The Great London [Search results for Genetics

  • Genetics: First fine-scale genetic map of the British Isles

    Genetics: First fine-scale genetic map of the British Isles

    Many people in the UK feel a strong sense of regional identity, and it now appears that there may be a scientific basis to this feeling, according to a landmark new study into the genetic makeup of the British Isles.

    First fine-scale genetic map of the British Isles
    Subtle differences in the genes of more than 2,000 people in England, Scotland, Wales 
    and Northern Ireland reveal 17 distinct groups, represented by different symbols 
    and colors on the map [Credit: Stephen Leslie; Contains OS data 
    © Crown copyright and database right 2012; © EuroGeographics
     for some administrative boundaries]

    An international team, led by researchers from the University of Oxford, UCL (University College London) and the Murdoch Childrens Research Institute in Australia, used DNA samples collected from more than 2,000 people to create the first fine-scale genetic map of any country in the world.

    Their findings, published in Nature, show that prior to the mass migrations of the 20th century there was a striking pattern of rich but subtle genetic variation across the UK, with distinct groups of genetically similar individuals clustered together geographically.

    By comparing this information with DNA samples from over 6,000 Europeans, the team was also able to identify clear traces of the population movements into the UK over the past 10,000 years. Their work confirmed, and in many cases shed further light on, known historical migration patterns.

    Key findings

    • There was not a single "Celtic" genetic group. In fact the Celtic parts of the UK (Scotland, Northern Ireland, Wales and Cornwall) are among the most different from each other genetically. For example, the Cornish are much more similar genetically to other English groups than they are to the Welsh or the Scots.
    • There are separate genetic groups in Cornwall and Devon, with a division almost exactly along the modern county boundary.
    • The majority of eastern, central and southern England is made up of a single, relatively homogeneous, genetic group with a significant DNA contribution from Anglo-Saxon migrations (10-40% of total ancestry). This settles a historical controversy in showing that the Anglo-Saxons intermarried with, rather than replaced, the existing populations.
    • The population in Orkney emerged as the most genetically distinct, with 25% of DNA coming from Norwegian ancestors. This shows clearly that the Norse Viking invasion (9th century) did not simply replace the indigenous Orkney population.
    • The Welsh appear more similar to the earliest settlers of Britain after the last ice age than do other people in the UK.
    • There is no obvious genetic signature of the Danish Vikings, who controlled large parts of England ("The Danelaw") from the 9th century.
    • There is genetic evidence of the effect of the Landsker line -- the boundary between English-speaking people in south-west Pembrokeshire (sometimes known as "Little England beyond Wales") and the Welsh speakers in the rest of Wales, which persisted for almost a millennium.
    • The analyses suggest there was a substantial migration across the channel after the original post-ice-age settlers, but before Roman times. DNA from these migrants spread across England, Scotland, and Northern Ireland, but had little impact in Wales.
    • Many of the genetic clusters show similar locations to the tribal groupings and kingdoms around end of the 6th century, after the settlement of the Anglo-Saxons, suggesting these tribes and kingdoms may have maintained a regional identity for many centuries.

    The Wellcome Trust-funded People of the British Isles study analysed the DNA of 2,039 people from rural areas of the UK, whose four grandparents were all born within 80km of each other. Because a quarter of our genome comes from each of our grandparents, the researchers were effectively sampling DNA from these ancestors, allowing a snapshot of UK genetics in the late 19th Century. They also analysed data from 6,209 individuals from 10 (modern) European countries.

    To uncover the extremely subtle genetic differences among these individuals the researchers used cutting-edge statistical techniques, developed by four of the team members. They applied these methods, called fineSTRUCTURE and GLOBETROTTER, to analyse DNA differences at over 500,000 positions within the genome. They then separated the samples into genetically similar individuals, without knowing where in the UK the samples came from. By plotting each person onto a map of the British Isles, using the centre point of their grandparents' birth places, they were able to see how this distribution correlated with their genetic groupings.

    The researchers were then able to "zoom in" to examine the genetic patterns in the UK at levels of increasing resolution. At the broadest scale, the population in Orkney (islands to the north of Scotland) emerged as the most genetically distinct. At the next level, Wales forms a distinct genetic group, followed by a further division between north and south Wales. Then the north of England, Scotland, and Northern Ireland collectively separate from southern England, before Cornwall forms a separate cluster. Scotland and Northern Ireland then separate from northern England. The study eventually focused at the level where the UK was divided into 17 genetically distinct clusters of people.

    Dr Michael Dunn, Head of Genetics & Molecular Sciences at the Wellcome Trust, said: "These researchers have been able to use modern genetic techniques to provide answers to the centuries' old question -- where we come from. Beyond the fascinating insights into our history, this information could prove very useful from a health perspective, as building a picture of population genetics at this scale may in future help us to design better genetic studies to investigate disease."

    Source: Wellcome Trust [March 18, 2015]

  • Genetics: A federal origin of Stone Age farming

    Genetics: A federal origin of Stone Age farming

    The transition from hunter-gatherer to sedentary farming 10,000 years ago occurred in multiple neighbouring but genetically distinct populations according to research by an international team including UCL.

    A federal origin of Stone Age farming
    The Fertile Crescent (shaded) on a political map of the Near and South East. In blue are the the archaeological sites
     in Iran with genomes from the Neolithic period that are ancestral to modern-day South Asians. In red are Neolithic
     sites with genomes that are ancestral to all European early farmers [Credit: ©: Joachim Burger, JGU]

    “It had been widely assumed that these first farmers were from a single, genetically homogeneous population. However, we’ve found that there were deep genetic differences in these early farming populations, indicating very distinct ancestries,” said corresponding author Dr Garrett Hellenthal, UCL Genetics.

    The study, published today in >Science and funded by Wellcome and Royal Society, examined ancient DNA from some of the world’s first farmers from the Zagros region of Iran and found it to be very different from the genomes of early farmers from the Aegean and Europe. The team identified similarities between the Neolithic farmer’s DNA and that of living people from southern Asia, including from Afghanistan, Pakistan, Iran, and Iranian Zoroastrians in particular.

    “We know that farming technologies, including various domestic plants and animals, arose across the Fertile Crescent, with no particular centre” added co-author Professor Mark Thomas, UCL Genetics, Evolution & Environment.

    “But to find that this region was made up of highly genetically distinct farming populations was something of a surprise. We estimated that they separated some 46 to 77,000 years ago, so they would almost certainly have looked different, and spoken different languages. It seems like we should be talking of a federal origin of farming.”

    A federal origin of Stone Age farming
    An approximately 10,000 year old skull from the Neolithic Tepe Abdul Hossein 
    [Credit: © Fereidoun Biglari, National Museum of Iran]

    The switch from mobile hunting and gathering to sedentary farming first occurred around 10,000 years ago in south-western Asia and was one of the most important behavioural transitions since humans first evolved in Africa some 200,000 years ago. It led to profound changes in society, including greater population densities, new diseases, poorer health, social inequality, urban living, and ultimately, the rise of ancient civilizations.

    Animals and plants were first domesticated across a region stretching north from modern-day Israel, Palestine and Lebanon to Syria and eastern Turkey, then east into, northern Iraq and north-western Iran, and south into Mesopotamia; a region known as the Fertile Crescent.

    “Such was the impact of farming on our species that archaeologists have debated for more than 100 years how it originated and how it was spread into neighbouring regions such as Europe, North Africa and southern Asia,” said co-author Professor Stephen Shennan, UCL Institute of Archaeology.

    “We’ve shown for the first time that different populations in different parts of the Fertile Crescent were coming up with similar solutions to finding a successful way of life in the new conditions created by the end of the last Ice Age.”

    A federal origin of Stone Age farming
    Analysis of ancient DNA in the laboratory [Credit: ©: JGU Palaeogenetics Group]

    By looking at how ancient and living people share long sections of DNA, the team showed that early farming populations were highly genetically structured, and that some of that structure was preserved as farming, and farmers, spread into neighbouring regions; Europe to the west and southern Asia to the east.

    “Early farmers from across Europe, and to some extent modern-day Europeans, can trace their DNA to early farmers living in the Aegean, whereas people living in Afghanistan, Pakistan, Iran and India share considerably more long chunks of DNA with early farmers in Iran. This genetic legacy of early farmers persists, although of course our genetic make-up subsequently has been reshaped by many millennia of other population movements and intermixing of various groups,” concluded Dr Hellenthal.

    Source: University College London [July 14, 2016]

  • Fossils: Mammal diversity exploded immediately after dinosaur extinction

    Fossils: Mammal diversity exploded immediately after dinosaur extinction

    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.

    Mammal diversity exploded immediately after dinosaur extinction
    Leptictis [Credit: Dr Thomas Halliday]

    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]

  • Evolution: Sex cells evolved to pass on quality mitochondria

    Evolution: Sex cells evolved to pass on quality mitochondria

    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.

    Sex cells evolved to pass on quality mitochondria
    One of a series of ova made in a spell of reproductive mitochondrial interest. The ovum about to ovulate has differentiated 
    from the rest of the surrounding tissue and is getting ready to leave the ovary. Its mitochondria are organized mainly 
    around the nucleus. The cell is full of potential and force. A big journey of life may be about to start 
    [Credit: Odra Noel]

    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]

  • Breaking News: Natural selection, key to evolution, also can impede formation of new species

    Breaking News: Natural selection, key to evolution, also can impede formation of new species

    An intriguing study involving walking stick insects led by the University of Sheffield in England and the University of Colorado Boulder shows how natural selection, the engine of evolution, can also impede the formation of new species.

    Natural selection, key to evolution, also can impede formation of new species
    A new study involving CU-Boulder looks at the role of natural selection on
     three types of stick insect belonging to the species Timema cristinae. 
    The illustration shows how green, striped, and melanistic, or brown 
    varieties have evolved camouflaged appearances matching them 
    to certain areas on two separate species of shrub 
    [Credit: Rosa Marin]

    The team studied a plant-eating stick insect species from California called Timema cristinae known for its cryptic camouflage that allows it to hide from hungry birds, said CU-Boulder Assistant Professor Samuel Flaxman. T. cristinae comes in several different types -- one is green and blends in with the broad green leaves of a particular shrub species, while a second green variant sports a white, vertical stripe that helps disguise it on a different species of shrub with narrow, needle-like leaves.

    While Darwinian natural selection has begun pushing the two green forms of walking sticks down separate paths that could lead to the formation of two new species, the team found that a third melanistic, or brown variation of T. cristinae appears to be thwarting the process, said Flaxman. The brown version is known to successfully camouflage itself among the stems of both shrub species inhabited by its green brethren, he said.

    Using field investigations, laboratory genetics, modern genome sequencing and computer simulations, the team concluded the brown version of T. cristinae is shuttling enough genes between the green stick insects living on different shrubs to prevent strong divergent adaptation and speciation. The brown variant of the walking stick species also is favored by natural selection because it has a slight advantage in mate selection and a stronger resistance to fungal infections than its green counterparts.

    "This is one of the best demonstrations we know of regarding the counteractive effects of natural selection on speciation," said Flaxman of CU-Boulder's Department of Ecology and Evolutionary Biology, second author on the new study. "We show how the brown population essentially carries genes back and forth between the green populations, acting as a genetic bridge that causes a slowdown in divergence."

    A paper on the subject appeared in a recent issue of the journal Current Biology. Other study co-authors were from the University of Sheffield, Royal Holloway University of London, Utah State University, the University of Nevada, Reno and the University of Lausanne in Switzerland.

    "This movement of genes between environments slows down the genetic divergence of these stick insect populations, impeding the formation of new species," said Aaron Comeault, a former CU-Boulder graduate student and lead study author who conducted the research while at the University of Sheffield. Comeault is now a postdoctoral researcher at the University of North Carolina at Chapel Hill.

    The new results underscore how combining natural history and cutting-edge genetics can help researchers gain a better understanding of how evolution operates in nature. It also shows how natural selection can sometimes promote but other times hinder the formation of new species, according to the research team.

    Walking sticks are one of nature's oddest insect groups and range in size from the half-inch long T. cristinae to species in Borneo and Vietnam that are more than a foot long. Most walking sticks rely on plant mimicry to protect them from predators.

    Source: University of Colorado at Boulder [August 06, 2015]

  • Fossils: Mammals evolved faster after dinosaur extinction

    Fossils: Mammals evolved faster after dinosaur extinction

    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.

    Mammals evolved faster after dinosaur extinction
    Late cretaceous dinosaurs [Credit: UCL]

    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]

  • Early Humans: Modern humans out of Africa sooner than thought

    Early Humans: Modern humans out of Africa sooner than thought

    Human teeth discovered in southern China provide evidence that our species left the African continent up to 70,000 years earlier than prevailing theories suggest, a study published on Wednesday said.

    Modern humans out of Africa sooner than thought
    47 human teeth found in the Fuyan Cave, Daoxian, in southern China 
    [Credit: AFP/S. Xing and X-J. Wu]

    Homo sapiens reached present-day China 80,000-120,000 years ago, according to the study, which could redraw the migration map for modern humans.

    "The model that is generally accepted is that modern humans left Africa only 50,000 years ago," said Maria Martinon-Torres, a researcher at University College London and a co-author of the study.

    "In this case, we are saying the H. sapiens is out of Africa much earlier," she told the peer-reviewed journal Nature, which published the study.

    While the route they travelled remains unknown, previous research suggests the most likely path out of East Africa to east Asia was across the Arabian Peninsula and the Middle East.

    The findings also mean that the first truly modern humans -- thought to have emerged in east Africa some 200,000 years ago -- landed in China well before they went to Europe.

    There is no evidence to suggest that H. sapiens entered the European continent earlier than 45,000 years ago, at least 40,000 years after they showed up in present-day China.

    The 47 teeth exhumed from a knee-deep layer of grey, sandy clay inside the Fuyan Cave near the town of Daoxian closely resemble the dental gear of "contemporary humans," according to the study.

    They could only have come from a population that migrated from Africa, rather than one that evolved from an another species of early man such as the extinct Homo erectus, the authors said.

    The scientists also unearthed the remains of some 38 mammals, including specimens of five extinct species, one of them a giant panda larger than those in existence today.

    Modern humans out of Africa sooner than thought
    The location and interior views of the Fuyan Cave, with dating sample (lower left), 
    plan view of the excavation area with stratigraphy layer marked (C) 
    and the spatial relationship of the excavated regions 
    [Credit: AFP/Y-J Cai, X-X Yang, and X-J Wu]

    No tools were found.

    "Judging by the cave environment, it may not have been a living place for humans," lead author Wu Liu from the Chinese Academy of Science in Beijing told AFP.

    The study, published in the journal Nature, also rewrites the timeline of early man in China.

    Up to now, the earliest proof of H. sapiens east of the Arabian Peninsula came from the Tianyuan Cave near Beijing, and dated from no more than 40,000 years ago.

    The new discovery raises questions about why it took so long for H. sapiens to find their way to nearby Europe.

    "Why is it that modern humans -- who were already at the gates -- didn't really get into Europe?", Martinon-Torres asked.

    Wu and colleagues propose two explanations.

    The first is the intimidating presence of Neanderthal man. While this species of early human eventually died out, they were spread across the European continent up until at least some 50,000 years ago.

    "The classic idea is that H. sapiens... took over the Neanderthal empire, but maybe Neanderthals were a kind of ecological barrier, and Europe was too small a place" for both, Martinon-Torres said.

    Modern humans out of Africa sooner than thought
    Human upper teeth found in the Fuyan Cave, Daoxian, 
    in southern China [Credit: AFP/S. Xing and X-J. Wu]

    Another impediment might have been the cold.

    Up until the Ice Age ended 12,000 years ago, ice sheets stretched across a good part of the European continent, a forbidding environment for a new species emerging from the relative warmth of East Africa.

    "H. sapiens originated in or near the tropics, so it makes sense that the species' initial dispersal was eastwards rather than northwards, where winter temperatures rapidly fell below freezing," Robin Dennell of the University of Exeter said in a commentary, also in Nature.

    Martinon-Torres laid out some of the questions to be addressed in future research, using both genetics and fossil records.

    "What are the origins of these populations, and what was their fate? Did they vanish? Could they be the ancestors of later and current populations that entered Europe?"

    She also suggested there might have been "different movements and migrations" out of Africa, not just one.

    Besides the prehistoric panda, called Ailuropoda baconi, the scientists found an extinct species of a giant spotted hyaena.

    An elephant-like creature called Stegodon orientalis and a giant tapir, also present, were species that may have survived into the era when the Chinese had developed writing, some 3500 years ago.

    The cache of teeth nearly went unnoticed, Wu told AFP.

    He and his Chinese colleagues discovered the cave -- and its menagerie of long-deceased animals -- in the 1980s, but had no inkling that it also contained human remains.

    But 25 years later, while revisiting the site, Wu had a hunch.

    "By thinking about the cave environment, we realised that human fossils might be found there," he told AFP by email. "So we started a five-year excavation."

    Author: Marlowe Hood | Source: AFP [October 14, 2015]

  • Genetics: A 100-million-year partnership on the brink of extinction

    Genetics: A 100-million-year partnership on the brink of extinction

    A relationship that has lasted for 100 million years is at serious risk of ending, due to the effects of environmental and climate change. A species of spiny crayfish native to Australia and the tiny flatworms that depend on them are both at risk of extinction, according to researchers from the UK and Australia.

    A 100-million-year partnership on the brink of extinction
    A light microscope image of the five tentacle temnocephalan Temnosewellia c.f rouxi from cultured redclaw crayfish 
    [Credit: David Blair/James Cook University]

    Look closely into one of the cool, freshwater streams of eastern Australia and you might find a colourful mountain spiny crayfish, from the genus Euastacus. Look even closer and you could see small tentacled flatworms, called temnocephalans, each only a few millimetres long. Temnocephalans live as specialised symbionts on the surface of the crayfish, where they catch tiny food items, or inside the crayfish's gill chamber where they can remove parasites. This is an ancient partnership, but the temnocephalans are now at risk of coextinction with their endangered hosts. Coextinction is the loss of one species, when another that it depends upon goes extinct.

    In a new study, researchers from the UK and Australia reconstructed the evolutionary and ecological history of the mountain spiny crayfish and their temnocephalan symbionts to assess their coextinction risk. This study was based on DNA sequences from crayfish and temnocephalans across eastern Australia, sampled by researchers at James Cook University, sequenced at the Natural History Museum, London and Queensland Museum, and analysed at the University of Sydney and the University of Cambridge. The results are published in the >Proceedings of the Royal Society B.

    "We've now got a picture of how these two species have evolved together through time," said Dr Jennifer Hoyal Cuthill from Cambridge's Department of Earth Sciences, the paper's lead author. "The extinction risk to the crayfish has been measured, but this is the first time we've quantified the risk to the temnocephalans as well -- and it looks like this ancient partnership could end with the extinction of both species."

    Mountain spiny crayfish species diversified across eastern Australia over at least 80 million years, with 37 living species included in this study. Reconstructing the ages of the temnocephalans using a 'molecular clock' analysis showed that the tiny worms are as ancient as their crayfish hosts and have evolved alongside them since the Cretaceous Period.

    >A symbiotic relationship that has existed since the time of the dinosaurs is at risk of ending,> as habitat loss and environmental change mean that a species of Australian crayfish >and the tiny worms that depend on them are both at serious risk of extinction >[Credit: David Blair/James Cook University]
    Today, many species of mountain spiny crayfish have small geographic ranges. This is especially true in Queensland, where mountain spiny crayfish are restricted to cool, high-altitude streams in small pockets of rainforest. This habitat was reduced and fragmented by long-term climate warming and drying, as the continent of Australia drifted northwards over the last 165 million years. As a consequence, mountain spiny crayfish are severely threatened by ongoing climate change and the International Union for the Conservation of Nature (IUCN) has assessed 75% of these species as endangered or critically endangered.

    "In Australia, freshwater crayfish are large, diverse and active 'managers', recycling all sorts of organic material and working the sediments," said Professor David Blair of James Cook University in Australia, the paper's senior author. "The temnocephalan worms associated only with these crayfish are also diverse, reflecting a long, shared history and offering a unique window on ancient symbioses. We now risk extinction of many of these partnerships, which will lead to degradation of their previous habitats and leave science the poorer."

    The crayfish tend to have the smallest ranges in the north of Australia, where the climate is the hottest and all of the northern species are endangered or critically endangered. By studying the phylogenies (evolutionary trees) of the species, the researchers found that northern crayfish also tended to be the most evolutionarily distinctive. This also applies to the temnocephalans of genus Temnosewellia, which are symbionts of spiny mountain crayfish across their geographic range. "This means that the most evolutionarily distinctive lineages are also those most at risk of extinction," said Hoyal Cuthill.

    The researchers then used computer simulations to predict the extent of coextinction. This showed that if all the mountain spiny crayfish that are currently endangered were to go extinct, 60% of their temnocephalan symbionts would also be lost to coextinction. The temnocephalan lineages that were predicted to be at the greatest risk of coextinction also tended to be the most evolutionarily distinctive. These lineages represent a long history of symbiosis and coevolution of up to 100 million years. However they are the most likely to suffer coextinction if these species and their habitats are not protected from ongoing environmental and climate change.

    "The intimate relationship between hosts and their symbionts and parasites is often unique and long lived, not just during the lifespan of the individual organisms themselves but during the evolutionary history of the species involved in the association," said study co-author Dr Tim Littlewood of the Natural History Museum. "This study exemplifies how understanding and untangling such an intimate relationship across space and time can yield deep insights into past climates and environments, as well as highlighting current threats to biodiversity."

    Source: University of Cambridge [May 24, 2016]

  • Genetics: DNA analysis reveals Roman London was a multi-ethnic melting pot

    Genetics: DNA analysis reveals Roman London was a multi-ethnic melting pot

    A DNA analysis of four ancient Roman skeletons found in London shows the first inhabitants of the city were a multi-ethnic mix similar to contemporary Londoners, the Museum of London said on Monday.

    DNA analysis reveals Roman London was a multi-ethnic melting pot
    The displayed skeleton of "The Harper Road Woman", one of four 
    ancient Roman skeletons that have undergone DNA analysis 
    [Credit: Museum of London/AFP]

    Two of the skeletons were of people born outside Britain -- one of a man linked genealogically to eastern Europe and the Near East, the other of a teenage girl with blue eyes from north Africa.

    The injuries to the man's skull suggest that he may have been killed in the city's amphitheatre before his head was dumped into an open pit.

    Both the man and the girl were suffering from periodontal disease, a type of gum disease.

    The other two skeletons of people believed to have been born in Britain were of a woman with maternal ancestry from northern Europe and of a man also with links through his mother to Europe or north Africa.

    "We have always understood that Roman London was a culturally diverse place and now science is giving us certainty," said Caroline McDonald, senior curator of Roman London at the museum.

    "People born in Londinium lived alongside people from across the Roman Empire exchanging ideas and cultures, much like the London we know today," she said.

    The museum said in a statement that this was "the first multidisciplinary study of the inhabitants of a city anywhere in the Roman Empire".

    The Romans founded Britain's capital city in the middle of the first century AD, under the emperor Claudius.

    Britain's University of Durham researched stable isotopes from tooth enamel to determine migration patterns.

    A tooth from each skeleton was also sent to McMaster University in Canada for DNA analysis that established the hair and eye colour of each individual and identified the diseases they were suffering from.

    McMaster University also examined the mitochondrial DNA (mtDNA) to identify maternal ancestry.

    The exhibition of the four skeletons, entitled "Written in Bone", opens on Friday.

    Source: AFP [November 24, 2015]

  • Breaking News: Complex genetic ancestry of Americans uncovered

    Breaking News: Complex genetic ancestry of Americans uncovered

    By comparing the genes of current-day North and South Americans with African and European populations, an Oxford University study has found the genetic fingerprints of the slave trade and colonization that shaped migrations to the Americas hundreds of years ago.

    Complex genetic ancestry of Americans uncovered
    A 1770 painting showing Spanish, Peruvian and mixed-race people
    [Credit: WikiCommons]

    The study published in Nature Communications found that:

    • While Spaniards provide the majority of European ancestry in continental American Hispanic/Latino populations, the most common European genetic source in African-Americans and Barbadians comes from Great Britain.
    • The Basques, a distinct ethnic group spread across current-day Spain and France, provided a small but distinct genetic contribution to current-day Continental South American populations, including the Maya in Mexico.
    • The Caribbean Islands of Puerto Rico and the Dominican Republic are genetically similar to each other and distinct from the other populations, probably reflecting a different migration pattern between the Caribbean and mainland America.
    • Compared to South Americans, people from Caribbean countries (such as the Barbados) had a larger genetic contribution from Africa.
    • The ancestors of current-day Yoruba people from West Africa (one of the largest African ethnic groups) provided the largest contribution of genes from Africa to all current-day American populations.
    • The proportion of African ancestry varied across the continent, from virtually zero (in the Maya people from Mexico) to 87% in current-day Barbados.
    • South Italy and Sicily also provided a significant European genetic contribution to Colombia and Puerto Rico, in line with the known history of Italian emigrants to the Americas in the late 19th and early 20th century.
    • One of the African-American groups from the USA had French ancestry, in agreement with historical French immigration into the colonial Southern United States.
    • The proportion of genes from European versus African sources varied greatly from individual to individual within recipient populations.

    The team, which also included researchers from UCL (University College London) and the Universita' del Sacro Cuore of Rome, analysed more than 4,000 previously collected DNA samples from 64 different populations, covering multiple locations in Europe, Africa and the Americas. Since migration has generally flowed from Africa and Europe to the Americas over the last few hundred years, the team compared the 'donor' African and European populations with 'recipient' American populations to track where the ancestors of current-day North and South Americans came from.

    'We found that the genetic profile of Americans is much more complex than previously thought,' said study leader Professor Cristian Capelli from the Department of Zoology.

    The research team analysed DNA samples collected from people in Barbados, Columbia, the Dominican Republic, Ecuador, Mexico, Puerto Rico and African-Americans in the USA.

    They used a technique called haplotype-based analysis to compare the pattern of genes in these 'recipient populations' to 'donor populations' in areas where migrants to America came from.

    'We firstly grouped subsets of people in Africa and Europe who were genetically similar and used this fine scale resolution to find which combinations of these clusters resulted in the sort of mixtures that we now see in people across the Americas', said the study's first author, Dr Francesco Montinaro from the Department of Zoology.

    'We can see the huge genetic impact that the slave trade had on American populations and our data match historical records', said study author Dr Garrett Hellenthal from the UCL Genetics Institute, 'The majority of African Americans have ancestry similar to the Yoruba people in West Africa, confirming that most African slaves came from this region. In areas of the Americas historically under Spanish rule, populations also have ancestry related to what is now Senegal and Gambia. Records show that around a third of the slaves sent to Spanish America in the 17th Century came from this region, and we can see the genetic evidence of this in modern Americans really clearly.'

    These genetic findings also uncover previously unknown migration. ‘We found a clear genetic contribution from the Basques in modern-day Maya in Mexico’, said Professor Capelli. ‘This suggests that the Basque also took part in the colonisation of the Americas, coming over either with the Spanish conquistadores or in later waves of migration’.

    'The differences in European ancestry between the Caribbean islands and mainland American population that we found were also previously unknown. It is likely that these differences reflect different patterns of migration between the Caribbean and mainland America.'

    'These results show just how powerful a genetic approach can be when it comes to uncovering hidden patterns of ancestry. We hope to use the same approach to look at other populations with diverse genetic contributions, such as Brazilians,' said Professor Capelli.

    Source: University of Oxford [March 24, 2015]

  • Scotland: Patrick Matthew: Evolution's overlooked third man

    Scotland: Patrick Matthew: Evolution's overlooked third man

    The horticulturist who came up with the concept of ‘evolution by natural selection’ 27 years before Charles Darwin did should be more widely acknowledged for his contribution, states a new paper by a King’s College London geneticist.

    Patrick Matthew: Evolution's overlooked third man
    Patrick Matthew [Credit: The Patrick Matthew Project]

    The paper, published in the Biological Journal of the Linnean Society, argues that Patrick Matthew deserves to be considered alongside Charles Darwin and Alfred Russel Wallace as one of the three originators of the idea of large-scale evolution by natural selection.

    Furthermore, Matthew’s version of evolution by natural section captures a valuable aspect of the theory that isn't so clear in Darwin's version – namely, that natural selection is a deductive certainty more akin to a ‘law’ than a hypothesis or theory to be tested.

    Patrick Matthew (1790-1874) was a Scottish landowner with a keen interest in politics and agronomy.  He established extensive orchards of apples and pears on his estate at Gourdie Hill, Perthshire, and became adept in horticulture, silviculture and agriculture.

    Whilst Darwin and Wallace’s 1858 paper to the Linnean Society, On the Origin of Species, secured their place in the history books, Matthews had set out similar ideas 27 years earlier in his book On Naval Timber and Arboriculture. The book, published in 1831, addressed best practices for the cultivation of trees for shipbuilding, but also expanded on his concept of natural selection.

    “There is a law universal in nature, tending to render every reproductive being the best possibly suited to its condition that its kind, or that organized matter, is susceptible of, which appears intended to model the physical and mental or instinctive powers, to their highest perfection, and to continue them so. This law sustains the lion in his strength, the hare in her swiftness, and the fox in his wiles.”  (Matthew, 1831: 364)

    In 1860, Matthew wrote to point out the parallels with his prior work, several months after the publication of On the origin of species.  Darwin publically wrote in 1860 “I freely acknowledge that Mr. Matthew has anticipated by many years the explanation which I have offered of the origin of species”, while Wallace wrote publically in 1879 of “how fully and clearly Mr. Matthew apprehended the theory of natural selection, as well as the existence of more obscure laws of evolution, many years in advance of Mr. Darwin and myself”, and further declared Matthew to be “one of the most original thinkers of the first half of the 19th century”.  However, both asserted their formulations were independent of Matthew’s.

    Even if Matthew did not influence Darwin and Wallace, his writings provide a valuable third point of reference on the notion of macroevolution by natural selection, argues the paper’s author, Dr Michael Weale. Dr Weale has created a public website to act as an online repository of the writings by Patrick Matthew, including some of his lesser-known work.

    Dr Michael Weale, from the Department of Medical and Molecular Genetics at King’s College London, said: ‘Whilst Darwin and Wallace both deserve recognition for their work, Matthew, the outsider who deduced his idea as part of a grand scheme of a purposeful universe, is the overlooked third man in the story. Matthew’s story is an object lesson in the perils of low-impact publishing. Despite its brevity, and to some extent because of it, Matthew’s work merits our renewed attention.’

    Source: King's College London [April 20, 2015]

  • Genetics: Tweak in gene expression may have helped humans walk upright

    Genetics: Tweak in gene expression may have helped humans walk upright

    Consider the engineering marvel that is your foot. Be it hairy or homely, without its solid support you'd be hard-pressed to walk or jump normally.

    Tweak in gene expression may have helped humans walk upright
    Researchers have identified a change in gene expression between humans and primates that may have helped give us this 
    edge when it comes to walking upright. And they did it by studying a tiny fish called the threespine stickleback that has 
    evolved radically different skeletal structures to match environments around the world  
    [Credit: Flickr/Emilian Robert Vicol]

    Now, researchers at the Stanford University School of Medicine and the HudsonAlpha Institute for Biotechnology in Huntsville, Alabama, have identified a change in gene expression between humans and primates that may have helped give us this edge when it comes to walking upright. And they did it by studying a tiny fish called the threespine stickleback that has evolved radically different skeletal structures to match environments around the world.

    "It's somewhat unusual to have a research project that spans from fish all the way to humans, but it's clear that tweaking the expression levels of molecules called bone morphogenetic proteins can result in significant changes not just in the skeletal armor of the stickleback, but also in the hind-limb development of humans and primates," said David Kingsley, PhD, professor of developmental biology at Stanford. "This change is likely part of the reason why we've evolved from having a grasping hind foot like a chimp to a weight-bearing structure that allows us to walk on two legs."

    Kingsley, who is also a Howard Hughes Medical Institute investigator, is the senior author of a paper describing the work that will be >published in Cell. The lead author is former Stanford postdoctoral scholar Vahan Indjeian, PhD, now head of a research group at Imperial College London.

    Adapting to different environments

    The threespine stickleback is remarkable in that it has evolved to have many different body structures to equip it for life in different parts of the world. It sports an exterior of bony plates and spines that act as armor to protect it from predators. In marine environments, the plates are large and thick; in freshwater, the fish have evolved to have smaller, lighter-weight plates, perhaps to enhance buoyancy, increase body flexibility and better slip out of the grasp of large, hungry insects. Kingsley and his colleagues wanted to identify the regions of the fish's genome responsible for the skeletal differences that have evolved in natural populations.

    The researchers identified the area of the genome responsible for controlling armor plate size, and then looked for differences there in 11 pairs of marine and freshwater fish with varying armor-plate sizes. They homed in on a region that includes the gene for a bone morphogenetic protein family member called GDF6. Due to changes in the regulatory DNA sequence near this gene, freshwater sticklebacks express higher levels of GDF6, while their saltwater cousins express less. Strikingly, marine fish genetically engineered to contain the regulatory sequence of freshwater fish expressed higher levels of GDF6 and developed smaller armor plates, the researchers found.

    Regulatory regions in humans vs. chimps

    Kingsley and his colleagues wondered whether changes in GDF6 expression levels might also have contributed to critical skeletal modifications during human evolution. The possibility was not as far-fetched as it might seem. Other studies by evolutionary biologists, including Kingsley, have shown that small changes in the regulatory regions of key developmental genes can have profound effects in many vertebrates.

    They began by working with colleagues in the laboratory of Gill Bejerano, PhD, Stanford associate professor of developmental biology, of computer science and of pediatrics, to compare differences in the genomes of chimps and humans. In previous surveys, they found over 500 places in which humans have lost regulatory regions that are conserved from chimps and many other mammals. Two of these occur near the GDF6 gene. They homed in on one in particular.

    "This regulatory information was shared through about 100 million years of evolution," said Kingsley. "And yet, surprisingly, this region is missing in humans."

    To learn more about what the GDF6 regulatory region might be controlling, the researchers used the chimp regulatory DNA to control the production of a protein that is easy to visualize in mice. Laboratory mice with the chimp regulatory DNA coupled to the reporter protein strongly and specifically expressed the protein in their hind limbs, but not their forelimbs, and in their lateral toes, but not the big toes of the hind limbs. Mice genetically engineered to lack the ability to produce GDF6 in any part of their bodies had skull bones that were smaller than normal and their toes were shorter than those of their peers. Together, these findings gave the researchers a clue that GDF6 might play a critical role in limb development and evolution.

    The big toe: an explanation

    The fact that humans are missing the hind-limb-regulatory region probably means that we express less of the gene in our legs and feet during development, but comparable amounts in our nascent arms, hands and skulls. Loss of this particular regulatory sequence would also shorten lateral toes but not the first toe of feet. This may help explain why the big toe is aligned with other short, lateral toes in humans. Such a modification would create a more sturdy foot with which to walk upright.

    "These bone morphogenetic proteins are strong signals for bone and cartilage growth in all types of animals," said Kingsley.

    "You can evolve new skeletal structures by changing where and when the signals are expressed, and it's very satisfying to see similar regulatory principles in action whether you are changing the armor of a stickleback, or changing specific hind-limb structures during human evolution."

    Author: Krista Conger | Source: Stanford University Medical Center [January 07, 2016]

  • Genetics: Mummies from Hungary reveal TB's Roman lineage

    Genetics: Mummies from Hungary reveal TB's Roman lineage

    Bodies found in a 200 year-old Hungarian crypt have revealed the secrets of how tuberculosis (TB) took hold in 18th century Europe, according to a research team led by the University of Warwick.

    Mummies from Hungary reveal TB's Roman lineage
    One of the 265 mummies resting in cardboard boxes in the Hungarian 
    Natural History Museum in Budapest, Hungary
    [Credit: AP/Bela Szandelszky]

    A new study published in Nature Communications details how samples taken from naturally mummified bodies found in an 18th century crypt in the Dominican church of Vác in Hungary have yielded 14 tuberculosis genomes, suggesting that mixed infections were common when TB was at peak prevalence in Europe.

    The research team included collaborators from the Universities of Warwick and Birmingham, University College London, the Hebrew University in Jerusalem and the Hungarian Natural History Museum in Budapest. Lead author Professor Mark Pallen, from Warwick Medical School, said the discovery was significant for current and future infection control and diagnosis.

    Professor Pallen said: “Microbiological analyses of samples from contemporary TB patients usually report a single strain of tuberculosis per patient. By contrast, five of the eight bodies in our study yielded more than one type of tuberculosis – remarkably from one individual we obtained evidence of three distinct strains.”

    The team used a technique called “metagenomics” to identify TB DNA in the historical specimens—that is direct sequencing of DNA from samples without growing bacteria or deliberately fishing out TB DNA. This approach draws on the remarkable throughput and ease of use of modern DNA sequencing technologies.

    Gemma Kay, first author on the paper says: “Poignantly, we found evidence of an intimate link between strains from in a middle-aged mother and her grown-up daughter, suggesting both family members died from this devastating infection.”

    The team used the 18th century sequences to date the origin of the lineage of TB strains commonly found in Europe and America to the late Roman period, which fits in with the recent controversial suggestion that the most recent common ancestor of all TB strains occurred as recently as six thousand years ago.

    Professor Pallen said: “By showing that historical strains can be accurately mapped to contemporary lineages, we have ruled out, for early modern Europe, the kind of scenario recently proposed for the Americas—that is wholesale replacement of one major lineage by another—and have confirmed the genotypic continuity of an infection that has ravaged the heart of Europe since prehistoric times.”

    Professor Pallen added that with TB resurgent in many parts of the world, the struggle to contain this ancient infection was far from over. He concludes: “We have shown that metagenomic approaches can document past infections. However, we have also recently shown that metagenomics can identify and characterize pathogens in contemporary samples, so such approaches might soon also inform current and future infectious disease diagnosis and control.”

    For more photos of the Hungarian mummies visit the website Morbid Anatomy.

    Source: University of Warwick [April 07, 2015]

  • Genetics: Genes for nose shape found

    Genetics: Genes for nose shape found

    Genes that drive the shape of human noses have been identified by a UCL-led study. The four genes mainly affect the width and 'pointiness' of noses which vary greatly between different populations. The new information adds to our understanding of how the human face evolved and may help contribute to forensic DNA technologies that build visual profiles based on an individual's genetic makeup.

    Genes for nose shape found
    Variation between nose shape and the specific genes responsible 
    [Credit: Dr Kaustubh Adhikari, UCL]

    The study, published today in >Nature Communications, analysed a population of over 6,000 people with varied ancestry across Latin America to study the differences in normal facial features and identify the genes which control the shape of the nose and chin.

    The researchers identified five genes which play a role in controlling the shape of specific facial features. DCHS2, RUNX2, GLI3 and PAX1 affect the width and pointiness of the nose and another gene -- EDAR -- affects chin protrusion.

    "Few studies have looked at how normal facial features develop and those that have only looked at European populations, which show less diversity than the group we studied. What we've found are specific genes which influence the shape and size of individual features, which hasn't been seen before.

    "Finding out the role each gene plays helps us to piece together the evolutionary path from Neanderthal to modern humans. It brings us closer to understanding how genes influence the way we look, which is important for forensics applications," said the first author of the report, Dr Kaustubh Adhikari, UCL Cell & Developmental Biology.

    People have different shaped facial features based on their genetic heritage and this is partly due to how the environment influenced the evolution of the human genome. The nose, for example, is important for regulating the temperature and humidity of the air we breathe in so developed different shapes in warmer and cooler climates.

    "It has long been speculated that the shape of the nose reflects the environment in which humans evolved. For example, the comparatively narrower nose of Europeans has been proposed to represent an adaptation to a cold, dry climate. Identifying genes affecting nose shape provides us with new tools to examine this question, as well as the evolution of the face in other species. It may also help us understand what goes wrong in genetic disorders involving facial abnormalities," explained Professor Andrés Ruiz-Linares UCL Biosciences, who led the study.

    The team collected and analysed DNA samples from 6,630 volunteers from the CANDELA cohort recruited in Brazil, Colombia, Chile, Mexico and Peru. After an initial screen, a sample size of 5,958 was used. This group included individuals of mixed European (50%), Native American (45%) and African (5%) ancestry, resulting in a large variation in facial features.

    Both men and women were assessed for 14 different facial features and whole genome analysis identified the genes driving differences in appearance.

    A subgroup of 3,000 individuals had their features assessed using a 3D reconstruction of the face in order to obtain exact measurements of facial features and the results identified the same genes.

    The study identified genes that are involved in bone and cartilage growth and the development of the face. GLI3, DCHS2 and PAX1 are all genes known to drive cartilage growth -- GLI3 gave the strongest signal for controlling the breadth of nostrils, DCHS2 was found to control nose 'pointiness' and PAX1 also influences nostril breadth. RUNX2 which drives bone growth was seen to control nose bridge width.

    The genes GLI3, DCHS2 and RUNX2 are known to show strong signals of recent selection in modern humans compared to archaic humans such as Neanderthals and Denisovans; GLI3 in particular undergoing rapid evolution.

    Source: University College London [May 19, 2016]

  • Genetics: Scientists sequence ancient British 'gladiator' genomes from Roman York

    Genetics: Scientists sequence ancient British 'gladiator' genomes from Roman York

    Cutting-edge genome technology in Trinity College Dublin has cast more light on a mystery that has perplexed archaeologists for more than a decade. The origins of a set of Roman-age decapitated bodies, found by York Archaeological Trust at Driffield Terrace in the city, have been explored, revealing a Middle Eastern body alongside native British.

    Scientists sequence ancient British 'gladiator' genomes from Roman York
    One of the skeletons excavated by York Archaeological Trust at Driffield Terrace
    [Credit: York Archaeological Trust]

    Archaeologists have speculated that the skeletons belonged to gladiators, although they could also have been soldiers or criminals. Several suffered perimortem decapitation and were all of a similar age – under 45 years old. Their skulls were buried with the body, although not positioned consistently – some were on the chest, some within the legs, and others at the feet.

    Although examining the skeletons revealed much about the life they lived – including childhood deprivation and injuries consistent with battle trauma – it was not until genomic analysis by a team from Trinity College Dublin, led by Professor of Population Genetics, Dan Bradley, that archaeologists could start to piece together the origins of the men.

    The Trinity College team recently published the first prehistoric Irish genomes and this analysis by Trinity PhD Researcher, Rui Martiniano, also breaks new ground as it represents the first genome analysis of ancient Britons.

    From the skeletons of more than 80 individuals, Dr Gundula Muldner of the University of Reading, Dr Janet Montgomery of the University of Durham and Malin Holst and Anwen Caffel of York Osteoarchaeology selected seven for whole genome analyses. Despite variation in isotope levels which suggested some of the 80 individuals lived their early lives outside Britain, most of those sampled had genomes similar to an earlier Iron Age woman from Melton, East Yorkshire. The poor childhood health of these men suggests that they were locals who endured childhood stress, but their robust skeletons and healed trauma, suggest that they were used to wielding weapons.

    Scientists sequence ancient British 'gladiator' genomes from Roman York
    The Roman-age skeletons from Driffield Terrace laid out in York's Guildhall 
    [Credit: York Archaeological Trust]

    The nearest modern descendants of the Roman British men sampled live not in Yorkshire, but in Wales. A man from a Christian Anglo-Saxon cemetery in the village of Norton, Teesside, has genes more closely aligned to modern East Anglia and Dutch individuals and highlights the impact of later migrations upon the genetic makeup of the earlier Roman British inhabitants.

    However, one of the decapitated Romans had a very different story, of Middle Eastern origin he grew up in the region of modern day Palestine, Jordan or Syria before migrating to this region and meeting his death in York.

    "Archaeology and osteoarchaeology can tell us a certain amount about the skeletons, but this new genomic and isotopic research can not only tell us about the body we see, but about its origins, and that is a huge step forward in understanding populations, migration patterns and how people moved around the ancient world," says Christine McDonnell, Head of Curatorial and Archive Services for York Archaeological Trust.

    "This hugely exciting, pioneering work will become the new standard for understanding the origins of skeletons in the future, and as the field grows, and costs of undertaking this kind of investigation fall, we may be able to refine our knowledge of exactly where the bodies were born to a much smaller region. That is a remarkable advance."

    Scientists sequence ancient British 'gladiator' genomes from Roman York
    The Roman skeletons were found at Driffield Terrace in York with their skulls placed between their legs,
     at their feet or on their chests [Credit: York Archaeological Trust]

    As well as Trinity College Dublin, the multi-disciplinary scientific analysis involved scientists from the University of York and The York Archaeological Trust, as well as the universities of Durham, Reading and Sheffield, University College London and the University Medical Centre in Utrecht. The research also included experts from York Osteoarchaeology Ltd, City of York Council and the Natural History Museum.

    The Roman skeletons sampled were all male, under 45 years old and most had evidence of decapitation. They were taller than average for Roman Britain and displayed evidence of significant trauma potentially related to interpersonal violence. All but one would have had brown eyes and black or brown hair but one had distinctive blue eyes and blond hair similar to the single Anglo-Saxon individual.

    The demographic profile of the York skeletons resembles the population structure in a Roman burial ground believed to be for gladiators at Ephesus. But the evidence could also fit with a military context—the Roman army had a minimum recruitment height and fallen soldiers would match the age profile of the York cemetery.

    Professor Dan Bradley, Trinity, said: "Whichever the identity of the enigmatic headless Romans from York, our sample of the genomes of seven of them, when combined with isotopic evidence, indicate six to be of British origin and one to have origins in the Middle East. It confirms the cosmopolitan character of the Roman Empire even at its most northerly extent."

    PhD Researcher and lead author, Rui Martiniano, Trinity, said: "This is the first refined genomic evidence for far-reaching ancient mobility and also the first snapshot of British genomes in the early centuries AD, indicating continuity with an Iron Age sample before the migrations of the Anglo-Saxon period."

    Professor Matthew Collins, of the BioArCh research facility in the Department of Archaeology at York, who co-ordinated the report on the research, "These genomes give the first snapshot of British genomes in the early centuries AD, showing continuity with the earlier Iron Age and evidence of migrations in the Anglo-Saxon period."

    The paper is published in >Nature Communications.

    Source: Trinity College Dublin [January 20, 2016]

  • Genetics: Scientists propose new evolution model for tropical rainforests

    Genetics: Scientists propose new evolution model for tropical rainforests

    Scientists from Wageningen UR and other institutes are proposing a new research model - the turnover model - as a way of answering the question why there are always so many plant species in tropical rainforests.

    Scientists propose new evolution model for tropical rainforests
    In their publication in New Phytologist magazine, the Dutch, British and Swiss scientists show that major evolutionary changes, such as the origin of large groups of species, occur with a reasonably constant frequency while the origin of new species is an explosive process.

    Various models

    Darwin’s contemporary Alfred Russel Wallace already argued that the Tropics are, in essence, a museum of biodiversity. As tropical climates are stable, Wallace suggested that species would gradually increase in number over longer time periods, the so-called museum model. More recently, however, it was suggested that the Pleistocene ice ages, and the impact thereof on the climate in the Tropics, resulted in recent explosions of speciation, the so-called cradle model.

    Both models are supported by previous research into patterns of diversification in tropical plants. This research is performed by means of reconstructed ‘phylogenetic trees’; genealogical trees that show the interrelated  descent of plant species. Where analyses of plant families focused on studying as many evolutionary lines as possible from the family, diversity was shown to increase gradually. For instance, the development of diversity in important tropical plant groups such as palm trees, the leguminous family and the soursop family, appear to follow the museum model. However, within these large plant families there are also plant genera that seem to follow the cradle model: so-called radiations in which many different species developed recently and over a short period of time.

    Equatiing seems impossible

    Equating these two models seems an impossible task. How can a large plant family that presents an explosive increase in the number of species diversify as an entire family following the museum model? The answer lies in analysing more species per family, and better modelling speciation over long periods in evolution via the computer.

    Scientists propose new evolution model for tropical rainforests
    In the turnover evolution model arise evolutionary lines with a more 
    or less constant speed, while the individual species formation 
    takes place abruptly and then happens explosively 
    [Credit: Wageningen University]

    Mahogany trees

    Scientists from Wageningen UR, Kew (London) and Zürich compiled the largest amount of data so far for the Meliaceae , or mahogany family. This family mainly grows in the Tropics, and is known for valuable wood such as mahogany and Spanish cedar. Parts of the nuclear and chloroplast genome of approximately 35% of the species were sequenced; a technology in which all the building blocks of the DNA are mapped.

    The analysis of evolutionary diversification showed that the diversity of larger groups, such as plant genera and families, does develop in accordance with the museum model, i.e., with a certain constant frequency in the origin of new branches. The scientists showed that, in addition to this ‘museum fundament’, the origin of individual species is an explosive process which occurs in accordance with the cradle model.

    ‘Young’ species

    The research shows that the mahogany family developed approximately 68 million years ago. The circa 200 mahogany species that grow in the South American rainforests are largely the result of two explosions in speciation (radiations) that occurred independently in two evolutionary lines in the late Miocene epoch, which was less than 10 million years ago.

    An interesting aspect of this explosive origin of large numbers of species within the mahogany family is that it involves two different groups within the family which independently evolved the same ecological adaptations, such as plant height and an adaptation of seeds to the same animal species that distribute them. In addition, the two groups show a similar speed of speciation. These abrupt increases in speciation speed occurred after the mahogany family had left its original habitat (tropical dry forests and seasonal forests) and colonised the rainforests, where they were faced with different climate conditions.

    New model for evolution

    The results of the study show that most mahogany species in the Tropics are relatively recent. It can be assumed that this also applies to other families. The authors propose a new model, the turnover model, in which the number of evolutionary lines increases with a more or less constant speed, while speciation occurs separately and in a more explosive way.

    Source: Wageningen University [June 19, 2015]

  • Genetics: Obesity in humans linked to fat gene in prehistoric apes

    Genetics: Obesity in humans linked to fat gene in prehistoric apes

    A genetic mutation in extinct European apes that enabled them to convert fruit sugar into fat could be a cause of the modern obesity epidemic and diabetes, according to scientists. Fossil evidence reveals that apes living around 16 million years ago, in what was then subtropical Europe, began to suffer as global cooling subsequently changed the forest, making the fruit they ate scarce.

    Obesity in humans linked to fat gene in prehistoric apes
    Extinct European apes evolved into today's great apes and the earliest hominids 
    [Credit: Nathan Thompson, Lucille Betti-Nash, and Deming Yang]

    Experts suggest that a mutation in the uricase gene which helps to convert fruit sugar (fructose) occurred around 15 million years ago. This aided apes in adding on fat layers so they could survive famines and harsh winters.

    Persistence of the same mutation in all modern great apes and all modern humans, along with the fossil evidence, suggests that the now extinct European apes evolved into today's great apes and the earliest hominids.

    Scientists have spent decades researching the genetic causes of obesity which is rarely found in other animals – apart from domesticated pets. The latest research focuses on fructose: a sugar which breaks down to form uric acid in the blood, according to a Sunday Times report.

    The Western diet contains so much uric acid that it cannot be removed quickly enough, but triggers liver cells to turn fructose into fat, with the effect of humans adding on extra weight. The uricase mutation predisposes humans to obesity and diabetes in modern times. The results suggest a need to eat and drink much less fructose to fight obesity and prevent its dangerous complications.

    "The gene enables uric acid levels to spike in response to two types of food," wrote Peter Andrews, professor of anthropology at University College London in Scientific American, co-authored with Richard Johnson, a professor of medicine in the US. "Those like beer that produce a lot of uric acid [directly] and those that contain a lot of fructose. These include honey and processed food that are high in table sugar or high-fructose corn syrup. When uric acid spikes we become susceptible to obesity and diabetes."

    Obesity is considered as one of the biggest public health challenges of the century. Statistics show that it is affecting more than 500 million people worldwide. In the US alone, obesity costs at least $200 billion each year.

    This medical condition also contributes to potentially fatal disorders such as cancer, type 2 diabetes and cardiovascular disease.

    Author: Fiona Keating | Source: International Business Times [November 20, 2015]

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