Is the Climate Right for Pleistocene Rewilding? Using Species Distribution Models to Extrapolate Climatic Suitability for Mammals across Continents

Species distribution models (SDMs) are increasingly used for extrapolation, or predicting suitable regions for species under new geographic or temporal scenarios. However, SDM predictions may be prone to errors if species are not at equilibrium with climatic conditions in the current range and if training samples are not representative. Here the controversial “Pleistocene rewilding” proposal was used as a novel example to address some of the challenges of extrapolating modeled species-climate relationships outside of current ranges. Climatic suitability for three proposed proxy species (Asian elephant, African cheetah and African lion) was extrapolated to the American southwest and Great Plains using Maxent, a machine-learning species distribution model. Similar models were fit for Oryx gazella, a species native to Africa that has naturalized in North America, to test model predictions. To overcome biases introduced by contracted modern ranges and limited occurrence data, random pseudo-presence points generated from modern and historical ranges were used for model training. For all species except the oryx, models of climatic suitability fit to training data from historical ranges produced larger areas of predicted suitability in North America than models fit to training data from modern ranges. Four naturalized oryx populations in the American southwest were correctly predicted with a generous model threshold, but none of these locations were predicted with a more stringent threshold. In general, the northern Great Plains had low climatic suitability for all focal species and scenarios considered, while portions of the southern Great Plains and American southwest had low to intermediate suitability for some species in some scenarios. The results suggest that the use of historical, in addition to modern, range information and randomly sampled pseudo-presence points may improve model accuracy. This has implications for modeling range shifts of organisms in response to climate change.     

Phylogeographic lineages and species comparisons in conservation analyses: a case study of california herpetofauna

Many phylogeographic studies have revealed strongly diverged lineages within species that are masked by a lack of congruent morphological differentiation. To assess the extent to which the genetic component of diversity affects conservation assessments, we compared spatial patterns of endemism and conservation value for 22 species of Californian amphibians and reptiles with the 75 phylogeographic lineages that they contain. We used bioclimatic distribution modeling with environmental layers to generate 5-km spatial-resolution maps of predicted distribution for each species and lineage. We found concentrations of lineage breaks across the Central Valley, San Francisco Bay, the Sierra Nevada, and the Tehachapi and Trinity ranges. Subdivision of the ranges of species into phylogeographic units revealed novel areas of endemism. Several areas of very high conservation value for lineages were not evident in the species-level analysis. These observations illustrate the importance of considering multiple levels of biodiversity in conservation assessments.     

Genetic analysis of the cultivated potato Solanum tuberosum L. Phureja Group using RAPDs and nuclear SSRs

The Solanum tuberosum L. Phureja Group consists of potato landraces widely grown in the Andes from western Venezuela to central Bolivia, and forms an important breeding stock due to their excellent culinary properties and other traits for developing modern varieties. They have been distinguished by short-day adaptation, diploid ploidy (2n = 2x = 24), and lack of tuber dormancy. This nuclear simple sequence repeat (nSSR or microsatellite) study complements a prior random amplified polymorphic DNA (RAPD) study to explore the use of these markers to form a core collection of cultivar groups of potatoes. Like this prior RAPD study, we analyzed 128 accessions of the Phureja Group using nuclear microsatellites (nSSR). Twenty-six of the 128 accessions were invariant for 22 nSSR markers assayed. The nSSR data uncovered 25 unexpected triploid and tetraploid accessions. Chromosome counts of the 102 accessions confirmed these nSSR results and highlighted seven more triploids or tetraploids. Thus, these nSSR markers (except 1) are good indicators of ploidy for diploid potatoes in 92% of the cases. The nSSR and RAPD results: (1) were highly discordant for the remaining 70 accessions that were diploid and variable in nSSR, (2) show the utility of nSSRs to effectively uncover many ploidy variants in cultivated potato, (3) support the use of a cultivar-group (rather than a species) classification of cultivated potato, (4) fail to support a relationship between genetic distance and geographic distance, (5) question the use of any single type of molecular marker to construct core collections.     

Managing Potato Biodiversity to Cope with Frost Risk in the High Andes: A Modeling Perspective

Austral summer frosts in the Andean highlands are ubiquitous throughout the crop cycle, causing yield losses. In spite of the existing warming trend, climate change models forecast high variability, including freezing temperatures. As the potato center of origin, the region has a rich biodiversity which includes a set of frost resistant genotypes. Four contrasting potato genotypes –representing genetic variability- were considered in the present study: two species of frost resistant native potatoes (the bitter Solanum juzepczukii, var. Luki, and the non-bitter Solanum ajanhuiri, var. Ajanhuiri) and two commercial frost susceptible genotypes (Solanum tuberosum ssp. tuberosum var. Alpha and Solanum tuberosum ssp. andigenum var. Gendarme). The objective of the study was to conduct a comparative growth analysis of four genotypes and modeling their agronomic response under frost events. It included assessing their performance under Andean contrasting agroecological conditions. Independent subsets of data from four field experiments were used to parameterize, calibrate and validate a potato growth model. The validated model was used to ascertain the importance of biodiversity, represented by the four genotypes tested, as constituents of germplasm mixtures in single plots used by local farmers, a coping strategy in the face of climate variability. Also scenarios with a frost routine incorporated in the model were constructed. Luki and Ajanhuiri were the most frost resistant varieties whereas Alpha was the most susceptible. Luki and Ajanhuiri, as monoculture, outperformed the yield obtained with the mixtures under severe frosts. These results highlight the role played by local frost tolerant varieties, and featured the management importance –e.g. clean seed, strategic watering- to attain the yields reported in our experiments. The mixtures of local and introduced potatoes can thus not only provide the products demanded by the markets but also reduce the impact of frosts and thus the vulnerability of the system to abiotic stressors.     

An improved method using densitometry for evaluating severity of laser photocoagulation induced CNV

Laser photocoagulation induced choroidal neovascularization currently is the most effective model available for the study of this disease in terms of efficacy of new drugs and therapies. Previously, evaluating the extent of choroidal neovascularization using this model was time- consuming and required the use of experienced personnel. We describe a new method for simple and rapid evaluation of laser induced choroidal neovascularization using densitometry. Fluorescein angiograms of a laser photocoagulated rat eye were scanned into a computer. Densitometry software subsequently was used to calculate the severity of the laser lesions. The densitometry method proved effective for calculating the extent of laser induced choroidal neovascularization. In addition, this method was more rapid than visual evaluations and less likely to produce errors.     

Diet of bluegill Lepomis macrochirus in a South African reservoir during winter and summer

Alien fishes are considered a major threat to aquatic biodiversity in South Africa, yet relatively little regional information on their biology and ecology is available for many of these species. Seasonal changes in the diet of the bluegill Lepomis macrochirus in Howieson’s Poort Dam, Grahamstown, were assessed during summer and winter in 2014–2015, using stomach content analysis. In winter, juvenile and adult fish diets were dominated by crustacean zooplankton and insects, respectively. In summer, juvenile fish fed on crustaceans and insects, whereas adults consumed mostly fish eggs, indicating a potential impact by these invasive fish on native fish through oophagy.     

A novel Atg5-shRNA mouse model enables temporal control of Autophagy in vivo

Macroautophagy/autophagy is an evolutionarily conserved catabolic pathway whose modulation has been linked to diverse disease states, including age-associated disorders. Conventional and conditional whole-body knockout mouse models of key autophagy genes display perinatal death and lethal neurotoxicity, respectively, limiting their applications for in vivo studies. Here, we have developed an inducible shRNA mouse model targeting Atg5, allowing us to dynamically inhibit autophagy in vivo, termed ATG5i mice. The lack of brain-associated shRNA expression in this model circumvents the lethal phenotypes associated with complete autophagy knockouts. We show that ATG5i mice recapitulate many of the previously described phenotypes of tissue-specific knockouts. While restoration of autophagy in the liver rescues hepatomegaly and other pathologies associated with autophagy deficiency, this coincides with the development of hepatic fibrosis. These results highlight the need to consider the potential side effects of systemic anti-autophagy therapies.     

Locating pleistocene refugia: comparing phylogeographic and ecological niche model predictions

Ecological niche models (ENMs) provide a means of characterizing the spatial distribution of suitable conditions for species, and have recently been applied to the challenge of locating potential distributional areas at the Last Glacial Maximum (LGM) when unfavorable climate conditions led to range contractions and fragmentation. Here, we compare and contrast ENM-based reconstructions of LGM refugial locations with those resulting from the more traditional molecular genetic and phylogeographic predictions. We examined 20 North American terrestrial vertebrate species from different regions and with different range sizes for which refugia have been identified based on phylogeographic analyses, using ENM tools to make parallel predictions. We then assessed the correspondence between the two approaches based on spatial overlap and areal extent of the predicted refugia. In 14 of the 20 species, the predictions from ENM and predictions based on phylogeographic studies were significantly spatially correlated, suggesting that the two approaches to development of refugial maps are converging on a similar result. Our results confirm that ENM scenario exploration can provide a useful complement to molecular studies, offering a less subjective, spatially explicit hypothesis of past geographic patterns of distribution.