Inbreeding and population/demographic shifts could have led to Neanderthal extinction

By: Thomas Schmitt Attorney on November 27, 2019 / comment : 0 Anthropology, Early Humans, Europe, Genetics, Near East, Ticker

Small populations, inbreeding, and random demographic fluctuations could have been enough to cause Neanderthal extinction, according to a study published in the open-access journal PLOS ONE by Krist Vaesen from Eindhoven University of Technology, the Netherlands, and colleagues.

Small populations, inbreeding, and random demographic fluctuations could have been enough to cause Neanderthal extinction, according to a new study [Credit: Petr Kratochvil (CC0)]

Paleoanthropologists agree that Neanderthals disappeared around 40,000 years ago--about the same time that anatomically modern humans began migrating into the Near East and Europe. However, the role modern humans played in Neanderthal extinction is disputed. In this study, the authors used population modelling to explore whether Neanderthal populations could have vanished without external factors such as competition from modern humans.

Using data from extant hunter-gatherer populations as parameters, the authors developed population models for simulated Neanderthal populations of various initial sizes (50, 100, 500, 1,000, or 5,000 individuals). They then simulated for their model populations the effects of inbreeding, Allee effects (where reduced population size negatively impacts individuals' fitness), and annual random demographic fluctuations in births, deaths, and the sex ratio, to see if these factors could bring about an extinction event over a 10,000-year period.

The population models show that inbreeding alone was unlikely to have led to extinction (this only occurred in the smallest model population). However, reproduction-related Allee effects where 25 percent or fewer Neanderthal females gave birth within a given year (as is common in extant hunter-gatherers) could have caused extinction in populations of up to 1,000 individuals. In conjunction with demographic fluctuations, Allee effects plus inbreeding could have caused extinction across all population sizes modelled within the 10,000 years allotted.

The population models are limited by their parameters, which are based on modern human hunter-gatherers and exclude the impact of the Allee effect on survival rates. It's also possible that modern humans could have impacted Neanderthal populations in ways which reinforced inbreeding and Allee effects, but are not reflected in the models.

However, by showing demographic issues alone could have led to Neanderthal extinction, the authors note these models may serve as a "null hypothesis" for future competing theories--including the impact of modern humans on Neanderthals.

The authors add: "Did Neanderthals disappear because of us? No, this study suggests. The species' demise might have been due merely to a stroke of bad, demographic luck."

Source: Public Library of Science [November 27, 2019]

Unique sled dogs helped the inuit thrive in the North American Arctic

By: Thomas Schmitt Attorney on November 27, 2019 / comment : 0 Archaeology, Arctic, Genetics, Indigenous Cultures, North America, Ticker

A unique group of dogs helped the Inuit conquer the tough terrain of the North American Arctic, major new analysis of the remains of hundreds of animals shows.

A team of Greenland sled dogs working in Greenland’s Disko Bay  [Credit: Tatiana Feuerborn]

The study shows that the Inuit brought specialised dogs with them when they migrated from Alaska and Siberia instead of adopting local dogs they would have come across during their migration. They instead maintained their own dogs, suggesting they were keen to enhance or keep the special features they had. By analysing the shape of elements from 391 dogs, the study shows that the Inuit had larger dogs with a proportionally narrower cranium to these earlier dogs. The Inuit dogs are the direct ancestors of modern Arctic sledge dogs, although their appearance has continued to change over time.

Experts had thought the Inuit used dogs to pull sledges, and this is the first study which shows they introduced a new dog population to the region to do this. These dogs then spread across the North American Arctic alongside Inuit migrants.

Dr Carly Ameen, an archaeologist from the University of Exeter who led the study, said: "Dogs have lived in North America for as long as humans, but we show here that the Inuit brought new dogs to the region which were genetically distinct and physically different from earlier dogs.

"Thousands of years ago there was not the huge number of dog breeds as we know them today. Through analysing the DNA and morphology of the remains of hundreds of dogs we've found that the dogs used by the Inuit had distinctive skull and teeth shapes, and would have likely looked different in life to dogs already in the Arctic."

The ancestors of these dogs arrived with the Inuit to the North American Arctic [Credit: Tatiana Feuerborn]

Experts also examined the DNA from 921 dogs and wolves who lived during the last 4,500 years. This analysis of the DNA, and the locations and time periods in which they were found, shows dogs from Inuit sites occupied from around 2,000 years ago were genetically different from the dogs already in the region.

Study co-lead author Tatiana Feuerborn, from the Globe Institute in Denmark and the Centre for Palaeogenetics in Sweden, said: "Archaeological evidence has shown us that before the Inuit arrived in North America dog sledging was a rarity. Our analysis of the DNA suggests dogs brought by the Inuit were distinct from the earlier dogs of the North American Arctic to fill specialist role in helping communities thrive in this hostile environment by aiding with transportation and hunting. The genetic legacy of these Inuit dogs can still be seen today in Arctic sledge dogs."

The Inuit were specialised sea mammal hunters, and were more mobile than other groups living in the Arctic, migrating huge distances across the region over 1,000 years ago, with the help of dog sledges and water craft. Today, sledge dogs whose origins can be traced back to the Inuit period continue to be an important part of Arctic communities.

The article is published in the journal Proceedings of the Royal Society B.

Source: University of Exeter [November 27, 2019]

Researchers show how feathers propel birds through air and history

By: Thomas Schmitt Attorney on November 27, 2019 / comment : 0 Biology, Early Birds, Evolution, Fossils, Genetics

New research from an international team led by USC scientists set out to learn how feathers developed and helped birds spread across the world. Flight feathers, in particular, are masterpieces of propulsion and adaptation, helping penguins swim, eagles soar and hummingbirds hover.

A Taiwan blue magpie in flight [Credit: Shao Huan Lang]

Despite such diversity, the feather shares a common core design: a one-style-fits-all model with option trims for specialized performance. This simplicity and flexibility found in nature holds promise for engineers looking for better ways to build drones, wind turbines, medical implants and other advanced materials.

Those findings, published in Cell, offer an in-depth look at the form and function of a feather based on a comparative analysis of their physical structure, cellular composition and evolution. The study compares feathers of 21 bird species from around the world.

"We've always wondered how birds can fly in so many different ways, and we found the difference in flight styles is largely due to the characteristics of their flight feathers," said Cheng-Ming Chuong, the study's lead author and a developmental biologist in the Department of Pathology at the Keck School of Medicine of USC. "We want to learn how flight feathers are made so we can better understand nature and learn how biological architecture principles can benefit modern technology."

To gain a comprehensive understanding of the flight feather, Chuong formed a multi-disciplinary international team with Wen Tau Juan, a biophysicist at the Integrative Stem Cell Center, China Medical University in Taiwan. The work involved experts in stem cells, molecular biology, anatomy, physics, bio-imaging, engineering, materials science, bioinformatics and animal science. The bird species studied include ostrich, sparrow, eagle, chickens, ducks, swallow, owl, penguin, peacock, heron and hummingbird, among others.

They compared feathers using fossils, stem cells and flight performance characteristics. They focused on the feather shaft, or rachis, that supports the feather much like a mast holds a sail, bearing the stress between wind and wing. They also focused on the vane, the lateral branches astride the shaft that give the feather its shape to flap the air. And they examined how evolution shaped the barbs, ridges and hooks that help a feather hold its form and lock with adjacent feathers like Velcro to form a wing. The goal was to understand how a simple filament appendage on dinosaurs transformed into a three-level branched structure with different functions.

For birds such as ducks, eagles and sparrows that fly in different modes, the scientists noted significant differences in the feather shaft compared to ground-hugging birds. On the rigid exterior, the shaft cortex was thinner and lightweight, while the interior was filled with porous cells resembling bubble wrap, aligned into bands of various orientations and reinforced with ridges that operate like tiny lateral beams. Together, it forms a light, hollow and buoyant structure to enable flight. Cross-sections of feather shafts of different birds show highly specialized shapes and orientations of the inner core and outer cortex.

This picture shows a the asymmetric vane and tapering main shaft of a single flight feather from a goshawk [Credit: Hao Howard Wu & Wen Tau Juan]

"The flight feather is made of two highly adaptable architectural modules, light and strong materials that can develop into highly adaptable configurations," Chuong said.

The researchers discovered two different molecular mechanisms guiding feather growth. Cortex thickness was governed by bone morphogenetic proteins, which are molecular signals for tissue growth. The porous feather interior, or medulla, relied upon a different mechanism known as transforming growth factor beta (TGF-b). Both components originate as stem cells in the bird's skin.

By contrast, feathers in flightless birds were simpler, consisting of a dense cortex exterior that is more rigid and sturdy with fewer internal struts and cells found in flying birds. The features were especially pronounced for penguins, which use wings as paddles under the water.

As part of the study, the researchers looked at nearly 100 million-year-old feathers, found embedded in amber in Myanmar. These fossils show early feathers lacked one key feature that modern birds have. Specifically, the researchers report how fossil feathers had barb branches and barbules, which form a feather vane by overlapping, but not hooklets. The hooklets, which act like clasps to turn fluffy feathers into a tight flat plane for high-performance flight, evolved later. The scientists also identified WNT2B, another growth factor, as the agent that controls hooklet formation. These also originated from epidermal stem cells.

Taken together, the findings show how feathered dinosaurs and early birds could form a primitive vane by overlapping barbule plates, although that wasn't aerodynamically fit to carry much load. As more complex composite features occurred in the wing, it got heavier, so feather shafts became stronger yet more lightweight, which led to stiffer feathers and sturdy wings that powered flight to carry birds around the world.

"Our findings suggest the evolutionary trends of feather shaft and vane are balanced for the best flight performance of an individual bird and become part of the selective basis of speciation," the study says. "The principles of functional architectures we studied here may also stimulate bio-inspired designs and fabrication of future composite materials for architectures of different scales, including wind turbines, artificial tissues, flying drones."

Source: University of Southern California [November 27, 2019]

Did human hunting activities alone drive great auks' extinction?

By: Thomas Schmitt Attorney on November 26, 2019 / comment : 0 Early Birds, Fossils, Genetics, Iceland, North America, Palaeontology, Scotland

New insight on the extinction history of a flightless seabird that vanished from the shores of the North Atlantic during the 19th century has been published in eLife.

A mounted great auk skin, The Brussels Auk (RBINS 5355), from the collections at the Royal Belgian Institute of Natural Sciences (RBINS) [Credit: Thierry Hubin, RBINS]

The findings suggest that intense hunting by humans could have caused the rapid extinction of the great auk, showing how even species that exist in large and widespread populations can be vulnerable to exploitation.

Great auks were large, flightless diving birds thought to have existed in the millions. They were distributed around the North Atlantic, with breeding colonies along the east coast of North America and especially on the islands off Newfoundland. They could also be found on islands off the coasts of Iceland and Scotland, as well as throughout Scandinavia.

But these birds had a long history of being hunted by humans. They were poached for their meat and eggs during prehistoric times, and this activity was further intensified in 1500 AD by European seamen visiting the fishing grounds of Newfoundland. Their feathers later became highly sought after in the 1700s, contributing further to their demise.

"Despite the well-documented history of exploitation since the 16th century, it is unclear whether hunting alone could have been responsible for the species' extinction, or whether the birds were already in decline due to natural environmental changes," says lead author Jessica Thomas, who completed the work as part of her PhD studies at Bangor University, UK, and the University of Copenhagen, Denmark, and is now a postdoctoral researcher at Swansea University, Wales, UK.

Great auk humeri from Funk Island. These samples are part of the great auk collection at the American Museum of Natural History [Credit: J. Thomas]

To investigate this further, Thomas and her collaborators carried out combined analyses of ancient genetic data, GPS-based ocean current data, and population viability - a process that looks at the probability of a population going extinct within a given number of years. They sequenced complete mitochondrial genomes of 41 individuals from across the species' geographic range and used their analyses to reconstruct the birds' population structure and dynamics throughout the Holocene period, the last 11,700 years of Earth's history.

"Taken together, our data don't suggest that great auks were at risk of extinction prior to intensive human hunting behaviour in the early 16th century," explains co-senior author Thomas Gilbert, Professor of Evolutionary Genomics at the University of Copenhagen. "But critically, this doesn't mean that we've provided solid evidence that humans alone were the cause of great auk extinction. What we have demonstrated is that human hunting pressure was likely to have caused extinction even if the birds weren't already under threat from environmental changes."

Gilbert adds that their conclusions are limited by a couple of factors. The mitochondrial genome represents only a single genetic marker and, due to limited sample preservation and availability, the study sample size of 41 is relatively small for population genetic analyses.

"Despite these limitations, the findings help reveal how industrial-scale commercial exploitation of natural resources have the potential to drive an abundant, wide-ranging and genetically diverse species to extinction within a short period of time," says collaborator Gary Carvalho, Professor in Zoology (Molecular Ecology) at Bangor University. This echoes the conclusions of a previous study* on the passenger pigeon, a bird that existed in significant numbers before going extinct in the early 20th century.

"Our work also emphasises the need to thoroughly monitor commercially harvested species, particularly in poorly researched environments such as our oceans," concludes co-senior author Michael Knapp, Senior Lecturer in Biological Anthropology and Rutherford Discovery Fellow at the University of Otago, New Zealand. "This will help lay the platform for sustainable ecosystems and ensure more effective conservation efforts."

Source: eLife [November 26, 2019]

Aquatic microorganisms offer important window on the history of life

By: Thomas Schmitt Attorney on November 25, 2019 / comment : 0 Biology, Evolution, Fossils, Genetics

The air, earth and water of our planet are pulsating with living things. Yet, a vast and diverse web of life exists, about which almost nothing is known. This is the world of flagellates, tiny organisms that persist in staggering numbers in many diverse ecosystems around the world.

The graphic shows a tree of life for complex forms known as Eukaryotes, that arose mysteriously around 1.2-2 billions years ago from a progenitor known as LECA (for Last Eukaryote Common Ancestor.) Jeremy Wideman and his colleagues used a new method to sequence mitochondrial DNA for around 100 species of flagellates--tiny aquatic organisms that populate many branches of the tree. These are seen on the graphic as red dots marking the particular lineages these flagellates belong to [Credit: Shireen Dooling]

According to Jeremy Wideman, a researcher at the Biodesign Center for Mechanisms in Evolution at Arizona State University, we have a great deal to learn from these delicate and wildly varied creatures. Among other surprises, flagellates could provide valuable clues about a shadowy event that may have occurred 1.5-2 billion years ago, (no one is really sure of the timing), with the arrival of a new type of cell.

Known as LECA, it was a sort of primal egg out of which the astonishing profusion of complex life--from flagellate organisms, fungi and plants, to insects, zebra, and humans, exploded and spread over the earth.

In new research published in the journal Nature Microbiology, Wideman and his colleagues, including Prof. Thomas Richards at the University of Exeter describe a new method for investigating the genomes of eukaryotic flagellate organisms, which have been notoriously tricky to pinpoint and sequence.

Specifically, they explored samples of mitochondrial DNA, sequencing around 100 such genomes for previously undocumented flagellates. The new technique could help scientists like Wideman begin to fill in the largely blank region of the eukaryotic puzzle, where flagellate life flourishes.

Cellular worlds

Wideman, originally a traditional cell biologist, became frustrated with the many unaddressed questions in the field, recently joining the emerging discipline of evolutionary cell biology. This rapidly advancing research area uses cells as fundamental units for the study of evolutionary processes and imports concepts from evolutionary biology to better understand how cells work. "I'm literally a cell biologist that wants to know more about things we know nothing about," he says.

Evolutionary cell biology is a profoundly transdisciplinary endeavor, fusing evolutionary theory, genomics and cell biology with quantitative branches of biochemistry, biophysics, and population genetics.

Flagellates include many parasites implicated in human disease, from the intestinal bug Giardia to more damaging trypanosomes, and leishmania. Flagellates also perform more benevolent tasks. As the major consumers of bacteria and other protists in aquatic ecosystems, they help ensure the recycling of limiting nutrients.

Single-celled eukaryotic organisms, which include flagellates, constitute the overwhelming majority of eukaryotic diversity, vastly outpacing the more familiar multicellular plants, animals, and fungi. Despite their importance and ubiquity across the globe, flagellates are, as Wideman stresses, an almost entirely unknown inhabitant of the living world and one of the most enigmatic. When viewed under a microscope, their often science fiction-like appearance is markedly distinct from the kinds of eukaryotic cells commonly described in biology textbooks. Their emergence from comparatively rudimentary prokaryotes marks the most momentous transition in the history of life on earth.

"Novel lineages of heterotrophic flagellates are being discovered at an alarming, rate," Wideman says. "In the last two years 2 kingdom level lineages have been discovered (see here and here), meaning lineages that have been evolving independently of animals and fungi for over a billion years." Nevertheless, researchers have barely scratched the surface of this astonishing diversity and new methods must be brought to bear to speed up the quest. (Heterotrophs are organisms that cannot synthesize their own food, relying instead on other organisms for nutrition.)

Microbial safari

Any drop of pond, lake or ocean water is likely to contain many flagellates, but separating them from a multitude of non-flagellates and accurately reading their genomes by conventional means has been slow and painstaking work. Only a minute fraction of extant flagellates have known genomic sequences and it's even possible that the overwhelming majority have never actually been seen. According to Wideman, flagellate life forms represent the 'dark matter' of the eukaryotic universe.

"Heterotrophic flagellates are the target," Wideman says. "They're not a lineage. They're many, many lineages that are from all over the tree of life. LECA, the Last Eukaryotic Common Ancestor, was a heterotrophic flagellate, which means, that every major lineage (of eukaryotes) evolved from some sort of heterotrophic flagellate."

To access the elusive flagellate mitochondrial DNA, the researchers exploited a feature common to all flagellates and from which they take their name--the existence of flagella, which, unlike in animal sperm are on the front of cells and are often used to pull them forward like a microscopic breast stroke but are also involved in sensation, feeding, and perhaps other, as-yet unknown functions.

Flagella are rich in a particular protein known as tubulin. The new method for identifying flagellates and distinguishing them from their aquatic neighbors--primarily algae and bacteria--capitalizes on this fact by applying a selective stain to flagella-bearing organisms, activated by their high tubulin content. (Algal cells are naturally marked by their chloroplasts, which the flagellates of interest in the new study lack.)

Samples of sea water collected in 2014 off the coast of California provided a test case. Using the technique, the researchers gathered a windfall of mitochondrial sequence data, significantly expanding the catalog of flagellates identified by molecular means. Indeed, they doubled the existing mitochondrial DNA library for flagellate organisms. "We got many, many different kinds of organisms. So it was a very rich sample and very few were identical," Wideman says.

In search of LECA

Apart from the mystery of life's origin, the puzzle of where eukaryotes came from and how the LECA event transpired is the most important and vexing unanswered question in all of biology. (It has been dubbed the black hole at the heart of the living world.)

Correctly establishing the sequence of events underlying the crucial innovations within eukaryotes, from whence all complex life sprang, will take much more research in unexplored regions of the existing eukaryotic domain, particularly, the flagellates. Wideman believes the rapid advance of techniques for identifying and sequencing these organisms, such as the one outlined in the new study, offer hope such questions may one day find answers.

Author: Richard Harth | Source: Arizona State University [November 25, 2019]

Unravelling gene expression

By: Thomas Schmitt Attorney on November 21, 2019 / comment : 0 Biology, Evolution, Genetics

The DNA of a single cell is 2-3 meters long end-to-end. To fit and function, DNA is packaged around specialized proteins. These DNA-protein complexes are called nucleosomes, and they are a small part of a larger structure called chromatin. Nucleosomes can be thought of as the cell's DNA storage and protection unit.

The pioneer transcription factor Rap1 pries open compact chromatin structure to activate genes [Credit: Beat Fierz, EPFL]

When a particular gene needs to be expressed, the cell requires access to the protected DNA within chromatin. This means that the chromatin structure must be opened and the nucleosomes must be removed to expose the underlying target gene.

This takes place in the orchestrated process of "chromatin remodeling", which regulates gene expression and involves a multitude of actors. Unravelling this pivotal step not only furthers our fundamental understanding, but may also help in the development of genetic engineering tools.

Now the lab of Beat Fierz at EPFL, has been able to uncover the first steps in the chromatin-opening process at the level of a single molecule, using a combination of chemical biology and biophysical methods. Published in Molecular Cell, the work looks at the role of a group of proteins called "pioneer transcription factors". These proteins bind to specific DNA regions within chromatin that are themselves shielded from other proteins. Little is known about how these factors overcome the barriers of the chromatin maze.

The graphical abstract of the paper, showing the way Rap1 accesses chromatin [Credit: M. Mivelaz et al. 2019]

Fierz's lab looked at yeast, which is a model organism for human genetics. The method involved replicating the architecture of yeast genes, combined with single-molecule fluorescence. The researchers studied a yeast pioneer transcription factor called Rap1, and found that it choreographs chromatin remodeling, allowing access to other proteins required for gene expression that were previously obstructed.

To do this, Rap1 first binds chromatin and then influences the action of a large molecular machine called "Remodeling the Structure of Chromatin" (RSC), displacing nucleosomes and paving the way to the now-exposed DNA for other proteins involved in controlling gene expression.

By revealing the physico-chemical mechanism of how Rap1 gains access to chromatin and opens it up, the EPFL study proposes a biological model for other pioneer transcription factors, but also provides the tools for investigating them at the level of a single molecule.

Source: Ecole Polytechnique Federale de Lausanne [November 21, 2019]

Self-restrained genes enable evolutionary novelty

By: Thomas Schmitt Attorney on November 21, 2019 / comment : 0 Biology, Evolution, Genetics

Changes in the genes that control development can potentially make large contributions to evolution by generating new morphologies in plants and animals. However, because developmental genes frequently influence many different processes, changes to their expression carry a risk of "collateral damage". Scientists at the Max Planck Institute for Plant Breeding Research in Cologne, and collaborators, have now shown how gene self-repression can reduce the potential side effects of novel gene expression so that new forms can evolve. This self-regulation occurs via a distinctive molecular mechanism employing small regions of genomic DNA called low-affinity transcription factor binding sites.

A confocal micrograph of a young leaf of Cardamine hirsuta (hairy bittercress) with emerging leaflets, showing distribution of the RCO protein. Cell outlines are shown in gray. RCO shown here in red colour is active at the base of initiating leaflets where it reduces  growth, leading to the formation of leaflets that are separated from each other  [Credit: Neha Bhatia and Peter Huijser]

Suppose a bird develops a modified wing shape, which makes flying easier and could be beneficial to its survival. If this gene change also altered the bird's color, making it less attractive to mates, then the advantageous wing-shape modification would be unlikely to persist. So, how then does nature balance the potential for novelty, with the risk of side effects that may prevent novelty from arising? Using the evolution of leaf shape as an example, an international team led by Director Miltos Tsiantis has provided fresh insight into this question.

This new study was done in the hairy bittercress, a small weed that the Tsiantis group has developed into a model system for understanding evolution of plant form. It builds on previous work from the group in which a gene called RCO was found to have driven leaf shape diversification in mustard plants by acquiring a novel expression pattern.

RCO encodes a transcription factor, a type of protein that can turn other genes on or off, and RCO's new expression pattern resulted in the emergence of the more complex leaf shapes found in bittercress. The researchers have now shown that this change in gene expression was accompanied by RCO acquiring the ability to repress its own activity. Mike Levine, Director of the Lewis-Sigler Institute for Integrative Genomics at Princeton University who was not involved in the study, finds this particular insight "very compelling". As the self-repression of RCO "limits the scope of its activity", Levine explains, it "thereby blocks potentially deleterious influences on cell development and function".

Stimulating cytokinin

As a next step, the scientists identified the genes targeted by RCO, and found that many of them are responsible for coordinating local levels of cytokinin - a widely acting plant hormone known to affect cell growth. Importantly, when the self-regulation of RCO is modified, RCO stimulates cytokinin excessively and leaf shape is altered in ways that can negatively affect plant fitness. This finding confirms the idea that self-repression of RCO could be essential for the persistence of RCO-induced novel leaf morphologies.

What's particularly interesting is that this self-repression of RCO occurs in a very distinctive way. The scientists discovered that it is based on many weak interactions between the RCO protein and RCO regulatory DNA at low-affinity binding sites. "This finding is exciting", explains Tsiantis, "because low-affinity binding sites can evolve relatively quickly, thus offering an easy way for evolution to keep changes in gene expression in check, by lowering a regulator's expression".

Soft repression

Indeed, this latest work from Tsiantis's team directly demonstrates that low-affinity transcription factor binding sites can play a major role in the generation of morphological novelty. By providing a tool to "softly" repress RCO expression, these sites dampen the effects of RCO expression changes and allow cytokinin levels to be fine-tuned. This in turn promotes the appearance of more complex leaf shapes, e.g., by precisely regulating the outgrowth of lobes or leaflets along the margins of developing leaves.

These results will stimulate further efforts to understand the influence of low-affinity transcription factor binding sites on development, diversity and disease. For example, there is increasing awareness that changes in the regulation of developmental genes are a major contributor to human disease, and that other regulatory changes can reduce disease severity or protect individuals who carry disease variants. While the specific DNA sequences underlying these effects are often unknown, this latest work highlights low-affinity transcription factor binding sites as excellent candidate regions for identifying causal sequences of disease susceptibility, and for understanding variation in trait diversity more broadly in complex eukaryotes.

The study is published in Current Biology.

Source: Max Planck Society [November 21, 2019]

Researchers sequence genome of the 'devil worm'

By: Thomas Schmitt Attorney on November 21, 2019 / comment : 0 Biology, Evolution, Genetics

When scientists discovered a worm deep in an aquifer nearly one mile underground, they hailed it as the discovery of the deepest-living animal ever found. Now American University researchers, reporting in Nature Communications, have sequenced the genome of the unique animal, referred to as the 'Devil Worm' for its ability to survive in harsh, subsurface conditions. The Devil Worm's genome provides clues to how an organism adapts to lethal environmental conditions. Future research into how it evolved could help humans learn lessons for how to adapt to a warming climate.

H. Mephisto (the Devil Worm) (microscopic image, magnified 200x) [Credit: Prof. John Bracht, American University]

In 2008, Gaetan Borgonie from the University of Ghent and Princeton University geoscientist Tullis Onstott discovered the microscopic Devil Worm while investigating subterrestrial bacterial communities in active gold mines in South Africa. Borgonie and his team were stunned to discover the worm, a complex, multi-cellular animal thriving in an environment thought only livable for microbes, with high temperatures, little oxygen and high amounts of methane.

Researchers named the worm Halicephalobus mephisto, in honor of Mephistopheles, a subterranean demon from the medieval German legend Faust.

The Devil Worm is the first subterrestrial animal to have its genome sequenced. The genome offers evidence of how life can exist below Earth's surface and opens up a new way of understanding how life can survive beyond Earth, said John Bracht, assistant professor of biology at American University who led the genome sequencing project.

The sequencing revealed that the genome encodes an unusually large number of heat-shock proteins known as Hsp70, which is notable because many nematode species whose genomes are sequenced do not reveal such a large number. Hsp70 is a well-studied gene that exists in all life forms and restores cellular health due to heat damage.

Many of the Hsp70 genes in the Devil Worm's genome were copies of themselves. The genome also has extra copies of AIG1 genes, known cellular survival genes in plants and animals. More research will be needed, but Bracht believes the presence of copies of the gene signifies the worm's evolutionary adaptation.

"The Devil Worm can't run away; it's underground," Bracht explained. "It has no choice but to adapt or die. We propose that when an animal cannot escape intense heat, it starts making additional copies of these two genes to survive."

By scanning other genomes, Bracht identified other cases where the same two gene families, Hsp70 and AIG1, are expanded. The animals he identified are bivalves, a group of mollusks including clams, oysters and mussels. They are heat-adapted like the Devil Worm. This suggests that the pattern identified in the Devil Worm may extend more generally to organisms unable to escape environmental heat. This work was also recently published in the Journal of Molecular Evolution with an AU Biology undergraduate first author, Megan Guerin.

Bracht got the chance to sequence the unique worm's genome as a post-doctoral fellow at Princeton University. He carried the project over to American University when he joined the biology faculty in 2014. Two biology master's students working in his lab, Deborah Weinstein and Sarah Allen, contributed research and writing of the Nature Communications paper and are first and second authors, respectively, on the manuscript. Kathryn Walters-Conte, Ph.D., director of AU's Master's in Biotechnology program, also contributed to the paper.

Nearly a decade ago, the Devil Worm was unknown and living below the Earth's surface. Now it's a subject of study in science laboratories, including Bracht's. When Bracht brought Devil Worms from a laboratory in South Africa that cultures them to his laboratory at AU, he recalls saying to his students that aliens landed at AU. The metaphor isn't a stretch. NASA supports research of the Devil Worm for what it can teach scientists about the search for life beyond Earth.

"Part of this work entails looking for 'biosignatures' of life--stable chemical clues left behind by living things. We focus on a ubiquitous biosignature of organic life--genomic DNA--obtained from an animal that has adapted to an environment once considered uninhabitable to complex life: the deep terrestrial subsurface," Bracht said. "It is work that might prompt us to broaden the search for extraterrestrial life to 'uninhabitable' exoplanets' deep subterrestrial regions."

Nematodes are well suited to studies of evolutionary adaptation, Bracht said. They have adapted to a diverse set of environments and are among the most abundant animals on earth. Future work involving the Devil Worm in Bracht's lab will pinpoint Hsp70's function, such as inactivating the gene to test its response to heat stress. Other work could involve gene-transfer studies in C.elegans, a type of heat-intolerant microscopic roundworm, to see if it becomes heat-resilient.

Source: American University [November 21, 2019]

Breakthrough method of identifying sex and species of million-year-old fossils

By: Thomas Schmitt Attorney on November 19, 2019 / comment : 0 Anthropology, Early Humans, Early Mammals, Fossils, Genetics

Reid Ferring, a professor in the University of North Texas Department of Geography and the Environment, is part of an international team of scientists who have developed a breakthrough method of identifying the sex and species of animal in fossils more than a million years old.

UNT Professor Reid Ferring holds that cast of a skull found at the Dmanisi site [Credit: University of North Texas]

"This is very exciting because our current method for determining sex and species, examination of extracted DNA, was limited to approximately 200,000 years. Through palaeoproteomics, the study of ancient proteins, we can now look back over a million years," said Ferring.

Ferring believes that palaeoproteomics will prove to be the key for establishing the evolutionary line between the earliest hominids and modern man. The reason, according to Ferring, is that proteins like collagen, which is found in tendons, ligaments, skin, bone and teeth, last much longer than DNA in fossilized material.

"We have thousands of hominid fossils in collections and museums around the world from all time periods," he said. "We have five complete skulls from the Dmanisi site in the country of Georgia that I know are almost two million years old. There are so many samples that can now be labeled and differentiated between species of the same line. We are on the edge of learning much more about our ancestors and ourselves than at any point in history."

Ferring added that the breakthrough came when the team was able to sample collagen from 1.7 million-year-old fossilized animal teeth found at the Dmanisi site. Using that protein, the team determined that the animal was a Stephanorhinus, an extinct form of rhinoceros. The team could then fit the Stephanorhinus into the modern rhinoceros' evolutionary line and differentiate it from ones that came before and after.

Palaeoproteomics is a very new field and, as such, scientists are very careful to document and confirm each part of the process. Ferring was one of more than 40 prominent researchers of different specialties, nationalities and backgrounds who participated in the groundbreaking project.

"I was brought in not because I am an expert on ancient proteins, but because I am a geologist and archaeologist who has been working at the Dmanisi site every summer for the last 27 years," Ferring said. "The whole surface of the site is covered with ruins of Bronze Age and medieval structures including a fortress and a seventh century Orthodox Church. All of the materials we excavated were found under 20 feet of volcanic ash containing thousands of animal bones and artifacts."

As the project geologist, Ferring documented and profiled the sediments in the area of the original find to provide context for all the materials that were dated and the fossils recovered. Based on the depth of the find and the type of minerals surrounding it, he was able to place the age of the Stephanorhinus teeth at more than 1.7 million years old.

In September, the journal Nature printed a paper titled "Early Pleistocene Enamel Proteome from Dmanisi Resolves Stephanorhinus Phylogeny" that describes the methods used and data collected by the international Stephanorhinus team. The paper was co-authored by Ferring.

Source: University of North Texas [November 19, 2019]

First detection of sugars in meteorites gives clues to origin of life

By: Thomas Schmitt Attorney on November 19, 2019 / comment : 0 Astrobiology, Astronomy, Genetics, Origin of Life, Universe

An international team has found sugars essential to life in meteorites. The new discovery adds to the growing list of biologically important compounds that have been found in meteorites, supporting the hypothesis that chemical reactions in asteroids—the parent bodies of many meteorites—can make some of life's ingredients. If correct, meteorite bombardment on ancient Earth may have assisted the origin of life with a supply of life's building blocks.

This is a mosaic image of asteroid Bennu, from NASA’s OSIRIS-REx spacecraft. The discovery of sugars in meteorites supports the hypothesis that chemical reactions in asteroids – the parent bodies of many meteorites – can make some of life’s ingredients [Credit: NASA/Goddard/University of Arizona]

The team discovered ribose and other bio-essential sugars including arabinose and xylose in two different meteorites that are rich in carbon, NWA 801 (type CR2) and Murchison (type CM2). Ribose is a crucial component of RNA (ribonucleic acid). In much of modern life, RNA serves as a messenger molecule, copying genetic instructions from the DNA molecule (deoxyribonucleic acid) and delivering them to molecular factories within the cell called ribosomes that read the RNA to build specific proteins needed to carry out life processes.

"Other important building blocks of life have been found in meteorites previously, including amino acids (components of proteins) and nucleobases (components of DNA and RNA), but sugars have been a missing piece among the major building blocks of life," said Yoshihiro Furukawa of Tohoku University, Japan, lead author of the study published in the Proceedings of the National Academy of Sciences. "The research provides the first direct evidence of ribose in space and the delivery of the sugar to Earth. The extraterrestrial sugar might have contributed to the formation of RNA on the prebiotic Earth which possibly led to the origin of life."

"It is remarkable that a molecule as fragile as ribose could be detected in such ancient material," said Jason Dworkin, a co-author of the study at NASA's Goddard Space Flight Center in Greenbelt, Maryland. "These results will help guide our analyses of pristine samples from primitive asteroids Ryugu and Bennu, to be returned by the Japan Aerospace Exploration Agency's Hayabusa2 and NASA's OSIRIS-REx spacecraft."

Artist’s concept of meteors impacting ancient Earth. Some scientists think such impacts may have delivered water and other  molecules useful to emerging life on Earth [Credit: NASA's Goddard Space Flight Center Conceptual Image Lab]

An enduring mystery regarding the origin of life is how biology could have arisen from non-biological chemical processes. DNA is the template for life, carrying the instructions for how to build and operate a living organism. However, RNA also carries information, and many researchers think it evolved first and was later replaced by DNA. This is because RNA molecules have capabilities that DNA lacks. RNA can make copies of itself without "help" from other molecules, and it can also initiate or speed up chemical reactions as a catalyst. The new work gives some evidence to support the possibility that RNA coordinated the machinery of life before DNA.

"The sugar in DNA (2-deoxyribose) was not detected in any of the meteorites analyzed in this study," said Danny Glavin, a co-author of the study at NASA Goddard. "This is important since there could have been a delivery bias of extraterrestrial ribose to the early Earth which is consistent with the hypothesis that RNA evolved first."

The team discovered the sugars by analyzing powdered samples of the meteorites using gas chromatography mass spectrometry, which sorts and identifies molecules by their mass and electric charge. They found that the abundances of ribose and the other sugars ranged from 2.3 to 11 parts per billion in NWA 801 and from 6.7 to 180 parts per billion in Murchison.

This is a model of the molecular structure of ribose and an image of the Murchison meteorite. Ribose and other sugars were found in this meteorite [Credit: Yoshihiro Furukawa]

Since Earth is awash with life, the team had to consider the possibility that the sugars in the meteorites simply came from contamination by terrestrial life. Multiple lines of evidence indicate contamination is unlikely, including isotope analysis. Isotopes are versions of an element with different mass due to the number of neutrons in the atomic nucleus. For example, life on Earth prefers to use the lighter variety of carbon (12C) over the heavier version (13C). However, the carbon in the meteorite sugars was significantly enriched in the heavy 13C, beyond the amount seen in terrestrial biology, supporting the conclusion that it came from space.

The team plans to analyze more meteorites to get a better idea of the abundance of the extraterrestrial sugars. They also plan to see if the extraterrestrial sugar molecules have a left-handed or right-handed bias. Some molecules come in two varieties that are mirror images of each other, like your hands. On Earth, life uses left-handed amino acids and right-handed sugars. Since it's possible that the opposite would work fine—right-handed amino acids and left-handed sugars—scientists want to know where this preference came from. If some process in asteroids favors the production of one variety over the other, then maybe the supply from space via meteorite impacts made that variety more abundant on ancient Earth, which made it more likely that life would end up using it.

Authors: Bill Steigerwald & Nancy Jones | Source: NASA [November 19, 2019]

Coming to a Head: Insights from a Vampire of the Deep

By: Thomas Schmitt Attorney on November 18, 2019 / comment : 0 Biology, Evolution, Genetics

Lamprey are blood-sucking vampire-like fish that attach to and eventually kill game fish, making them the bane of many a fisherman's existence. Like something out of a horror film, these parasites use radial rows of sharp teeth to dig into the skin of their host and extract blood and other fluids for food. But to Caltech scientists, these gruesome pests hold important clues to the evolution and success of vertebrates.

Credit: Megan Martik

The eel-like fish do not have a jaw, but because lamprey are the most primitive animals with a backbone (vertebrates) on Earth, comparing them to more recently evolved vertebrates could offer insight into how the jaw and other structures of the head evolved over time. This has important implications for understanding behaviors such as predation that rely heavily on the power of the jaw.

Caltech scientists have discovered that a population of embryonic stem cells called neural crest cells may help explain how vertebrates progressively evolved a more and more efficient head. Neural crest cells originate within the developing central nervous system before migrating throughout the embryo. They are a major player in the development of the jaws and other important components of the head and face, making them a good candidate for a role in vertebrate head evolution.

The research was conducted in the laboratory of Marianne Bronner, Albert Billings Ruddock Professor of Biology and director of the Beckman Institute. A paper describing work appeared in the journal Nature.

"Lamprey are like living fossils, and we use them to guess what primitive vertebrates might have looked like," says Bronner. "In the 1980s, it was proposed that the neural crest was a vertebrate invention that enabled acquisition of a 'new head.' We wanted to test this by looking at neural crest genes in lamprey."

The study, led by postdoctoral scholar Megan Martik, began by comparing the genetic makeup of lamprey neural crest with that of chicken embryos. The team discovered that the lamprey neural crest cells lacked important genes that are present in the head neural crest of birds and mammals, and critical for making advanced structures like the jaw.

The team wondered how the neural crest ultimately acquired the genes. To look for clues, they examined the neural crest genes of animals that have jaws, such as sharks and zebrafish, and evolved after lamprey but well before chickens and other birds. Martik and her colleagues found that the genetic program that helped to make the head more sophisticated was created by the progressive addition of genes to the neural crest repertoire as the vertebrate tree of life advanced and new species evolved.

Author: Alison Koontz | Source: California Institute of Technology [November 18, 2019]

New method takes analysis of genetic libraries to next level

By: Thomas Schmitt Attorney on November 18, 2019 / comment : 0 Biology, Evolution, Genetics, Wildlife

Uppsala researchers have developed a new method for investigating dynamic processes in large genetic libraries. By using this method to study cell cycle regulation, they help paint a clearer picture of the elusive control mechanism. The study is published in the journal Nature Methods.

Credit: Bill Oxford/Getty Images

Modern gene technology makes it possible to quickly and inexpensively introduce thousands of different DNA modifications in human cells or bacteria to create genetic libraries. The CRISPR/Cas9 system, a.k.a. 'the gene snipper', can be modified and used to alter the expression of thousands of different proteins. By labelling each modification with a genetic barcode, it is possible to keep track of which cell carries which change.

At the same time, recent developments in optics and image analysis have made it possible to investigate the chemical processes inside the cell with exceedingly high precision. In principle, it is possible to 'film' basic biological processes such as protein expression or cell division at the molecular level inside a living cell.

Now imagine it were possible to combine these advanced optical methods with large-scale genetic engineering. Let us say we are interested in a particular biological process. We could, in theory, identify all the genes involved in this process by observing the biology in a genetic library. Studies that have so far taken several years could be conducted in a single experiment - in theory.

The challenges that have previously prevented scientists from putting theory into practice have primarily been technical. How do you keep track of thousands of different cells so that you can first examine their biology and then read the genetic barcode?

A group of Uppsala researchers rose to the challenge, and now presents the DuMPLING method (Dynamic u-fluidic Microscopy-based Phenotyping of a Library before IN situ Genotyping). This method enables the examination of an entire library of living cells in a single microfluidic chip.

"The method is exceptionally potent and allows us to link genetic information to complex cell behaviour at an entirely new level," says Johan Elf, Professor of Physical Biology, who leads the study.

Among other things, Elf and his team study the bacterial cell cycle. In all cells, including human cells, it is vital that all DNA is copied exactly once before each cell division. If this is not the case, the cell is at risk of losing genetic material or accumulating DNA with equally devastating consequences. Although cell cycle regulation has been studied for decades, it is still unclear how cells achieve the strict control that is required.

"We can develop models that can reproduce the mechanism, but since we don't know all the players yet, it's hard to test if the models are biologically relevant. With this new method, it will be possible to identify the unknown components," says Daniel Camsund, researcher in molecular cell biology at Uppsala University.

The researchers created a genetic library where they decreased the expression of various known cell cycle regulators as well as some unknown genes and then used the DuMPLING method to study how the cell cycle was affected by these modifications. The next step is the game-changer. When all cell cycle data is collected, the nutrient solution in the chip is replaced with a solution that preserves the cells and fixes them in their positions. The genetic barcode can now be read using microscopy and colour-coded pieces of DNA.

"It's fascinating to see how the colour code develops, but fortunately, we're not decoding it manually. We have software that makes the identification," says Jimmy Larsson, researcher in molecular cell biology at Uppsala University

The results are encouraging. From the data, the researchers can identify most of the known regulatory elements, which means that the method works. Since the DuMPLING produces time-resolved data, it is also possible to tell how the cell cycle is affected by the various modifications. In the next phase, the team plans to expand the library to include all genes in the bacterial genome. Hopefully, this will take research one step closer to a complete description of the cell cycle control mechanism.

Source: Uppsala University [November 18, 2019]

Early DNA lineages from Finland shed light on the diverse origins of the contemporary population

By: Thomas Schmitt Attorney on November 15, 2019 / comment : 0 Archaeology, Europe, Finland, Genetics, Northern Europe

A new genetic study carried out at the University of Helsinki and the University of Turku demonstrates that, at the end of the Iron Age, Finland was inhabited by separate and differing populations, all of them influencing the gene pool of modern Finns. The study is so far the most extensive investigation of the ancient DNA of people inhabiting the region of Finland.

Medieval burial site of Kalmistomaki in Kylalahti, Hiitola in Russia [Credit: Stanislav Belskiy]

In the study, published in Scientific Reports, genes were investigated from archaeological bone samples of more than one hundred individuals who lived between the 4th and 19th centuries AD. Most of the samples originated in the Iron Age and the Middle Ages. Mitochondrial DNA (mtDNA), which is passed down by mothers to all of their offspring, was extracted from the individuals, thus uncovering the population history of women.

Based on the findings, the people who inhabited Finland in the Iron Age (approximately 300-1300 AD) and the Middle Ages (approximately 1200-1500 AD) shared mitochondrial lineages with today's Finns. However, significant differences were seen in the genome of individuals buried in different burial sites in the Iron Age in particular. mtDNA lineages typical of Stone Age hunter-gatherers were common among those buried in Luistari, Eura (southwest Finland), and Kirkkailanmaki, Hollola (southern Finland).

The Iron Age and the medieval burial sites investigated in the study include Levanluhta in Isokyro, Luistari in Eura, Kirkkailanmaki in Hollola, Kalmistomaki in Kylalahti, Hiitola, and Tuukkala in Mikkeli (marked in the map with dark grey colouring) [Credit: SUGRIGE-HANKE]

In Kylalahti, Hiitola (Republic of Karelia, Russia) and Tuukkala, Mikkeli (eastern Finland), the most common findings were lineages characteristic of ancient European farmer populations. The fifth Iron Age burial site included in the study is located in Levanluhta, western Finland. Many of the individuals buried there represented mtDNA lineages associated with the modern Sami.

"All of the above originally independent lineages remain common in Finland to this day. This indicates that the studied Iron Age populations have had an impact on the gene pool of contemporary Finns," says doctoral student Sanni Oversti from the Faculty of Biological and Environmental Sciences, University of Helsinki, Finland.

The researchers posit that the differences found in the Iron Age populations of western and eastern Finland are opposite to those found in today's Finns: the lineages associated with ancient farmers were more common in the east, while the lineages inherited from hunter-gatherers were more prevalent in the west. Farmer populations arriving in Finland not only from the west and south but also from the east provides a potential explanation for this.

Source: University of Helsinki [November 15, 2019]

Lichens are way younger than scientists thought

By: Thomas Schmitt Attorney on November 15, 2019 / comment : 0 Biology, Evolution, Genetics

You've probably seen a lichen, even if you didn't realize it. If you've ever meandered through the forest and wondered what the crusty stuff on trees or rocks was, they're lichens, a combination of algae and fungi living together almost as if they were one organism. And since they can grow on bare rocks, scientists thought that lichens were some of the first organisms to make their way onto land from the water, changing the planet's atmosphere and paving the way for modern plants. A new study in Geobiology upends this history by delving deep into the DNA of the algae and fungi that form lichens and showing the lichens likely evolved millions of years after plants.

Crustose Ophioparma lichen [Credit: (c) Matthew P. Nelsen, Field Museum]

"When we look at modern ecosystems, and we see a bare surface like a rock, oftentimes lichens are the first thing to grow there, and eventually you'll get plants growing on there too," says Matthew Nelsen, lead author of the paper and a research scientist at the Field Museum. "People have thought that maybe that's the way ancient colonization of land worked, but we're seeing that these lichens actually came later in the game than plants."

Four hundred and eighty-five million years ago, Earth was very different from what we see today. Hardly anything lived on land. But lichens can live in extreme conditions. They can grow on bare rocks and break them down, helping to create the soil needed by complex plants with roots (called "vascular plants"). Scientists thought that lichens must have arrived on land before the vascular plants did and made the environment more hospitable. But Nelsen and his colleagues' work calls this timeline into question.

Nelsen didn't set out to disrupt lichen's status as some of the land's first colonizers. He was initially interested in finding out how the algae-fungus relationship that makes up lichens came to be. If lichens could update their relationship status on Facebook, it would definitely be "it's complicated." They're a product of symbiosis, a relationship where two species live together and both benefit. In this instance, the algae--or specialized blue-green algae called cyanobacteria--provide food and the fungi wraps around it creating a shelter. "The question of when lichens evolved and how many times fungi evolved the ability to form symbiotic relationships with algae has been a bit contentious in the past," says Nelsen.

Crustose Porpidia lichen growing on a rock [Credit: (c) Matthew P. Nelsen, Field Museum]

But to accurately determine when lichens evolved, scientists needed to examine the evolutionary history of both the fungi and algae that make them up. The early lichen fossil record isn't very clear; it can be hard to tell lichen fossils apart from other fossils, and all the fossils that scientists know for sure are lichens are younger than the oldest complex plant fossils. So, the researchers used the fossils that were available to extrapolate the ages of family trees of lichen-forming fungi and algae. They compared these family trees with ages of fossil plants. The verdict: lichens probably evolved long after complex plants.

"Lichens aren't as old as we thought they were. They're a younger, newer sort of symbiosis and haven't been around forever, covering the earth long before there were plants and animals running around," says Nelsen.

Unearthing the age of lichens makes it clear that the pattern of modern lichens showing up on rocks before plants doesn't mean that lichens evolved before plants. "It provides a snapshot into what was going on deep in time on Earth, and when some of these groups started appearing," says Nelsen. And since lichens growing on soil can make the ground wetter, hold the soil in place, and influence the kind of nutrients present in soil, learning when lichens arrived on the scene use us a clearer picture of the world in which complex plants evolved.

By understanding what the Earth was like hundreds of millions of years ago, we can examine how it's changed and gain more insight into the current state of our planet. For the researchers, it's similar to the feeling you might get when learning about your family history from an ancestry DNA kit.

"It reshapes our understanding of the early evolution of complex ecosystems on Earth," says Nelsen.

Source: Field Museum [November 15, 2019]

Genetic analysis of sacred ibis mummies sheds light on early Egyptian practices

By: Thomas Schmitt Attorney on November 14, 2019 / comment : 0 Archaeology, Egypt, Genetics, Near East

New genetic research into the mummification of ibises found in Egyptian catacombs has shed light on how Ancient Egyptians obtained millions of the ‘wise’ birds to sacrifice annually.

The ibises were mummified and placed in clay jars by temple priests then offered to Thoth  who had the appearance of a man but the head of an ibis [Credit: Griffith University]

The research, led by Griffith University, investigated historical suggestions that Sacred Ibis were farmed on an industrial scale in order to provide the God of Wisdom Thoth with millions of sacrificed birds each year.

Mitogenomic analyses by the team revealed high genetic diversity among the mummified ibises from various sites. This suggests that mass-scale farming was unlikely and instead supported the possibility that temple priests and locals were able to tame and increase wild populations each year.

Researchers from Australia, New Zealand, the United Kingdom, South Africa Denmark and Egypt contributed to the study, which has been published in PLOS ONE.

Dr Sally Wasef and Professor David Lambert from Griffith’s Australian Research Centre for Human Evolution analysed the mitogenomes (DNA transmitted from the mother only to offspring) of 26 modern Sacred Ibis samples collected from throughout Africa. 

In addition, 14 ancient Egyptian from five major Sacred Ibis burial sites scattered around Egypt were examined genetically.

Radiocarbon dating revealed that most of the ancient Egyptian ibis mummy samples were aged to ~600BC.

About 15,000 birds were estimated to be mummified and offered annually at each temple site, of which there were many throughout Egypt.  Hence, the yearly total of sacrificed birds was likely in the millions.

The ibises were mummified and placed in clay jars by temple priests then offered to Thoth who had the appearance of a man but the head of an ibis. The mummies were stacked floor-to-ceiling in many rooms lining the catacomb streets.

A Scene from the Books of the Dead (The Egyptian museum) showing the ibis-headed God Thoth  recording the result of the final judgement. B and D Example of the millions of votive mummies presented as offerings by pilgrims to the God Thoth. C Pottery jars containing ‘votive’ mummies stacked in the North Ibis catacomb at Saqqara [Credit: Wasef et al. 2019]

Dr Wasef said contrary to historical belief that the millions of the birds were industrially farmed for yearly sacrifice, analysis of the mitogenomes of the mummified birds from the various sites showed a high genetic diversity among them.

“This suggests it is unlikely that Sacred Ibis were farmed on a mass scale as the genetic consequences of that would have been low genetic diversity owing to the shared DNA between in-breeding family groups over time,” she said.

“If the ancient Egyptians had bred the Ibis in local homes or wetlands surrounding the temples, it would have been just a short-term practice to support the considerable yearly demand. It seems clear that they did not establish long-term industrial scale farms to have millions of birds to sacrifice each year. We suggest that the genetic data indicates that the local people obtained wild ibis yearly, tamed them and raised them for mummification, so it was also beneficial for the community and the economy.”

Dr Wasef adds that had there been an industrial-scale farming operation, the expedition team would not have found ‘fake’ mummies (mummified feathers and nests) in the temple catacombs as there would have been plenty of ibises to sacrifice and offer.

Professor Lambert remarked: “mitogenomic analyses outlined here are appropriate in this case because the timeframe under study was short, being only 2000-3000 years.”

Thoth was the god of wisdom, magic, writing, and the moon. His head was shaped like that of an ibis. The ancient Egyptians believed the Sacred Ibis – very similar species to Australia’s white ibis – was very wise in drinking only clean water.

“Here in Australia we call the ibis a ‘bin chicken’, but if you did the same in ancient Egypt you would be put to death,” Dr Wasef said.

“To ancient Egyptians the Sacred Ibis was a God, something to be revered and worshiped. So this research hopefully might result in our humble ‘bin chicken’ being seen in a new light.”

Author: Carley Rosengreen | Source: Griffith University [November 14, 2019]