Biology subjects

Velasco, J. A.

Publications and source records attributed to Velasco, J. A..

3 recordsLinked to original sources

bioRxiv2018

Akaike information criteria and predictive geographical accuracy are not related in ecological niche modeling

AimEcological niche modeling (ENM) is an approach used to estimate species presence given its environmental preferences. Model complexity in ENMs has increasingly gained relevance in the last years. In particular, in Maxent algorithm is captured using the Akaike Information Criteria (AIC) based on the number of parameters and likelihoods of continuous raw outputs. However, it is not clear whether best-selected models using AIC are the models with the highest classification rate of correct presences and absences. Here, we test for a link between model complexity and accuracy of geographical predictions of Maxent models.\n\nInnovationWe created a set of virtual species and generate true geographical predictions for each one. We build a set of Maxent models using presence data from each virtual species with different regularization and features schemes. We compared AICc values for each model with the scores of standard validation metrics (e.g., Kappa, TSS) and with the number of pixels correctly predicted as presences, absences or both.\n\nMain ConclusionsWe found that binary predictions (i.e., presence-absence maps) selected as best models for AIC tend to predict incorrectly sites as presences and absences using independent datasets. We suggest that information criteria as AIC should be avoided when users are interested in binary predictions. Future applications that capture model complexity in ENM applications should be evaluated using standard validation metrics.

ecology↗

bioRxiv2018

Mapping diversification metrics in macroecological studies: Prospects and challenges

The intersection of macroecology and macroevolution is one of the most active research areas today. Macroecological studies are increasingly using phylogenetic diversification metrics to explore the role of evolutionary processes in shaping present-day patterns of biodiversity. Evolutionary explanations of species richness gradients are key for our understanding of how diversity accumulated in a region. For instance, the present-day diversity in a region can be a result of in situ diversification, extinction, or colonization from other regions, or a combination of all of these processes. However, it is unknown whether these metrics capture well these diversification and dispersal processes across geography. Some metrics (e.g., mean root distance -MRD-; lineage diversification-rate -DR-; evolutionary distinctiveness -ED-) seem to provide very similar geographical patterns regardless of how they were calculated (e.g., using branch lengths or not). The lack of appropriate estimates of extinction and dispersal rates in phylogenetic trees can limit our conclusions about how species richness gradients emerged. With a review of the literature and complemented by an empirical comparison, we show that phylogenetic metrics by itself are not capturing well the speciation, extinction and dispersal processes across the geographical gradients. Furthermore, we show how new biogeographic methods can improve our inference of past events and therefore our conclusions about the evolutionary mechanisms driving regional species richness. Finally, we recommend that future studies include several approaches (e.g., spatial diversification modelling, parametric biogeographic methods) to disentangle the relative the role of speciation, extinction and dispersal in the generation and maintenance of species richness gradients.

ecology↗

bioRxiv2017

Climatic niche dynamics and its role in the insular endemism of Anolis lizards

We evaluated the tempo and mode of climatic niche evolution in the radiation of Caribbean Anolis lizards and the role of climate in shaping their exceptional insular endemism. Using phylogenetic comparative methods, climatic niche data and a calibrated phylogeny, we reconstructed climatic niche dynamics across time and space for Caribbean Anolis lizards. We found evidence of several instances of niche shifts through the Caribbean Anolis radiation. Caribbean anole species have diversified mainly along a precipitation rather than a temperature gradient. Only a few lineages have colonized both cold and hot conditions. Furthermore, most of the single-island endemic species are climatically restricted to its native islands and a small set of species might the potential to colonize other islands given its climatic niche requirements. Overall, we found evidence that climate niche conservation has played a role structuring current insular Anolis endemism. The observed climatic dissimilarity across the Greater Antilles likely limit successful population establishment of potential exotic insular species.

evolutionary biology↗