The Great London:
Early Mammals

The diversity of mammals on Earth exploded straight after the dinosaur extinction event, according to UCL researchers. New analysis of the fossil record shows that placental mammals, the group that today includes nearly 5000 species including humans, became more varied in anatomy during the Paleocene epoch - the 10 million years immediately following the event.

Senior author, Dr Anjali Goswami (UCL Genetics, Evolution & Environment), said: "When dinosaurs went extinct, a lot of competitors and predators of mammals disappeared, meaning that a great deal of the pressure limiting what mammals could do ecologically was removed. They clearly took advantage of that opportunity, as we can see by their rapid increases in body size and ecological diversity. Mammals evolved a greater variety of forms in the first few million years after the dinosaurs went extinct than in the previous 160 million years of mammal evolution under the rule of dinosaurs."

The Natural Environment Research Council-funded research, published today in the Biological Journal of the Linnean Society, studied the early evolution of placental mammals, the group including elephants, sloths, cats, dolphins and humans. The scientists gained a deeper understanding of how the diversity of the mammals that roamed the Earth before and after the dinosaur extinction changed as a result of that event.

Placental mammal fossils from this period have been previously overlooked as they were hard to place in the mammal tree of life because they lack many features that help to classify the living groups of placental mammals. Through recent work by the same team at UCL, this issue was resolved by creating a new tree of life for placental mammals, including these early forms, which was described in a study published in Biological Reviews yesterday.

First author of both papers, Dr Thomas Halliday (UCL Earth Sciences and Genetics, Evolution & Environment), said: "The mass extinction that wiped out the dinosaurs 66 million years ago is traditionally acknowledged as the start of the 'Age of Mammals' because several types of mammal appear for the first time immediately afterwards.

"Many recent studies suggest that little changed in mammal evolution during the Paleocene but these analyses don't include fossils from that time. When we look at the mammals that were present, we find a burst of evolution into new forms, followed by specialisation that finally resulted in the groups of mammals we see today. The earliest placental mammal fossils appear only a few hundred thousand years after the mass extinction, suggesting the event played a key role in diversification of the mammal group to which we belong."

The team studied the bones and teeth of 904 placental fossils to measure the anatomical differences between species. This information was used to build an updated tree of life containing 177 species within Eutheria (the group of mammals including all species more closely related to us than to kangaroos) including 94 from the Paleocene - making it the tree with the largest representation from Paleocene mammals to date. The new tree was analysed in time sections from 140 million years ago to present day, revealing the change in the variety of species.

Three different methods were used by the team to investigate the range and variation of the mammals present and all showed an explosion in mammal diversity after the dinosaur extinction. This is consistent with theories that mammals flourished when dinosaurs were no longer hunting them or competing with them for resources.

Dr Anjali Goswami (UCL Genetics, Evolution & Environment), added: "Extinctions are obviously terrible for the groups that go extinct, non-avian dinosaurs in this case, but they can create great opportunities for the species that survive, such as placental mammals, and the descendants of dinosaurs: birds."

Professor Paul Upchurch (UCL Earth Sciences), co-author of the Biological Reviews study, added: "Several previous methodological studies have shown that it is important to include as many species in an evolutionary tree as possible: this generally improves the accuracy of the tree. By producing such a large data set, we hope that our evolutionary tree for Paleocene mammals is more robust and reliable than any of the previous ones. Moreover, such large trees are very useful for future studies of large-scale evolutionary patterns, such as how early placental mammals dispersed across the continents via land bridges that no longer exist today."

The team are now investigating rates of evolution in these mammals, as well as looking at body size more specifically. Further work will involve building data from DNA into these analyses, to extend these studies to modern mammals.

Source: University College London [December 21, 2015]

Mammals immortalise their genes through eggs and sperm to ensure future generations inherit good quality mitochondria to power the body's cells, according to new UCL research.

Before now, it was not known why mammals rely on dedicated sex cells that are formed early in development (a germline) to make offspring whereas plants and other simple animals, such as corals and sponges, use sex cells produced later in life from normal body tissues.

In a new study, published today in >PLOS Biology and funded by Natural Environment Research Council, Engineering & Physical Sciences Research Council and the Leverhulme Trust, UCL scientists developed an evolutionary model to investigate how these differences evolved over time and discovered that the germline in mammals developed in response to selection on mitochondria (the powerhouses of cells).

First author and UCL PhD student, Arunas Radzvilavicius, said: "There have been many theories about why mammals have a specialised germline when plants and other ancient animals don't. Some suggest it was due to complexity of tissues or a selfish conflict between cells. The distinction between sex cells and normal body tissues seems to be necessary for the evolution of very complex specialised tissues like brain.

"Surprisingly, we found that these aren't the reason. Rather, it's about the number of genetic mutations in mitochondrial DNA over time, which differs between organisms, and the variation between cells caused by the mitochondria being randomly partitioned into daughter cells at each division."

In plants, mitochondrial mutations creep in slowly, so a germline isn't needed as mutations are corrected by natural selection. Mitochondrial variation is maximised by forming the next generation from the same cells used to make normal tissue cells. When the cells divide to form new daughter cells, some receive more mutant mitochondria than others and these cells are then removed through natural selection, preserving the reproductive cells containing higher quality mitochondria.

In mammals, genetic errors in mitochondria accumulate more quickly due to our higher metabolic rate so using cells that have undergone lots of division cycles would be a liability. Mitochondria are therefore only passed along to the next generation through a dedicated female germline in the form of large eggs. This protects against errors being introduced as eggs undergo many fewer replication cycles than cells in other tissues such as the gut, skin and blood.

The germline ensures that the best quality mitochondria are transferred but restricts the genetic variation in the next generation of cells in the developing embryo. This is corrected for by mammals generating far too many egg cells which are removed during development. For example, humans are born with over 6 million egg-precursor cells, 90% of which are culled by the start of puberty in a mysterious process called atresia.

Senior author, Dr Nick Lane (UCL CoMPLEX and Genetics, Evolution & Environment) added: "We think the rise in mitochondrial mutation rate likely occurred in the Cambrian explosion 550 million years ago when oxygen levels rose. This was the first appearance of motile animals in the fossil record, things like trilobites that had eyes and armour plating - predators and prey. By moving around they used their mitochondria more and that increased the mutation rate. So to avoid these mutations accumulating they needed to have fewer rounds of cell division, and that meant sequestering a specialized germline."

Co-author, Professor Andrew Pomiankowski (UCL Genetics, Evolution & Environment), concluded: "Without a germline, animals with complex development and brains could not exist. Scientists have long tried to explain the evolution of the germline in terms of complexity. Who would have thought it arose from selection on mitochondrial genes? We hope our discovery will transform the way researchers understand animal development, reproduction and aging."

Source: University College London [December 20, 2016]

Placental mammals consist of three main groups that diverged rapidly, evolving in wildly different directions: Afrotheria (for example, elephants and tenrecs), Xenarthra (such as armadillos and sloths) and Boreoeutheria (all other placental mammals). The relationships between them have been a subject of fierce controversy with multiple studies coming to incompatible conclusions over the last decade leading some researchers to suggest that these relationships might be impossible to resolve.

There are thus many outstanding questions such as which is the oldest sibling of the three? Did the mammals go their separate ways due to South America and Africa breaking apart? And if not, when did placentals split up?

"This has been one of the areas of greatest debate in evolutionary biology, with many researchers considering it impossible to resolve," said lead author Dr Tarver of Bristol's School of Earth Sciences. "Now we've proven these problems can be solved -- you just need to analyse genome-scale datasets using models that accurately reflect genomic evolution."

The researchers assembled the largest mammalian phylogenomic dataset ever collected before testing it with a variety of models of molecular evolution, choosing the most robust model and then analysing the data using several supercomputer clusters at the University of Bristol and the University of Texas Advanced Computing Centre. "We tested it to destruction," said Dr Tarver. "We threw the kitchen sink at it."

"A complication in reconstructing evolutionary histories from genomic data is that different parts of genomes can and often do give conflicting accounts of the history," said Dr Siavash Mirarab at the University of California San Diego, USA. "Individual genes within the same species can have different histories. This is one reason why the controversy has stood so long -- many thought the relationships couldn't be resolved."

To address the complexities of analysing large numbers of genes shared among many species, the researchers paired two fundamentally different approaches -- concatenated and coalescent-based analyses -- to confirm the findings. When the dust settled, the team had a specific family tree showing that Atlantogenata (containing the sibling groups of African Afrotheria and the South American Xenarthra) is the sister group to all other placentals.

Because many conflicting family trees have already been published, the team then gathered three of the most influential rivals and tested them against each other with the same model. All of the previous studies suddenly fell into line, their data agreeing with Tarver and colleagues.

With the origins of the family tree resolved, what does this mean for placental mammals? The researchers folded in another layer -- a molecular clock analysis. "The molecular clock analysis uses a combination of fossils and genomic data to estimate when these lineages diverged from each other," said author Dr Mario Dos-Reis of Queen Mary London, UK. "The results show that the afrotherians and xenarthrens diverged from one another around 90 million years ago."

Previously, scientists thought that when Africa and South America separated from each other over 100 million years ago, they broke up the family of placental mammals, who went their separate evolutionary ways divided by geography. But the researchers found that placental mammals didn't split up until after Africa and South America had already separated.

"We propose that South America's living endemic Xenarthra (for exmaple, sloths, anteaters, and armadillos) colonized the island-continent via overwater dispersal," said study author Dr Rob Asher of the University of Cambridge, UK.

Dr Asher suggests that this isn't as difficult as you might think. Mammals are among the great adventurers of the animal kingdom, and at the time the proto-Atlantic was only a few hundred miles wide. We already know that New World monkeys crossed the Atlantic later, when it was much bigger, probably on rafts formed from storm debris. And, of course, mammals repeatedly colonised remote islands like Madagascar.

"You don't always need to overturn the status quo to make a big impact," said Dr Tarver. "All of the competing hypotheses had some evidence to support them -- that's precisely why it was the source of such controversy. Proving the roots of the placental family tree with hard empirical evidence is a massive accomplishment."

The findings are published in Genome Biology and Evolution journal.

Source: University of Bristol [February 15, 2016]

A new UCL study examines how the baculum (penis bone) evolved in mammals and explores its possible function in primates and carnivores—groups where many species have a baculum, but some do not.

The baculum has been described as "the most diverse of all bones", varying dramatically in length, width and shape in the male mammals where it is present.

The research, published today in the Royal Society journal >Proceedings of the Royal Society B, shows that the ancestral mammal, like humans, did not have a baculum - but both ancestral primates and carnivores did. The work uncovers that the baculum first evolved in mammals between 145 and 95 million years ago.

The study found that prolonged intromission - defined as penetration for longer than 3 minutes - was correlated with baculum presence across the course of primate evolution. Prolonged intromission was also found to predict a longer baculum in primates and carnivores.

High levels of postcopulatory sexual competition between males also predicted longer bacula in primates.

First author, Matilda Brindle (UCL Anthropology), said: "Our findings suggest that the baculum plays an important role in supporting male reproductive strategies in species where males face high levels of postcopulatory sexual competition. Prolonging intromission helps a male to guard a female from mating with any competitors, increasing his chances of passing on his genetic material."

The findings of the study may also provide clues as to why humans do not have a baculum.

When any cultural aspects of sex are removed and a male's aim is solely to ejaculate, humans have a short intromission duration.

In species where mating occurs between multiple males and multiple females (known as polygamy), there is acute competition between males to fertilise a female. However, human mating systems are not like this. Instead humans tend to be monogamous or, more rarely, polygynous (where one male mates with multiple females). In these circumstances, only one male has access to a female and postcopulatory competition between males is absent or very low level.

Brindle added: "Interestingly, humans have neither prolonged intromission durations, nor high levels of postcopulatory sexual competition. Given the results of our study, this may help to unravel the mystery of why the baculum was lost in the human lineage."

Chimpanzees and bonobos, humans' closest relatives, have very small bacula (between about 6-8mm) and short intromission durations (around 7 seconds for chimpanzees and 15 seconds for bonobos). However, they are characterised by polygamous mating systems, so they experience high levels of postcopulatory competition between males. The researchers suggest that this may be why these species have retained a baculum - albeit a small one.

Co-author, Dr Kit Opie (UCL Anthropology), commented: "After the human lineage split from chimpanzees and bonobos and our mating system shifted towards monogamy, probably after 2mya, the evolutionary pressures retaining the baculum likely disappeared. This may have been the final nail in the coffin for the already diminished baculum, which was then lost in ancestral humans."

Source: University College London [December 14, 2016]

An ancient relative of the giraffe was a huge, heavy animal with thick legs, a flat face and massive, curly horns flaring out from its skull, said a study Wednesday.

Dubbed Sivatherium giganteum, the impressive creature would have been shorter than today's giraffe, with a less elongated neck, a trio of British scientists wrote in the Royal Society journal >Biology Letters.

Using bones dug up in India in the 1830s and now in London's Natural History Museum, the team built a computerised 3D reconstruction of an animal they said would have stood about 1.8 metres (5.9 feet) tall at the shoulder and weighed about 1.2 tonnes.

"This was a heavy animal with thick legs," co-author Christopher Basu told AFP.

Added to the large, flattened horns or "ossicones" on the top of the skull, each about 70 centimetres (28 inches) long, it also had two smaller, pointy horns just over the eyes.m

"It would have been an impressive and strong animal," said Basu. "It's face would have looked very different from a giraffe. Giraffe's have very long, pointed skulls. Sivatherium had a very short, flattened skull."

It lived somewhere between the last five million and 12,000 years ago in Africa and Asia.

Related to the giraffe and its cousin the okapi, Sivatherium was possibly the largest ruminant animal—those with multi-compartmented stomachs—to ever have lived.

The first scientists to study Sivatherium bones misclassified the animal as an archaic link between modern ruminants and a long-extinct relative of elephants and rhinoceroses.

For the new study, the skeleton was reconstructed using 26 fossil bones from three individual animals. The ribs, back and pelvis are missing.

"We estimated what these might look like from giraffe and okapi anatomy—the two living relatives," said Basu.

Source: AFP [January 13, 2016]

Uplift associated with the Great Rift Valley of East Africa and the environmental changes it produced have puzzled scientists for decades because the timing and starting elevation have been poorly constrained.

Now paleontologists have tapped a fossil from the most precisely dated beaked whale in the world -- and the only stranded whale ever found so far inland on the African continent -- to pinpoint for the first time a date when East Africa's mysterious elevation began.

The 17 million-year-old fossil is from the beaked Ziphiidae whale family. It was discovered 740 kilometers inland at an elevation of 620 meters in modern Kenya's harsh desert region, said vertebrate paleontologist Louis L. Jacobs, Southern Methodist University, Dallas.

At the time the whale was alive, it would have been swimming far inland up a river with a low gradient ranging from 24 to 37 meters over more than 600 to 900 kilometers, said Jacobs, a co-author of the study.

The study, published in the Proceedings of the National Academy of Sciences, provides the first constraint on the start of uplift of East African terrain from near sea level.

"The whale was stranded up river at a time when east Africa was at sea level and was covered with forest and jungle," Jacobs said. "As that part of the continent rose up, that caused the climate to become drier and drier. So over millions of years, forest gave way to grasslands. Primates evolved to adapt to grasslands and dry country. And that's when -- in human evolution -- the primates started to walk upright."

Identified as a Turkana ziphiid, the whale would have lived in the open ocean, like its modern beaked cousins. Ziphiids, still one of the ocean's top predators, are the deepest diving air-breathing mammals alive, plunging to nearly 10,000 feet to feed, primarily on squid.

In contrast to most whale fossils, which have been discovered in marine rocks, Kenya's beached whale was found in river deposits, known as fluvial sediments, said Jacobs, a professor in the Roy M. Huffington Department of Earth Sciences of SMU's Dedman College of Humanities and Sciences. The ancient large Anza River flowed in a southeastward direction to the Indian Ocean. The whale, probably disoriented, swam into the river and could not change its course, continuing well inland.

"You don't usually find whales so far inland," Jacobs said. "Many of the known beaked whale fossils are dredged by fishermen from the bottom of the sea."

Determining ancient land elevation is very difficult, but the whale provides one near sea level.

"It's rare to get a paleo-elevation," Jacobs said, noting only one other in East Africa, determined from a lava flow.

Beaked whale fossil surfaced after going missing for more than 30 years

The beaked whale fossil was discovered in 1964 by J.G. Mead in what is now the Turkana region of northwest Kenya.

Mead, an undergraduate student at Yale University at the time, made a career at the Smithsonian Institution, from which he recently retired. Over the years, the Kenya whale fossil went missing in storage. Jacobs, who was at one time head of the Division of Paleontology for the National Museums of Kenya, spent 30 years trying to locate the fossil. His effort paid off in 2011, when he rediscovered it at Harvard University and returned it to the National Museums of Kenya.

The fossil is only a small portion of the whale, which Mead originally estimated was 7 meters long during its life. Mead unearthed the beak portion of the skull, 2.6 feet long and 1.8 feet wide, specifically the maxillae and premaxillae, the bones that form the upper jaw and palate.

The researchers reported their findings in "A 17 million-year-old whale constrains onset of uplift and climate change in East Africa" online at the PNAS web site.

Modern cases of stranded whales have been recorded in the Thames River in London, swimming up a gradient of 2 meters over 70 kilometers; the Columbia River in Washington state, a gradient of 6 meters over 161 kilometers; the Sacramento River in California, a gradient of 4 meters over 133 kilometers; and the Amazon River in Brazil, a gradient of 1 meter over 1,000 kilometers.

Source: Southern Methodist University [March 17, 2015]

Our ancestors evolved three times faster in the 10 million years after the extinction of the dinosaurs than in the previous 80 million years, according to UCL researchers.

The team found the speed of evolution of placental mammals -- a group that today includes nearly 5000 species including humans -- was constant before the extinction event but exploded after, resulting in the varied groups of mammals we see today.

Lead researcher, Dr Thomas Halliday (UCL Genetics, Evolution & Environment), said: "Our ancestors -- the early placental mammals - benefitted from the extinction of non-avian dinosaurs and dwindling numbers of competing groups of mammals. Once the pressure was off, placental mammals suddenly evolved rapidly into new forms.

"In particular, we found a group called Laurasiatheria quickly increased their body size and ecological diversity, setting them on a path that would result in a modern group containing mammals as diverse as bats, cats, rhinos, whales, cows, pangolins, shrews and hedgehogs."

The team found that the last common ancestor for all placental mammals lived in the late Cretaceous period, about three million years before the non-avian dinosaurs became extinct 66 million years ago. This date is 20 million years younger than suggestions from previous studies which used molecular data from living mammals and assumed a near-constant rate of evolution.

In this study, funded by the Natural Environment Research Council and published in >Proceedings B of the Royal Society, the researchers analysed fossils from the Cretaceous to the present day, and used the dates of their occurrence in the fossil record to estimate the timing of divergences based on an updated tree of life. The new tree was released by the same team in 2015 and has the largest representation of Paleocene mammals to date.

The scientists measured all the small changes in the bones and teeth of 904 placental fossils and mapped the anatomical differences between species on the tree of life. From measuring the number of character changes over time for each branch, they found the average rate of evolution for early placental mammals both before and after the dinosaur extinction event. They compared the average rate of evolution over the geological stages before the extinction and the geological stages after to see what impact it had.

Senior author, Professor Anjali Goswami (UCL Genetics, Evolution & Environment and UCL Earth Sciences), said: "Our findings refute those of other studies which overlooked the fossils of placental mammals present around the last mass extinction. Using rigorous methods, we've successfully tracked the evolution of early placental mammals and reconstructed how it changed over time. While the rate differed between species, we see a clear and massive spike in the rates of evolution straight after the dinosaurs become extinct, suggesting our ancestors greatly benefitted from the demise of the dinosaurs. The huge impact of the dinosaur extinction on the evolution of our ancestors really shows how important this event was in shaping the modern world."

Professor Paul Upchurch (UCL Earth Sciences), co-author of the study, added: "Our large and refined data set allows us to build a clearer picture of evolutionary history. We plan on using it to study other large-scale evolutionary patterns such as how early placental mammals dispersed across the continents via land bridges that no longer exist today."

Source: University College London [June 28, 2016]

Scientists from the Universities of Bristol and Málaga have proposed that the long extinct marsupial lion hunted in a very unique way -- by using its teeth to hold prey before dispatching them with its huge claws.

The marsupial lion, or Thylacoleo carnifex, was a predator in the Pleistocene era of Australia and was about the same size as a large jaguar.

It was known to have existed from around two-and-a-half-million years ago until as recently as a few tens of thousands of years ago.

The animal is depicted on native Australian cave art and some speculate it still survives as the "Queensland Tiger."

As its name suggests, the marsupial lion has long been presumed to be a cat-like predator, despite lacking large canine teeth -- instead it had large, protruding incisors that have been suggested to be canine substitutes.

Thylacoleo was a powerful beast but, as other researchers have noted, it had limbs of different proportions to a lion, suggesting it was not a fast.

It also sported a very large claw on its hand, similar to the dew claw of cats but of a much bigger size, with a bony sheath foisted on a mobile first digit (thumb).

The new study, >published in Paleobiology by Christine Janis, a Marie Curie Research Fellow at the University of Bristol (currently on a leave of absence from a professorship at Brown University, USA) with colleagues Borja Figueirido and Alberto Martín-Serra from the University of Málaga, Spain looked at the elbow joints of a large number of living mammals.

This showed a strong association between the anatomy of the humerus (upper arm bone) where it articulates with the forelimb and the locomotor behaviour of mammals.

Animals more specialized for running (like a dog) have a joint indicating movement limited for back and forwards, stabilising their bodies on the ground, while animals more specialised for climbing (like a monkey) have a joint that allows for rotation of the hand around the elbow. Modern cats, which (unlike dogs) use their forelimbs to grapple with their prey, have an elbow joint of intermediate shape.

Christine Janis said: "If Thylacoleo had hunted like a lion using its forelimbs to manipulate its prey, then its elbow joint should have been lion-like."

"But, surprisingly, it a unique elbow-joint among living predatory mammals -- one that suggested a great deal of rotational capacity of the hand, like an arboreal mammal, but also features not seen in living climbers, that would have stabilized the limb on the ground (suggesting that it was not simply a climber)."

Christine Janis and colleagues proposed that this unique elbow joint, in combination with the huge "dew claw" on a mobile thumb, would have allowed the marsupial lion to use that claw to kill its prey.

In contrast the large incisors were blunt. While Thylacoleo had massive shearing teeth in the back of its jaw, the incisors appear to have functioned better for gripping than for piercing flesh in a killing bite.

They concluded that, unlike a real lion, which holds its prey with its claws, and kills it with its teeth, the marsupial lion -- unlike any living predator -- used its teeth to hold its prey, while it despatched it with its huge claws.

Source: University of Bristol [August 16, 2016]

From skeletal remains found among ancient owl pellets, a team of scientists has recovered the first ancient DNA of the extinct West Indian mammal Nesophontes, meaning "island murder." They traced its evolutionary history back to the dawn of mammals 70 million years ago.

The authors, including Selina Brace, Jessica Thomas, Ian Barnes et al., published their findings in the advanced online edition of >Molecular Biology and Evolution.

The insect-eating creature existed in the Caribbean islands until the 16th century when, perhaps, they were outcompeted as the first Spanish ships arrived—-introducing rats as stowaways. "Nesophontes was just one of the dozens of mammals that went extinct in the Caribbean during recent times," said Professor Ian Barnes, Research Leader at London's Natural History Museum.

Scientists used a 750-year-old specimen to generate many thousands of base pairs of DNA sequence data. This allowed the research team to uncover its evolutionary origins and finally resolve the relationships between its closest relatives, the insectivores, a group including shrews, hedgehogs and moles. Phylogenetic and divergence time scenarios clearly demonstrate that Nesophontes is a deeply distinct sister group to another group of living native Caribbean insectivores, the solenodons. The time of the split between these two correlates with an era when the northern Caribbean was formed of volcanic islands, well before the origins of the islands we see today.

Obtaining DNA from tropical fossils is notoriously difficult, and the team made use of the latest developments in ancient DNA technology to conduct the study.

"Once we'd dealt with the tiny size of the bone samples, the highly degraded state of the DNA, and the lack of any similar genomes to compare to, the analysis was a piece of cake," said Natural History Museum scientist Dr. Selina Brace.

The findings will be of considerable interest for evolutionary biologists studying mammalian biogeography, and the significant role that humans may have played in a recent extinction.

Source: Oxford University Press [September 13, 2016]