Jason L. Brown

SDMtoolbox: a python-based GIS toolkit for landscape genetic, biogeographic and species distribution model analyses

Summary 1. Species distribution models (SDMs) are broadly used in ecological and evolutionary studies. Almost all SDM methods require extensive data preparation in a geographic information system (GIS) prior to model building. Often, this step is cumbersome and, if not properly done, can lead to poorly parameterized models or in some cases, if too difficult, prevents the realization of SDMs. Further, for many studies, the creation of SDMs is not the final result and the post-modelling processing can be equally arduous as other steps. 2. SDMtoolbox is designed to facilitate many complicated pre- and post-processing steps commonly required for species distribution modelling and other geospatial analyses. SDMtoolbox consists of 59 Python script-based GIS tools developed and compiled into a single interface. 3. A large set of the tools were created to complement SDMs generated in Maxent or to improve the predictive performance of SDMs created in Maxent. However, SDMtoolbox is not limited to analyses of Maxent models, and many tools are also available for additional analyses or general geospatial processing: for example, assessing landscape connectivity of haplotype networks (using least-cost corridors or least-cost paths); correcting SDM over-prediction; quantifying distributional changes between current and future SDMs; or for calculating several biodiversity metrics, such as corrected weighted endemism. 4. SDMtoolbox is a free comprehensive python-based toolbox for macroecology, landscape genetic and evolutionary studies to be used in ArcGIS 10.1 (or higher) with the Spatial Analyst extension. The toolkit simplifies many GIS analyses required for species distribution modelling and other analyses, alleviating the need for repetitive and time-consuming climate data pre-processing and post-SDM analyses.

A Key Ecological Trait Drove the Evolution of Biparental Care and Monogamy in an Amphibian

Linking specific ecological factors to the evolution of parental care pattern and mating system is a difficult task of key importance. We provide evidence from comparative analyses that an ecological factor (breeding pool size) is associated with the evolution of parental care across all frogs. We further show that the most intensive form of parental care (trophic egg feeding) evolved in concert with the use of small pools for tadpole deposition and that egg feeding was associated with the evolution of biparental care. Previous research on two Peruvian poison frogs (Ranitomeya imitator and Ranitomeya variabilis) revealed similar life histories, with the exception of breeding pool size. This key ecological difference led to divergence in parental care patterns and mating systems. We present ecological field experiments that demonstrate that biparental care is essential to tadpole survival in small (but not large) pools. Field observations demonstrate social monogamy in R. imitator, the species that uses small pools. Molecular analyses demonstrate genetic monogamy in R. imitator, the first example of genetic monogamy in an amphibian. In total, this evidence constitutes the most complete documentation to date that a single ecological factor drove the evolution of biparental care and genetic and social monogamy in an animal.

Noninvasive measurement of blood flow and extraction fraction

We describe the theory of a technique for the noninvasive measurement of organ blood flow which is based on the principle of fractionation of cardiac output and is applicable with any recirculating gamma emitting tracer. The technique effectively determines the count rate that would be recorded over the organ if the tracer behaved like radiolabelled microspheres and was completely trapped in the organs vascular bed on first pass. After correction for organ depth, the estimated first pass activity plateau, expressed as a fraction of the injected dose, is equal to the organs fraction of the cardiac output (CO). By extending the theory, organ extraction fraction of extractable tracers or mean transit time of nonextractable tracers can be measured. Renal blood flow (RBF) to the normal left kidney in 18 subjects without evidence of renal disease was estimated by the technique to be 10.4% CO (S.D. 1.2), for the right kidney 9.0% CO(S.D. 1.1), and for both, 19.4% CO (S.D. 1.5). In a separate series of eight patients, RBF values were highly reproducible when obtained on successive days (standard deviation of change: 0.67% CO for the left kidney, 0.63% CO for the right and 0.78% CO for both). The extraction fraction of DTPA (filtration fraction) was 8.5% (1.7) in the left kidney and 9.7% (2.1) in the right kidney. This parameter was less reproducible than RBF, with standard deviations of the changes equal to 1.17% for the left kidney and 1.31% for the right. Stable, well-functioning, renal allografts in children had a mean blood flow of 20.6% CO (S.D. 3.7). Transplant blood flow in eight patients with rejection was less than 5.2% CO. In patients without splenomegaly, splenic blood flow, splenic extraction fraction of sulphur colloid and splenic red cell mean transit time were 4.3% CO (S.D. 0.9), 41% (S.D. 13.8), and 36.9 s (S.D. 4.6), respectively.

Spatially explicit models of dynamic histories: examination of the genetic consequences of Pleistocene glaciation and recent climate change on the American Pika

A central goal of phylogeography is to identify and characterize the processes underlying divergence. One of the biggest impediments currently faced is how to capture the spatiotemporal dynamic under which a species evolved. Here, we described an approach that couples species distribution models (SDMs), demographic and genetic models in a spatiotemporally explicit manner. Analyses of American Pika (Ochotona princeps) from the sky islands of the central Rocky Mountains of North America are used to provide insights into key questions about integrative approaches in landscape genetics, population genetics and phylogeography. This includes (i) general issues surrounding the conversion of time‐specific SDMs into simple continuous, dynamic landscapes from past to current, (ii) the utility of SDMs to inform demographic models with deme‐specific carrying capacities and migration potentials as well as (iii) the contribution of the temporal dynamic of colonization history in shaping genetic patterns of contemporary populations. Our results support that the inclusion of a spatiotemporal dynamic is an important factor when studying the impact of distributional shifts on patterns of genetic data. Our results also demonstrate the utility of SDMs to generate species‐specific predictions about patterns of genetic variation that account for varying degrees of habitat specialization and life history characteristics of taxa. Nevertheless, the results highlight some key issues when converting SDMs for use in demographic models. Because the transformations have direct effects on the genetic consequence of population expansion by prescribing how habitat heterogeneity and spatiotemporal variation is related to the species‐specific demographic model, it is important to consider alternative transformations when studying the genetic consequences of distributional shifts.

Phytotelm size in relation to parental care and mating strategies in two species of Peruvian poison frogs

Summary Factors contributing to the evolution of reproductive strategies have been of great interest to evolutionary biologists. In tropical amphibians predation and competition have been suggested to play a major role. Poison frogs of the family Dendrobatidae display a trend towards the use of very small pools and increased parental care, particularly in the genus Dendrobates. Some species with female parental care, asymmetrical biparental care and biparental care, have evolved novel behaviors in association with the use very small phytotelmata. It has been hypothesized that selection pressure imposed by predation and competition favored the use of small phytotelmata, and this, in turn, produced selection for trophic egg provisioning to ameliorate the lack of available nutrients. To elucidate the ecological factors associated with the transition from uniparental male care to biparental care and associated changes in social behaviors, we evaluated key behavioral and ecological differences between Dendrobates imitator and D. variabilis. Dendrobates imitator used significantly smaller phytotelmata in different plant species than D. variabilis for tadpole and embryo deposition. The parental strategy of D. variabilis was limited to male parental care, whereas D. imitator exhibited biparental care. Males and females of D. variabilis were observed to have a promiscuous mating system with little mate fidelity. This contrasted with D. imitator, where paired males and females were observed interacting daily and were never observed courting additional mates. Our results are consistent with the hypothesis that a key ecological difference between these species, involving the size of pools typically used for reproduction, is strongly associated with the evolution of biparental care and monogamy in D. imitator.

Divergence in parental care, habitat selection and larval life history between two species of Peruvian poison frogs: an experimental analysis

Changes in the nature of the ecological resources exploited by a species can lead to the evolution of novel suites of behaviours. We identified a case in which the transition from large pool use to the use of very small breeding pools in neotropical poison frogs (family Dendrobatidae) is associated with the evolution of a suite of behaviours, including biparental care (from uniparental care) and social monogamy (from promiscuity). We manipulated breeding pool size in order to demonstrate experimentally that breeding habitat selection strategy has evolved in concert with changes in parental care and mating system. We also manipulated intra‐ and interspecific larval interactions to demonstrate that larval adaptation to the use of very small pools for breeding affected the evolution of larval competition and cannibalism. Our results illustrate the intimate connection between breeding pool ecology, parental care and mating strategies in Peruvian poison frogs.

CITES Designation for Endangered Rosewood in Madagascar

Predicted forest losses and a recent government ban on logging build support for trade protection of Malagasy rosewood. Logging in Madagascar, one of the worlds most threatened biodiversity hot spots (1, 2), has rapidly increased amid political turmoil since a transitional government assumed power in March 2009 (1, 3). With as much as 90% of the countrys primary forest already lost, continued logging will mean species extinctions across all biotic elements of Madagascars ecosystems, where rates of endemism are unparalleled (2, 4, 5). We demonstrate immediate risk for rosewood (genus Dalbergia) species extinctions and thus the need for protection via international trade regulation under the Convention on International Trade in Endangered Species of Wild Fauna and Flora (CITES). Protection of Malagasy rosewood species, which suffer from targeted logging because of their high value in international markets, would not only avoid their extinction but also extend the benefits of protection to all biota within these threatened ecosystems.

Single Assay for Simultaneous Detection and Differential Identification of Human and Avian Influenza Virus Types, Subtypes, and Emergent Variants

For more than four decades the cause of most type A influenza virus infections of humans has been attributed to only two viral subtypes, A/H1N1 or A/H3N2. In contrast, avian and other vertebrate species are a reservoir of type A influenza virus genome diversity, hosting strains representing at least 120 of 144 combinations of 16 viral hemagglutinin and 9 viral neuraminidase subtypes. Viral genome segment reassortments and mutations emerging within this reservoir may spawn new influenza virus strains as imminent epidemic or pandemic threats to human health and poultry production. Traditional methods to detect and differentiate influenza virus subtypes are either time-consuming and labor-intensive (culture-based) or remarkably insensitive (antibody-based). Molecular diagnostic assays based upon reverse transcriptase-polymerase chain reaction (RT-PCR) have short assay cycle time, and high analytical sensitivity and specificity. However, none of these diagnostic tests determine viral gene nucleotide sequences to distinguish strains and variants of a detected pathogen from one specimen to the next. Decision-quality, strain- and variant-specific pathogen gene sequence information may be critical for public health, infection control, surveillance, epidemiology, or medical/veterinary treatment planning. The Resequencing Pathogen Microarray (RPM-Flu) is a robust, highly multiplexed and target gene sequencing-based alternative to both traditional culture- or biomarker-based diagnostic tests. RPM-Flu is a single, simultaneous differential diagnostic assay for all subtype combinations of type A influenza viruses and for 30 other viral and bacterial pathogens that may cause influenza-like illness. These other pathogen targets of RPM-Flu may co-infect and compound the morbidity and/or mortality of patients with influenza. The informative specificity of a single RPM-Flu test represents specimen-specific viral gene sequences as determinants of virus type, A/HN subtype, virulence, host-range, and resistance to antiviral agents.

Broad Spectrum Respiratory Pathogen Analysis of Throat Swabs from Military Recruits Reveals Interference Between Rhinoviruses and Adenoviruses

Military recruits experience a high incidence of febrile respiratory illness (FRI), leading to significant morbidity and lost training time. Adenoviruses, group A Streptococcus pyogenes, and influenza virus are implicated in over half of the FRI cases reported at recruit training center clinics, while the etiology of the remaining cases is unclear. In this study, we explore the carriage rates and disease associations of adenovirus, enterovirus, rhinovirus, Streptococcus pneumoniae, Haemophilus influenzae, and Neisseria meningitidis in military recruits using high-density resequencing microarrays. The results showed that rhinoviruses, adenoviruses, S. pneumoniae, H. influenzae, and N. meningitidis were widely distributed in recruits. Of these five agents, only adenovirus showed significant correlation with illness. Among the samples tested, only pathogens associated with FRI, such as adenovirus 4 and enterovirus 68, revealed strong temporal and spatial clustering of specific strains, indicating that they are transmitted primarily within sites. The results showed a strong negative association between adenoviral FRI and the presence of rhinoviruses in recruits, suggesting some form of viral interference.

Current State of Conservation Knowledge on Threatened Amphibian Species in Peru

This study documents the current state of conservation knowledge on threatened amphibian species in Peru. Following the International Union for the Conservation of Nature (IUCN) classification system, we considered species in the following categories: Critically Endangered, Endangered, Vulnerable, and Near Threatened. Even though only the first three categories are regarded as threatened by IUCN, we included the fourth category to make comparisons with the list of threatened species issued by the Peruvian government. We used the Global Amphibian Assessments database and the list issued in Peru for this comparison. We conducted separate field surveys in 17 regions of Peru to evaluate the presence/absence of threatened amphibian species and species that are potentially threatened. We also used the Declining Amphibian Database-DAPTF, to compare our results with previous assessments on population declines, and the World Wildlife Funds Wildfinder database, to determine in which Neotropical ecoregion each species occurs. We compiled data on 83 species, 44 of which are recognized as threatened by the IUCN and/or the Peruvian government. The remaining 39 species should be re-assessed as they face various threats. A re-evaluation of current estimates is needed as only 8% of all species recorded in Peru are recognized as threatened by the government, whereas the global estimate of threatened species is about 32%. In addition to using IUCN criteria, this re-assessment should follow national guidelines standardized in Peru and be in accordance with the Convention on International Trade in Endangered Species of Wild Fauna and Flora (CITES). Because the habitat of almost 40% of threatened species reported herein still remains unprotected, and data on chytridiomycosis and other threats are lacking for most taxa, it is crucial to develop strategies for habitat conservation and research on disease dynamics in natural populations.