Protein Sequencing Solves Darwinian Mystery Of Strange South American Mammals

Protein Sequencing Solves Darwinian Mystery Of Strange South American Mammals

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Published today in Nature, their remarkable technical feat in obtaining a molecular phylogeny based on Pleistocene protein sequences is a first, which could herald a new chapter in palaeontology.

Researchers in the University’s BioArCh research facility and Centre of Excellence in Mass Spectrometry were called in by the Natural History Museum and the American Museum of Natural History to resolve the long-standing question of the fossils of Toxodon and Macrauchenia, the South American native ungulates or hooved mammals—the last of which disappeared only 10,000 years ago.

The research shows that South American ungulates, similar to those whose fossils were found by Darwin 180 years ago in Uruguay and Argentina, are actually related to mammals like horses rather than elephants and other species with ancient evolutionary ties to Africa as some taxonomists have maintained

Previously, attempts by scientists to pinpoint the origin of animals using morphology-based analysis and ancient DNA, had failed. The latter approach was compromised because scientists were unable to recover any identifiable mammalian DNA from fossil specimens. This is likely to be the case for large numbers of important fossils from tropical or temperate deposits, as DNA preservation is ultimately controlled by the thermal history of the material.

But the structural protein, collagen, is likely to survive around ten times longer than DNA so the York scientists used proteomic analysis to screen 48 fossil bone samples of Toxodon platensis and Macrauchenia patachonica, discovered in the 19th century in the same area as those recovered by Darwin.  This produced sequences covering more than 90 per cent of the collagen molecule, effectively providing a phylogenetic barcode for the two species.

The York research team was headed by Professor Matthew Collins, of BioArCh, and Professor Jane Thomas-Oates, director of York’s Centre of Excellence in Mass Spectrometry, and included PhD student Frido Welker and Dr Jessica Thomas from the University’s Department of Biology.

Dr Thomas, who conducted the phylogenetic analysis, said “By producing the most comprehensive example of sequencing of its type, we have been able to resolve the taxonomic placement of these mammals, and solve a question that has baffled paleaontologists for more than a century.”

Professor Collins said: “We now have the potential to address many more of these challenges and to explore the evolutionary process much further back in prehistory.”

Frido Welker, a Ph.D. student at the Max Planck Institute for Evolutionary Anthropology and in BioArCh at York, said:  “We are developing new proteomic techniques and applying them to the archaeological and palaeoanthropological record. To get 90 per cent sequence coverage for both species is a direct result of those efforts, and truly fantastic given the burial time and location.”

Professor Thomas-Oates, of the University’s Department of Chemistry, added: “Our long-standing collaboration with scientists at Bruker Daltonics made it possible to analyse these samples using the most up to date mass spectrometric instrumentation.  The outstanding quality of the data was crucial in enabling us to determine the collagen sequences.”

Professor Ian Barnes, a curator at the Natural History Museum said: “Although the bones of these animals had been studied for over 180 years, no clear picture of their origins had been reached. Our analyses began by investigating ancient DNA to try to resolve the problem.”

Ross MacPhee, a curator in the American Museum of Natural History’s Department of Mammalogy said: “Fitting South American ungulates to the mammalian family tree has always been a major challenge for paleontologists, because anatomically they were these weird mosaics, exhibiting features found in a huge variety of quite unrelated species living all over the place.

“This is what puzzled Darwin and his collaborator Richard Owen so much in the early 19th century. With all of these conflicting signals, they couldn’t say whether these ungulates were related to giant rodents, or elephants, or camels—or what have you.”

With modern techniques of phylogenetic interpretation, the researchers were able to conclusively show that the closest living relatives of these species were the perissodactyls, the group that includes horses, rhinos, and tapirs. This makes them part of Laurasiatheria, one of the major groups of placental mammals. The molecular evidence corroborates a view held by some leading paleontologists that the ancestors of these South American ungulates came from North America more than 60 million years ago, probably just after the mass extinction that killed off non-avian dinosaurs and many other vertebrates. Because the South American ungulates were such a large and varied group, it is not clear whether other lineages not studied by the researchers all had the same origin.

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Earliest-Known Arboreal And Subterranean Ancestral Mammals Discovered

Earliest-Known Arboreal And Subterranean Ancestral Mammals Discovered

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The fossils of two interrelated ancestral mammals, newly discovered in China, suggest that the wide-ranging ecological diversity of modern mammals had a precedent more than 160 million years ago.

With claws for climbing and teeth adapted for a tree sap diet, Agilodocodon scansorius is the earliest-known tree-dwelling mammaliaform (long-extinct relatives of modern mammals). The other fossil, Docofossor brachydactylus, is the earliest-known subterranean mammaliaform, possessing multiple adaptations similar to African golden moles such as shovel-like paws. Docofossor also has distinct skeletal features that resemble patterns shaped by genes identified in living mammals, suggesting these genetic mechanisms operated long before the rise of modern mammals.

These discoveries are reported by international teams of scientists from the University of Chicago and Beijing Museum of Natural History in two separate papers published Feb. 13 in Science.

“We consistently find with every new fossil that the earliest mammals were just as diverse in both feeding and locomotor adaptations as modern mammals,” said Zhe-Xi Luo, PhD, professor of organismal biology and anatomy at the University of Chicago and an author on both papers. “The groundwork for mammalian success today appears to have been laid long ago.”

Agilodocodon and Docofossor provide strong evidence that arboreal and subterranean lifestyles evolved early in mammalian evolution, convergent to those of true mammals. These two shrew-sized creatures – members of the mammaliaform order Docodonta – have unique adaptations tailored for their respective ecological habitats.

Agilodocodon, which lived roughly 165 million years ago, had hands and feet with curved horny claws and limb proportions that are typical for mammals that live in trees or bushes. It is adapted for feeding on the gum or sap of trees, with spade-like front teeth to gnaw into bark. This adaptation is similar to the teeth of some modern New World monkeys, and is the earliest-known evidence of gumnivorous feeding in mammaliaforms. Agilodocodonalso had well-developed, flexible elbows and wrist and ankle joints that allowed for much greater mobility, all characteristics of climbing mammals.

“The finger and limb bone dimensions of Agilodocodon match up with those of modern tree-dwellers, and its incisors are evidence it fed on plant sap,” said study co-author David Grossnickle, graduate student at the University of Chicago. “It’s amazing that these arboreal adaptions occurred so early in the history of mammals and shows that at least some extinct mammalian relatives exploited evolutionarily significant herbivorous niches, long before true mammals.”

Docofossor, which lived around 160 million years ago, had a skeletal structure and body proportions strikingly similar to the modern day African golden mole. It had shovel-like fingers for digging, short and wide upper molars typical of mammals that forage underground, and a sprawling posture indicative of subterranean movement.

Docofossor had reduced bone segments in its fingers, leading to shortened but wide digits. African golden moles possess almost the exact same adaptation, which provides an evolutionary advantage for digging mammals. This characteristic is due to the fusion of bone joints during development – a process influenced by the genes BMP and GDF-5. Because of the many anatomical similarities, the researchers hypothesize that this genetic mechanism may have played a comparable role in early mammal evolution, as in the case of Docofossor.

The spines and ribs of both Agilodocodon and Docofossoralso show evidence for the influence of genes seen in modern mammals. Agilodocodon has a sharp boundary between the thoracic ribcage to lumbar vertebrae that have no ribs. However, Docofossor shows a gradual thoracic to lumber transition. These shifting patterns of thoracic-lumbar transition have been seen in modern mammals and are known to be regulated by the genes Hox 9-10 and Myf 5-6. That these ancient mammaliaforms had similar developmental patterns is an evidence that these gene networks could have functioned in a similar way long before true mammals evolved.

“We believe the shortened digits of Docofossor, which is a dead ringer for modern golden moles, could very well have been caused by BMP and GDF,” Luo said. “We can now provide fossil evidence that gene patterning that causes variation in modern mammalian skeletal development also operated in basal mammals all the way back in the Jurassic.”

Early mammals were once thought to have limited ecological opportunities to diversify during the dinosaur-dominated Mesozoic era. However, Agilodocodon,Docofossor and numerous other fossils – includingCastorocauda, a swimming, fish-eating mammaliaform described by Luo and colleagues in 2006 – provide strong evidence that ancestral mammals adapted to wide-ranging environments despite competition from dinosaurs.

“We know that modern mammals are spectacularly diverse, but it was unknown whether early mammals managed to diversify in the same way,” Luo said. “These new fossils help demonstrate that early mammals did indeed have a wide range of ecological diversity. It appears dinosaurs did not dominate the Mesozoic landscape as much as previously thought.”

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Manatees

Manatees

Manatees (family Trichechidae, genus Trichechus) are large, fully aquatic, mostly herbivorous marine mammals sometimes known as sea cows. There are three accepted living species of Trichechidae, representing three of the four living species in the order Sirenia: the Amazonian manatee (Trichechus inunguis), the West Indian manatee (Trichechus manatus), and the West African manatee (Trichechus senegalensis). They measure up to 13 feet (4.0 m) long, weigh as much as 1,300 pounds (590 kg), and have paddle-like flippers. The name manatí comes from the Taíno, a pre-Columbian people of the Caribbean, meaning “breast”.

The Manatee! A female sea cow can give birth to a single calf every three years. The calf begins feeding on plants when it’s a few weeks old, but continues to nurse from its mother for about 12 to 18 months. This long period of nursing allows the calf to learn migration routes, foods, and preferred feeding areas from its mother. As of April 2012, it is estimated there are less than 3,000 left, about ten percent die each year, injured and killed in accidents involving boats.


Info via: http://en.wikipedia.org/wiki/Manatee

Flying fish a fascinating sight

Flying fish a fascinating sight

21 December 2012

Spotfin Flyingfish captured on film by ecologist Rohan Clarke at Ashmore Reef off the Kimberley coast.

A chance sighting of the exotic Spotfin Flyingfish captured on film by ecologist Rohan Clarke during a recent research trip has been recognised in a premier natural history photography competition.

The photo snapped at Ashmore Reef off the Kimberley coast, Western Australia, during a research trip has won the Animal Behaviour category of this year’s ANZANG wildlife photography competition in the Australasian region.

Dr Clarke, from Monash University’s School of Biological Sciences, said the photo was captured when the spectacular fish was spooked by the boat during the cruise to an overnight anchorage.


“Spotfin Flyingfish began exploding out of the water all around us,” Dr Clarke said.

“The glassy, mirror-like sea and evening light provided a perfect opportunity to hang off the bow with the camera and snap one in mid-flight as it fled the moving boat.”

Dr Clarke and his research team are studying seabirds of the Kimberley to gauge the long-term effects of the 2009 Montara oil spill. Ashmore Reef is home to other exotic winged creatures including the Masked Booby, Wedge-Tailed Shearwater, Lesser Noddy and Nankeen Night-Heron.

The 20cm long Spotfin Flyingfish can accelerate to around 40km/h underwater before breaking the surface and extending its wings. They are capable of flights of a hundred metres or more.

When not conducting research, Dr Clarke has concentrated on building a quality collection of natural history images. With images of Australian birds, reptiles, amphibians and mammals his collection is one of the largest achieved by a single photographer in Australia, South-east Asia andthe Pacific region.

The collection can be viewed via Dr Clarke’s website – Wildlife Images.

Editors note: Full article can be found here.

Credit: http://www.monash.edu.au