The Great London:
Genetics

Using a technique that can tell if a species has passed by from just a sample of water, scientists are developing new ways to assess ecosystems.

All animals shed fragments of DNA as they go about their lives – in faeces, mucous, sperm and eggs, shed skin, hair and, eventually, their carcasses.

These traces of genetic material can persist in the environment for some time – a matter of weeks in water and up to a few centuries in soil. With new, more sensitive DNA amplification and sequencing techniques, scientists can collect and analyse these fragments in water and soil samples and identify individual species that have passed by.

One area where environmental DNA, or eDNA, is finding practical use is in environmental assessments, for example to check whether any protected species are present before construction works are carried out. Already, Defra in the UK have approved the use of eDNA sampling to assess the presence of protected great crested newts in ponds.

Now, in a new partnership between Imperial College London and environmental ecology consultancy Thomson Ecology, scientists are hoping to expand the use of eDNA. They want to create protocols to assess whether different areas are home to key protected species, including crayfish, water voles, otters and reptiles.

As well as looking at key protected species for conservation, the team want to use eDNA for biosecurity, by identifying invasive species. For example, as well as native crayfish, some UK waters have been occupied by invasive American Signal Crayfish, which outcompete the native species and damage the local environment. Early detection of invasive crayfish could mean they are dealt with sooner, and cause less damage.

Ultimately, the researchers hope to be able to use eDNA to profile entire ecosystems, analysing water samples to get a snapshot of all the organisms present in the local environment that have shed some DNA.

Victoria Priestley, who is taking on this task for her PhD thesis in the Department of Life Sciences at Imperial, said: "I think eDNA surveys represent a sea change in how we approach survey and monitoring of species.

"There is a lot of effort going into eDNA research globally and once it becomes more established, we should be able to assess what species are present in an area much more quickly. Ultimately we should be able to use it to create a clearer and more detailed picture of global biodiversity."

Efficient Environmental Assessments

Currently, species are assessed based on intensive field surveys, requiring taxonomic expertise and often involving tagging animals and repeat visits to a site. However, Professor Vincent Savolainen, from the Department of Life Sciences at Imperial, is developing new protocols for various species.

This is paving the way for much simpler and more cost-effective surveying for environmental assessments. Professor Savolainen said: "This research will contribute to developing new indices to meet goals of the Intergovernmental Science-Policy Platform on Biodiversity and Ecosystem Services (IPBES), the body that assesses the state of biodiversity and of the ecosystem services it provides to society, in response to requests from decision makers."

Although sequencing techniques have improved dramatically in the last few decades, challenges remain in analysing eDNA. The fragments degrade over time, a process enhanced by temperature, microbes, enzymes and salinity.

The rate that eDNA is 'shed' from species to species and individual to individual also requires more research, as does the role of predators in moving eDNA between sites, and especially how eDNA is distributed in aquatic environments.

However, Priestley is positive that eDNA surveys have a bright future: "There is still some way to go before whole-ecosystem eDNA monitoring is standard practice, but I believe that at least in the near future, eDNA will increasingly be one of the options in the survey toolkit, working alongside traditional methods to obtain the best ecological survey data in the most efficient way."

Positive Partnership

Professor Tom Welton, Dean of the Faculty of Natural Sciences, said partnerships like this one help translate research into real-world applications: "This exciting collaboration demonstrates that research across the whole breadth of natural sciences at Imperial, even on newts, has practical applications to real world problems.

"Our partnership with Thomson Ecology will allow our research to have a positive impact on environmental protection and conservation."

Author: Hayley Dunning | Source: Imperial College London [November 25, 2016]

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]

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.

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]

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.

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.

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."

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]

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 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.

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]

Scientists used the full DNA sequences of Schistosoma mansoni parasites from Africa and the French Caribbean to discover the fluke's origins, map its historic transmission and identify the secrets of its success. Their findings, published in Scientific Reports, show how the global slave trade transported the disease from Senegal and Cameroon to Guadeloupe. Further genomic comparison with a closely related schistosome species that infects rodents reveals how the parasite has adapted to infecting human beings.

Schistosoma mansoni is a blood fluke (flatworm) that infects more than 250 million people worldwide and causes more than 11,000 deaths each year. Six years ago the Sanger Institute published the parasite's first full DNA sequence (genome); this latest study used that 'genetic map' to construct and compare the genomes of S. mansoni parasites gathered from across Africa and the New World, the majority of which were held at the Schistosomiasis Collection in the Natural History Museum, London.

By analysing the differences between the human-infecting S. mansoni and its close relative, the rodent-infecting S. rodhaini, the scientists calculated that the two species evolved from a common ancestor approximately 107,000 to 148,000 years ago in East Africa. This finding suggests that the species is much 'younger' than previously thought.

"The timing of the separation of the two species coincidences with the first archaeological evidence of fishing in Africa," explains Thomas Crellen, first author of the study from Imperial College London, the Sanger Institute and the Royal Veterinary College London. "The parasite develops in freshwater and infects people by burrowing through their skin. The introduction of fishing would have meant that people spent more time in the water, greatly increasing their chances of being infected."

Analysing the differences between genomes from different locations also revealed the darker side of human history.

"Comparing the S. mansoni genomes suggests that flukes in West Africa split from their Caribbean counterparts at some point between 1117AD and 1742AD, which overlaps with the time of the 16th-19th Century Atlantic Slave Trade," says Professor Joanne Webster from Imperial College London and the Royal Veterinary College. "During this period more than 22,000 African people were transported from West Africa to Guadeloupe by French slave ships, and the fluke was carried with them."

Comparing the genomes of S. mansoni with S. rodhaini also revealed the genetic variations that have been positively selected over time in the human-infecting fluke and have been "fixed" into its DNA. It is likely that these variations are the evolutionary adaptations that have occurred to enable the fluke to successfully tunnel into, and thrive within, human beings.

"When we looked for the differences between human-infecting S. mansoni DNA and its rodent infecting cousin S. rodhaini, we found two important variations. We found that changes to two genes in S. mansoni's DNA -- VAL21 and an elastase gene -appear to be important in allowing the fluke to enter and live in humans," says Dr James Cotton, senior author of the study from the Sanger Institute. "VAL genes produce proteins that cause allergic responses, so it is possible that the variation in VAL21 helps the fluke to hide from our immune systems. The elastase gene helps the parasite to burrow in to the body, by breaking down elastin -- a major component of human skin."

It is hoped that exploring the genetic makeup of the fluke it will be possible to discover more about the processes the parasite relies on to infect humans and offer new opportunities to develop preventive and therapeutic interventions.

Source: Wellcome Trust Sanger Institute [February 17, 2016]

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.

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]

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.

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.

'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]

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.

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]

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.

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.

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]

Scientists have discovered that stunted growth can be a genetic response to ocean acidification, enabling some sea creatures to survive high carbon dioxide levels, both in the future and during past mass extinctions.

Using natural CO2 seeps as test sites, the international team of marine scientists and palaeontologists have studied the way in which sea snails cope in more acidic conditions ‒ simulating the change in seawater chemistry that will occur in future as more atmospheric CO2 is absorbed by the ocean.

The researchers say their findings, published in Nature Climate Change, provide an explanation as to why marine species that survived previous mass extinction events were much smaller – a phenomenon known as the ‘Lilliput effect’.

The research was funded by the EU MedSeA project and the UK Ocean Acidification Research Programme, and involved researchers from 10 institutions including Plymouth University, the University of Southampton, the Natural History Museum, London, and colleagues in Italy, Monaco, Norway and New Caledonia.

Its results provide a stark warning about the impact that continuing ocean acidification could have on marine ecosystems unless we drastically slow the rate of carbon dioxide emissions.

Dr Vittorio Garilli, at Paleosofia-APEMA, Palermo, said: “Two species of snails growing at shallow water CO2 seeps were smaller than those found in normal pH conditions, and adapted their metabolic rates to cope with the acidified seawater. These physiological changes allowed the animals to maintain calcification and to partially repair shell dissolution.”

Professor Jason Hall-Spencer, of the School of Marine Science and Engineering at Plymouth University, said: “Organisms that have been exposed to elevated CO2 levels over multiple generations provide valuable insights both into changes we can expect in marine ecosystems as CO2 emissions continue to rise unchecked, and into past mass extinctions."

“Not only do they demonstrate a similar magnitude and direction of body size change as fossil organisms, but they also reveal the physiological advantages of dwarfing,” added Professor Marco Milazzo at Palermo University.

Measurements showed that the shells from high CO2 seawater were about a third smaller than those in “normal” environments. Some of the snails were taken to the Marine Environmental Studies Laboratory at the International Atomic Energy Agency in Monaco, where their calcification rates were measured in aquaria.

Study co-leader Dr Riccardo Rodolfo-Metalpa, from the Institut de Recherche pour le Développement, said: “They developed a surprising ability to calcify and cope with shell dissolution at pH values which were thought too low for calcification to occur.”

The results – published in the paper Physiological advantages of dwarfing in surviving extinctions in high CO2 oceans – confirmed the theory that the snails had adapted to the conditions over many generations.

Professor Richard Twitchett, of the Department of Earth Sciences at the Natural History Museum, said: “The fossil record shows us that mass extinctions and dwarfing of marine shelled species are repeatedly associated with episodes of past global warming. It is likely that similar changes will increasingly affect modern marine ecosystems, especially as the current rate of ocean acidification and warming is so rapid."

Professor Hall-Spencer added: “It is critical that we understand the mechanisms by which certain species survive chronic exposure to elevated CO2 since emissions of this gas are already having adverse effects on marine foodwebs and putting food security at risk.”

Author: Andrew Merrington | Source: University of Plymouth [April 21, 2015]

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.

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]

Archaeologists from the British museum have reconstructed an ancient man's face, allowing visitors to see what he looked like for the first time.

The man lived 9,500 years ago in the holy city of Jericho, now found in the Palestinian territories near the West Bank.

The 'Jericho skull' was found by British archaeologists in 1953, but until now nobody knew what the he had looked like.

Scientists still don't know the man's true identity, but they speculate that he was once someone of great importance.

This is based on the amount of care people had taken to fill his skull with plaster once he had died, almost 10,000 years ago.

Back then, plastered skulls were a form of ritual burial, like the Egyptians' infamous mummification burials.

The gruesome practice involved removing the corpse's skull and filling it with plaster, before painting over the dead person's face and filling his eye sockets with shells.

These remains were likely put on display for locals while the rest of the body was buried under the family home.

The Jericho skull was found nestled alongside several other plastered skulls, but was by far the most well-preserved of the group.

'He was certainly a mature individual when he died, but we cannot say exactly why his skull, or for that matter the other skulls that were buried alongside him, were chosen to be plastered,' British Museum curator Alexandra Fletcher told >Seeker.

'It may have been something these individuals achieved in life that led to them being remembered after death.'

Before the reconstruction, the ancient skull showed few human features due to the plaster pasting over most of its features.

To investigate the grim burial practice, the scientists sent the skull off for a scan at the Imaging and Analysis Centre at London's Natural History Museum.

Here, a complete micro-CT scan unveiled a ream of new information about the skull, and inspired the Museum to undertake a full plaster reconstruction.

Through the CT scans, the team discovered that the ancient man was missing a jaw underneath the plaster, and had lines of decaying teeth.

They could see he had suffered a broken nose at some point in his life.

He had also undergone head-binding, a traditional practice in which the skull of a human being is deformed intentionally, usually by forcefully distorting a child's skull.

'Head binding is something that many different peoples have undertaken in various forms around the world until very recently,' Fletcher told Seeker.

'In this case, the bindings have made the top and back of the head broader - different from other practices that aim for an elongated shape. I think this was regarded as a 'good look' in Jericho at this time.'

All of the newly gathered details allowed the team to make an accurate plaster reconstruction of the man's head.

And while the fascinating new model provides fresh insight into the man's life, plenty more work needs to be done to discover more about his history and culture.

The team hopes to gather DNA samples from the skull in future, laying out 10,000 year-old genes for investigation.

But the process would be risky - it's likely to damage the skull and useful results aren't guaranteed.

'If we were able to extract DNA from the human remains beneath the plaster, there is currently a very slight chance that we would be able to find out this individual's hair and eye colour,' Fletcher said.

'I say a slight chance because the DNA preservation in such ancient human remains can be too poor to obtain any information.'

The reconstructed face will be on display at the British Museum in London from next Thursday until mid-February.

Author: Harry Pettit | Source: Daily Mail Online [December 09, 2016]

Scientists have developed the largest ever family tree of a major group of flowering plants called monocots, which could help protect their diversity.

Monocots account for a quarter of all flowering plants. They are among the most diverse and economically important plants on the planet, but their evolutionary lines have never been properly mapped. Monocots include staples such as corn, rice, wheat and barley; many tropical fruits such as pineapples and bananas; and other foods such as dates and sugarcane. Monocots such as grasses, bamboo, palms, and their derivations including fibres, are used as key building materials in many countries such as in China.

Now, researchers at Imperial College London have created the most up-to-date family tree or phylogenetic tree, which traces the lines of evolutionary descent of monocots. The researchers analysed DNA samples from across the globe, aiming to determine what factors affected the diversity of monocot species.

Their work could help scientists to conserve the biodiversity of monocots and lead to new types of uses for these plants, such as in the development of new medicines.

Professor Vincent Savolainen, study co-author from the Department of Life Sciences at Imperial College London, said: "Monocots are so important in our lives, providing us with essential food and building materials. Our study is not only the most detailed family tree of monocot species ever developed, it is also importantly helping us to understand what factors affect their diversity. This could lead to better methods for conserving and protecting them.

"It may also lead to new uses for them such as in medicines. Sometimes the best active compound to use in medicine is found in a different species to the one in which it was initially discovered. Therefore, testing close evolutionary relatives may reveal a slightly different molecule that has a stronger effect in combatting one particular disease."

As expected, the team in today's study found that biological factors - such as the way different monocots evolved to take advantage of their environment - played a part in their diversity. However, the researchers discovered that the most important factors in the diversity of monocots in any given region were geographical factors such as the habitat size, its latitude, and altitude.

In particular, they found that the size of the habitat accounted for a third of the species diversity. They suggest this is likely because a bigger habitat means that there are generally more resources and less competition, which enables more species to thrive together rather than compete against each other. They also found that species diversity was reduced at higher altitudes. This may be because temperatures are lower and there is less water available, which causes fiercer competition among monocots for fewer resources.

The researchers were also able to verify previous findings that monocot species are most varied around the equator, and that the closer monocots are to the poles, the fewer species are available. This might be due to higher UV radiation at the equator, causing more genetic mutations and species variation in equatorial regions as a result.

This research analyses 1,987 of the 2,713 types of monocot worldwide. Researchers in this field will now look to increase their sampling to ultimately encompass the roughly 400,000 plant species, to create the entire botanical 'tree of life'.

The study was published in >Botanical Journal of the Linnean Society.

Author: Caroline Brogan | Source: Imperial College London [November 09, 2016]

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.

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]

Ten pigtails of hair thought to be from seven mutineers of "Mutiny on the Bounty" fame and three of their female Polynesian companions will be analysed in a new collaboration between the Pitcairn Islands Study Centre at Pacific Union College (California, US) and the forensic DNA group at King's College London (UK).

The forensic DNA group at King's has been sent hair strands from the ten pigtails, which are currently on display in the California-based centre, to help establish as much information as possible on their origins.

As the pigtails purportedly date back to the pre-1800s, the King's team will first attempt to extract DNA from the historical hair samples after cleaning the outside and then digesting the hair matrix using a chemical process. Nuclear DNA is not found in hair shafts, only the roots which are not available here; however, mitochondrial DNA may be present. If sufficient mitochondrial DNA can be collected, the first step will be to investigate the ancestral origins of the owners of the pigtails.

Unlike nuclear DNA, mitochondrial DNA does not discriminate between all individuals as people sharing a common maternal ancestor will also share a similar profile. However, this type of DNA can provide some indication of maternal geographic origin e.g. whether someone is likely to be of European descent, so the team will aim to establish whether the hair samples do indeed come from seven Europeans and three Polynesian individuals, as the documentation accompanying the samples suggests.

Further, more detailed identification will require genealogical methods to trace the ancestors of the pigtail owners, to be able to link samples to names from historical records and other sources of information. A lot has been written about the possible descendants of the mutineers but this information will not be helpful with regards to the male mutineers; instead, their maternal line will need be traced. The study will therefore try to identify their maternal ancestors, such as their respective mothers and maternal grandmothers, and research other direct female descendants down to individuals living today.

Dr Denise Syndercombe-Court, project lead from the Analytical and Environmental Sciences Division at King's College London, said: "First, we will have to determine whether we can recover mitochondrial DNA of appropriate quality to be analysed. The hairs, if from the mutineers, are over two hundred years old and we have no idea what environments they might have been exposed to in the intervening time."

"Potentially as problematic will be the genealogical research as civil registration in the UK did not start until 1837, some 50 years after the mutiny and so, at best, the death of the mother may be listed in these records but other processes would need to be used to gather more information. Because of the patrilineal transmission of surnames we would not even expect to find someone who believes they may be linked to the mutineers and so we will have to depend on this research and hope for the agreed consent from any identified living descendant to act as a modern day reference. We do not anticipate that this will be easy and it will require other interested parties to get involved in this part of the study."

Herbert Ford, Director of the Pitcairn Islands Study Centre, said: "This hair is a gift from Joy Allward, wife of the late Maurice Allward of Hatfield, UK, who successfully bid for the hair at a Sotheby's auction in London in 2000."

"If the tests and genealogical studies of this hair authenticates that it is of seven of the nine mutineers who hid out from British justice on Pitcairn Island in 1790, it will be the only tangible physical evidence of their having existed. There is only one known mutineer grave on Pitcairn, that of John Adams. Of the whereabouts of the remains of the eight others, we can only speculate."

The pigtails on display in the US were housed in a nineteenth-century cylindrical tobacco tin. Also with the locks of hair was a handkerchief said to have belonged to Sarah, the daughter of William McCoy, one of the Bounty mutineers.

A worn, faded label with the pigtails notes that it is attached to the hair of William McCoy. The mutineer McCoy died on Pitcairn Island in 1800. Notes written on the label also state that the pigtails are of seven of the mutineers of H.M.S. Bounty and "also that of three of the Tahitian women," who accompanied the mutineers to Pitcairn in 1789.

Further information on the label notes that "The holders of the hair have been (1) Teio, wife of McCoy. (2) Mrs. Sarah Christian. (3) F. G. Mitchell. Given to F. G. Mitchell, 22nd June 1849 (Jubilee Day) by Mrs. Sarah Nobbs."

The story of the mutiny that took place on the ship H.M.S. Bounty in the South Pacific Ocean in 1789 was made famous by the publication of a trilogy of books published in the 1930s. Following the publication of the books, a number of Hollywood-type motion pictures about the Bounty mutiny were shown worldwide over the next four decades.

Source: King's College London [August 22, 2016]

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.

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.

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]

The first eukaryote is thought to have arisen when simpler archaea and bacteria joined forces. But in an Opinion paper published in >Trends in Cell Biology, researchers propose that new genomic evidence derived from a deep-sea vent on the ocean floor suggests that the molecular machinery essential to eukaryotic life was probably borrowed, little by little over time, from those simpler ancestors.

"We are beginning to think of eukaryotic origins as a slow process of growing intimacy--the result of a long, slow dance between kingdoms, and not a quick tryst, which is the way it is portrayed in textbooks," says Mukund Thattai of the National Centre for Biological Sciences in India.

The eukaryotic cells of plants, animals, and protists are markedly different from those of their single-celled, prokaryotic relatives, the archaea and bacteria. Eukaryotic cells are much larger and have considerably more internal complexity, including many internal membrane-bound compartments.

Although scientists generally agree that eukaryotes can trace their ancestry to a merger between archaea and bacteria, there's been considerable disagreement about what the first eukaryote and its immediate ancestors must have looked like. As Thattai and his colleagues Buzz Baum and Gautam Dey of University College London explain in their paper, that uncertainty has stemmed in large part from the lack of known intermediates that bridge the gap in size and complexity between prokaryotic precursors and eukaryotes. As a result, they say, the origin of the first eukaryotic cell has remained "one of the most enduring mysteries in modern biology."

That began to change last year with the discovery of DNA sequences for an organism that no one has ever actually seen living near a deep-sea vent on the ocean floor. The genome of the archaeon known as Lokiarchaeum ('Loki' for short) contains more "eukaryotic signature proteins" (ESPs) than any other prokaryote. Importantly, among those ESPs are proteins (small Ras/Arf-type GTPases) critical for eukaryotes' ability to direct traffic amongst all those intercellular compartments.

The authors consider the available data to explore an essential question: what might the archaeal ancestor of all eukaryotes look like? "If we could turn back the clock and peer inside this cell, would its cellular organization have been like that of an archaeal cell or more eukaryote-like?" Dey says.

As the closest known archaeal relative of eukaryotes, Loki helps to answer that question. The researchers say that the ESPs found in Loki are unlikely to work in the same way they do in eukarytoes. That's because Loki doesn't appear to have enzymes required for ESP association with membranes or key building blocks of the membrane trafficking machinery.

"However," Baum says, "the genome can be seen as 'primed' for eukaryogenesis. With the acquisition of a number of key genes and lipids from a bacterial symbiont, it would be possible for Loki-type cells to evolve a primitive membrane trafficking machinery and compartmentalization."

The researchers predict that, when Loki is finally isolated or cultured, "it will look more like an archaeon than a proto-eukaryote and will not have internal compartments or a vesicle-trafficking network." But its morphology and/or cell cycle might have complexities more often associated with eukaryotes.

Baum and Dey say they now plan to explore the basic cell biology of the related archaea Sulfolobus acidocaldarius, first isolated from an acidic hot spring in Yellowstone National Park.

"We believe it will be very difficult to crack the mysteries of eukaryogenesis without first understanding the archaeal cell biology," Dey says. "We are currently developing tools in the lab to study the cell cycle and cellular morphology of Sulfolobus at the single-cell level under the microscope. We would also love to catch a glimpse of Loki."

Source: Cell Press [June 16, 2016]

In tropical climes, animals and plants aren't adapted to surviving freezing temperatures - and why would they be? It's never all that cold near the Equator, even at altitude. But in places like the Rocky Mountains, where temperatures can climb into the 100s and dip below freezing, species are hardier and more equipped to deal with such fluctuations.

These divergent climate tolerances play crucial roles in how species evolve. Colorado State University research offers new insight into this long-held understanding of species diversity.

A study led by CSU biologists shows that insect populations in the tropics exhibit a higher number of distinct species than in the Rockies. But the distinctions between those species consist of subtle, genetic differences that aren't readily visible. These are called cryptic species - by the looks of things identical, but actually genetically distinct.

The study supports a classic theory dating back to the 1960s. The saying goes that "mountain passes are higher in the tropics" - that is, tropical mountain passes are stronger barriers to the dispersal of organisms than temperate-zone passes of equivalent altitudes. That's indeed true, and the CSU researchers have now found that that species differentiation is more subtle - cryptic - than previously understood.

The study, published in >Proceedings of the Royal Society London B - Biological Sciences will be featured on the journal's printed cover. The lead author is Brian Gill, a graduate student co-advised by Chris Funk in the College of Natural Sciences' Department of Biology and Boris Kondratieff in the College of Agricultural Sciences' Department of Bioagricultural Sciences and Pest Management. Gill led a field team that traversed watersheds in the wilds of Colorado's Rocky Mountains and in the remote Ecuadorean Andes to collect and analyze thousands of mayflies at comparable elevations. Mayflies are common aquatic insects that play key roles in stream food webs and other ecological processes.

Comparing mayfly specimens between the Rockies and the Andes, the researchers identified higher species richness in Ecuador than in Colorado - a disparity rooted in high levels of cryptic tropical diversity. They used a genetic analysis called DNA barcoding to parse out these subtle species differences, which would not be apparent using standard taxonomy.

In fact, by standard taxonomic methods, it would appear that Colorado had a greater abundance of mayfly species. But the subtle, molecular-level differences unveiled by the DNA analyses tipped the scale well in favor of species richness for tropical mayflies.

"Since there is this high climatic zonation in the tropics and narrow thermal tolerances, there are more opportunities for populations to become divergent and isolated, which is what you need for speciation to happen," Gill explained. By comparison, temperate species and their tolerance to a wider range of conditions leads to more gene flow, which limits the number of distinct species that can evolve.

"We think our results can contribute to the discussion about species vulnerability and how it varies across the planet," Gill said.

The next step is to provide better support for latitudinal differences in physiology, and more insight into how species disperse. For those follow-up studies, the researchers will continue to work with collaborators at CSU, Cornell University, University of Nebraska Lincoln, Universidad San Francisco de Quito, and Universidad Tecnológica Indoamérica.

Source: Colorado State University [June 15, 2016]