More Evidence South American Notoungulates are Perissodactyls

Ancient collagen reveals evolutionary history of the endemic South American ‘ungulates’

Author:

Buckley

Abstract:

Since the late eighteenth century, fossils of bizarre extinct creatures have been described from the Americas, revealing a previously unimagined chapter in the history of mammals. The most bizarre of these are the ‘native’ South American ungulates thought to represent a group of mammals that evolved in relative isolation on South America, but with an uncertain affinity to any particular placental lineage. Many authors have considered them descended from Laurasian ‘condylarths’, which also includes the probable ancestors of perissodactyls and artiodactyls, whereas others have placed them either closer to the uniquely South American xenarthrans (anteaters, armadillos and sloths) or the basal afrotherians (e.g. elephants and hyraxes). These hypotheses have been debated owing to conflicting morphological characteristics and the hitherto inability to retrieve molecular information. Of the ‘native’ South American mammals, only the toxodonts and litopterns persisted until the Late Pleistocene–Early Holocene. Owing to known difficulties in retrieving ancient DNA (aDNA) from specimens from warm climates, this research presents a molecular phylogeny for both Macrauchenia patachonica (Litopterna) and Toxodon platensis (Notoungulata) recovered using proteomics-based (liquid chromatography–tandem mass spectrometry) sequencing analyses of bone collagen. The results place both taxa in a clade that is monophyletic with the perissodactyls, which today are represented by horses, rhinoceroses and tapirs.

This came out just a hair behind the other paper.   I wonder which one was submitted first?

Mystery Solved: South American Ungulates (NotoUngulates) are Crown Perissodactyls (Horse, Rhino Cousins)

Ancient proteins resolve the evolutionary history of Darwin’s South American ungulates

Authors:

Welker et al

Abstract:

No large group of recently extinct placental mammals remains as evolutionarily cryptic as the approximately 280 genera grouped as ‘South American native ungulates’. To Charles Darwin , who first collected their remains, they included perhaps the ‘strangest animal[s] ever discovered’. Today, much like 180 years ago, it is no clearer whether they had one origin or several, arose before or after the Cretaceous/Palaeogene transition 66.2 million years ago or are more likely to belong with the elephants and sirenians of superorder Afrotheria than with the euungulates (cattle, horses, and allies) of superorder Laurasiatheria . Morphology-based analyses have proved unconvincing because convergences are pervasive among unrelated ungulate-like placentals. Approaches using ancient DNA have also been unsuccessful, probably because of rapid DNA degradation in semitropical and temperate deposits. Here we apply proteomic analysis to screen bone samples of the Late Quaternary South American native ungulate taxa Toxodon (Notoungulata) and Macrauchenia (Litopterna) for phylogenetically informative protein sequences. For each ungulate, we obtain approximately 90% direct sequence coverage of type I collagen α1- and α2-chains, representing approximately 900 of 1,140 amino-acid residues for each subunit. A phylogeny is estimated from an alignment of these fossil sequences with collagen (I) gene transcripts from available mammalian genomes or mass spectrometrically derived sequence data obtained for this study. The resulting consensus tree agrees well with recent higher-level mammalian phylogenies. Toxodon and Macrauchenia form a monophyletic group whose sister taxon is not Afrotheria or any of its constituent clades as recently claimed , but instead crown Perissodactyla (horses, tapirs, and rhinoceroses). These results are consistent with the origin of at least some South American native ungulates from ‘condylarths’, a paraphyletic assembly of archaic placentals. With ongoing improvements in instrumentation and analytical procedures, proteomics may produce a revolution in systematics such as that achieved by genomics, but with the possibility of reaching much further back in time.

pop sci link.

DNA of Extinct Pleistocene Quaternary Macropod (kangaroos, wallabies) Studied

Late Pleistocene Australian Marsupial DNA Clarifies the Affinities of Extinct Megafaunal Kangaroos and Wallabies

Authors:

Llamas et al

Abstract:

Understanding the evolution of Australia’s extinct marsupial megafauna has been hindered by a relatively incomplete fossil record and convergent or highly specialized morphology, which confound phylogenetic analyses. Further, the harsh Australian climate and early date of most megafaunal extinctions (39–52 ka) means that the vast majority of fossil remains are unsuitable for ancient DNA analyses. Here, we apply cross-species DNA capture to fossils from relatively high latitude, high altitude caves in Tasmania. Using low-stringency hybridization and high-throughput sequencing, we were able to retrieve mitochondrial sequences from two extinct megafaunal macropodid species. The two specimens, Simosthenurus occidentalis (giant short-faced kangaroo) and Protemnodon anak (giant wallaby), have been radiocarbon dated to 46–50 and 40–45 ka, respectively. This is significantly older than any Australian fossil that has previously yielded DNA sequence information. Processing the raw sequence data from these samples posed a bioinformatic challenge due to the poor preservation of DNA. We explored several approaches in order to maximize the signal-to-noise ratio in retained sequencing reads. Our findings demonstrate the critical importance of adopting stringent processing criteria when distant outgroups are used as references for mapping highly fragmented DNA. Based on the most stringent nucleotide data sets (879 bp for S. occidentalis and 2,383 bp for P. anak), total-evidence phylogenetic analyses confirm that macropodids consist of three primary lineages: Sthenurines such as Simosthenurus (extinct short-faced kangaroos), the macropodines (all other wallabies and kangaroos), and the enigmatic living banded hare-wallaby Lagostrophus fasciatus (Lagostrophinae). Protemnodon emerges as a close relative of Macropus (large living kangaroos), a position not supported by recent morphological phylogenetic analyses.

Royal Tyrrell Museum Lecture Series: Resurrecting Physiological Traits

Hummingbirds Split From Swifts During the Eocene Paleogene in Asia, but had Explosive Evolutionary Radition In South America

The first comprehensive map of hummingbirds' 22-million-year-old family tree—reconstructed based on careful analysis of 284 of the world's 338 known species—tells a story of rapid and ongoing diversification. The decade-long study reported in the Cell Press journal Current Biology on April 3 also helps to explain how today's hummingbirds came to live where they do.

Part of the secret to the birds' remarkable success lies in the formation of nine principal groups or clades, hummingbirds' unique relationship to flowering plants, and the birds' continued spread into new geographic areas, the researchers say.

"Hummingbirds have essentially been reinventing themselves throughout their 22-million-year history," says Jim McGuire of the University of California, Berkeley.

While all hummingbirds depend on flower nectar to fuel their high metabolisms and hovering flight, coordinated changes in flower and bill shape have helped to drive the formation of new species of both hummingbirds and plants. Remarkably, as many as 25 hummingbird species are able to coexist in some places.

"One of the really cool features of hummingbird evolution is that they all eat the same thing yet have diversified dramatically," McGuire says. "It really is a big surprise that hummingbirds have divided the nectarivore niche so extensively."

The new, time-calibrated evolutionary tree shows that ancestral hummingbirds split from the swifts and treeswifts about 42 million years ago, probably in Eurasia. By about 22 million years ago, the ancestral species of all modern hummingbirds had made its way to South America, and that's when things really took off.

link.

Fossil Feather "Melanosomes" may Really be Bacterial Biofilms

Paleontologists studying fossilized feathers have proposed that the shapes of certain microscopic structures inside the feathers can tell us the color of ancient birds. But new research from North Carolina State University demonstrates that it is not yet possible to tell if these structures – thought to be melanosomes – are what they seem, or if they are merely the remnants of ancient bacteria.

Melanosomes are small, pigment-filled sacs located inside the cells of feathers and other pigmented tissues of vertebrates. They contain melanin, which can give feathers colors ranging from brownish-red to gray to solid black. Melanosomes are either oblong or round in shape, and the identification of these small bodies in preserved feathers has led to speculation about the physiology, habitats, coloration and lifestyles of the extinct animals, including dinosaurs, that once possessed them.

But melanosomes are not the only round and oblong microscopic structures that might show up in fossilized feathers. In fact, the microbes that drove the decomposition of the animal prior to fossilization share the same size and shape as melanosomes, and they would also be present in feathers during decay.

Alison Moyer, a Ph.D. candidate in paleontology at NC State, wanted to find out whether these structures could be definitively identified as either melanosome or microbe. Using black and brown chicken feathers – chickens are one of the closest living relatives to both dinosaurs and ancient birds – Moyer grew bacteria over them to replicate what we see in the fossil record. She used three different types of microscopy to examine the patterns of biofilm growth, and then compared those structures to melanosomes inside of chicken feathers that she had sliced open. Finally, she compared both microbes and actual melanosomes to structures in a fossilized feather from Gansus yumenensis, an avian dinosaur that lived about 120 million years ago, and to published images of fossil "melanosomes" by others. Her findings led to more questions.

"These structures could be original to the bird, or they could be a biofilm which has grown over and degraded the feather – if the latter, they would also produce round or elongated structures that are not melanosomes," Moyer says. "Melanosomes are embedded in keratin, which is a very tough protein, so they're hard to see unless there's been some degradation. But the bacteria are doing the degrading, and so that may be what we're seeing, rather than the melanosome itself. It's impossible to say with certainty what these structures are without more data, including fine scale chemical data."

The research appears online in Scientific Reports. Possible next steps for Moyer include testing for the presence of keratin or bacteria within the fossils, by looking for their molecular signals.

link.

Frasnian Devonian Fossil Yields 70 Different Steroids, Setting Record for Oldest Organic Molecular Fossils Found

Curtin University PhD candidate Ines Melendez says the lipids are 380 million years old, or about 250 million years older than what had been the oldest known find of its kind.

"This is the first detailed molecular study … on a carbonate concretion from the Devonian Reef," she says.

Her supervisor, Professor Kliti Grice, says the fossil was originally a crustacean that died in the oceans around the time of the Devonian mass-extinctions (more than 360 million years ago).

It fed on smaller organisms in the oxygenated upper layer of water, and when it died it sank into a lower layer of anoxic water.

"Sulfate reducers degrade that organic matter anerobically, yielding hydrogen sulfide utilised in photosynthesis by organisms called Chlorobi at the interface between the oxygenated and anoxic layers," Prof Grice says.

Ms Melendez says these microbes then formed a community around the dead crustacean.

"There was so much organic matter that they didn't degrade everything," she says.

"The conditions helped these organisms to start to precipitate carbonate—whatever was left was encapsulated inside and wasn't used any more.

"In that way the concretion kept growing."

She analysed the fossil, finding molecules of 70 different steroids.

link.