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Researchers have genetically transformed the Common Primrose (Primula vulgaris) for the first time in a development that could shed light on one of the plant world's most renowned reproductive systems.

Credit: John Innes Historical Collection

The complicated sex life of Primula was a subject that fascinated Charles Darwin and generations of geneticists that followed because it's one of the best examples of heteromorphic flower development.

Heteromorphy (or heterostyly) is a phenomenon in which plants exhibit two or three distinct forms of flowers based on the position of the male and female sex organs. Now, some of the secrets that eluded Darwin could be revealed following the biotechnological success announced by researchers from the John Innes Centre, the University of East Anglia (UEA) and the Earlham Institute.

The technology known as Agrobacterium-mediated plant transformation involves using soil bacteria to insert or modify genes in a plant genome. Genetic transformation is a valuable tool that allows researchers to study gene function and genetically controlled characteristics in organisms.

It is a research method routinely used on model organisms such as Nicotiana benthamiana and Arabidopsis thaliana to understand the molecular workings of plants. However, these species cannot be used to study heteromorphy because their flowers are all homomorphic which means they are able to self-fertilise.

"Now we have a transformation system we can use gene editing tools such as CRISPR-Cas9 to work out exactly what the gene function is that controls heteromorphy in the Primula family," says Sadiye Hayta, of the John Innes Centre.

"Longer term, there may be implications for commercial crops. If we understand the roles of these different genes we could take them over to a commercial crop and use it in a hybrid system," she adds.

Until now attempts to transform Primula have been unsuccessful because the plant has proved resistant to laboratory regeneration of whole plants from tissue culture.

The new transformation protocols reported in the peer-reviewed journal Plant Methods will allow the scientists of today to study the Primula at a molecular level.

The flowering plant is one of the best-known examples of heteromorphic flower development. This reproductive system enthralled not only Darwin but many leading geneticists from the early 1900s including William Bateson, the first director of the John Innes Centre and colleagues JBS Haldane, Cyril Darlington and Dorothea de Winton.

Darwin, in a landmark paper of 1862, worked out the functional significance of the different anatomical formations: they made the plants self-incompatible. This is Nature's way of promoting cross-pollination to maintain genetic variation in the population, driving natural selection.

Fundamental research into heteromorphy has continued. In a research paper in 2016 a John Innes Centre - University of East Anglia team led by Professor Philip Gilmartin identified the S-Locus supergene that controls heteromorphy as described by Darwin.

Armed with this fundamental knowledge and a the newly announced transformation system, scientists can delve deeper into the mysteries of heteromorphy.

Co-author Mark Smedley, of the John Innes Centre says: "It is not every day you get to work on a paper that references Darwin. This is a fundamental story that scientists have been trying to unravel for 200 years."

Professor Philip Gilmartin of the UEA whose laboratory started out on this scientific mission more than 20 years ago, said: "The development of a Primula transformation system is an important component of our lab's long-term study to identify and characterise the genes that control development of the two forms of Primula flower studied by Charles Darwin."

It's a piece of research that would have excited Darwin. Towards the end of his illustrious career the author of On the Origin of Species remarked:

"I do not think anything in my scientific life has given me so much satisfaction as making out the meaning of the structure of these plants."

Source: John Innes Centre [December 11, 2018]

Populations of indigenous people in southern Africa carry a gene that causes lighter skin, and scientists have now identified the rapid evolution of this gene in recent human history.

San man of Namibia [Credit: Ian Beatty/WikiCommons]

The gene that causes lighter skin pigmentation, SLC24A5, was introduced from eastern African to southern African populations just 2,000 years ago. Strong positive selection caused this gene to rise in frequency among some KhoeSan populations.

UC Davis anthropologist Brenna Henn and colleagues have shown that a gene for lighter skin spread rapidly among people in southern Africa in the last 2,000 years.

This is a "rare example of intense, ongoing adaptation in recent human history and is the first known example of adaptive gene flow at a pigmentation locus in humans," according to the paper published online in the Proceedings of the National Academy of Sciences.

The findings are based on research by multiple scientists. The primary author, Meng Lin, conducted the research as a graduate student at Stony Brook University, working with anthropologist Brenna Henn, now of the University of California, Davis, Genome Center and Department of Anthropology. Lin is now a post-doctoral researcher in genetics at the University of Southern California.

In previous work, the researchers looked at pigmentation variation in two KhoeSan populations from South Africa by performing a genome-wide association analysis in about 450 individuals. They followed up on the top associated gene, SLC24A5, by simulating population histories with and without positive selection. The DNA and pigmentation sampling took place in the Northern Cape of South Africa in the southern Kalahari Desert and Richtersveld regions.

Gene plays a role in lighter skin pigmentation

Individuals who carry two copies of the lighter pigmentation gene are 14 percent lighter-skinned than the population average, the researchers said. The gene SLC24A5 plays a key role in the genetic basis of light skin pigmentation.

While light skin is often associated with European ancestry, even in South Africa, the present-day Khoekhoe and San did not experience enough recent migration to account for the frequency of the gene. Rather, strong positive selection during the past 2,000 years was the only way to explain the current distribution. The gene, which is also present in people from the Near East and eastern Africa, was probably initially brought into the region by only a small number of individuals.

The actual source of the positive selection is not clear. The researchers theorize that a shift from consuming vitamin D-rich marine animals to consuming pasture animals, or a reduction in exposure to ultraviolent rays, might have changed skin pigmentation over time.

"While the biological cause of the selective event merits further investigation, we have demonstrated an unusual rapid case of selection for lighter skin pigmentation based on a recently introduced allele less that 2,000 years ago, the first case of pigmentation adaptation from migration in humans," the paper concludes.

Author: Karen Nikos-Rose | Source: UC Davis [December 10, 2018]

A QUT-led collaboration with University of Adelaide reveals that Australia's pint-sized banded hare-wallaby is the closest living relative of the giant short-faced kangaroos which roamed the continent for millions of years, but died out about 40,000 years ago.

The diminutive banded hare-wallaby linked to the giant Sthenurinae kangaroos [Credit: Queensland University of Technology]

Published in Systematic Biology, the research involved the first near-complete mitochondrial (mt) genome sequencing from extinct Australian megafauna.

- DNA was sequenced from inner ear bones (petrous bones) of a 45,000-year-old giant short-faced kangaroo, Simosthenurus occidentalis, part of the Sthenurinae sub-family, found at Mt Cripps in Tasmania

- These are the longest DNA sequences ever recovered from Australia's extinct megafauna, with more than 16,000 base pairs of mtDNA, which is used to help understand evolutionary relationships

- The results support an evolutionary link between giant short-faced kangaroos (Sthenurinae) and the threatened banded hare-wallaby, Lagostrophus fasciatus

- The study also combined the DNA evidence with fossil and anatomical data to trace body size change over the evolutionary history of kangaroos and wallabies

The analysis was conducted by QUT evolutionary biologists Ph.D. researcher Manuela Cascini and Associate Professor Matthew Phillips, from the Science and Engineering Faculty, in collaboration with University of Adelaide's Professor Alan Cooper and Dr. Kieren Mitchell, who undertook the DNA sequencing at the Australian Centre for Ancient DNA.

Credit: Queensland University of Technology

Lead author Ms Cascini, a molecular biologist who moved from Italy to undertake her Ph.D. research with Associate Professor Phillips, said her project also involved analysis of mtDNA sequenced from the inner ear bones of another ancient extinct macropod that was found in Tasmania – the giant wallaby, Protemnodon anak, which weighed up to 150 kilograms.

Small fragments of ancient DNA sequenced from this giant wallaby species and from the giant short-faced kangaroo were first reported on by University of Adelaide scientists in 2015.

"Our analysis confirmed their conclusion that the giant wallabies are close relatives of the iconic living Macropus genus of kangaroos and wallabies," Ms Cascini said.

"However that earlier study provided insufficient DNA to confidently place the giant short-faced kangaroos on the evolutionary tree.

"We've now been able to show the strongest evidence yet that the closest living relative of these massive Sthenurinae kangaroos, which weighed up to about 240 kilograms, is the tiny, 2-kilogram banded hare-wallaby. These wallabies live in the wild only on islands off Western Australia and are classified as vulnerable."

Largest of the extinct giant short-faced kangaroos, Procoptodon goliah, featured on an Australia Post stamp  [Credit: Queensland University of Technology]

Associate Professor Phillips said the larger amount of mtDNA sequenced in this study by the University of Adelaide collaborators helped enable the strong finding on the banded hare-wallaby link.

"This is by far the most genetic data that anyone has extracted out of Australian megafauna, and it was taken from the petrous bones which are denser and often seem to hold DNA better," he said.
"You find a lot of ancient DNA studies of megafauna from permafrost in northern Europe and northern America because the cold helps preserve the DNA. But in Australia the hotter climate and older age of the megafauna is far less favourable for DNA preservation."

Dr. Mitchell said Tasmania's cooler climate and higher-altitude caves "make for much better DNA preservation than we find elsewhere in Australia, so we focused our hunt for high-quality megafaunal DNA there".

Associate Professor Phillips said other findings of the study on the evolution of kangaroos and wallabies (macropods) included:

- The macropod ancestors diverged from tree-living possums around 41 to 46 million years ago

- They remained small, in the 2-15 kg range, while Australia was more dominated by rainforest

- As the climate cooled and dried, and as the forests opened up over the past 10 million years, at least four different kangaroo lineages independently evolved to megafaunal size (more than 44 kg)

- This includes the short-faced kangaroos, the giant Protemnodon wallabies, and the living red and grey kangaroos.

Author: Rose Trapnell | Source: Queensland University of Technology [December 10, 2018]

Barely living "zombie" bacteria and other forms of life constitute an immense amount of carbon deep within Earth's subsurface -- 245 to 385 times greater than the carbon mass of all humans on the surface, according to scientists nearing the end of a 10-year international collaboration to reveal Earth's innermost secrets.

A nematode (eukaryote) in a biofilm of microorganisms. This unidentified nematode (Poikilolaimus sp.) from Kopanang gold mine in South Africa, lives 1.4 km below the surface [Credit: Gaetan Borgonie, Extreme Life Isyensya, Belgium]

On the eve of the American Geophysical Union's annual meeting, scientists with the Deep Carbon Observatory today reported several transformational discoveries, including how much and what kinds of life exist in the deep subsurface under the greatest extremes of pressure, temperature, and low nutrient availability.

Drilling 2.5 kilometers into the seafloor, and sampling microbes from continental mines and boreholes more than 5 km deep, scientists have used the results to construct models of the ecosystem deep within the planet.

With insights from now hundreds of sites under the continents and seas, they have approximated the size of the deep biosphere -- 2 to 2.3 billion cubic km (almost twice the volume of all oceans) -- as well as the carbon mass of deep life: 15 to 23 billion tonnes (an average of at least 7.5 tonnes of carbon per cu km subsurface).

The work also helps determine types of extraterrestrial environments that could support life.

Among many key discoveries and insights:

- The deep biosphere constitutes a world that can be viewed as a sort of "subterranean Galapagos" and includes members of all three domains of life: bacteria and archaea (microbes with no membrane-bound nucleus), and eukarya (microbes or multicellular organisms with cells that contain a nucleus as well as membrane-bound organelles)

- Two types of microbes -- bacteria and archaea -- dominate Deep Earth. Among them are millions of distinct types, most yet to be discovered or characterized. This so-called microbial "dark matter" dramatically expands our perspective on the tree of life. Deep Life scientists say about 70% of Earth's bacteria and archaea live in the subsurface

- Deep microbes are often very different from their surface cousins, with life cycles on near-geologic timescales, dining in some cases on nothing more than energy from rocks

- The genetic diversity of life below the surface is comparable to or exceeds that above the surface

- While subsurface microbial communities differ greatly between environments, certain genera and higher taxonomic groups are ubiquitous -- they appear planet-wide

- Microbial community richness relates to the age of marine sediments where cells are found -- suggesting that in older sediments, food energy has declined over time, reducing the microbial community

- The absolute limits of life on Earth in terms of temperature, pressure, and energy availability have yet to be found. The records continually get broken. A frontrunner for Earth's hottest organism in the natural world is Geogemma barossii, a single-celled organism thriving in hydrothermal vents on the seafloor. Its cells, tiny microscopic spheres, grow and replicate at 121 degrees Celsius (21 degrees hotter than the boiling point of water). Microbial life can survive up to 122°C, the record achieved in a lab culture (by comparison, the record-holding hottest place on Earth's surface, in an uninhabited Iranian desert, is about 71°C -- the temperature of well-done steak)

- The record depth at which life has been found in the continental subsurface is approximately 5 km; the record in marine waters is 10.5 km from the ocean surface, a depth of extreme pressure; at 4000 meters depth, for example, the pressure is approximately 400 times greater than at sea level

- Scientists have a better understanding of the impact on life in subsurface locations manipulated by humans (e.g., fracked shales, carbon capture and storage)

Candidatus Desulforudis audaxviator (the purplish, blue rod-shaped cells straddling orange carbon spheres) is a species of bacteria that survives on hydrogen. Scientists found it living within a fluid and gas-filled fracture 2.8 km beneath Earth's surface at a mine near Johannesburg, South Africa. The genus name Desulforudis comes from the Latin for "from sulfur"  and "rod," noting its shape and its ability to get energy from sulfates. And audaxviator? From Jules Verne's Journey to the Center of the Earth, and a message in Latin deciphered by Verne's protagonist, Professor Lidenbrock, which read  in part: "descend, bold traveler, and attain the center of the Earth" [Credit: Greg Wanger, California Institute of Technology, USA, and Gordon Southam University of Queensland, Australia]

Ever-increasing accuracy and the declining cost of DNA sequencing, coupled with breakthroughs in deep ocean drilling technologies (pioneered on the Japanese scientific vessel Chikyu, designed to ultimately drill far beneath the seabed in some of the planet's most seismically-active regions) made it possible for researchers to take their first detailed look at the composition of the deep biosphere.

There are comparable efforts to drill ever deeper beneath continental environments, using sampling devices that maintain pressure to preserve microbial life (none thought to pose any threat or benefit to human health).

To estimate the total mass of Earth's subcontinental deep life, for example, scientists compiled data on cell concentration and microbial diversity from locations around the globe.

Led by Cara Magnabosco of the Flatiron Institute Center for Computational Biology, New York, and an international team of researchers, subsurface scientists factored in a suite of considerations, including global heat flow, surface temperature, depth and lithology -- the physical characteristics of rocks in each location -- to estimate that the continental subsurface hosts 2 to 6 × 10^29 cells.

Combined with estimates of subsurface life under the oceans, total global Deep Earth biomass is approximately 15 to 23 petagrams (15 to 23 billion tonnes) of carbon.

Says Mitch Sogin of the Marine Biological Laboratory Woods Hole, USA, co-chair of DCO's Deep Life community of more than 300 researchers in 34 countries: "Exploring the deep subsurface is akin to exploring the Amazon rainforest. There is life everywhere, and everywhere there's an awe-inspiring abundance of unexpected and unusual organisms.

"Molecular studies raise the likelihood that microbial dark matter is much more diverse than what we currently know it to be, and the deepest branching lineages challenge the three-domain concept introduced by Carl Woese in 1977. Perhaps we are approaching a nexus where the earliest possible branching patterns might be accessible through deep life investigation.

"Ten years ago, we knew far less about the physiologies of the bacteria and microbes that dominate the subsurface biosphere," says Karen Lloyd, University of Tennessee at Knoxville, USA. "Today, we know that, in many places, they invest most of their energy to simply maintaining their existence and little into growth, which is a fascinating way to live.

"Today too, we know that subsurface life is common. Ten years ago, we had sampled only a few sites - the kinds of places we'd expect to find life. Now, thanks to ultra-deep sampling, we know we can find them pretty much everywhere, albeit the sampling has obviously reached only an infinitesimally tiny part of the deep biosphere."

"Our studies of deep biosphere microbes have produced much new knowledge, but also a realization and far greater appreciation of how much we have yet to learn about subsurface life," says Rick Colwell, Oregon State University, USA. "For example, scientists do not yet know all the ways in which deep subsurface life affects surface life and vice versa. And, for now, we can only marvel at the nature of the metabolisms that allow life to survive under the extremely impoverished and forbidding conditions for life in deep Earth."

"A decade ago, we had no idea that the rocks beneath our feet could be so vastly inhabited. Experimental investigations told us that microbes could potentially survive to great depth; at that time, we had no evidence, and this has become real ten years later. This is simply fascinating and will surely foster enthusiasm to look for the biotic-abiotic fringe on Earth and elsewhere," said Isabelle Daniel, University of Lyon 1, France.

This is a species of Methanobacterium, which produces methane. Found in samples from a buried coal bed 2 km below the  Pacific Ocean floor off the coast of Japan, this specimen was retrieved during an Integrated Ocean Drilling Program  (now the International Ocean Discovery Program) expedition aboard the Drilling Vessel Chikyu. Bar represents 10 μm (micrometers, or 0.0004 inch) [Credit: Hiroyuki Imachi (Japan Agency for Marine-Earth Science and Technology (JAMSTEC)]

Among the many remaining enigmas of deep life on Earth:

Movement: How does deep life spread -- laterally through cracks in rocks? Up, down? How can deep life be so similar in South Africa and Seattle, Washington? Did they have similar origins and were separated by plate tectonics, for example? Or do the communities themselves move? What roles do big geological events (such as plate tectonics, earthquakes; creation of large igneous provinces; meteoritic bombardments) play in deep life movements?

Origins: Did life start deep in Earth (either within the crust, near hydrothermal vents, or in subduction zones) then migrate up, toward the sun? Or did life start in a warm little surface pond and migrate down? How do subsurface microbial zombies reproduce, or live without dividing for millions to tens of millions of years?

Energy: Is methane, hydrogen, or natural radiation (from uranium and other elements) the most important energy source for deep life? Which sources of deep energy are most important in different settings? How do the absence of nutrients, and extreme temperatures and pressure, impact microbial distribution and diversity in the subsurface?

"Even in dark and energetically challenging conditions, intraterrestrial ecosystems have uniquely evolved and persisted over millions of years. Expanding our knowledge of deep life will inspire new insights into planetary habitability, leading us to understand why life emerged on our planet and whether life persists in the Martian subsurface and other celestial bodies,"  according to Fumio Inagaki, Japan Agency for Marine-Earth Science and Technology.

"While we are far from being able to quantify it, we believe Deep Life has an important impact on global biogeochemical cycles and chemical equilibria in habitable rocks. Deep Life plays a role in aquifer quality, for example, or carbon capture and storage (CCS). Unfortunately, the deep biosphere is very poorly considered in engineering operations carried out in the subsurface. We recently demonstrated the high reactivity of deep biota to CO2 injections (CCS), which ultimately led to the bioclogging of the injection well, and surrounding reservoir," adds Benedicte Menez, Institut de Physique du Globe de Paris, France.

Source: Deep Carbon Observatory [December 10, 2018]

Otago researchers have discovered a rare case of genetic population discontinuity on the Mediterranean Island of Ibiza. Essentially, the original genetic signature of the founding female population, handed down through centuries on Ibiza has been replaced, prompting a change in understanding of the island’s genetic history.

Set of figurines from Es Culleram. Archaeological Museum of Ibiza and Formentera [Credit: © Ministerio de Cultura]

Ancient DNA from Ibiza demonstrates a clear genetic discontinuity in the maternal lineages of the early Phoenician settlers and the modern inhabitants of the island according to a study published in Scientific Reports.

The study was led by Professor Lisa Matisoo-Smith and her team from the University of Otago, New Zealand, and Professor Pierre Zalloua of the Lebanese American University, Beirut, with the collaboration of researchers from the Institute of Evolutionary Biology (Universitat Pompeu Fabra-CSIC), Barcelona, the Archaeological Museum of Ibiza and archaeologists from Lebanon and Italy.

The team analysed mitochondrial DNA (mtDNA), which is maternally inherited, from archaeological Phoenician remains and from modern inhabitants of Ibiza. They also obtained whole genome data (representing their total ancestry from both parents) from one ancient Phoenician individual.

Arriving from Cadiz, on the Iberian mainland, the Phoenicians first settled on the strategic island of Ibiza around 654 BCE and remained the main inhabitants of Ibiza for about seven centuries.

Burial rituals and other archaeological findings at the Puig des Molins necropolis of Ibiza provide evidence for a second population influx from Carthage or other Punic settlements in the Mediterranean, coinciding with a period of prosperity and major development of the island around 5th BCE. After the 2nd Punic War, Ibiza started a long process of integration of Ibiza into the Roman Empire, followed by the Islamic conquest of the island around 900 CE. Beginning around 1200 CE Ibiza was the recipient of migrations from the Iberian and Southern European mainland.

Based on the mtDNA results, the study showed clear genetic discontinuity between the early Phoenician settlers and the modern inhabitants of the island.

“Thus, the unusual genetic signature that has previously been identified in modern Ibizans does not appear to be the result of their Phoenician ancestry, at least from a maternal perspective”, explains Professor Matisoo-Smith.

Multiple population arrivals through invasions or other movements combined with periods of population instability after the early Phoenician settlement seems to have led to a reshuffling of the genetic makeup of this island.

“It is fascinating to see that the ancient maternal lineages were replaced over time. Today the mitochondrial DNA lineages in indigenous Ibizans appear to be most closely related to those of modern French, which may indicate a Catalonian connection,” adds Professor Zalloua.

While ancient DNA evidence generated over the last few years does now show us that there were population replacements in deep time, for example in Europe when farmers moved into western Europe several thousands of years ago and replaced many hunter-gatherer populations, we do not often see genetic replacement during more recent times.

Despite the lack of continuity observed in the mitochondrial genomes, previous Y chromosome analyses suggest that there is still some Phoenician signature in the modern Ibizan population. The whole genome data obtained from one ancient Phoenician from Ibiza belonged to an individual with a European maternal lineage but with a significant Eastern Mediterranean component to their genetic ancestry, indicating an admixed Phoenician community in Ibiza during the 3rd century BCE. This result is consistent with the archaeological evidence and further indicates that diversity and integration was a hallmark of Phoenician societies.

The results are consistent with historical evidence suggesting that Phoenician influence in the West was male dominated and indicates that there was not a total replacement of the Ibizan founding population, however, we now know that the genetic distinctness of the modern indigenous inhabitants of Ibiza is not due to Phoenician ancestry as has often been suggested. Further whole genome data is needed to help us understand why and how the genetic makeup of the Ibizan population changed over time. For example, disease or social impacts like war or famine may have played a major role in shaping the genetic makeup of the population of the island.

Source: University of Otago [December 07, 2018]

A team of researchers from France, Sweden, and Denmark have identified a new strain of Yersinia pestis, the bacteria that causes plague, in DNA extracted from 5,000-year-old human remains. Their analyses, published in the journal Cell, suggest that this strain is the closest ever identified to the genetic origin of plague. Their work also suggests that plague may have been spread among Neolithic European settlements by traders, contributing to the settlements' decline at the dawn of the Bronze Age.

The remains of a 20-year old woman (Gokhem2) from around 4900 BP that was killed by the first plague pandemic. She was one of the victims of a plague pandemic  that likely lead to the decline of the Neolithic societies in Europe [Credit: Karl-Göran Sjögren/University of Gothenburg]

"Plague is maybe one of the deadliest bacteria that has ever existed for humans. And if you think of the word 'plague,' it can mean this infection by Y. pestis, but because of the trauma plague has caused in our history, it's also come to refer more generally to any epidemic. The kind of analyses we do here let us go back through time and look at how this pathogen that's had such a huge effect on us evolved," says senior author Simon Rasmussen, a metagenomics researcher at the Technical University of Denmark and the University of Copenhagen.

To better understand the evolutionary history of the plague, Rasmussen and his colleagues trawled through publicly available genetic data from ancient humans, screening for sequences similar to more modern plague strains. They found a strain they had never seen before in the genetic material of a 20-year-old woman who died approximately 5,000 years ago in Sweden. The strain had the same genes that make the pneumonic plague deadly today and traces of it were also found in another individual at the same grave site -- suggesting that the young woman did likely die of the disease.

This strain of the plague is the oldest that's ever been discovered. But what makes it particularly interesting is that, by comparing it to other strains, the researchers were able to determine that it's also the most basal -- meaning that it's the closest strain we have to the genetic origin of Y. pestis. It likely diverged from other strains around 5,700 years ago, while the plague that was common in the Bronze Age and the plague that is the ancestor of the strains in existence today diverged 5,300 and 5,100 years ago, respectively. This suggests that there were multiple strains of plague in existence at the end of the Neolithic period.

Rasmussen also believes that this finding offers a new theory about how plague spreads. Massive human migrations from the Eurasian steppe down into Europe are known to have occurred around 5,000 years ago, but how these cultures were able to displace the Neolithic farming culture that was present in Europe at the time is still debated. Previous researchers have suggested that the invaders brought the plague with them, wiping out the large settlements of Stone Age farmers when they arrived.

How researchers believe the plague spread [Credit: Gothenburg University]

But if the strain of plague the researchers found in the Swedish woman diverged from the rest of Y. pestis 5,700 years ago, that means it likely evolved before these migrations began and around the time that the Neolithic European settlements were already starting to collapse.

At the time, mega-settlements of 10,000-20,000 inhabitants were becoming common in Europe, which made job specialization, new technology, and trade possible. But they also may have been the breeding ground for plague. "These mega-settlements were the largest settlements in Europe at that time, ten times bigger than anything else. They had people, animals, and stored food close together, and, likely, very poor sanitation. That's the textbook example of what you need to evolve new pathogens," says Rasmussen.

"We think our data fit. If plague evolved in the mega-settlements, then when people started dying from it, the settlements would have been abandoned and destroyed. This is exactly what was observed in these settlements after 5,500 years ago. Plague would also have started migrating along all the trade routes made possible by wheeled transport, which had rapidly expanded throughout Europe in this period," he says.

Eventually, he suggests, the plague would have arrived through these trade interactions at the small settlement in Sweden where the woman his team studied lived. Rasmussen argues that the woman's own DNA also provides further evidence for this theory -- she isn't genetically related to the people who invaded Europe from the Eurasian steppe, supporting the idea that this strain of plague arrived before the mass migrations did. The archaeology also supports this hypothesis, as there were still no signs of the invaders by the time she died.

Some of the remains examined [Credit: Karl-Göran Sjögren/ University of Gothenburg]

Of course, there are some limitations to what the data from this study can tell us. Most importantly, the researchers have not yet identified the plague in individuals from the mega-settlements where it may have evolved. "We haven't really found the smoking gun, but it's partly because we haven't looked yet. And we'd really like to do that, because if we could find plague in those settlements, that would be strong support for this theory," says Rasmussen.

Regardless, he believes that this study is a step toward understanding how plague -- and other pathogens -- became deadly. "We often think that these superpathogens have always been around, but that's not the case," he says. "Plague evolved from an organism that was relatively harmless. More recently, the same thing happened with smallpox, malaria, Ebola, and Zika. This process is very dynamic -- and it keeps happening. I think it's really interesting to try to understand how we go from something harmless to something extremely virulent."

Source: Cell Press [December 06, 2018]

University of Otago researchers have discovered information about a gene that sets primates—great apes and humans—apart from other mammals, through the study of a rare developmental brain disorder.

Brain organoids, or "mini-brains" growing in culture [Credit: Dr Adam O'Neill]

Dr. Adam O'Neill carried out the research as part of his Ph.D. at the University of Otago, under the supervision of Professor Stephen Robertson, discovering that the PLEKHG6 gene has qualities that drives aspects of brain development differently in primates compared to other species.

"Broadly speaking, this gene can be thought of as one of the genetic factors that make us human in a neurological sense," Dr. O'Neill who now works in the Department of Physiological Genomics at Ludwig Maximilian Universität in Munich, Germany, explains.

Professor Robertson says the research, just published in international journal Cell Reports, aimed to address the idea that there must be genes that humans have that have made our brains bigger and better functioning in some respects than other animals. However, that increased complexity could come at a cost, potentially predisposing humans to the development of a whole suite of neurological or psychiatric conditions.

"Such genes have been hard to find, but using an approach where we studied children with a certain brain malformation called periventricular nodular heterotopia, we found a 'damaged' genomic element in a child that had the attributes of such a primate specific genetic factor," he explains. In this particular condition a subset of neurons in the developing brain fail to take up their correct position resulting in a variety of symptoms including epilepsy and delayed development.

Dr. O'Neill and research collaborators from Max Planck Institute of Psychiatry, Germany, then set forth to test the point that the gene drives aspects of brain development that are unique to primates. Some amazing data was found using a novel approach through studying human "mini-brains" in culture. It is now possible to take a skin cell and transform it using a set of genetic tricks, so that it can be triggered to form a tiny brain-like structure in culture in the lab.

Their results showed that the particular genetic change that disabled a component of this gene (PLEKHG6) altered its ability to support the growth and proliferation of specialised stem cells in the developing brain. In addition, some of these cells also failed to migrate to their correct position in the growing "mini-brain" during the first few weeks of brain development.

Professor Robertson says it has been known for a while that these stem cells behave differently between primates/humans and other animals, but understanding what genes regulate these differences has been a mystery.

"Adam's achievement has been to show that this particular component of the PLEKHG6 gene is one such regulator that humans have 'acquired' very recently in their evolution to make their brains 'exceptional'."

Dr. O'Neill says there are very few genetic elements that are primate specific in our genome, so this discovery adds to a very short list of genetic factors that, at least in one sense, make us human.

"Such an understanding positions us to better understand how a brain builds itself- knowledge that will add to our ability to design strategies to repair the damaged brain, especially early in infancy where there are still lots of stem cells around," Dr. O'Neill says.

The work also helps provide more information about the list of genes that are altered to cause this particular type of brain malformation.

"Personally, I also think it does underscore how it is very subtle nuanced differences that separate us from other animals. Our anthropocentrism could be a whole lot more humble," Dr. O'Neill says.

Source: University of Otago [December 06, 2018]

Like other organisms, bacteria constantly have to fight to survive in hostile living conditions. Together with colleagues in Finland, researchers at the Max Planck Institute for Evolutionary Biology in Plön have discovered that bacteria adapt to their environment more slowly and less efficiently as soon as they are exposed to two stress factors rather than one. This is due to mutations in different genes. The slower rate of evolution led to smaller population sizes. This means that evolution can take divergent paths if an organism is exposed to several stress factors.

The single-cell organism Tetrahymena thermophila (green) with its bacterial prey (purple) [Credit: Matti Jalasvuori]

Bacteria rarely live alone; they are usually part of a community of species that is exposed to various stress factors. They can often react to these factors by adapting to new environmental conditions with astonishing speed. Antibiotics that enter soil and water via waste water and accumulate there in low concentrations can trigger the evolution of resistance in bacteria – even though these concentrations are so low that they inhibit bacterial growth only slightly or not at all. However, bacteria do not only have to fight antibiotics; they also have to deal with predators. This is why they often grow in large colonies that cannot be consumed by predatory organisms.

Typically, scientists investigate the effects that a single stress factor has on an organism. Researchers at the Max Planck Institute for Evolutionary Biology in Plön and the Universities of Helsinki and Jyväskylä, Finland, have now investigated the question of how microorganisms behave when they are confronted with more than one stress factor. "We simulated natural environmental conditions in the lab and exposed bacteria to both predators and antibiotics. This allows us to estimate how likely it is to find evolution of resistance to antibiotics outdoors," explains study leader Lutz Becks.

Antibiotics and predators

In the scientists' laboratory, the bacterium Pseudomonas fluorescence had to cope with both antibiotics and the predatory single-cell organism Tetrahymena thermophila. After just a short time, the team of researchers noticed that the bacterial population was changing: the bacteria were much slower and less effective in developing resistance and protecting themselves from being consumed than others of the species that were only exposed to one of these factors. Moreover, resistance against the antibiotic was much less common. "The bacteria were clearly unable to optimize both attributes at the same time," says Becks.

In the next step, the scientists analysed the genetic basis of these adaptations. Their results show that mutations for improved protection from predators appear in the same numbers and at the same places in the bacterial genome if only the predatory ciliates are present. The same applies to mutations that cause resistance to antibiotics. However, other mutations occur as soon as both stress factors influence the bacteria and the bacteria have to fight both predators and antibiotics. This causes both the bacteria's protection against predators and resistance to antibiotics to evolve more slowly and be less efficient.

Because the bacteria are less able to protect themselves from predators if they are confronted by the predatory ciliates and antibiotics simultaneously, their numbers are fewer than when they only have to defend themselves from predators. Several stress factors therefore appear to have a strong influence on whether and how often resistance to antibiotics develops and how large the population of bacteria can become.

"Microbial populations – whether in a lake or in the gut – are complex communities in which many species have to compete for resources. The various stress factors to which microbes are exposed have an enormous effect on their evolution and survival rate. It will take some time until we fully understand the interaction of all these factors and the influence of antibiotics and pesticides," explains Becks.

The study is published in Nature Ecology & Evolution.

Source: Max Planck Society [December 06, 2018]

Parrots are famously talkative, and a blue-fronted Amazon parrot named Moises - or at least its genome - is telling scientists volumes about the longevity and highly developed cognitive abilities that give parrots so much in common with humans. Perhaps someday, it will also provide clues about how parrots learn to vocalize so well.

This photograph shows an Amazona aestiva taking care of the nest in Pantanal [Credit: Glaucia Seixas]

Morgan Wirthlin, a BrainHub post-doctoral fellow in Carnegie Mellon University's Computational Biology Department and first author of a report to appear in the journal Current Biology, said she and her colleagues sequenced the genome of the blue-fronted Amazon and used it to perform the first comparative study of parrot genomes.

By comparing the blue-fronted Amazon with 30 other long- and short-lived birds -- including four additional parrot species -- she and colleagues at Oregon Health and Science University (OHSU), the Federal University of Rio de Janeiro and other entities identified a suite of genes previously not known to play a role in longevity that deserve further study. They also identified genes associated with longevity in fruit flies and worms.

"In many cases, this is the first time we've connected those genes to longevity in vertebrates," she said.

This photograph shows Amazona aestiva chicks in Pantanal [Credit: Glaucia Seixas]

Wirthlin, who began the study while a Ph.D. student in behavioral neuroscience at OHSU, said parrots are known to live up to 90 years in captivity -- a lifespan that would be equivalent to hundreds of years for humans. The genes associated with longevity include telomerase, responsible for DNA repair of telomeres (the ends of chromosomes), which are known to shorten with age. Changes in these DNA repair genes can potentially turn cells malignant. The researchers have found evidence that changes in the DNA repair genes of long-lived birds appear to be balanced with changes in genes that control cell proliferation and cancer.

The researchers also discovered changes in gene-regulating regions of the genome -- which seem to be parrot-specific -- that were situated near genes associated with neural development. Those same genes are also linked with cognitive abilities in humans, suggesting that both humans and parrots evolved similar methods for developing higher cognitive abilities.

This photograph shows an Amazona aestiva taking care of the nest in Pantanal [Credit: Glaucia Seixas]

"Unfortunately, we didn't find as many speech-related changes as I had hoped," said Wirthlin, whose research is focused on the evolution of vocal behaviors, including speech. Animals that learn songs or speech are relatively rare -- parrots, hummingbirds, songbirds, whales, dolphins, seals and bats -- which makes them particularly interesting to scientists, such as Wirthlin, who hope to gain a better understanding of how humans evolved this capacity.

"If you're just analyzing genes, you hit the end of the road pretty quickly," she said. That's because learned speech behaviors are thought be more of a function of gene regulation than of changes in genes themselves. Doing comparative studies of these "non-coding" regulatory regions, she added, is difficult, but she and Andreas Pfenning, assistant professor of computational biology, are working on the computational and experimental techniques that may someday reveal more of their secrets.

Author: Byron Spice | Source: Carnegie Mellon University [December 06, 2018]

Botryllus schlosseri, a marine invertebrate that lives in underwater colonies resembling fuzzy pinheads clinging to rocks, has a blood-forming system with uncanny similarities to that of humans, according to scientists at Stanford University.

Under the microscope, a Botryllus colony looks like a bouquet of flowers, although in reality each “petal” is a separate organism with its own heart, gills, digestive system, brain and blood cells [Credit: Stanford Hopkins Marine Station]

In a study published in Nature, the researchers report that these lowly sea creatures may provide a way to understand our own blood-forming system, improve our immune function and find new immune-associated tools for biological discovery.

"The mammalian and Botryllus blood-forming systems also share hundreds of homologous genes, even though the two species are separated by over 500 million years of evolution," said former postdoctoral scholar Benyamin Rosental, PhD.

Rosental shares lead authorship of the study with graduate student Mark Kowarsky. The senior authors are Irving Weissman, MD, the Virginia and D.K. Ludwig Professor for Clinical Innovation in Cancer Research and professor of pathology and of developmental biology; Stephen Quake, PhD, the Lee Otterson Professor in the School of Engineering and professor of bioengineering and of applied physics; and senior research scientist Ayelet Voskoboynik, PhD.

The researchers isolated the Botryllus stem cells that are the foundation of its blood and immune system, as well as the progenitor cells they make on their way to becoming adult blood and immune cells. "Out of all the invertebrates, the Botryllus blood stem cells and progenitors are the most similar to vertebrate blood cells, so it is possible, if not likely, that they are the 'missing link' between vertebrates and invertebrates," said Weissman, who also directs the Stanford Institute for Stem Cell Biology and Regenerative Medicine and the Ludwig Cancer Center at Stanford.

Odd characteristics

Botryllus is an organism with many odd characteristics. It lives part of its life as a free-swimming chordate "tadpole" -- an animal without vertebrae but with a spinal bundle called a notochord. Then it attaches itself to a rock, undergoes metamorphosis to lose its notochord, tail, body muscles and one of its two brains, and settles down to live in colonies with other Botryllus organisms on the subtidal surface.

The separate Botryllus organisms in the colony share a common blood supply, and even exchange cells [Credit: Stanford Hopkins Marine Station]

Under the microscope, a Botryllus colony looks like a bouquet of flowers, although in reality each "petal" is a separate organism with its own heart, gills, digestive system, brain and blood cells. The separate Botryllus organisms in the colony share a common blood supply, and even exchange cells. This blood sharing allows stem cells for sperm and eggs and stem cells for body tissues to be shared throughout the growing colony.

The researchers showed that there are close parallels between the blood systems in Botryllus and in mammals. They found that Botryllus has a sort of incubator of specialized cells, called a niche, that holds and supports blood stem cells and is a lot like the blood stem cell niche in mammalian bone marrow. They also found that Botryllus blood stem cells will find their own way from blood vessels to the niche, exactly as they do in mammals. And they found 327 genes involved in blood cell formation in Botryllus that are similar to genes involved in blood formation in mammals.

Previously, researchers in the Weissman lab showed that a single variant of a gene called BHF regulated whether separate Botryllus organisms would send out blood vessels from their own bodies and merge with adjacent individuals, or undergo an immune rejection, preventing blood cell exchanges. The new study identifies how BHF regulates whether organisms fuse together in the colony: If the protein produced by the gene is recognized as compatible by the other colony, it prevents the activation of a rejection process that is similar to the way that the human immune system's natural killer cells attacks tissues that are not "self."

An excellent model

The discovery of such strong parallels between the two systems offers researchers an excellent model for studying many biological phenomena in mammals, the researchers said. "Blood stem cells in mammals are hard to find and, when found, it's very hard to follow what is going on in the blood stem cell niche," Voskoboynik said. "Botryllus is a translucent organism, so we can easily spot the niche and visually follow the migration of each type of cell from one part of their body to the other."

It's also easy to observe how the cells in individual organisms interact when one mounts an immune attack against the other, or the two individuals fuse blood vessels. This could provide scientists with a better understanding of why an organism accepts or rejects foreign cells, knowledge that could give insights into organ transplant acceptance and rejection, Voskoboynik said.

"With its primitive but effective immune system, Botryllus may also give us insights into how we can boost our own immune responses to pathogens and cancer," Voskoboynik said. "But in addition to any practical benefits this research may produce, we are delighted to explore this important guidepost on the path to understanding the evolution of vertebrates, and of their blood-forming and immune systems. Isn't that what curiosity-driven science is supposed to do?"

Author: Christopher Vaughan | Source: Stanford Medicine [December 05, 2018]

Researchers at the RIKEN Center for Biosystems Dynamics (BDR) and collaborators have described for the first time the development of the hagfish inner ear. Published in the journal Nature, the study provides a new story for inner ear evolution that began with the last common ancestor of modern vertebrates.

The eel-shaped, slime-producing hagfish is a living fossil, remaining unchanged in its structure and habits for over 300 million years [Credit: Gerald & Buff Corsi/Getty Images]

Comparing organs among related animals can be helpful when trying to understand the evolutionary process, and will ultimately help us better understand organogenesis--the process through which organs develop. This underlying philosophy helped guide the collaborative effort to study the inner ear led by Shigeru Kuratani at RIKEN BDR.

The story begins with a difference between jawed and jawless vertebrates. Jawed vertebrates like humans have inner ears with three semicircular canals, which are what allow us to sense our position and stay balanced in the world, and especially to sense 3-D acceleration. The fossil record shows that a group of jawless fish from the Paleozoic era only had two semicircular canals. In order to understand the evolutionary changes that led three canals, the team looked at the only two types of jawless vertebrates that still exist on earth: lampreys and hagfish.

Lampreys are thought to have two semicircular canals, while hagfish only have one. However, hagfish are no longer thought to be more primitive than lampreys. A series of molecular biological experiments was able to clarify the issue. Analyzing the regulatory genes that control the development of the semicircular canals showed that the basic pattern of inner ear development is similar for all vertebrates, including lampreys and hagfish. Key genes, such as Tbx1 and Patched were expressed at the same places with the same timing across all three types of vertebrate.

The anterior and posterior canals in jawed vertebrates appear to be genetically homologous to the anterior and posterior parts of the lamprey canal, while the pattern for the single hagfish canal is likely an evolved trait, not a primitive condition. The difference between the jawed and lawless fish is the presence of the common crus, a structure that connects the anterior and posterior canals in jawed vertebrates. The current study could not determine whether the common crus is something that jawed vertebrates gained or something that was lost in jawless vertebrates.

Further analysis focused on the Otx1 gene. This gene is required for proper development of the lateral canal, the third canal that is unique to jawed vertebrates. The researchers found that despite the lack of a lateral canal, lampreys and hagfish both expressed Otx1 in the proper location during development. This was somewhat surprising as its expression was thought to be an advent that led to the evolution of the lateral canal. Instead, it appears that Otx1 expression in the otic vesicle is an ancient feature for all vertebrates.

A more complete understanding will be possible by performing studies with an animal that represents the lineages before jawed and jawless vertebrates diverged.

Source: RIKEN [December 05, 2018]

On 3 December 2018, the laboratory of Professor Axel Meyer, University of Konstanz published new findings of an experimental evolutionary project that ran for 30 years on the genomic mechanisms of sex determination in swordtail fish in the journal Nature Communications. Dr Paolo Franchini, evolutionary biologist and Junior Research Group Leader at the University of Konstanz is the lead author of this collaboration with the laboratory of Professor Manfred Schartl of the University of Würzburg

Xiphophorus maculatus hellerii [Credit: Manfred Schartl/Paolo Franchini]

The diversity of sex determination systems is remarkably diverse among fishes compared to mammals that all have a stereotypic XX, XY sex-chromosomal mechanism to determine sex. Why and how the genomic mechanisms and the evolutionary causes behind such diversity in sex determination in fish are so variable remained unknown.

Evolutionary biologist Dr Paolo Franchini with his collaborators has now been able to describe such a mechanism and its exact function in this study entitled "Long-term experimental hybridisation results in the evolution of a new sex chromosome in swordtail fish".

Professor Manfred Schartl, Head of the Department for Physiological Chemistry at the Biocenter of the University of Würzburg, initiated this experiment that included hybridisation with backcrossing by two Xiphophorus fish species with different sex chromosome systems three decades ago. Hybrid origins of species, the result of the crossing of two genetically different species, are found frequently in fish populations.

"What we know from the study of these systems in natural habitats is that hybridisation is a crucial mechanism for the evolution of new species", explains Paolo Franchini. In the experiment the researchers could study the effects of hybridisation on the genomic mechanism of sex-determination.

Determining the sex of these fish is easy: as its name suggests, the male swordtail fish has a sword-like elongated caudal fin; the female, on the other hand, is rounder and fuller and does not have a swordtail. In this long-term laboratory study the effects of hybridisation that is thought to have resulted in at least two swordtail species in nature on the genome and the mechanisms that determine sex could be studied in detail.

In an experimental design that makes it possible to track crossings of more than 100 generations over more than 30 years, a female Xiphophorus maculatus was crossed repeatedly with a male Xiphophorus hellerii.

These two species have different sex chromosome systems. In further steps, the new hybrid fish originating from the cross was backcrossed again with the male species, and this design was repeated for more than 100 generations.

Paolo Franchini explains further: "We found out that introgression - the movement of genetic material from one species to another - and the selection of pigmentation phenotypes results in the retention of an unexpectedly large maternally derived genomic region."

During the hybridisation process, the sex-determining region on the X chromosome of one parent was transferred to an autosome of the hybrid fish. This transfer led to the evolution of a completely new sex chromosome.

"Our results show above all the complexity of factors that contribute to patterns observed in hybrid genomes including such fundamental issues such as sex determination", summarises Paolo Franchini. The work proves that hybridisation can catalyse the rapid evolution of a new sex chromosome and thus makes an essential contribution to an experiment launched more than 30 years ago.

Source: University of Konstanz [December 05, 2018]

An international group of scientists led by researchers from the University of Bristol have advanced our understanding of how ancient animals saw the world by combining the study of fossils and genetics.

A fossil trilobite with its complex eye. These ancient animals were inferred to have minimally possessed four opsins, like many modern arthropods, and should have therefore been able to see colours [Credit: University of Bristol]

Ancestors of insects and crustaceans that lived more than 500 million years ago in the Cambrian period were some of the earliest active predators, but not much is known about how their eyes were adapted for hunting.

Work published in the Proceedings of the Royal Society B suggests that when fossil and genetic data are assessed in tandem, previously inaccessible and exciting conclusions about long dead species can be made.

By examining the morphological characteristics of fossils' eyes, alongside the genetic visual pigment clues, a cross-disciplinary team led by a collaboration between the University of Bristol's Davide Pisani, Professor of Phylogenomics in the School of Earth Sciences and Nicholas Roberts, Professor of Sensory Ecology in the School of Biological Sciences, were able to find that ancient predators with more complex eyes are likely to have seen in colour.

Professor Pisani remarked: "Being able to combine fossil and genetic data in this way is a really exciting frontier of modern palaeontological and biological research. Vision is key to many animals' behaviour and ecology, and understanding how extinct animals perceived their environment will help enormously to clarify how they evolved."

By calculating the time of emergence of different visual pigments, and then comparing them to the inferred age of origin of key fossil lineages, the researchers were able to work out the number of pigments likely to have been possessed by different fossil species. They found that fossil animals with more complex eyes appeared to have more visual pigments, and that the great predators of the Cambrian period may have been able to see in colour.

Dr James Fleming, Professor Pisani and Roberts' former PhD student, explained: "Animal genomes and therefore opsin genes (constituting the base of different visual pigments) evolve by processes of gene duplication. The opsin and the pigment that existed before the duplication is like a parent, and the two new opsins (and pigments) that emerge from the duplication process are like children on a family tree.

"We calculated the birth dates of these children and this allowed understanding of what the ancient world must have seemed like to the animals that occupied it. We found that while some of the fossils we considered had only one pigment and were monochromat, i.e. they saw the world as if looking into a black and white TV, forms with more complex eyes, like iconic trilobites, had many pigments and most likely saw their world in colours."

The combinations of complex eyes and multiple kinds of visual pigments are what allows animals to distinguish between different objects based on colour alone - what we know as colour vision.

Professor Roberts commented: "It is remarkable to see how in only a very few million years the view those animals' had of their world changed from greys to the colourful world we see today."

The project involved scientists from all across the world - from the UK as well as Denmark, Italy, Korea and Japan, where Dr Fleming has now moved to work as a postdoctoral researcher. Each of them brought their own specialities to this multidisciplinary work, providing expertise in genetics, vision, taxonomy and palaeontology.

Source: University of Bristol [December 04, 2018]