics of Mexican birds.
Abstract: BACKGROUND Faunal change is a basic and fundamental element in ecology, biogeography, and conservation biology, yet vanishingly few detailed studies have documented such changes rigorously over decadal time scales. This study responds to that gap in knowledge, providing a detailed analysis of Digital Accessible Knowledge of the birds of Mexico, designed to marshal DAK to identify sites that were sampled and inventoried rigorously prior to the beginning of major global climate change (1980). METHODS We accumulated DAK records for Mexican birds from all relevant online biodiversity data portals. After extensive cleaning steps, we calculated completeness indices for each 0.05° pixel across the country; we also detected 'hotspots' of sampling, and calculated completeness indices for these broader areas as well. Sites were designated as well-sampled if they had completeness indices above 80% and >200 associated DAK records. RESULTS We identified 100 individual pixels and 20 broader 'hotspots' of sampling that were demonstrably well-inventoried prior to 1980. These sites are catalogued and documented to promote and enable resurvey efforts that can document events of avifaunal change (and non-change) across the country on decadal time scales. CONCLUSIONS Development of repeated surveys for many sites across Mexico, and particularly for sites for which historical surveys document their avifaunas prior to major climate change processes, would pay rich rewards in information about distributional dynamics of Mexican birds.

Journal ArticleDOI
TL;DR: The Biodiversity Informatics Training Curriculum represents an integration of three years of teaching and interaction by many instructors and students in a series of interactions in courses across Africa, which are compiled into a first field-wide curriculum.
Abstract: The Biodiversity Informatics Training Curriculum represents an integration of three years of teaching and interaction by many instructors and students in a series of interactions in courses across Africa. Digital videos of these courses--shared openly via YouTube--have been compiled into a first field-wide curriculum, which is presented herein. The compilation is, in effect, a digital textbook covering the entire field of biodiversity informatics.

Dataset
01 Jan 2016
TL;DR: This study derived a picture of the potential transmission geography of Ebola virus species and Marburg, paired with views of the spatial uncertainty associated with model-to-model variation in predictions, to understand the relationship between known filovirus occurrences and environmental characteristics.
Abstract: Filoviruses represent a significant public health threat worldwide. West Africa recently experienced the largest-scale and most complex filovirus outbreak yet known, which underlines the need for a predictive understanding of the geographic distribution and potential for transmission to humans of these viruses. Here, we used ecological niche modeling techniques to understand the relationship between known filovirus occurrences and environmental characteristics. Our study derived a picture of the potential transmission geography of Ebola virus species and Marburg, paired with views of the spatial uncertainty associated with model-to-model variation in our predictions. We found that filovirus species have diverged ecologically, but only three species are sufficiently well known that models could be developed with significant predictive power. We quantified uncertainty in predictions, assessed potential for outbreaks outside of known transmission areas, and highlighted the Ethiopian Highlands and scattered areas across East Africa as additional potentially unrecognized transmission areas.

Journal ArticleDOI
TL;DR: Phylogenetic patterns, divergence times, and biogeographic analyses suggest a South American ancestor for T. assimilis, which split from T. albicollis between 1.4 and 3.0 Ma ago, and genetic divergence, reciprocal monophyly, an ancient disjunction, and clear phenotypic differences suggest that the population from the Chocó region, T. a.
Abstract: It is suggested that dispersal and vicariance led to speciation in Mesoamerican taxa during the Pleistocene, as a consequence of climatic fluctuations and resulting range disjunctions, but few biogeographic studies have been developed to assess their relative roles. Based on a mitochondrial DNA dataset, we analyzed the evolutionary history of Turdus assimilis, a species distributed in Mesoamerica and northwestern South America. Phylogenetic patterns, divergence times, and biogeographic analyses suggest a South American ancestor for T. assimilis, which split from T. albicollis between 1.4 and 3.0 Ma ago. The analysis suggests the colonization of Mesoamerica and the Choco region by small numbers of founder individuals. Furthermore, genetic divergence, reciprocal monophyly, an ancient disjunction, and clear phenotypic differences suggest that the population from the Choco region, T. a. daguae, represents a separate species from T. assimilis.

Journal ArticleDOI
17 Jun 2016-Science
TL;DR: Spectral analysis of bathymetry in a region they highlight as being fault controlled, however, shows strong evidence for a signal from sea level variation.
Abstract: Comment on “Sensitivity of seaf oor bathymetry to climate-driven f uctuations in mid-ocean ridge magma supply” Peter Huybers, Charles Langmuir, Richard F. Katz, David Ferguson, Cristian Proistosescu, Suzanne Carbotte Olive et al. (Reports, 16 October 2015, p. 310) argue that ~10% fl uctuations in melt supply do not produce appreciable changes in ocean ridge bathymetry on time scales less than 100,000 years and thus cannot refl ect sea level forcing. Spectral analysis of bathymetry in a region they highlight as being fault controlled, however, shows strong evidence for a signal from sea level variation. Full text at http://dx.doi.org/10.1126/science.

06 Jun 2016
TL;DR: This occurrence-environment mapping approach provides predictions that can guide education and mitigation efforts in the broader East African region and were better than random expectations in predicting infection risk of A. lumbricoides.
Abstract: Background: Despite being identified as a major health concern and neglected tropical disease, Ascariasis, caused by Ascaris lumbricoides , a soil-transmitted helminth, ranks among the most common infections worldwide. Methods: Based on prevalence data from the community surveys across East Africa for 1975-2009, we used ecological niche modeling to summarize and predict the spatial distribution of A. lumbricoides ’ transmission risk.  Results: Projection of this model across East Africa identified 51.4% of the region as suitable for A. lumbricoides transmission, with least suitable areas in the Sahara and the Somali-Chalbi deserts. Partial area under the curve (AUC) tests based on independent data showed that our model predictions were better than random expectations in predicting infection risk of A. lumbricoides ; the model successfully identified areas of high and low infection risk in Ethiopia and Eritrea. Conclusions: Although preliminary, this occurrence-environment mapping approach provides predictions that can guide education and mitigation efforts in the broader East African region.

16 Nov 2016
TL;DR: The authors presented as part of the GIS Day@KU symposium on November 16, 2016, which was held at the University of KU. For more information about GIS day@ku activities, please see http://gis.ku.edu/gisday/2016/.
Abstract: This presentation was given as part of the GIS Day@KU symposium on November 16, 2016. For more information about GIS Day@KU activities, please see http://gis.ku.edu/gisday/2016/.