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The total-evidence approach to divergence time dating uses molecular and morphological data from extant and fossil species to infer phylogenetic relationships, species divergence times, and macroevolutionary parameters in a single coherent framework. Current model-based implementations of this approach lack an appropriate model for the tree describing the diversification and fossilization process and can produce estimates that lead to erroneous conclusions. We address this shortcoming by providing a total-evidence method implemented in a Bayesian framework. This approach uses a mechanistic tree prior to describe the underlying diversification process that generated the tree of extant and fossil taxa. Previous attempts to apply the total-evidence approach have used tree priors that do not account for the possibility that fossil samples may be direct ancestors of other samples, that is, ancestors of fossil or extant species or of clades. The fossilized birth–death (FBD) process explicitly models the diversification, fossilization, and sampling processes and naturally allows for sampled ancestors. This model was recently applied to estimate divergence times based on molecular data and fossil occurrence dates. We incorporate the FBD model and a model of morphological trait evolution into a Bayesian total-evidence approach to dating species phylogenies. We apply this method to extant and fossil penguins and show that the modern penguins radiated much more recently than has been previously estimated, with the basal divergence in the crown clade occurring at \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{upgreek} \usepackage{mathrsfs} \setlength{\oddsidemargin}{-69pt} \begin{document} }{}${\sim}12.7$\end{document} Ma and most splits leading to extant species occurring in the last 2 myr. Our results demonstrate that including stem-fossil diversity can greatly improve the estimates of the divergence times of crown taxa. The method is available in BEAST2 (version 2.4) software www.beast2.org with packages SA (version at least 1.1.4) and morph-models (version at least 1.0.4) installed. [Birth–death process; calibration; divergence times; MCMC; phylogenetics.]

Avian diversification has been influenced by global climate change, plate tectonic movements, and mass extinction events. However, the impact of these factors on the diversification of the hyperdiverse perching birds (passerines) is unclear because family level relationships are unresolved and the timing of splitting events among lineages is uncertain. We analyzed DNA data from 4,060 nuclear loci and 137 passerine families using concatenation and coalescent approaches to infer a comprehensive phylogenetic hypothesis that clarifies relationships among all passerine families. Then, we calibrated this phylogeny using 13 fossils to examine the effects of different events in Earth history on the timing and rate of passerine diversification. Our analyses reconcile passerine diversification with the fossil and geological records; suggest that passerines originated on the Australian landmass ∼47 Ma; and show that subsequent dispersal and diversification of passerines was affected by a number of climatological and geological events, such as Oligocene glaciation and inundation of the New Zealand landmass. Although passerine diversification rates fluctuated throughout the Cenozoic, we find no link between the rate of passerine diversification and Cenozoic global temperature, and our analyses show that the increases in passerine diversification rate we observe are disconnected from the colonization of new continents. Taken together, these results suggest more complex mechanisms than temperature change or ecological opportunity have controlled macroscale patterns of passerine speciation.

It has long been appreciated that analyses of genomic data (e.g., whole genome sequencing or sequence capture) have the potential to reveal the tree of life, but it remains challenging to move from sequence data to a clear understanding of evolutionary history, in part due to the computational challenges of phylogenetic estimation using genome-scale data. Supertree methods solve that challenge because they facilitate a divide-and-conquer approach for large-scale phylogeny inference by integrating smaller subtrees in a computationally efficient manner. Here, we combined information from sequence capture and whole-genome phylogenies using supertree methods. However, the available phylogenomic trees had limited overlap so we used taxon-rich (but not phylogenomic) megaphylogenies to weave them together. This allowed us to construct a phylogenomic supertree, with support values, that included 707 bird species (~7% of avian species diversity). We estimated branch lengths using mitochondrial sequence data and we used these branch lengths to estimate divergence times. Our time-calibrated supertree supports radiation of all three major avian clades (Palaeognathae, Galloanseres, and Neoaves) near the Cretaceous-Paleogene (K-Pg) boundary. The approach we used will permit the continued addition of taxa to this supertree as new phylogenomic data are published, and it could be applied to other taxa as well.

Penguin feathers are highly modified in form and function, but there have been no fossils to inform their evolution. A giant penguin with feathers was recovered from the late Eocene (~36 million years ago) of Peru. The fossil reveals that key feathering features, including undifferentiated primary wing feathers and broad body contour feather shafts, evolved early in the penguin lineage. Analyses of fossilized color-imparting melanosomes reveal that their dimensions were similar to those of non-penguin avian taxa and that the feathering may have been predominantly gray and reddish-brown. In contrast, the dark black-brown color of extant penguin feathers is generated by large, ellipsoidal melanosomes previously unknown for birds. The nanostructure of penguin feathers was thus modified after earlier macrostructural modifications of feather shape linked to aquatic flight.

Penguins have undergone dramatic changes associated with the evolution of underwater flight and subsequent loss of aerial flight, which are manifest and well documented in the musculoskeletal system and integument. Significant modification of neurosensory systems and endocranial spaces may also be expected along this locomotor transition. However, no investigations of the brain and sensory organs of extinct stem lineage Sphenisciformes have been carried out, and few data exist even for extant species of Spheniscidae. In order to explore neuroanatomical evolution in penguins, we generated virtual endocasts for the early Miocene stem penguin Paraptenodytes antarcticus, three extant penguin species (Pygoscelis antarctica, Aptenodytes patagonicus, Spheniscus magellanicus), and two outgroup species (the common loon Gavia immer and the Laysan albatross Phoebastria immutabilis). These endocasts yield new anatomical data and phylogenetically informative characters from the brain, carotid arteries, pneumatic recesses, and semicircular canal system. Despite having undergone over 60 million years of evolution since the loss of flight, penguins retain many attributes traditionally linked to flight. Features associated with visual acuity and proprioception, such as the sagittal eminence and flocculus, show a similar degree of development to those of volant birds in the three extant penguins and Paraptenodytes antarcticus. These features, although clearly not flight-related in penguins, are consistent with the neurological demands associated with rapid manoeuvring in complex aquatic environments. Semicircular canal orientation in penguins is similar to volant birds. Interestingly, canal radius is grossly enlarged in the fossil taxon Pa. antarcticus compared to living penguins and outgroups. In contrast to all other living birds, the contralateral anterior tympanic recesses of extant penguins do not communicate. An interaural pathway connecting these recesses is retained in Pa. antarcticus, suggesting that stem penguins may still have employed this connection, potentially to enhance directional localization of sound. Paedomorphosis, already identified as a potential factor in crown clade penguin skeletal morphology, may also be implicated in the failure of an interaural pathway to form during ontogeny in extant penguins.

New penguin fossils from the Eocene of Peru force a reevaluation of previous hypotheses regarding the causal role of climate change in penguin evolution. Repeatedly it has been proposed that penguins originated in high southern latitudes and arrived at equatorial regions relatively recently (e.g., 4–8 million years ago), well after the onset of latest Eocene/Oligocene global cooling and increases in polar ice volume. By contrast, new discoveries from the middle and late Eocene of Peru reveal that penguins invaded low latitudes >30 million years earlier than prior data suggested, during one of the warmest intervals of the Cenozoic. A diverse fauna includes two new species, here reported from two of the best exemplars of Paleogene penguins yet recovered. The most comprehensive phylogenetic analysis of Sphenisciformes to date, combining morphological and molecular data, places the new species outside the extant penguin radiation (crown clade: Spheniscidae) and supports two separate dispersals to equatorial (paleolatitude ≈14°S) regions during greenhouse earth conditions. One new species, Perudyptes devriesi , is among the deepest divergences within Sphenisciformes. The second, Icadyptes salasi , is the most complete giant (>1.5 m standing height) penguin yet described. Both species provide critical information on early penguin cranial osteology, trends in penguin body size, and the evolution of the penguin flipper.

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