Skull sheds light on human-Neanderthal relationship

Retrieved from a cave in northern Israel, the partial skull provides the first evidence that Homo sapiens inhabited that region at the same time as Neanderthals. (Reuters: Nikola Solic)

A partial skull, found in a cave in Israel, is shedding light on the pivotal moment in early human history when our species left Africa and encountered our close cousins the Neanderthals.

Anthropologist Israel Hershkovitz, from Tel Aviv University, called the skull "an important piece of the puzzle of the big story of human evolution."

The findings of the research, led by Hershkovitz, are published today in the journal Nature.

The upper part of the skull - the domed portion without the face or jaws - was unearthed in Manot Cave in Israel's Western Galilee.

Scientific dating techniques determined the skull was about 55,000 years old, a time period when members of our species were thought to have been marching out of Africa,

The researchers say characteristics of the skull suggest the individual was closely related to the first Homo sapiens populations that later colonized Europe.

They also say the skull provides the first evidence that Homo sapiens inhabited that region at the same time as Neanderthals, our closest extinct human relative.

Previous genetic evidence suggests our species and Neanderthals interbred around the time the skull is dated to, with all people of Eurasian ancestry still retaining a small amount of Neanderthal DNA as a result.

"It is the first direct fossil evidence that modern humans and Neanderthals inhabited the same area at the same time," says palaeontologist Bruce Latimer of Case Western Reserve University in Cleveland, another of the researchers.

"The co-existence of these two populations in a confined geographic region at the same time that genetic models predict interbreeding promotes the notion that interbreeding may have occurred in the Levant region," Hershkovitz says.

The robust, large-browed Neanderthals prospered across Europe and Asia from about 350,000 to 40,000 years ago, going extinct sometime after Homo sapiens arrived.

Scientists say our species first appeared about 200,000 years ago in Africa and later migrated outwards. The cave is located along the sole land route for ancient humans to take from Africa into the Middle East, Asia and Europe.

Latimer says he suspects the skull belonged to a woman, although the researchers could not say definitively.

The cave, sealed off for 30,000 years, was discovered in 2008 during sewage line construction work. Hunting tools, perforated seashells perhaps used ornamentally and animal bones have been excavated from the cave, along with further human remains.

Source: ABC

‘Fury’ tanks in safe hands

Fury Sherman. Credit: Image courtesy of Bournemouth University

BU research engineers have been working on military vehicles that feature in Brad Pitt's new movie.

Set in the Second World War and currently in UK cinemas, 'Fury' sees Pitt's character Wardaddy command a Sherman tank.

Scenes from the movie were filmed at the Tank Museum at Bovington, where the BU research team are investigating how to preserve these historic vehicles.

The team have worked on the Sherman and Tiger 1, which can be seen in the Fury movie trailer (2 minutes 26 seconds in). Researchers Adil Saeed, Dr Zulfiqar Khan, and Professor Mark Hadfield from BU's Sustainable Design Research Centre have published widely on these particular vehicles.

Dr Zulfiqar Khan said, "This movie reflects the importance of the research, which examines how we can preserve these vehicles for the benefit of society for lengths of time that far exceed the basis any normal design intent.

"The centenary of the First World War and the passing of the generation that fought in the Second World War, means the conservation of significantly degraded vehicle collections has taken on a new importance."

The Tank Museum at Bovington is one of the largest military vehicle museums in the world, boasting a collection of over 300 military vehicles with historic significance. Structural deterioration through corrosion, corrosion fatigue, stress corrosion cracking and mechanical failures are a threat to these vehicles in terms of conservation.

The only operational Tiger tank in the world is currently at The Tank Museum at Bovington. This and other vehicles had to be conserved sustainably, while operating modestly for the annual Tank Fest and other events.

Dr Khan concluded, "The opportunity of collaborative research with The Tank Museum at Bovington to develop sustainable methodology of conserving historic military tanks brought us face to face with the history. This research investigated the state of the structural integrity of vehicles used in WW1, WW2 and post war.

"The outcomes of the research informed the current design of control environment in The Tank Museum. In addition a separate research project looked into the cost implications of project management of The Tank Museum.

"This kind of activity is important in engaging new generations with science, technology, maths and mechanical engineering design solutions."

The research has led to further collaborations with Defence Science & Technology Laboratory Ministry of Defence to develop corrosion condition monitoring and predictive modelling techniques.

Source: Bournemouth University

Genes tell story of birdsong and human speech

The activity of genes related to singing shows a unique pattern in the brain of an Australian Budgerigar.
Credit: Duke University

His office is filled with all sorts of bird books, but Duke neuroscientist Erich Jarvis didn't become an expert on the avian family tree because of any particular interest in our feathered friends. Rather, it was his fascination with how the human brain understands and reproduces speech that brought him to the birds.

"We've known for many years that the singing behavior of birds is similar to speech in humans -- not identical, but similar -- and that the brain circuitry is similar, too," said Jarvis, an associate professor of neurobiology at the Duke University Medical School and an investigator at the Howard Hughes Medical Institute. "But we didn't know whether or not those features were the same because the genes were also the same."

Now scientists do know, and the answer is yes -- birds and humans use essentially the same genes to speak.

After a massive international effort to sequence and compare the entire genomes of 48 species of birds representing every major order of the bird family tree, Jarvis and his colleagues found that vocal learning evolved twice or maybe three times among songbirds, parrots and hummingbirds.

Even more striking is that the set of genes involved in each of those song innovations is remarkably similar to the genes involved in human speaking ability.

The findings are part of a package of eight scientific papers in a Dec. 12 special issue of Science and 21 additional papers appearing nearly simultaneously in Genome Biology, GigaScience and other journals. Jarvis' name appears on 20 papers and he is a corresponding author for 8 of them.

Jarvis co-led the Avian Phylogenomics Consortium with Guojie Zhang of the National Genebank at BGI in China and the University of Copenhagen and M. Thomas P. Gilbert of the Natural History Museum of Denmark. His Duke lab contributed to preparing samples, sequencing and annotating the genomes, performing the analyses and coordinating the overall project.

The Jarvis lab in the Bryan Research Building prepared DNA of many of the species, pulling it from little chunks of frozen, pink bird flesh collected over the past 30 years by museums and other institutions around the world. To ensure the DNA being sequenced really belonged to the Golden-collared manakin and not an undergraduate lab assistant, the lab has been kept spotlessly clean and many of its tools are used only once, to avoid the possibility of subsequent contamination.

"We change gloves a lot," said Carole Parent, the lab research analyst who set up a DNA isolation pipeline for the next stage of the project to sequence still more birds and supervised sample prep with a team of Duke undergrads and a student from East Chapel Hill High School.

All of this meticulous and somewhat tedious work has given Jarvis and hundreds of colleagues around the world a crack at an unprecedented amount of genomic data generated by BGI in China. The whole-genome comparison of the 48 bird species required new algorithms written at the University of Illinois and University of Texas that ran for 400 years of CPU time on three supercomputers in the U.S.

Of the 29 papers covering everything from penguin evolution to color vision, eight are devoted to bird song.

One of the Dec. 12 papers in Science found there is a consistent set of just over 50 genes that show higher or lower activity in the brains of vocal learning birds and humans. These changes were not found in the brains of birds that do not have vocal learning and of non-human primates that do not speak, according to this Duke team, which was led by Jarvis; Andreas Pfenning, a graduate of the Ph.D. program in computational biology and bioinformatics (CBB); and Alexander Hartemink, professor of computer science, statistical science and biology.

"This means that vocal learning birds and humans are more similar to each other for these genes in song and speech brain areas than other birds and primates are to them," Jarvis said.

These genes are involved in forming new connections between neurons of the motor cortex and neurons that control the muscles that produce sound.

A companion study by another CBB doctorate, Rui Wang, looked at the specialized activity of a pair of genes involved in the regions of the brain that control song and speech. This study, appearing in the Journal of Comparative Neurology, found that these genes are down- and up-regulated in one brain region of song-learning birds during the juvenile period of their vocal learning , changes that last into adulthood. This study, and that of Pfenning, hypothesize that changes in these genes could be critical for the evolution of song in birds and speech in humans.

"You can find those same genes in the genomes of all species, but they're active at much higher or lower levels in the specialized song or speech brain regions of vocal learning birds and humans," Jarvis said. "What this suggests to me is that when vocal learning evolves, there may be a limited way in which the brain circuits can evolve."

Another paper in Science from Duke, led by post-doc Osceola Whitney, Pfenning, Hartemink and Anne West, an associate professor of neurobiology, looked at gene activation in different areas of the brain during singing. This team found activation of 10 percent of the expressed genome during singing, with diverse activation patterns in different song-learning regions of the brain. The diverse gene patterns are best explained by epigenetic differences in the genomes of the different brain regions, meaning that individual cells in different brain regions can regulate genes at a moment's notice when the birds sing.

Among the three main groups of vocal learning birds, parrots are clearly different in their ability to mimic human speech. Mukta Chakraborty, a postdoc in the Jarvis lab, led a project that used the activity of some of the specialized genes to discover that the parrot's speech center is organized somewhat differently. It has what the researchers call a "song-system-within-a-song-system" in which the area of the brain with different gene activity for producing song has an outer ring of still more differences in gene expression.

Parrots are very social animals, Chakraborty said, and having the ability to quickly pick up "dialects" of parrot speech may account for their super-charged speech center. The "shell" or outer regions were found to be proportionally larger in the parrot species, which are believed to have the highest vocal, cognitive and social abilities. These species include Amazon parrots, the African Grey and the Blue and Gold Macaw.

Jarvis was also part of a team with Claudio Mello and his Ph.D. student Morgan Wirthlin at Oregon Health & Science University that found ten more genes that are unique to song-control regions of songbirds. This paper appears in BMC Genomics.

A paper in Science led by Zhang, Gilbert and Jarvis found the genomes of vocal learners are more rapidly evolving and have more chromosomal rearrangements compared to other bird species. This genomic comparison also found similar changes occurred independently in in the song-learning area of different birds' brains.

Jarvis said knowing more of this history of how speech evolved in birds makes vocal learning birds even more valuable model organisms for helping to answer the questions he and other researchers are addressing about human speech.

"Speech is difficult to study in human brains," he said. "Whales and elephants learn speech and songs, but they're too big to house in the lab. Now that we have a deeper understanding of how similar birdsong brain regions are to human speech regions at the genetic level, I think they'll be a better model than ever."

Jarvis' general exploration of the bird brain over his 16 years at Duke has also led to several unexpected discoveries unrelated to song.

In 2005, he and colleagues found a center of the brain in migratory birds that apparently enables sensing of magnetic fields through "night vision." That year he also led a revision of the understanding of bird brain organization and vertebrate brain evolution. Last year, he led a re-drawing of the geography of the bird brain based on analysis of 52 genes that are active in 23 areas of the brains of eight species of birds. This new map shows neuron groupings in the birds' brains to be organized in columns like the brains of humans and other mammals.

He also branched out a bit and learned about the brain structures that enable mice to "sing" in ultrasonic ranges beyond human hearing.

Jarvis said this first wave of findings from the Avian Phylogenomics Consortium is just the beginning of an exciting new era of genomic analysis. The international group is already sequencing more birds at the whole-genome level.

"This is an exciting moment," said Jarvis, who is also a member of the Duke Institute for Brain Sciences. "Lots of fundamental questions now can be resolved with more genomic data from a broader sampling. I got into this project because of my interest in birds as a model for vocal learning and speech production in humans, and it has opened up some amazing new vistas on brain evolution."

Source: Duke University

Hox cluster found in Crown of Thorns starfish a surprise

A Crown of Thorns starfish, Acanthaster planci, feeding on several species of Montipora corals. The image was taken off the coast of Okinawa near Sesoko Island. Credit: Yuna Zayasu

New research published in the journal genesis, by Kenneth Baughman, Dr. Eiichi Shoguchi, Professor Noriyuki Satoh of the Marine Genomics Unit at the Okinawa Institute of Science and Technology Graduate University, and collaborators from Australia, reports an intact Hox cluster in the Crown of Thorns starfish, Acanthaster planci. This surprising result contrasts with the relatively disorganized Hox cluster found in sea urchins, which are also echinoderms, classification of animals including starfish, sea lilies, and sea cucumbers. Stanford University Professor Christopher Lowe, who studies developmental biology in echinoderms, summarizes the paper: "The translocation of the Hox cluster in echinoderms has been a major red herring for understanding their evolution. It's really good to have some hard data showing that some echinoderms exhibit some oddities that are not representative of all echinoderms."

The Hox cluster is a classic example of an 'evo-devo' genetic toolkit. The term "evo-devo" refers to the study of genetic programs that control development, which can be compared between species, and thus, across evolutionary time. 

The Hox genes coordinate segmental identity along the head to tail (anterior-posterior) axis. The Hox cluster is evolutionarily conserved and has been 

repurposed repeatedly during the evolution of the animal body plan, or how animals are shaped. Past studies have shown that Hox clusters organize the development of brain and central nervous system regions in chordates, limb bud identity in vertebrates, and, classically, antennae or wing segment identity in fruit flies.

Generally, the Hox cluster shows "colinearity," in which gene order correlates with the location of expression, or the developmental stage of expression. "For example, anterior Hox genes are expressed in regions that are closer to the head of an embryo, and are expressed sooner during development, versus the posterior Hox genes," explained Baughman. "Thus, we were surprised to see chordate-like Hox cluster organization in starfish, which have a radial body plan." Echinoderms are classical model organisms for embryology, and more recently evo-devo. Baughman added, "Interacting with the speakers and students of theOIST Winter Course 'Evolution of Complex Systems' (OWECS) allowed me to appreciate the importance of finding an intact Hox cluster in starfish."

The Crown of Thorns starfish, a predatory starfish which feeds on corals, is famous for its dramatic changes in population density on the reefs near Australia, as well as Okinawa. Over the past 50 years, this has resulted in a measurable loss of coral reefs. A recent 27-year reef monitoring study of the Great Barrier Reef estimated that the starfish accounts for 42% of the loss in coral cover, 2nd only to typhoons. While population control was the initial motivation for Crown of Thorns genome research, the Hox cluster report is one of the first to show that the species can be useful for studies in evolutionary-developmental biology. "We were excited to see the entire Hox cluster on a single genomic scaffold, a result which confirmed the remarkably high quality of the genomic data," said Prof. Satoh.

As is often the case with science, the discovery raises more questions than it answers. If starfish have a collinear Hox cluster, what accounts for their dramatic departures in body plan organization? Do starfish express Hox genes during development in a manner similar to chordates, as indicated by the organization of their Hox cluster? Baughman looks forward to addressing these questions and many more as part of his doctoral research. "I look forward to pursuing developmental biology studies that may suggest methods for mitigating damage to the coral reef caused by the Crown of Thorns starfish."

More research is being conducted at OIST on the Crown of Thorns starfish in the Marine Biophysics Unit by Masako Nakamura in cooperation with local fishermen. In addition to the research collaboration highlighted by the Hox publication, recent efforts by the Okinawa Prefectural Government and Australian Institute of Marine Science are also working on projects to protect the existing coral reefs from the Crown of Thorns starfish.

Source: Okinawa Institute of Science and Technology - OIST

Digging for answers: Gender inequality in archeology?

Dana Bardolph.
Credit: Image courtesy of University of California - Santa Barbara

On an archaeology field trip in New Mexico as an undergraduate in 2006, Dana Bardolph noticed something that struck her as an odd gender imbalance: The professor leading the dig was a men, while the graduate assistant and all but two of the 14 undergrads were women.

"And it just got me thinking," Bardolph recalled. "Is this reflective of the profession as a whole, or is it an anomaly?"

The question stayed with her, and four years ago she decided to search for an answer. Her findings -- generated after digging through more than 4,500 peer-reviewed papers in 11 archaeology journals covering a 23-year period -- are published in a recent issue of the archaeology journal American Antiquity.

Bardolph, a Ph.D. student in UC Santa Barbara's Department of Anthropology, found that female authors are significantly and consistently underrepresented in American archaeology journals. Indeed, although the gender ratio among researchers is roughly equal, in the journals Bardolph surveyed, female authors account for slightly less than 29 percent of articles published.

"I found that there was no significant difference between any of the regions, any of the journals, so it was really a ubiquitous pattern across the study samples," Bardolph said.

The results, she and researchers familiar with the paper said, have deep implications not just for women in the field but for the direction and substance of archaeology itself. Bardolph argues, based on feminist theory, that the low rates of publication perpetuate a marginalization of female researchers in academia and demonstrate what she called "a pernicious historical bias with regards to the visibility, recognition, presentation and circulation of women's writing."

Bardolph's adviser, Amber VanDerwarker, associate professor of anthropology and director of UCSB's Integrative Subsistence Laboratory, said the paper has the potential to catalyze a movement toward greater gender equity in publishing and academia. "It is hugely significant because there have been articles here and there that talk about this issue of gender equity in the field," she said, "and none of the studies has done this much data collection and analysis; this is the first study of this scale looking at publication rates."

Among the articles surveyed in the major journals, Bardolph found 71.4 percent were lead-authored by men and 28.6 percent by women. The regional journals revealed nearly identical numbers. In addition, the data were consistent over time.

While the data demonstrated a clear gender bias, what they didn't show is the source, said Bardolph, whose specialty is paleoethnobotany, a study of the relationship between humans and plants in the past.

The journals don't track submissions by gender, so there's no way to tell if men are being favored explicitly, she said. Other studies, however, have found that men submit papers far more often than women do, with equal rejection rates among the genders.

Based on her research, Bardolph said she suspects the bias is likely a result of authorial behavior rather than editorial or reviewer bias. Women, she noted, are more likely to take on "nurturing" roles in academia and accept positions in smaller teaching colleges as opposed to large research universities with their more abundant resources.

"When you have grad students you can collaborate with, you publish more than you would if you were doing everything by yourself," VanDerwarker said. "I spent a few years at a teaching college just struggling to keep up with the publication record."

Another potential factor Bardolph noted is more subjective: braving the sometimes-brutal journal submission process. The anonymity of peer reviewers occasionally engenders harsh rejections. And archaeology, which has long been dominated by men, is no exception.

"I think it's highly plausible that the issue of rejection ¾ and whether you do decide to revise and resubmit or discard the manuscript -- has a lot to do with confidence issues," Bardolph said. "I wouldn't be surprised if that was in fact the case, that perhaps women were revising and resubmitting less often than men."

For Bardolph, getting academia to acknowledge gender bias is just one step on a long road to equality. "People aren't really realizing this sort of inequality is still pervasive," she said. "My real goal is to bring awareness to the issue and to inspire people to delve more deeply into their particular subdisciplines and continue this type of research so we can continue to explore why these inequities perpetuate and think about what we can do about them."

Source: University of California - Santa Barbara

Were Neanderthals a sub-species of modern humans? New research says no

Depiction of Neanderthal (stock image). Credit: © procy_ab / Fotolia

In an extensive, multi-institution study led by SUNY Downstate Medical Center, researchers have identified new evidence supporting the growing belief that Neanderthals were a distinct species separate from modern humans (Homo sapiens), and not a subspecies of modern humans.

The study looked at the entire nasal complex of Neanderthals and involved researchers with diverse academic backgrounds. Supported by funding from the National Science Foundation and the National Institutes of Health, the research also indicates that the Neanderthal nasal complex was not adaptively inferior to that of modern humans, and that the Neanderthals' extinction was likely due to competition from modern humans and not an inability of the Neanderthal nose to process a colder and drier climate.

Samuel Márquez, PhD, associate professor and co-discipline director of gross anatomy in SUNY Downstate's Department of Cell Biology, and his team of specialists published their findings on the Neanderthal nasal complex in the November issue of The Anatomical Record, which is part of a special issue on The Vertebrate Nose: Evolution, Structure, and Function (now online).

They argue that studies of the Neanderthal nose, which have spanned over a century and a half, have been approaching this anatomical enigma from the wrong perspective. Previous work has compared Neanderthal nasal dimensions to modern human populations such as the Inuit and modern Europeans, whose nasal complexes are adapted to cold and temperate climates.

However, the current study joins a growing body of evidence that the upper respiratory tracts of this extinct group functioned via a different set of rules as a result of a separate evolutionary history and overall cranial bauplan (bodyplan), resulting in a mosaic of features not found among any population of Homo sapiens. Thus Dr. Márquez and his team of paleoanthropologists, comparative anatomists, and an otolaryngologist have contributed to the understanding of two of the most controversial topics in paleoanthropology -- were Neanderthals a different species from modern humans and which aspects of their cranial morphology evolved as adaptations to cold stress.

"The strategy was to have a comprehensive examination of the nasal region of diverse modern human population groups and then compare the data with the fossil evidence. We used traditional morphometrics, geometric morphometric methodology based on 3D coordinate data, and CT imaging," Dr. Márquez explained.

Anthony S. Pagano, PhD, anatomy instructor at NYU Langone Medical Center, a co-author, traveled to many European museums carrying a microscribe digitizer, the instrument used to collect 3D coordinate data from the fossils studied in this work, as spatial information may be missed using traditional morphometric methods. "We interpreted our findings using the different strengths of the team members," Dr. Márquez said, "so that we can have a 'feel' for where these Neanderthals may lie along the modern human spectrum."

Co-author William Lawson, MD, DDS, vice-chair and the Eugen Grabscheid research professor of otolaryngology and director of the Paleorhinology Laboratory of the Icahn School of Medicine at Mount Sinai, notes that the external nasal aperture of the Neanderthals approximates some modern human populations but that their midfacial prognathism (protrusion of the midface) is startlingly different. That difference is one of a number of Neanderthal nasal traits suggesting an evolutionary development distinct from that of modern humans. Dr. Lawson's conclusion is predicated upon nearly four decades of clinical practice, in which he has seen over 7,000 patients representing a rich diversity of human nasal anatomy.

Distinguished Professor Jeffrey T. Laitman, PhD, also of the Icahn School of Medicine and director of the Center for Anatomy and Functional Morphology, and Eric Delson, PhD, director of the New York Consortium in Evolutionary Primatology or NYCEP, are also co-authors and are seasoned paleoanthropologists, each approaching their fifth decade of studying Neanderthals. Dr. Delson has published on various aspects of human evolution since the early 1970's.

Dr. Laitman states that this article is a significant contribution to the question of Neanderthal cold adaptation in the nasal region, especially in its identification of a different mosaic of features than those of cold-adapted modern humans. Dr. Laitman's body of work has shown that there are clear differences in the vocal tract proportions of these fossil humans when compared to modern humans. This current contribution has now identified potentially species-level differences in nasal structure and function.

Dr. Laitman said, "The strength of this new research lies in its taking the totality of the Neanderthal nasal complex into account, rather than looking at a single feature. By looking at the complete morphological pattern, we can conclude that Neanderthals are our close relatives, but they are not us."

Ian Tattersall, PhD, emeritus curator of the Division of Anthropology at the American Museum of Natural History, an expert on Neanderthal anatomy and functional morphology who did not participate in this study, stated, "Márquez and colleagues have carried out a most provocative and intriguing investigation of a very significant complex in the Neanderthal skull that has all too frequently been overlooked." Dr. Tattersall hopes that "with luck, this research will stimulate future research demonstrating once and for all that Homo neanderthalensis deserves a distinctive identity of its own."

Source: SUNY Downstate Medical Center

Human faces are so variable because we evolved to look unique

The amazing variety of human faces -- far greater than that of most other animals -- is the result of evolutionary pressure to make each of us unique and easily recognizable. Credit: UC Berkeley

The amazing variety of human faces -- far greater than that of most other animals -- is the result of evolutionary pressure to make each of us unique and easily recognizable, according to a new study by University of California, Berkeley, scientists.

Our highly visual social interactions are almost certainly the driver of this evolutionary trend, said behavioral ecologist Michael J. Sheehan, a postdoctoral fellow in UC Berkeley's Museum of Vertebrate Zoology. Many animals use smell or vocalization to identify individuals, making distinctive facial features unimportant, especially for animals that roam after dark, he said. But humans are different.

"Humans are phenomenally good at recognizing faces; there is a part of the brain specialized for that," Sheehan said. "Our study now shows that humans have been selected to be unique and easily recognizable. It is clearly beneficial for me to recognize others, but also beneficial for me to be recognizable. Otherwise, we would all look more similar."

"The idea that social interaction may have facilitated or led to selection for us to be individually recognizable implies that human social structure has driven the evolution of how we look," said coauthor Michael Nachman, a population geneticist, professor of integrative biology and director of the UC Berkeley Museum of Vertebrate Zoology.

The study will appear Sept. 16 in the online journal Nature Communications.

In the study, Sheehan said, "we asked, 'Are traits such as distance between the eyes or width of the nose variable just by chance, or has there been evolutionary selection to be more variable than they would be otherwise; more distinctive and more unique?'"

As predicted, the researchers found that facial traits are much more variable than other bodily traits, such as the length of the hand, and that facial traits are independent of other facial traits, unlike most body measures. People with longer arms, for example, typically have longer legs, while people with wider noses or widely spaced eyes don't have longer noses. Both findings suggest that facial variation has been enhanced through evolution.

Finally, they compared the genomes of people from around the world and found 

more genetic variation in the genomic regions that control facial characteristics than in other areas of the genome, a sign that variation is evolutionarily advantageous.

"All three predictions were met: facial traits are more variable and less correlated than other traits, and the genes that underlie them show higher levels of variation," Nachman said. "Lots of regions of the genome contribute to facial features, so you would expect the genetic variation to be subtle, and it is. But it is consistent and statistically significant."

Using Army data

Sheehan was able to assess human facial variability thanks to a U.S. Army database of body measurements compiled from male and female personnel in 1988. The Army Anthropometric Survey (ANSUR) data are used to design and size everything from uniforms and protective clothing to vehicles and workstations.

A statistical comparison of facial traits of European Americans and African Americans -- forehead-chin distance, ear height, nose width and distance between pupils, for example -- with other body traits -- forearm length, height at waist, etc. -- showed that facial traits are, on average, more varied than the others. The most variable traits are situated within the triangle of the eyes, mouth and nose.

Sheehan and Nachman also had access to data collected by the 1000 Genome project, which has sequenced more than 1,000 human genomes since 2008 and catalogued nearly 40 million genetic variations among humans worldwide. Looking at regions of the human genome that have been identified as determining the shape of the face, they found a much higher number of variants than for traits, such as height, not involving the face.

Prehistoric origins

"Genetic variation tends to be weeded out by natural selection in the case of traits that are essential to survival," Nachman said. "Here it is the opposite; selection is maintaining variation. All of this is consistent with the idea that there has been selection for variation to facilitate recognition of individuals."

They also compared the human genomes with recently sequenced genomes of Neanderthals and Denisovans and found similar genetic variation, which indicates that the facial variation in modern humans must have originated prior to the split between these different lineages.

"Clearly, we recognize people by many traits -- for example their height or their gait -- but our findings argue that the face is the predominant way we recognize people," Sheehan said.

Source: University of California - Berkeley

Gene silencing instructions acquired through 'molecular memory' tags on chromatin

Epigenetic inheritance is a two-step process, with a heritable molecular memory first forming to maintain a chromatin state required later for actual silencing of a genetic locus. Credit: Craig Pikaard and Todd Blevins

Scientists at Indiana University have unlocked one of the mysteries of modern genetics: how acquired traits can be passed between generations in a process called epigenetic inheritance. The new work finds that cells don't know to silence some genes based on information hardwired into their DNA sequences, but recognize heritable chemical marks that are added to the genes. These chemical tags serve as a form of molecular memory, allowing cells to recognize the genes and remember to silence them again in each new generation.

The discovery made by a 12-member all-Indiana University team of scientists led by IU biologist and biochemist Craig Pikaard provides important new insight into how plant cells know to silence a genetic locus -- that specific place on a chromosome where a gene is located -- in every successive generation.

Rather than rely on intrinsic, DNA sequence-based information, the cells instead must recall the need to silence specific loci by relying on chemical marks displayed on the complex of DNA and proteins called chromatin. Addition, or removal, of one-carbon (methyl) or two-carbon (acetyl) chemical tags are ways of modifying chromatin that can impart additional, epigenetic (literally, "above genetic") information to a locus beyond the genetic information encoded in the DNA.

The ability to perpetuate chromatin marks serves as a form of epigenetic memory that confers what Pikaard calls silent locus identity, a pre-established state that is needed for the cell to deliver to the loci the machinery that actually accomplishes silencing in a multi-step process known as RNA-directed DNA methylation (RdDM). RdDM involves short-interfering RNAs (siRNA), tiny RNA molecules that are 24 nucleotides long and that guide the addition of methyl groups to matching DNA strands, ultimately rendering the genes inactive.

"Importantly, this work shows that silent locus identity is required for, but separable from, actual gene silencing," Pikaard said. "We've found that epigenetic inheritance is a two-step process, with the heritable specification of silent locus identity occurring before actual silencing of the locus can occur."

Scientists are interested in epigenetic inheritance because it's a process by which heritable modifications occur in gene function without changes in the base sequence of an organism's DNA being required. Disease states such as cancer, which occur sporadically during an individual's lifetime, are increasingly recognized as having an epigenetic basis. Pikaard said the new work not only sheds important new light on the mechanisms responsible for epigenetic inheritance, a topic of broad interest in the fields of genetics and chromosome biology, but it also helps explain the basis for the recruitment of two plant-specific gene silencing enzymes -- the RNA polymerases Pol IV and Pol V -- first identified by Pikaard in 1999.

Specifically, the researchers tested and identified the relationship between histone deacetylase 6 (HDA6), an enzyme that removes acetyl groups from histones, and the CG DNA sequence maintenance methyltransferase, MET1, and discovered that their partnership in maintenance methylation can explain the perpetuation of epigenetic memory that accounts for silent locus identity.

"Collectively, our results show that silent locus identity is perpetuated from generation to generation through the actions of HDA6 and MET1," Pikaard said. "These activities are not sufficient to silence the loci but maintain a chromatin state that is required for Pol IV recruitment, siRNA biogenesis and RdDM, which is what ultimately silences the loci." When the team removed the RdDM pathway in Pol IV and Pol V mutant strains of the model plant Arabidopsis thaliana (rockcress), all gene silencing was lost, but silent locus identity remained. They then removed the HDA6 and MET1-dependent process that specifies silent locus identity and, importantly, the epigenetic memory required for silent locus identity was lost and unable to be regained.

Source:Indiana University

Reshaping the horse through millennia: Sequencing reveals genes selected by humans in domestication

A man catches domestic Mongolian horses with a lasso in Khomiin Tal, Mongolia. Credit: Copyright: Ludovic Orlando.

Whole genome sequencing of modern and ancient horses unveils the genes that have been selected by humans in the process of domestication through the latest 5,500 years, but also reveals the cost of this domestication. A new study led by the Centre for GeoGenetics at the University of Copenhagen, in collaboration with scientists from 11 international universities, reports that a significant part of the genetic variation in modern domesticated horses could be attributed to interbreeding with the descendants of a now extinct population of wild horses. This population was distinct from the only surviving wild horse population, that of the Przewalski's horses. The study has been published in the scientific journal Proceedings of the National Academy of Sciences (PNAS).

The domestication of the horse some 5,500 years ago ultimately revolutionized human civilization and societies. Horses facilitated transportation as well as the circulation of ideas, languages and religions. Horses also revolutionized warfare with the advent of chariotry and mounted cavalry and beyond the battlefield horses greatly stimulated agriculture. However, the domestication of the horse and the subsequent encroachment of human civilization also resulted in the near extinction of wild horses.

The only surviving wild horse population, the Przewalski's horses from Mongolia, descends from mere 13 individuals, preserved only through a massive conservation effort. As a consequence of this massive loss of genetic diversity, the effects of horse domestication through times have been difficult to unravel on a molecular level. Says Dr. Ludovic Orlando, Associate Professor at the Centre for GeoGenetics, who led this work

"The classical way to evaluate the evolutionary impact of domestication consists of comparing the genetic information present amongst wild animals and their living domesticates. This approach is ill suited to horses as the only surviving population of wild horses has experienced a massive demographic decline in the 20th century. We therefore decided to sequence the genome of ancient horses that lived prior to domestication to directly assess how pre-domesticated horses looked like genetically."

Recent advances in ancient DNA research have opened the door for reconstructing the genomes of ancient individuals. In 2013, Ludovic Orlando and his team succeeded in decoding the genome of a ~700,000 year-old horse, which represents the oldest genome sequenced to date. This time, the researchers focused on much more recent horse specimens, dating from ~16,000 and ~43,000 years ago. These were carefully selected to unambiguously predate the beginning of domestication, some 5,500 years ago. The bone fossils were excavated in the Taymyr Peninsula, Russia, where arctic conditions favor the preservation of DNA.

The human reshaping of the horse

While the horse contributed to reshaping human civilization, humans in turn reshaped the horse to fit their diverse needs and the diverse environments they lived in. This transformation left specific signatures in the genomes of modern horses, which the ancient genomes helped reveal. The scientists were able to detect a set of 125 candidate genes involved in a wide range of physical and behavioral traits, by comparing the genomes of the two ancient horses with those of the Przewalski's horse and five breeds of domesticated horses. Says Dr. Dan Chang, post-doctoral researcher at the UCSC Paleogenomics Lab and co-leading author of the study:

"Our selection scans identified genes that were already known to evolve under strong selection in horses. This provided a nice validation of our approach."

Dr. Beth Shapiro, head of the UCSC Paleogenomics Lab continues: "We provide the most extensive list of gene candidates that have been favored by humans following the domestication of horses. This list is fascinating as it includes a number of genes involved in the development of muscle and bones. This probably reveals the genes that helped utilizing horses for transportation."

And Dr. Ludovic Orlando from the Centre for GeoGenetics at the University of Copenhagen concludes: "Perhaps even more exciting as it represents the hallmark of animal domestication, we identify genes controlling animal behavior and the response to fear. These genes could have been the key for turning wild animals into more docile domesticated forms."

The 'cost of domestication' in horses

However, the reshaping of the horse genome during their domestication also had significant negative impacts. This was apparent in the increasing levels of inbreeding found amongst domesticates, but also through an enhanced accumulation of deleterious mutations in their genomes relative to the ancient wild horses. This finding supports an earlier theory coined 'the cost of domestication', which predicted increasing genetic loads in domesticates compared to their wild ancestors. Says Professor Laurent Excoffier, University of Bern and group leader at the Swiss Institute for Bioinformatics:

"Domestication is generally associated with repeated demographic crashes. Yet, mutations that negatively impact genes are not eliminated by selection and can even increase in frequency when populations are small. Domestication thus generally comes at a cost, as deleterious mutations can accumulate in the genome. This had already been shown for rice and dogs. Horses now provide another example of this phenomenon."

This is something that was only detectable in the horse in comparison to the ancient genomes, as Przewalski's horses were found to show a proportion of deleterious mutations similar to domesticated horses. Says Hákon Jónsson, PhD-student at the Centre for GeoGenetics, co-leading author of the study: "The recent near extinction of the Przewalski's horse population resulted in the persistence of deleterious mutations in the population, following the same mechanism that once led to the accumulation of deleterious mutations in the genomes of domesticated horses. What is striking is that a similar order of magnitude 
was reached even though this occurred in a much shorter time scale than domestication."

An ancient contribution to the present

In addition, comparison of the ancient and modern genomes revealed that the ancient individuals contributed a significant amount of genetic variation to the modern population of domesticated horses, but not to the Przewalski's horses. This suggests that restocking from a wild population descendant from the ancient horses occurred during the domestication processes that ultimately led to the modern domesticated horses. Mikkel Schubert, PhD- student at the Centre for GeoGenetics, co-leading author of the study concludes:

"This confirms previous findings that wild horses were used to restock the population of domesticated horses during the domestication process. However, as we sequenced whole genomes, we can estimate how much of the modern horse genome has been contributed through this process. Our estimate suggests that at least 13%, and potentially up to as much as 60%, of the modern horse genome has been acquired by restocking from the extinct wild population. That we identified the population that contributed to this process demonstrates that it is possible to identify the ancestral genetic sources that ultimately gave rise to our domesticated horses."

Source: Faculty of Science - University of Copenhagen

A clear, molecular view of how human color vision evolved

Mountain Gorilla - Bwindi Uganda. “Gorillas and chimpanzees have human color vision,” Yokoyama says. “Or perhaps we should say that humans have gorilla and chimpanzee vision.” Credit: © Alexander / Fotolia

Many genetic mutations in visual pigments, spread over millions of years, were required for humans to evolve from a primitive mammal with a dim, shadowy view of the world into a greater ape able to see all the colors in a rainbow.

Now, after more than two decades of painstaking research, scientists have finished a detailed and complete picture of the evolution of human color vision. PLOS Genetics published the final pieces of this picture: The process for how humans switched from ultraviolet (UV) vision to violet vision, or the ability to see blue light.

"We have now traced all of the evolutionary pathways, going back 90 million years, that led to human color vision," says lead author Shozo Yokoyama, a biologist at Emory University. 

"We've clarified these molecular pathways at the chemical level, the genetic level and the functional level."

Co-authors of the PLOS Genetics paper include Emory biologists Jinyi Xing, Yang Liu and Davide Faggionato; Syracuse University biologist William Starmer; and Ahmet Altun, a chemist and former post-doc at Emory who is now at Fatih University in Istanbul, Turkey.

Yokoyama and various collaborators over the years have teased out secrets of the adaptive evolution of vision in humans and other vertebrates by studying ancestral molecules. The lengthy process involves first estimating and synthesizing ancestral proteins and pigments of a species, then conducting experiments on them. The technique combines microbiology with theoretical computation, biophysics, quantum chemistry and genetic engineering.

Five classes of opsin genes encode visual pigments for dim-light and color vision. Bits and pieces of the opsin genes change and vision adapts as the environment of a species changes.

Around 90 million years ago, our primitive mammalian ancestors were nocturnal and had UV-sensitive and red-sensitive color, giving them a bi-chromatic view of the world. By around 30 million years ago, our ancestors had evolved four classes of opsin genes, giving them the ability to see the full-color spectrum of visible light, except for UV.

"Gorillas and chimpanzees have human color vision," Yokoyama says. "Or perhaps we should say that humans have gorilla and chimpanzee vision."

For the PLOS Genetics paper, the researchers focused on the seven genetic mutations involved in losing UV vision and achieving the current function of a blue-sensitive pigment. 

They traced this progression from 90-to-30 million years ago.

The researchers identified 5,040 possible pathways for the amino acid changes required to bring about the genetic changes. "We did experiments for every one of these 5,040 possibilities," Yokoyama says. "We found that of the seven genetic changes required, each of them individually has no effect. It is only when several of the changes combine in a particular order that the evolutionary pathway can be completed."

In other words, just as an animal's external environment drives natural selection, so do changes in the animal's molecular environment.

In previous research, Yokoyama showed how the scabbardfish, which today spends much of its life at depths of 25 to 100 meters, needed just one genetic mutation to switch from UV to blue-light vision. Human ancestors, however, needed seven changes and these changes were spread over millions of years. "The evolution for our ancestors' vision was very slow, compared to this fish, probably because their environment changed much more slowly," 
Yokoyama says.

About 80 percent of the 5,040 pathways the researchers traced stopped in the middle, because a protein became non-functional. Chemist Ahmet Altun solved the mystery of why the protein got knocked out. It needs water to function, and if one mutation occurs before the other, it blocks the two water channels extending through the vision pigment's membrane.

"The remaining 20 percent of the pathways remained possible pathways, but our ancestors used only one," Yokoyama says. "We identified that path."

In 1990, Yokoyama identified the three specific amino acid changes that led to human ancestors developing a green-sensitive pigment. In 2008, he led an effort to construct the most extensive evolutionary tree for dim-light vision, including animals from eels to humans. At key branches of the tree, Yokoyama's lab engineered ancestral gene functions, in order to connect changes in the living environment to the molecular changes.

The PLOS Genetics paper completes the project for the evolution of human color vision. "We have no more ambiguities, down to the level of the expression of amino acids, for the mechanisms involved in this evolutionary pathway," Yokoyama says.

Source: Emory Health Sciences

Hunter-gatherer past shows our fragile bones result from inactivity since invention of farming

Hunter-gatherer bone mass compared to agriculturalist bone mass. Credit: Timothy Ryan

New research across thousands of years of human evolution shows that our skeletons have become much lighter and more fragile since the invention of agriculture -- a result of our increasingly sedentary lifestyles as we shifted from foraging to farming.

The new study, published today in the journal PNAS, shows that, while human hunter-gatherers from around 7,000 years ago had bones comparable in strength to modern orangutans, farmers from the same area over 6,000 years later had significantly lighter and weaker bones that would have been more susceptible to breaking.

Bone mass was around 20% higher in the foragers -- the equivalent to what an average person would lose after three months of weightlessness in space.

After ruling out diet differences and changes in body size as possible causes, researchers have concluded that reductions in physical activity are the root cause of degradation in human bone strength across millennia. It is a trend that is reaching dangerous levels, they say, as people do less with their bodies today than ever before.

Researchers believe the findings support the idea that exercise rather than diet is the key to preventing heightened fracture risk and conditions such as osteoporosis in later life: more exercise in early life results in a higher peak of bone strength around the age of 30, meaning the inevitable weakening of bones with age is less detrimental.

There is, in fact, no anatomical reason why a person born today could not achieve the bone strength of an orangutan or early human forager, say researchers; but even the most physically active people alive are unlikely to be loading bones with enough frequent and intense stress to allow for the increased bone strength seen in the 'peak point' of traditional hunter-gatherers and non-human primate bones.

"Contemporary humans live in a cultural and technological milieu incompatible with our evolutionary adaptations. There's seven million years of hominid evolution geared towards action and physical activity for survival, but it's only in the last say 50 to 100 years that we've been so sedentary -- dangerously so," said co-author Dr Colin Shaw from the University of Cambridge's Phenotypic Adaptability, Variation and Evolution (PAVE) Research Group.

"Sitting in a car or in front of a desk is not what we have evolved to do."

The researchers x-rayed samples of human femur bones from the archaeological record, along with femora from other primate species, focusing on the inside of the femoral head: the ball at the top of the femur which fits into the pelvis to form the hip joint, one of the most load-bearing bone connections in the body.

Two types of tissue form bone: the cortical or 'hard' bone shell coating the outside, and the trabecular or 'spongy' bone: the honeycomb-like mesh encased within cortical shell that allows flexibility but is also vulnerable to fracture.

The researchers analysed the trabecular bone from the femoral head of four distinct archaeological human populations representing mobile hunter-gatherers and sedentary agriculturalists, all found in the same area of the US state of Illinois (and likely to be genetically similar as a consequence).

The trabecular structure is very similar in all populations, with one notable exception: within the mesh, hunter-gatherers have a much higher amount of actual bone relative to air.

"Trabecular bone has much greater plasticity than other bone, changing shape and direction depending on the loads imposed on it; it can change structure from being pin or rod-like to much thicker, almost plate-like. In the hunter-gatherer bones, everything was thickened," said Shaw.

This thickening is the result of constant loading on the bone from physical activity as hunter-gatherers roamed the landscape seeking sustenance. This fierce exertion would result in minor damage that caused the bone mesh to grow back ever stronger and thicker throughout life -- building to a 'peak point' of bone strength which counter-balanced the deterioration of bones with age.

Shaw believes there are valuable lessons to be learnt from the skeletons of our prehistoric predecessors. "You can absolutely morph even your bones so that they deal with stress and strain more effectively. Hip fractures, for example, don't have to happen simply because you get older if you build your bone strength up earlier in life, so that as you age it never drops below that level where fractures can easily occur."

Other theories for humans evolving a lighter, more fragile skeleton include changes in diet or selection for a more efficient, lighter skeleton, which was never reversed.

While the initial switch to farming did cause a dip in human health due to monoculture diets that lacked variety, the populations tested were unaffected by this window in history. "Of course we need a level of calcium to maintain bone heath, but beyond that level excess calcium isn't necessary," said Shaw.

The research also counters the theory that, at some point in human evolution, our bones just became lighter -- perhaps because there wasn't enough food to support a denser skeleton. "If that was true, human skeletons would be entirely distinct from other living primates. We've shown that hunter-gatherers fall right in line with primates of a similar body size. Modern human skeletons are not systemically fragile; we are not constrained by our anatomy."

"The fact is, we're human, we can be as strong as an orangutan -- we're just not, because we are not challenging our bones with enough loading, predisposing us to have weaker bones so that, as we age, situations arise where bones are breaking when, previously, they would not have" Shaw said.

While the 7,000-year-old foragers had vastly stronger bones than the 700-year-old farmers, Shaw says that neither competes with even earlier hominids from around 150,000 years ago. 

"Something is going on in the distant past to create bone strength that outguns anything in the last 10,000 years."

The next step for Shaw's research team will be to look at how different types of loading and mobility shape bodies and bones by cross-referencing archaeological records with testing on modern ultra-marathon runners, who cover punishing distances over a range of terrains -- from the Himalayas to the Namibian desert. He hopes this future work will provide insight into the kind of mobility that gave our ancient ancestors such powerful physical strength.

Source: University of Cambridge

Genetically identical ants help unlock the secrets of larval fate

Cerapachys biroi ants, native to Asia and introduced globally on tropical and subtropical islands, have no queens and have minimal genetic variation, making them ideal for research on social behavior. Credit: Image courtesy of Rockefeller University

A young animal's genes are not the only genes that determine its fate. The genetic identity of its caretakers matters too. Researchers suspect the interaction between the two can sway the fate of the young animal, but this complex dynamic is difficult to pin down in lab experiments.

However, social insect researchers have found a solution. Rockefeller University's Daniel Kronauer, head of the Laboratory of Insect Social Evolution, and his colleagues are developing a species of small raider ants as a model organism in order to ask questions about the relationships between genes, social behavior and evolution.

In a pair of recent papers, the researchers first explain the unique, and potentially useful, biology of this 2.5-millimeter-long ant. Then, in work with collaborators at the University of Paris 13, they put it to work exploring the interaction between the larvae and their nursemaids, and the influence on the young ants' reproductive success as adults.

Clonal raider ants, the species Cerapachys biroi, reproduce by cloning, and they live in colonies of as many as a few hundred nearly genetically identical workers. This makes these ants ideal for studies testing how a particular genetic makeup responds to different conditions, the researchers write in Current Biology. With the help of collaborators at BGI China, researchers in Kronauer's lab have sequenced the clonal raider ant's genome. This is an important step toward using the ant in the sorts of experiments conducted for years in traditional model organisms, such as mice and fruit flies.

"We have shown that colony mates are extremely closely related to one another, with all of the individuals in a colony being essentially genetically identical. This gives us precise control in experiments because we don't need to account for individual genetic variation," says Peter Oxley, a postdoc in the laboratory who led work establishing the clonal raider ant as a promising new model organism.

In the second study, one of the first to make use of the clonal raider ant, a team led by Serafino Teseo of the University of Paris 13 used the unique aspects of the ants' biology to test the indirect role genes play in shaping the future identity of larvae and whole colonies by looking at the interaction between larvae and adults. They did so by observing the success of two ant clones, A and B, in pure colonies or mixed together into chimeric colonies. They also swapped broods, so A adults raised B larvae and vice versa.

It turned out that A and B larvae developed differently depending on whether A or B nurses raised them. Left alone, pure A colonies produced the most young after six generations, making them more successful than B. However, in mixed colonies, B did better because its larvae more frequently turned into large adults that specialize in egg-laying rather than smaller, foraging-focused individuals.

The researchers suspect an indirect genetic effect -- specifically, a social influence. To begin to tease apart the dynamic, they had adults from one clone raise larvae from the other. Again, B did better when raised by A nurses than any of the other combinations. The results were published in Nature Communications.

The B colony's strategy of favoring reproduction over foraging when raised by A colony nurses smacks of social parasitism, in which one organism exploits another's social behavior for its own benefit. "This doesn't mean B is a parasite in the making, just that uncoupling the normal interaction between larvae and their nearly identical adult nursemaids reveals the presence of this mechanism," Kronauer says.

The study shows that, in social species, genetic makeup alone does not provide enough information to predict social behavior. Instead, interactions between social partners, such as larvae and their caregivers, are crucial determinants and can lead to surprising outcomes.

Source: Rockefeller University