An updated paleontological timetree of lissamphibians,with comments on the anatomy of Jurassic crown-group salamanders (Urodela)

We present an update of our time-calibrated supertree of extant and extinct lissamphibians (Marjanovi? D, Laurin M. 2007. Fossils, molecules, divergence times, and the origin of lissamphibians. Syst Biol 56(3):369–388) and of the divergence dates that can be inferred from it. The present version contains 319 extinct species or possible species of lissamphibians, compared to 223 previously. Discoveries of new fossiliferous sites, advances in phylogeny and recently obtained radiometric dates have offered opportunities to test our results, including the conclusion that the fossil record of Lissamphibia is dense enough to provide reliable calibration constraints for molecular divergence dating. By and large, the results are upheld. Some of the divergence dates we infer from the tree are up to 15 Ma younger than we previously published, some are up to 15 Ma older, some have had their range of uncertainty drastically reduced and the maximum age for the origin of Urodela (the salamander crown group) is no longer well constrained. The dermal bone plates in the gill region of the Jurassic urodeles Beiyanerpeton, Seminobatrachus and Chunerpeton and the grooves for the lateral line organ on the skull of the first require either unexpected reversals or several independent losses in other lissamphibians and indeed other urodeles.     

The role of frugivory in the diversification of bats in the Neotropics

Aim Ecological interactions are among the most important biotic factors influencing the processes of speciation and extinction. Our aim was to test whether diversification rates of New World Noctilionoidea bats are associated with specialization for frugivory, and how this pattern differs between the mainland and the West Indies. Location The New World. Methods We reconstructed a time‐calibrated molecular phylogenetic hypothesis for the New World genera of the superfamily Noctilionoidea. We compiled data on diet, morphology, geographical distribution and number of ecoregions in which each genus occurs. Then, using the phylogenetic tree constructed, we tested whether diversification was driven by diet (animalivorous and sanguinivorous versus nectarivorous and frugivorous) and specialization for frugivory. Afterwards, we conducted phylogenetic comparative analyses to identify correlates of species richness and net diversification rates. Results The diversification rate was higher in mutualistic than in antagonistic clades in mainland and Antillean biogeographical scenarios, but only strictly frugivorous clades showed a markedly higher diversification rate than the rest of the genera. Geographical range and number of ecoregions were positively associated with species richness and diversification rate in continental and insular lineages. Lower body mass, lower forearm length and specialization for frugivory were significantly positively correlated with higher diversification rates in continental lineages, whereas these parameters were negatively correlated in Antillean lineages. Main conclusions The direction of the relationship of intrinsic factors (specialization for frugivory and body size) with diversification of noctilionoid bats depends on the biogeographical context, whereas the direction of the relationship of extrinsic factors (geographical range and number of ecoregions) with diversification is consistent in both mainland and the West Indian lineages.     

Molecular phylogeny and divergence times of deuterostome animals

The phylogenetic relationships among deuterostome animals have been debated for many years, and a diversity of hypotheses have been proposed based on both morphological and molecular data. Here we have assembled sequences of 217 nuclear-encoded proteins to address specific questions concerning their relationships and times of origin. We recovered significant support for urochordates as the closest relative of vertebrates with an analysis of 59 proteins (17,400 amino acids) and suggest that the basal position of urochordates found in previous molecular studies may have been the result of long-branch attraction biases. Our results also support Ambulacraria, the pairing of hemichordates with echinoderms (nine proteins; 2,382 amino acids), and Cyclostomata, the pairing of lampreys with hagfish (25 proteins; 6,895 amino acids). In addition, 325 shared proteins (102,110 amino acids) were obtained from the complete genomes of six vertebrates and a urochordate for phylogenetic analysis and divergence time estimation. An evolutionary timescale was estimated using a local (Bayesian) molecular clock method. We found that most major lineages of deuterostomes arose prior to the Cambrian Explosion of fossils (approximately 520 MYA) and that several lineages had originated before periods of global glaciation in the Precambrian.     

TimeTree 5: An Expanded Resource for Species Divergence Times

We present the fifth edition of the TimeTree of Life resource (TToL5), a product of the timetree of life project that aims to synthesize published molecular timetrees and make evolutionary knowledge easily accessible to all. Using the TToL5 web portal, users can retrieve published studies and divergence times between species, the timeline of a species’ evolution beginning with the origin of life, and the timetree for a given evolutionary group at the desired taxonomic rank. TToL5 contains divergence time information on 137,306 species, 41% more than the previous edition. The TToL5 web interface is now Americans with Disabilities Act-compliant and mobile-friendly, a result of comprehensive source code refactoring. TToL5 also offers programmatic access to species divergence times and timelines through an application programming interface, which is accessible at timetree.temple.edu/api. TToL5 is publicly available at timetree.org.     

Limitations of Phylogenomic Data Can Drive Inferred Speciation Rate Shifts

Biodiversity analyses of phylogenomic timetrees have produced many high-profile examples of shifts in the rate of speciation across the tree of life. Temporally correlated events in ecology, climate, and biogeography are frequently invoked to explain these rate shifts. In a re-examination of 15 genomic timetrees and 25 major published studies of the pattern of speciation through time, we observed an unexpected correlation between the timing of reported rate shifts and the information content of sequence alignments. Here, we show that the paucity of sequence variation and insufficient species sampling in phylogenomic data sets are the likely drivers of many inferred speciation rate shifts, rather than the proposed biological explanations. Therefore, data limitations can produce predictable but spurious signals of rate shifts even when speciation rates may be similar across taxa and time. Our results suggest that the reliable detection of speciation rate shifts requires the acquisition and assembly of long phylogenomic alignments with near-complete species sampling and accurate estimates of species richness for the clades of study.     

A newly recognized family from the Horn of Africa,the Heterocephalidae (Rodentia: Ctenohystrica)

The Ctenohystrica is one of the three major lineages of rodents and contains diverse forms related to gundis, porcupines, and guinea pigs. Phylogenetic analyses of this group using mitochondrial and nuclear gene sequences confirm the monophyly of the infraorder Hystricognathi and most of its recognized subclades, including both the Neotropical caviomorphs and the African phiomorphs, which are recovered as sister groups. Molecular timetrees calibrated with 22 securely placed fossils indicate that hystricognath superfamilies originated in the Eocene and Oligocene and most families had appeared by the end of the Oligocene, ～23 Mya. Divergences leading to hystricognath genera took place in the Miocene and Pliocene, with a single exception. The naked mole‐rat (Heterocephalus) diverged from other African mole‐rats (Bathyergidae) in the early Oligocene (～31.2 Mya), when the four caviomorph superfamilies (Erethizonoidea and Cavioidea at 32.4 Mya, Chinchilloidea and Octodontoidea at 32.8 Mya) were first appearing in South America. The extended independent evolution of Heterocephalus suggested by this analysis prompted a closer examination of mole‐rat characters. Heterocephalus indeed shares many characters with bathyergids, befitting their joint membership in the parvorder Bathyergomorphi and superfamily Bathyergoidea as well as their shared exploitation of subterranean lifestyles. However, a diverse array of cranial, dental, postcranial, external, and ecological characters distinguishes Heterocephalus from other African mole‐rats. These differences equal or exceed those used to diagnose caviomorph families and justify recognizing the naked mole‐rat in its own family, Heterocephalidae Landry, 1957. This taxonomic arrangement poses questions for the inter‐relationships of fossil and extant mole‐rats and brings time equivalence to the ranks assigned to the major clades of hystricognaths. © 2014 The Linnean Society of London