It is predicted that climate change will cause species extinctions and distributional shifts in coming decades, but data to validate these predictions are relatively scarce. Here, we compare recent and historical surveys for 48 Mexican lizard species at 200 sites. Since 1975, 12% of local populations have gone extinct. We verified physiological models of extinction risk with observed local extinctions and extended projections worldwide. Since 1975, we estimate that 4% of local populations have gone extinct worldwide, but by 2080 local extinctions are projected to reach 39% worldwide, and species extinctions may reach 20%. Global extinction projections were validated with local extinctions observed from 1975 to 2009 for regional biotas on four other continents, suggesting that lizards have already crossed a threshold for extinctions caused by climate change.

Phylogeographical inferences, applied in a comparative framework across multiple species at a regional scale, provide the means for detecting regional and landscape-level patterns of biodiversity, which are important for understanding macroecology and evolution in a geographical mosaic against a backdrop broadly impacted by geological events. Although information on Patagonian phylogeographical patterns has accumulated for both aquatic and terrestrial organisms in recent years, no attempt has been made to compare patterns across major organismal groups. In this review, we compiled studies on the phylogeography of co-distributed plants and terrestrial vertebrates from Patagonia. From each study, we extracted information on levels of genetic diversity, and inferred demographic processes and phylogeographical breaks, as well as on putative refugia, to produce the first summary of emerging phylogeographical patterns for this region. This review reveals some congruent phylogeographical patterns within and among plants and terrestrial vertebrates, and suggests that PreQuaternary as well as Quaternary geological events would have been important driving forces in the evolutionary history of Patagonian lineages. Different processes and directional range shifts suggest a mosaic of phylogeographical patterns, far more complex than the several north-south common patterns traditionally proposed.Las inferencias filogeográficas, dentro de un marco comparativo cuando incluyen varias especies a escala regional, permiten detectar patrones de biodiversidad regional y de paisaje (fisonómicos), importantes para entender tanto la macroecología como el impacto a gran escala de los eventos geológicos. En los últimos años, el conocimiento filogeográfico de Patagonia se ha acumulado para organismos acuáticos y terrestres, y aunque se han propuesto pocos patrones demográficos o espaciales cualitativamente concordantes, no se ha hecho ningún intento de revisar comparativamente algunos de esos patrones considerando grandes grupos de organismos. En esta revisión compilamos el conocimiento publicado sobre la filogeografía de plantas vasculares y vertebrados terrestres de Patagonia con el propósito de comparar niveles de diversidad genética, procesos demográficos, quiebres filogeográ-ficos y localización de posibles refugios, para producir el primer resumen de patrones filogeográficos emergentes

Species delimitation is a major research focus in evolutionary biology because accurate species boundaries are a prerequisite for the study of speciation. New species delimitation methods (SDMs) can accommodate nonmonophyletic species and gene tree discordance as a result of incomplete lineage sorting via the coalescent model, but do not explicitly accommodate gene flow after divergence. Approximate Bayesian computation (ABC) can incorporate gene flow and estimate other relevant parameters of the speciation process while testing alternative species delimitation hypotheses. We evaluated the accuracy of BPP, SpeDeSTEM, and ABC for delimiting species using simulated data and applied these methods to empirical data from lizards of the Liolaemus darwinii complex. Overall, BPP was the most accurate, ABC showed an intermediate accuracy, and SpeDeSTEM was the least accurate under most simulated conditions. All three SDMs showed lower accuracy when speciation occurred despite gene flow, as found in previous studies, but ABC was the method with the smallest decrease in accuracy. All three SDMs consistently supported the distinctness of southern and northern lineages within L. darwinii. These SDMs based on genetic data should be complemented with novel SDMs based on morphological and ecological data to achieve truly integrative and statistically robust approaches to species discovery.

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Recovery of evolutionary history and delimiting species boundaries in widely distributed, poorly known groups requires extensive geographic sampling, but sampling regimes are difficult to design a priori because evolutionary diversity is often "hidden" by inadequate taxonomy. Large data sets are needed, and these provide unique challenges for analysis when they span intra- and interspecific levels of divergence. However, protocols have been designed to combine methods of analysis for DNA sequences that exhibit both very shallow and relatively deeper divergences. In this study, we combined several tree-based phylogeny reconstruction methods with nested-clade analysis to extract maximum historical signal at various levels in the poorly known Liolaemus elongatus-kriegi lizard complex in temperate South America. We implemented a recently descrirbed tree-based protocol for DNA sequences to test for species boundaries, and we propose modifications to accommodate large data sets and gene regions with heterogeneous substitution rates. Combining haplotype trees with nested-clade analyses allowed testing of species boundaries on the basis of a priori defined criteria. The results obtained suggest that the number of putative species in the L. elongatus-kriegi complex could be doubled. We discuss these findings in the context of the advantages and limitations of a combined approach for retrieval of maximum historical information in large data sets and with reference to the yet formidable unresolved issues of sampling strategies.

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