Jakob Vinther

Recalibrating Equus evolution using the genome sequence of an early Middle Pleistocene horse

The rich fossil record of equids has made them a model for evolutionary processes. Here we present a 1.12-times coverage draft genome from a horse bone recovered from permafrost dated to approximately 560–780 thousand years before present (kyr bp). Our data represent the oldest full genome sequence determined so far by almost an order of magnitude. For comparison, we sequenced the genome of a Late Pleistocene horse (43 kyr bp), and modern genomes of five domestic horse breeds (Equus ferus caballus), a Przewalski’s horse (E. f. przewalskii) and a donkey (E. asinus). Our analyses suggest that the Equus lineage giving rise to all contemporary horses, zebras and donkeys originated 4.0–4.5 million years before present (Myr bp), twice the conventionally accepted time to the most recent common ancestor of the genus Equus. We also find that horse population size fluctuated multiple times over the past 2 Myr, particularly during periods of severe climatic changes. We estimate that the Przewalski’s and domestic horse populations diverged 38–72 kyr bp, and find no evidence of recent admixture between the domestic horse breeds and the Przewalski’s horse investigated. This supports the contention that Przewalski’s horses represent the last surviving wild horse population. We find similar levels of genetic variation among Przewalski’s and domestic populations, indicating that the former are genetically viable and worthy of conservation efforts. We also find evidence for continuous selection on the immune system and olfaction throughout horse evolution. Finally, we identify 29 genomic regions among horse breeds that deviate from neutrality and show low levels of genetic variation compared to the Przewalski’s horse. Such regions could correspond to loci selected early during domestication.

Ordovician faunas of Burgess Shale type

The renowned soft-bodied faunas of the Cambrian period, which include the Burgess Shale, disappear from the fossil record in the late Middle Cambrian, after which the Palaeozoic fauna dominates. The disappearance of faunas of Burgess Shale type curtails the stratigraphic record of a number of iconic Cambrian taxa. One possible explanation for this loss is a major extinction, but more probably it reflects the absence of preservation of similar soft-bodied faunas in later periods. Here we report the discovery of numerous diverse soft-bodied assemblages in the Lower and Upper Fezouata Formations (Lower Ordovician) of Morocco, which include a range of remarkable stem-group morphologies normally considered characteristic of the Cambrian. It is clear that biotas of Burgess Shale type persisted after the Cambrian and are preserved where suitable facies occur. The Fezouata biota provides a link between the Burgess Shale communities and the early stages of the Great Ordovician Biodiversification Event.

Plumage Color Patterns of an Extinct Dinosaur

Dinosaur Plumage Coloration and appearance provide important behavioral and evolutionary information in animals. However, for the most part, we do not know the coloration of fossil terrestrial animals. Li et al. (p. 1369, published online 4 February) have reconstructed the appearance of a theropod dinosaur by mapping features of its well-preserved feathers and comparing them with modern samples from birds. Feather color is partly determined by melanosome density and shape, and this information is preserved in a recently discovered fossil from China. The dinosaur was gray with white limbs and had a reddish crest and a speckled face. Comparison of melanosome shape and density between fossil feathers and modern ones reveals the appearance and color of a theropod. For as long as dinosaurs have been known to exist, there has been speculation about their appearance. Fossil feathers can preserve the morphology of color-imparting melanosomes, which allow color patterns in feathered dinosaurs to be reconstructed. Here, we have mapped feather color patterns in a Late Jurassic basal paravian theropod dinosaur. Quantitative comparisons with melanosome shape and density in extant feathers indicate that the body was gray and dark and the face had rufous speckles. The crown was rufous, and the long limb feathers were white with distal black spangles. The evolution of melanin-based within-feather pigmentation patterns may coincide with that of elongate pennaceous feathers in the common ancestor of Maniraptora, before active powered flight. Feathers may thus have played a role in sexual selection or other communication.

Cephalopod origin and evolution: A congruent picture emerging from fossils, development and molecules: Extant cephalopods are younger than previously realised and were under major selection to become agile, shell-less predators.

Cephalopods are extraordinary molluscs equipped with vertebrate‐like intelligence and a unique buoyancy system for locomotion. A growing body of evidence from the fossil record, embryology and Bayesian molecular divergence estimations provides a comprehensive picture of their origins and evolution. Cephalopods evolved during the Cambrian (∼530 Ma) from a monoplacophoran‐like mollusc in which the conical, external shell was modified into a chambered buoyancy apparatus. During the mid‐Palaeozoic (∼416 Ma) cephalopods diverged into nautiloids and the presently dominant coleoids. Coleoids (i.e. squids, cuttlefish and octopods) internalised their shells and, in the late Palaeozoic (∼276 Ma), diverged into Vampyropoda and the Decabrachia. This shell internalisation appears to be a unique evolutionary event. In contrast, the loss of a mineralised shell has occurred several times in distinct coleoid lineages. The general tendency of shell reduction reflects a trend towards active modes of life and much more complex behaviour.

Fossil Evidence for Evolution of the Shape and Color of Penguin Feathers

Feather of the Penguin Penguins are highly adapted for their cold, aquatic environment. Changes in their wings and feathers have allowed rapid swimming and protection from the near-freezing water. Clarke et al. (p. 954, published online 30 September; see the cover) describe an early penguin, dating to about 35 million years ago, that includes well-preserved feathers. The melanosomes in the feathers, which influence their strength, as well as their color, are like those of many other aquatic birds and unlike those of present-day penguins, even though the morphology of the wings and feathers had already been modified. Thus, in penguins, the shape and form of the feather evolved before microstructural changes occurred. The melanosome arrangement also suggests that the penguin was mostly gray-brown. A fossil penguin shows that the wing and feather form evolved before distinctive microstructural changes in the feathers. 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.

The colour of fossil feathers

Feathers are complex integumentary appendages of birds and some other theropod dinosaurs. They are frequently coloured and function in camouflage and display. Previous investigations have concluded that fossil feathers are preserved as carbonized traces composed of feather-degrading bacteria. Here, an investigation of a colour-banded feather from the Lower Cretaceous Crato Formation of Brazil revealed that the dark bands are preserved as elongate, oblate carbonaceous bodies 1–2 μm long, whereas the light bands retain only relief traces on the rock matrix. Energy dispersive X-ray analysis showed that the dark bands preserve a substantial amount of carbon, whereas the light bands show no carbon residue. Comparison of these oblate fossil bodies with the structure of black feathers from a living bird indicates that they are the eumelanin-containing melanosomes. We conclude that most fossil feathers are preserved as melanosomes, and that the distribution of these structures in fossil feathers can preserve the colour pattern in the original feather. The discovery of preserved melanosomes opens up the possibility of interpreting the colour of extinct birds and other dinosaurs.

A placozoan affinity for Dickinsonia and the evolution of late Proterozoic metazoan feeding modes

SUMMARY Dickinsonia is one of the most recognizable forms in the Ediacaran fauna, but its phylogenetic position has been contentious, and it has been placed in almost every kingdom of life. Here, it is hypothesized that the affinities of Dickinsonia lie with the Placozoa (Metazoa), an understudied phylum that is widespread in tropical seas worldwide. Modern placozoans show obvious differences in size and axial organization compared with Dickinsonia, but these differences can be accounted for by the stem‐group/crown‐group distinction. The affinity with placozoans is evidenced primarily by the unique feeding mode of Dickinsonia, which is demonstrated by a series of feeding traces. These traces indicate that Dickinsonia moved over the Ediacaran matgrounds, and digested the mat using its entire lower sole. The ability of Dickinsonia to move negates an algal, fungal, or sponge affinity, while the feeding mode, external digestion with a ventral sole, rules out placement within any sponge or eumetazoan lineage. The only organisms that both move and feed in this manner are placozoans. Recent molecular phylogenetic studies have demonstrated that placozoans lie above sponges but below Eumetazoa. We hypothesize that Dickinsonia and other externally digesting Ediacaran forms are either stem‐placozoans, or a series of extinct lineages above sponges and below eumetazoans on the metazoan tree. We discuss the potential evolutionary transitions between the main metazoan feeding modes in the context of the emerging molecular phylogeny, and suggest that aspects of the sponge and placozoan feeding strategies are relicts of nonuniformitarian Proterozoic ocean conditions.

Reconstruction of Microraptor and the Evolution of Iridescent Plumage

Flashy Feathers Feather colors play key roles in the lives of birds, functioning in everything from camouflage, to thermoregulation, to sexual signaling. Much recent research has revealed that some dinosaurs also had feathers, and examination of feather components in fossil and preserved feathers has begun to reveal how feather color may have played a role in the lives of these dinosaurs. Li et al. (p. 1215) compared the characteristics of the melanosomes of the paravian dinosaur Microraptor to those found in extant birds, which suggest that its feathers were black and iridescent. The existence of this subtle color reflectance, together with morphological aspects of the feathered tail, suggests an important role for signaling in the early evolution of feathers. Iridescence in the feathers of a feathered dinosaur suggests an early role for feathers in ornamental display and signaling. Iridescent feather colors involved in displays of many extant birds are produced by nanoscale arrays of melanin-containing organelles (melanosomes). Data relevant to the evolution of these colors and the properties of melanosomes involved in their generation have been limited. A data set sampling variables of extant avian melanosomes reveals that those forming most iridescent arrays are distinctly narrow. Quantitative comparison of these data with melanosome imprints densely sampled from a previously unknown specimen of the Early Cretaceous feathered Microraptor predicts that its plumage was predominantly iridescent. The capacity for simple iridescent arrays is thus minimally inferred in paravian dinosaurs. This finding and estimation of Microraptor feathering consistent with an ornamental function for the tail suggest a centrality for signaling in early evolution of plumage and feather color.

Direct chemical evidence for eumelanin pigment from the Jurassic period

Melanin is a ubiquitous biological pigment found in bacteria, fungi, plants, and animals. It has a diverse range of ecological and biochemical functions, including display, evasion, photoprotection, detoxification, and metal scavenging. To date, evidence of melanin in fossil organisms has relied entirely on indirect morphological and chemical analyses. Here, we apply direct chemical techniques to categorically demonstrate the preservation of eumelanin in two > 160 Ma Jurassic cephalopod ink sacs and to confirm its chemical similarity to the ink of the modern cephalopod, Sepia officinalis. Identification and characterization of degradation-resistant melanin may provide insights into its diverse roles in ancient organisms.

The Early Cambrian Halkieria is a mollusc

Halkieria evangelista was originally interpreted as a stem‐group brachiopod. It was later proposed that the brachiopods evolved from a halkieriid ancestor that curved ventrally, lost the foot and radula, developed a lophophore as a new feeding organ, and modified the sclerites to chaetae. Molluscan affinities have been discussed by a number of authors. We have studied some of the original material of Halkieria and found that all the characters that can be observed with certainty are compatible with characters in living molluscs. The combination of characters observed in Halkieria does not fit with any of the living classes of molluscs, so we propose placing it in a new class, Diplacophora. Living polyplacophorans have hairs secreted by a number of epithelial cells and containing nerve cells; they are clearly not homologous with annelid chaetae. Thus, there is no support for theories that regard Halkieria as belonging to the stem group of either the annelids or brachiopods.