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We investigated the pattern of genetic and morphological variation and the timing of diversification in a Neotropical direct developing frog, Pristimantis w-nigrum (Craugastoridae) to gain insight into the historical biogeography of the northern Andes. Phylogenetic inference and analyses of genetic differentiation at mitochondrial and nuclear markers reveal eight mitochondrial clades that display concordant and highly structured nuclear genetic variation along both eastern and western slopes of the Ecuadorian Andes. These eight phylogroups are deeply divergent and show little evidence of change in effective size over substantial periods of time. Consistent with other phylogenetic studies of vertebrates in the Andes, the timing of genetic divergence among lineages coincides with sequential bouts of Andean orogenesis during the late Miocene and early Pliocene. Morphometric analyses recover little morphological variation among populations in spite of considerable genetic divergence. The deep genetic differentiation among populations of P. w-nigrum suggests that this species harbors unrecognized diversity and may represent a complex of cryptic species. These results illuminate the evolutionary processes that generate diversity in tropical montane biomes and underscore the fact that cryptic diversity may be an important component of Neotropical montane biodiversity., (Copyright © 2013 Elsevier Inc. All rights reserved.)

Predicting where threatened species occur is useful for making informed conservation decisions. However, because they are usually rare, surveying threatened species is often expensive and time intensive. Here, we show how regions where common species exhibit high genetic and morphological divergence among populations can be used to predict the occurrence of species of conservation concern. Intraspecific variation of common species of birds, bats and frogs from Ecuador were found to be a significantly better predictor for the occurrence of threatened species than suites of environmental variables or the occurrence of amphibians and birds. Fully 93 per cent of the threatened species analysed had their range adequately represented by the geographical distribution of the morphological and genetic variation found in seven common species. Both higher numbers of threatened species and greater genetic and morphological variation of common species occurred along elevation gradients. Higher levels of intraspecific divergence may be the result of disruptive selection and/or introgression along gradients. We suggest that collecting data on genetic and morphological variation in common species can be a cost effective tool for conservation planning, and that future biodiversity inventories include surveying genetic and morphological data of common species whenever feasible.

We developed an approach that combines distribution data, environmental geographic information system layers, environmental niche models, and phylogenetic information to investigate speciation processes. We used Ecuadorian frogs of the family Dendrobatidae to illustrate our methodology. For dendrobatids there are several cases for which there is significant environmental divergence for allopatric and parapatric lineages. The consistent pattern that many related taxa or nodes exist in distinct environmental space reinforces Lynch and Duellman's hypothesis that differential selection likely played an important role in species differentiation of frogs in the Andes. There is also some evidence that the Río Esmeraldas basin is a geographic barrier to species distributed in low to middle elevations on the western side of the Andes. Another useful aspect of this approach is that it can point to common environmental parameters that correlate with speciation. For dendrobatids, sister clades generally segregate along temperature/elevational and/or seasonality axes. The joint analysis of environmental and geographic data for this group of dendrobatid frogs has identified potentially important speciation mechanisms and specific sister lineages that warrant intensive study to test hypotheses generated in this investigation. Further, the method outlined in this paper will be increasingly useful as knowledge of distribution and phylogeny of tropical species increases.