Phylogenetic evidence from freshwater crayfishes that cave adaptation is not an evolutionary dead-end.

Caves are perceived as isolated, extreme habitats with a uniquely specialized biota, which long ago led to the idea that caves are evolutionary dead-ends. This implies that cave-adapted taxa may be doomed for extinction before they can diversify or transition to a more stable state. However, this hypothesis has not been explicitly tested in a phylogenetic framework with multiple independently evolved cave-dwelling groups. Here, we use the freshwater crayfish, a group with dozens of cave-dwelling species in multiple lineages, as a system to test this hypothesis. We consider historical patterns of lineage diversification and habitat transition as well as current patterns of geographic range size. We find that while cave-dwelling lineages have small relative range sizes and rarely transition back to the surface, they exhibit remarkably similar diversification patterns to those of other habitat types and appear to be able to maintain a diversity of lineages through time. This suggests that cave adaptation is not a dead-end for freshwater crayfish, which has positive implications for our understanding of biodiversity and conservation in cave habitats

Two new species of freshwater crayfish of the genus Faxonius (Decapoda: Cambaridae) from the Ozark Highlands of Arkansas and Missouri

Fetzner Jr, James W., Taylor, Christopher A. (2018): Two new species of freshwater crayfish of the genus Faxonius (Decapoda: Cambaridae) from the Ozark Highlands of Arkansas and Missouri. Zootaxa 4399 (4): 491-520, DOI: https://doi.org/10.11646/zootaxa.4399.4.

Hylid Frog Phylogeny And Sampling Strategies For Speciose Clades

How should characters and taxa be sampled to resolve efficiently the phylogeny of ancient and highly speciose groups? We addressed this question empirically in the treefrog family Hylidae, which contains \u3e800 species and may be nonmonophyletic with respect to other anuran families. We sampled 81 species (54 hylids and 27 outgroups) for two mitochondrial genes (12S, ND1), two nuclear genes (POMC, c-myc), and morphology (144 characters) in an attempt to resolve higher-level relationships. We then added 117 taxa to the combined data set, many of which were sampled for only one gene (12S). Despite the relative incompleteness of the majority of taxa, the resulting trees placed all taxa in the expected higher-level clades with strong support, despite some taxa being \u3e90% incomplete. Furthermore, we found no relationship between the completeness of a taxon and the support (parsimony bootstrap or Bayesian posterior probabilities) for its localized placement on the tree. Separate analysis of the data set with the most taxa (12S) gives a somewhat problematic estimate of higher-level relationships, suggesting that data sets scored only for some taxa (ND1, nuclear genes, morphology) are important in determining the outcome of the combined analysis. The results show that hemiphractine hylids are not closely related to other hylids and should be recognized as a distinct family. They also show that the speciose genus Hyla is polyphyletic, but that its species can be arranged into three monophyletic genera. A new classification of hylid frogs is proposed. Several potentially misleading signals in the morphological data are discussed. Copyright © Society of Systematic Biologists

FileS1 - R scripts

R scripts used to execute the state-dependent diversification analyses and model adequacy tests

DatasetS4 - Bootstrap phylogenies

Time-calibrated bootstrap phylogenies (N=1000

Data from: Phylogenetic evidence from freshwater crayfishes that cave adaptation is not an evolutionary dead-end

Caves are perceived as isolated, extreme habitats with a set of uniquely specialized biota, which long ago led to the idea that caves are ‘evolutionary dead-ends.’ This suggests that cave-adapted taxa may be doomed for extinction before they can diversify or transition to a more stable state. However, this hypothesis has not been explicitly tested in a phylogenetic framework with multiple independent cave-dwelling groups. Here we use the freshwater crayfish, a group with dozens of cave-dwelling species in multiple lineages, as a system to test this hypothesis. We consider historical patterns of lineage diversification and habitat transition as well as current patterns of geographic range size. We find that while cave-dwelling lineages have small relative range sizes and rarely transition back to the surface, they exhibit remarkably similar diversification patterns to those of other habitat types and appear to be able to maintain a diversity of lineages through time. This suggests that cave-adaptation is not a ‘dead-end’ for freshwater crayfish, which has positive implications for our understanding of biodiversity and conservation in cave habitats