Phylogenomics reconciles molecular data with the rich fossil record on the origin of living turtles.

Although a consensus exists that all living turtles fall within either Pleurodira or Cryptodira clades, estimating when these lineages split is still under debate. Most molecular studies date the split in the Triassic Period, whereas a Jurassic age is unanimous among morphological studies. Each hypothesis implies different paleobiogeographical scenarios to explain early turtle evolution. Here we explored the rich turtle fossil record with the Fossilized Birth-Death (FBD) and the traditional node dating (ND) methods using complete mitochondrial genomes (147 taxa) and a set of nuclear orthologs with over 10 million bp (25 taxa) to date the major splits in Testudines. Our results support an Early Jurassic split (191-182 Ma) for the crown Testudines with great consistency across different dating methods and datasets, with a narrow confidence interval. This result is independently supported by the oldest fossils of Testudines that postdate the Middle Jurassic (174 Ma), which were not used for calibration in this study. This age coincides with the Pangaea fragmentation and the formation of saltwater barriers such as the Atlantic Ocean and the Turgai Strait, supporting that diversification in Testudines was triggered by vicariance. Our ages of the splits in Pleurodira coincide with the geologic events of the Late Jurassic and Early Cretaceous. Conversely, the early Cryptodira radiation remained in Laurasia, and its diversification ensued as all its major lineages expanded their distribution into every continent during the Cenozoic. We provide the first detailed hypothesis of the evolution of Cryptodira in the Southern Hemisphere, in which our time estimates are correlated with each contact between landmasses derived from Gondwana and Laurasia. Although most South American Cryptodira arrived through the Great American Biotic Interchange, our results indicate that the Chelonoidis ancestor probably arrived from Africa through the chain islands of the South Atlantic during the Paleogene. Together, the presence of ancient turtle diversity and the vital role that turtles occupy in marine and terrestrial ecosystems underline South America as a chief area for conservation.

Bootstrap and Rogue Identification Tests for Phylogenetic Analyses.

Most phylogenetic tree-generating programs produce a fully dichotomous phylogenetic tree. However, as different markers may produce distinct topologies for the same set of organisms, topological tests are used to estimate the statistical reliability of the clades. In this protocol, we provide step-by-step instructions on how to perform the widely used bootstrap test using MEGA. However, a single unstable lineage, also known as a rogue lineage, may decrease the bootstrap proportions in many branches of the tree. This occurs because rogue taxa tend to bounce between clades from one pseudo-replicate to the next, lowering bootstrap proportions for many correct clades. Thus, it is important to identify and exclude rogue taxa before initiating a final phylogenetic analysis; here, we provide this protocol using the RogueNaRok platform.

An African Origin of the Eurylaimides (Passeriformes) and the Successful Diversification of the Ground-Foraging Pittas (Pittidae).

The Eurylaimides is one of the few passerine groups with a pantropical distribution. In this study, we generated a multi-calibrated tree with 83% of eurylaimid species diversity based on 30 molecular loci. Particular attention was given to the monotypic Sapayoidae to reconstruct the biogeography of this radiation. We conducted several topological tests including nonoverlapping subsampling of the concatenated alignment and coalescent species tree reconstruction. These tests firmly placed the South American Sapayoidae as the sister group to all other Eurylaimides families (split at ∼28 Ma), with increasing branch support as highly variable sites were removed. This topology is consistent with the breakup of the insular connection between Africa and South America (Atlantogea) that took place between the middle Eocene and the early Oligocene. We recovered Africa as the cradle of the core Eurylaimides, and this result is supported by all African lineages corresponding to the oldest splits within each family in this group. Our timescale suggests that desertification and the uplift of the Tibetan Plateau caused a parallel divergence between African and Asian lineages in all major clades in the core Eurylaimides at 22-9 Ma. We also propose that the ground-foraging behavior in the Pittidae ancestor allowed the pitta lineage to thrive and coexist with the older arboreal lineages of the core Eurylaimides. In contrast, the diversification of pittas in Australia was likely hindered by direct competition with the endemic ground-foraging oscines that had been well established in that continent since the Eocene.

A Paleogene origin for crown passerines and the diversification of the Oscines in the New World.

In this study, we present a detailed family-level phylogenetic hypothesis for the largest avian order (Aves: Passeriformes) and an unmatched multi-calibrated, relaxed clock inference for the diversification of crown passerines. Extended taxon sampling allowed the recovery of many challenging clades and elucidated their position in the tree. Acanthisittia appear to have diverged from all other passerines at the early Paleogene, which is considerably later than previously suggested. Thus, Passeriformes may be younger and represent an even more intense adaptive radiation compared to the remaining avian orders. Based on our divergence time estimates, a novel hypothesis for the diversification of modern Suboscines is proposed. According to this hypothesis, the first split between New and Old World lineages would be related to the severing of the Africa-South America biotic connection during the mid-late Eocene, implying an African origin for modern Eurylaimides. The monophyletic status of groups not recovered by any subsequent study since their circumscription, viz. Sylvioidea including Paridae, Remizidae, Hyliotidae, and Stenostiridae; and Muscicapoidea including the waxwing assemblage (Bombycilloidea) were notable topological findings. We also propose possible ecological interactions that may have shaped the distinct Oscine distribution patterns in the New World. The insectivorous endemic Oscines of the Americas, Vireonidae (Corvoidea), Mimidae, and Troglodytidae (Muscicapoidea), probably interfered with autochthonous Suboscines through direct competition. Thus, the Early Miocene arrival of these lineages before any other Oscines may have occupied the few available niches left by Tyrannides, constraining the diversification of insectivorous Oscines that arrived in the Americas later. The predominantly frugivorous-nectarivorous members of Passeroidea, which account for most of the diversity of New World-endemic Oscines, may not have been subjected to competition with Tyrannides. In fact, the vast availability of frugivory niches combined with weak competition with the autochthonous passerine fauna may have been crucial for passeroids to thrive in the New World.