https://www.cs.princeton.edu/~schapire/papers/ecolmod.pdf

Maximum entropy modeling of species geographic distributions

Climate change over the past approximately 30 years has produced numerous shifts in the distributions and abundances of species and has been implicated in one species-level extinction. Using projections of species' distributions for future climate scenarios, we assess extinction risks for sample regions that cover some 20% of the Earth's terrestrial surface. Exploring three approaches in which the estimated probability of extinction shows a power-law relationship with geographical range size, we predict, on the basis of mid-range climate-warming scenarios for 2050, that 15-37% of species in our sample of regions and taxa will be 'committed to extinction'. When the average of the three methods and two dispersal scenarios is taken, minimal climate-warming scenarios produce lower projections of species committed to extinction ( approximately 18%) than mid-range ( approximately 24%) and maximum-change ( approximately 35%) scenarios. These estimates show the importance of rapid implementation of technologies to decrease greenhouse gas emissions and strategies for carbon sequestration.

/pdf/extinction-risk-from-climate-change-3pqx1sctsd.pdf

Extinction risk from climate change

In the last two decades, interest in species distribution models (SDMs) of plants and animals has grown dramatically. Recent advances in SDMs allow us to potentially forecast anthropogenic effects on patterns of biodiversity at different spatial scales. However, some limitations still preclude the use of SDMs in many theoretical and practical applications. Here, we provide an overview of recent advances in this field, discuss the ecological principles and assumptions underpinning SDMs, and highlight critical limitations and decisions inherent in the construction and evaluation of SDMs. Particular emphasis is given to the use of SDMs for the assessment of climate change impacts and conservation management issues. We suggest new avenues for incorporating species migration, population dynamics, biotic interactions and community ecology into SDMs at multiple spatial scales. Addressing all these issues requires a better integration of SDMs with ecological theory.

Predicting species distribution: offering more than simple habitat models.

The influence of diet on the distribution of nitrogen isotopes in animals was investigated by analyzing animals grown in the laboratory on diets of constant nitrogen isotopic composition. 
The isotopic composition of the nitrogen in an animal reflects the nitrogen isotopic composition of its diet. The δ^(15)N values of the whole bodies of animals are usually more positive than those of their diets. Different individuals of a species raised on the same diet can have significantly different δ^(15)N values. The variability of the relationship between the δ^(15)N values of animals and their diets is greater for different species raised on the same diet than for the same species raised on different diets. Different tissues of mice are also enriched in ^(15)N relative to the diet, with the difference between the δ^(15)N values of a tissue and the diet depending on both the kind of tissue and the diet involved. The δ^(15)N values of collagen and chitin, biochemical components that are often preserved in fossil animal remains, are also related to the δ^(15)N value of the diet. 
The dependence of the δ^(15)N values of whole animals and their tissues and biochemical components on the δ^(15)N value of diet indicates that the isotopic composition of animal nitrogen can be used to obtain information about an animal's diet if its potential food sources had different δ^(15)N values. The nitrogen isotopic method of dietary analysis probably can be used to estimate the relative use of legumes vs non-legumes or of aquatic vs terrestrial organisms as food sources for extant and fossil animals. However, the method probably will not be applicable in those modern ecosystems in which the use of chemical fertilizers has influenced the distribution of nitrogen isotopes in food sources. 
The isotopic method of dietary analysis was used to reconstruct changes in the diet of the human population that occupied the Tehuacan Valley of Mexico over a 7000 yr span. Variations in the δ^(15)C and δ^(15)N values of bone collagen suggest that C_4 and/or CAM plants (presumably mostly corn) and legumes (presumably mostly beans) were introduced into the diet much earlier than suggested by conventional archaeological analysis.

Influence of Diet On the Distribtion of Nitrogen Isotopes in Animals

Accurate modeling of geographic distributions of species is crucial to various applications in ecology and conservation. The best performing techniques often require some parameter tuning, which may be prohibitively time-consuming to do separately for each species, or unreliable for small or biased datasets. Additionally, even with the abundance of good quality data, users interested in the application of species models need not have the statistical knowledge required for detailed tuning. In such cases, it is desirable to use "default settings", tuned and validated on diverse datasets. Maxent is a recently introduced modeling technique, achieving high predictive accuracy and enjoying several additional attractive properties. The performance of Maxent is influenced by a moderate number of parameters. The first contribution of this paper is the empirical tuning of these parameters. Since many datasets lack information about species absence, we present a tuning method that uses presence-only data. We evaluate our method on independently collected high-quality presence-absence data. In addition to tuning, we introduce several concepts that improve the predictive accuracy and running time of Maxent. We introduce "hinge features" that model more complex relationships in the training data; we describe a new logistic output format that gives an estimate of probability of presence; finally we explore "background sampling" strategies that cope with sample selection bias and decrease model-building time. Our evaluation, based on a diverse dataset of 226 species from 6 regions, shows: 1) default settings tuned on presence-only data achieve performance which is almost as good as if they had been tuned on the evaluation data itself; 2) hinge features substantially improve model performance; 3) logistic output improves model calibration, so that large differences in output values correspond better to large differences in suitability; 4) "target-group" background sampling can give much better predictive performance than random background sampling; 5) random background sampling results in a dramatic decrease in running time, with no decrease in model performance.

https://onlinelibrary.wiley.com/doi/pdf/10.1111/j.0906-7590.2008.5203.x

Modeling of species distributions with Maxent: new extensions and a comprehensive evaluation

Incorporating connectivity into conservation planning: A multi-criteria case study from central Mexico

This study examined whether postdispersal fruit and seed removal by terrestrial mammals of common plant species was affected by the type of item, item density (low, medium, high), and habitat (gap, mid-succession, mature). Fruits of Brosimum alicastrum and Ficusyoponensis (Moraceae), Astrocaryum mexicanum (Palmae), and Nectandra ambigens (Lauraceae), and seeds of Omphalea oleifera (Euphorbiaceae) and Cymbopetalum baillonii (Annonaceae) were tested at the Los Tuxtlas rainforest in Mexico. Item removal from 108 experimental patches (N= 2340 fruits or seeds for each plant species tested) after 5 d was lower for F. yoponensis (6.6%) than for N. ambigens (68.8%), B. alicastrum (67.8%) C. baillonii (64.0%) and A. mexicanum (60.0%). No seeds of 0. oleifera were removed. A higher fruit or seed removal was observed from high density than low density food patches in A. mexicanum, C. baillonii and N. ambigens, but not in B. alicastrum and Fyoponensis. A higher fruit or seed removal was observed from food patches in mature forest than in gaps in all plant species tested. Similar removal values between open (open to all terrestrial mammals) and caged (open to small rodents) fruit and seed patches, abundant rodent live-trapping, and a scarcity of large terrestrial mammals, indicated that forest-dwelling small rodents were the main postdis- persal removal agents. Differences in plant species seedling recruitment resulting from small rodent food choices can partially determine long-term forest floristic composition at the Los Tuxtlas rainforest. RESUMEN. Se determino si la remocion postdispersion de frutos y semillas de plantas comunes, por parte de los mamiferos terrestres, es afectada por la especie de planta, la densidad de los lotes de frutos o semillas y por el habitat (claro, sucesion secundaria y selva madura). Frutos de Brosimum alicastrum y Ficus yoponensis (Moraceae), Astrocaryum mexicanum (Palmae) y Nectandra ambigens (Lauraceae) y semillas de Omphalea oleifera (Euphorbiaceae) y Cymbopetalum baillonii

Postdispersal fruit and seed removal by forest-dwelling rodents in a lowland rainforest in Mexico

Ecology of North American Triatominae.

The relative importance of plants and insects as sources of protein through the year was evaluated in 2 bat species in a seasonal forest in the neotropics using stable-isotope analysis of carbon and nitrogen. Artibeus jamaicensis, a frugivore, met almost all of its protein requirements from plants with no seasonal or sexual variation. In contrast, Glossophaga soricina, a nectarivore, relied mostly on insects, but in females, plants and insects were equally important in the early rainy season and in the mid dry season. Evidence of changes in food origin of protein associated with reproductive activity was not detected in either species.

Sources of protein in two species of phytophagous bats in a seasonal dry forest: evidence from stable-isotope analysis

We estimated the relative contribution of fruits and insects as sources of dietary protein in two species of Neotropical frugivorous bats (Artibeus jamaicensis and Sturnira lilium) using stable carbon and nitrogen isotope analyses. An insectivorous species (Pteronotus parnellii) was also included for comparison. We found constant patterns in stable carbon and nitrogen isotope composition in blood that separated the two species of frugivorous bats from the insectivorous bat. When we used these isotopic values (combined with those of dietary fruits and insects) to estimate the percent contribution of fruits and insects to the diet of the bats, we obtained different results, depending on assumptions and model adopted. We tested models using both δ15N and δ13C results simultaneously and separately and further used diet-tissue fractionation factors of 3‰ for nitrogen and 1 and 3.5‰ for carbon. We found that a carbon-based model with a diet-blood enrichment factor of 3.5‰ produced the most parsimonious...

Víctor Sánchez-Cordero

Papers

Incorporating connectivity into conservation planning: A multi-criteria case study from central Mexico

Postdispersal fruit and seed removal by forest-dwelling rodents in a lowland rainforest in Mexico

Ecology of North American Triatominae.

Sources of protein in two species of phytophagous bats in a seasonal dry forest: evidence from stable-isotope analysis

The Role of Fruits and Insects in the Nutrition of Frugivorous Bats: Evaluating the Use of Stable Isotope Models1