The Russian community of geneticists, clinicians and bioethicists have reached a consensus on the use of genome-editing technologies on human embryos and germ cells for clinical purposes. They consider that such experiments are premature at this point. Their view aligns with the position of the Russian ministry of health and sets the social context for further discussion of the technology.
Researchers from the University of Oxford have revealed that the genetic ancestries of many of sub-Saharan Africa's populations are the result of historical DNA mixing events, known as admixture, within the last 4,000 years.
Their study, to be published in the journal eLife, uncovers signatures of these admixture events through a large analysis of DNA from populations across the continent. The discovery provides a foundation for the recent genetic history of the continent, which could aid future studies of non-communicable and infectious diseases, such as malaria.
While admixture has been demonstrated in other regions of the world, the new analysis has allowed the team to characterise sub-Saharan Africa's mixing events in an unprecedented level of detail.
"As Africa has few written records of its history, it is somewhat unknown what important movements of people generated the populations in the continent today," says lead author George Busby, Statistical Geneticist at the Wellcome Trust Centre for Human Genetics.
"Looking at and comparing the differences in the genomes of people alive today can help us better understand and reconstruct the historical interactions that brought their ancestors together."
Using genetic markers, researchers have for the first time shown how cultivating a specific crop led to the expansion of a pollinator species. In this case, the researchers found that the spread of a bee species in pre-Columbian Central and North America was tied to the spread of squash agriculture.
"We wanted to understand what happens when the range of a bee expands," says Margarita López-Uribe, a postdoctoral researcher at North Carolina State University and lead author of a paper describing the work. "What does that mean for its genetic variability? And if the genetic variability declines, does that harm the viability of the species?"
To explore these questions, researchers looked at the squash bee (Peponapis pruinosa), which is indigenous to what is now central Mexico and the southwestern United States. Squash bees are specialists, collecting pollen solely from the flowers of plants in the genus Cucurbita, such as squash, zucchini and pumpkins.
Before contact with Europeans, native American peoples had begun cultivating Cucurbita crops. Over time, these agricultural practices spread to the north and east.
"We wanted to know whether P. pruinosa spread along with those crops," López-Uribe says.
To find out, researchers looked at DNA from squash bee individuals, collected from throughout the species' range. P. pruinosa can now be found from southern Mexico to California and Idaho in the west, and from Georgia in the southeast to Quebec in the north.
By assessing genetic markers in each bee's DNA, the researchers could identify genetic signatures associated with when and where the species expanded.
Two scientists have come up with a depressing new hypothesis that attempts to explain why cancer is so hard to stop.
Maybe, they suggest, cancer's not working against us. Maybe the disease is actually an evolutionary 'final checkpoint' that stops faulty DNA from being passed down to the next generation.
Three weeks ago, 130 scientists, entrepreneurs and policy leaders held an invitation-only, closed-door meeting at Harvard University to discuss an ambitious plan to create synthetic human genomes. Now, after a flurry of criticism over the secrecy of the effort, the participants have published their idea, declaring that they're launching a project to radically reduce the cost of synthesizing genomes -- a potentially revolutionary development in biotechnology that could enable technicians to grow human organs for transplantation.
Evidence for extensive horizontal gene transfer from the draft genome of a tardigrade
Authors:
Boothby et al
Abstract:
Horizontal gene transfer (HGT), or the transfer of genes between species, has been recognized recently as more pervasive than previously suspected. Here, we report evidence for an unprecedented degree of HGT into an animal genome, based on a draft genome of a tardigrade, Hypsibius dujardini. Tardigrades are microscopic eight-legged animals that are famous for their ability to survive extreme conditions. Genome sequencing, direct confirmation of physical linkage, and phylogenetic analysis revealed that a large fraction of the H. dujardini genome is derived from diverse bacteria as well as plants, fungi, and Archaea. We estimate that approximately one-sixth of tardigrade genes entered by HGT, nearly double the fraction found in the most extreme cases of HGT into animals known to date. Foreign genes have supplemented, expanded, and even replaced some metazoan gene families within the tardigrade genome. Our results demonstrate that an unexpectedly large fraction of an animal genome can be derived from foreign sources. We speculate that animals that can survive extremes may be particularly prone to acquiring foreign genes.
Genome of a tardigrade: Horizontal gene transfer or bacterial contamination?Seriously! You guys screwed up!
Authors:
Bemm et al
Extract:
We have read the article “Evidence for extensive horizontal gene transfer from the draft genome of a tardigrade” (1) with interest and were astonished by the high number of genes horizontally transferred into the tardigrade genome. Still, we were surprised by the reported genome size of greate than 200 Mbp, which is in stark contrast to a previously published size of ∼78 Mbp determined by the same group (2).
No evidence for extensive horizontal gene transfer from the draft genome of a tardigrade
Author:
Arakawa
Extract:
Through a draft genome sequencing of a tardigrade Hypsibius dujardini, Boothby et al. (1) report that “Approximately one-sixth of the genes in the tardigrade genome were found to have been acquired through horizontal transfer, a proportion nearly double the proportion of previous known cases of extreme horizontal gene transfer (HGT) in animals.” However, the authors also state that the “cultures are not axenic,” which means that they are highly prone to contamination.
Reply to Bemm et al. and Arakawa: Identifying foreign genes in independent Hypsibius dujardini genome assemblies
Authors:
Boothyby et al
Extract:
Our report (1) describing the discovery of extensive horizontal gene transfer in a tardigrade genome has raised questions from other groups who were sequencing the Hypsibius dujardini genome in parallel or who have done new experiments and analyses since our report (2⇓⇓–5). Bemm et al. (2) now report filtering our data for likely contaminants, resulting in a new, prefiltered genome assembly. Arakawa (3) has sequenced genomes of starved, washed, individual animals that had been treated with antibiotics for 48 h, and used this genomic sequence and RNA-Seq data to identify likely bona fide tardigrade contigs. Two other reports have contributed data and analysis: Delmont and Eren (4) used a newly published analysis and visualization platform, Anvi'o (6), to identify likely contaminants in our genome assembly, and Koutsovoulos et al. (5) applied useful taxon-annotated GC coverage plots (Blobplots) (7) to our data and reported an independent genome assembly.
A new study from Tel Aviv University, Cornell University and the Albert Einstein College of Medicine reveals genetic proof of the Jewish roots of the Bene Israel community in the western part of India. They have always considered themselves Jewish.
"Almost nothing is known about the Bene Israel community before the 18th century, when Cochin Jews and later Christian missionaries first came into contact with it," says first author Yedael Waldman of both TAU's Department of Molecular Microbiology and Cornell's Department of Biological Statistics and Computational Biology. "Beyond vague oral history and speculations, there has been no independent support for Bene Israel claims of Jewish ancestry, claims that have remained shrouded in legend."
Despite the urban myth reinforced by many a daytime talk show, researchers writing in Trends in Ecology & Evolution on April 5 say the emerging evidence consistently indicates that very few fathers have unknowingly raised children who were not biologically their own. The collective evidence for low rates of extra-pair paternity (EPP) challenges the notion that it pays, evolutionarily speaking, to sleep around, the researchers say.
"Media and popular scientific literature often claim that many alleged fathers are being cuckolded into raising children that biologically are not their own," said Maarten Larmuseau of KU Leuven in Belgium. "Surprisingly, the estimated rates within human populations are quite low--around 1 or 2 percent."
Those rates apparently haven't changed much either, despite the fact that people in the past didn't have access to modern contraceptives.
Molecular development of fibular reduction in birds and its evolution from dinosaurs
Authors:
Botelho et al
Abstract:
Birds have a distally reduced, splinter-like fibula that is shorter than the tibia. In embryonic development, both skeletal elements start out with similar lengths. We examined molecular markers of cartilage differentiation in chicken embryos. We found that the distal end of the fibula expresses Indian hedgehog (IHH), undergoing terminal cartilage differentiation, and almost no Parathyroid-related protein (PTHrP), which is required to develop a proliferative growth plate (epiphysis). Reduction of the distal fibula may be influenced earlier by its close contact with the nearby fibulare, which strongly expresses PTHrP. The epiphysis-like fibulare however then separates from the fibula, which fails to maintain a distal growth plate, and fibular reduction ensues. Experimental downregulation of IHH signaling at a postmorphogenetic stage led to a tibia and fibula of equal length: The fibula is longer than in controls and fused to the fibulare, whereas the tibia is shorter and bent. We propose that the presence of a distal fibular epiphysis may constrain greater growth in the tibia. Accordingly, many Mesozoic birds show a fibula that has lost its distal epiphysis, but remains almost as long as the tibia, suggesting that loss of the fibulare preceded and allowed subsequent evolution of great fibulo–tibial disparity.
Researchers at the University of British Columbia have identified a common ancestral gene that enabled the evolution of advanced life over a billion years ago.
The gene, found in all complex organisms, including plants and animals, encodes for a large group of enzymes known as protein kinases that enabled cells to be larger and to rapidly transfer information from one part to another.
"If the duplications and subsequent mutations of this gene during evolution didn't happen, then life would be completely different today," said Steven Pelech, a professor in Division of Neurology in the UBC Faculty of Medicine. "The most advanced life on our planet would probably still be bacterial slime."
Plants, animals, mushrooms and more all exist because they are made up of eukaryotic cells that are larger and far more complex than bacteria. Inside of these eukaryotic cells are hundreds of organelles that perform diverse functions to keep them living, just as different organs do for the human body.
The new research, published this week in the Journal of Biological Chemistry, identifies the gene that gave rise to protein kinases. On a cellular scale, these highly interactive signaling proteins play a role similar to the neurons in the brain by transferring information throughout the cell by a process known as protein phosphorylation.
This ability to transmit signals from one part of the cell to another not only enabled cells to become more complex internally, but also allowed cells to come together to form systems, paving the way for the evolution of intelligent life.
Many safety, technical and legal barriers still stand in the way of editing DNA in human embryos. But some scientists and ethicists say that it is important to think through the implications of embryo editing now — before these practical hurdles are overcome. What sort of world would these procedures create for those currently living with disease and for future generations?
The Spanish conquest of the Americas was devastating for native peoples. Many native men died in conflicts with the invaders. Male Spanish colonists often came without their wives and took native women as partners. A new genetic analysis of Panamanian men by a team including a Smithsonian scientist shows this historical legacy: only 22 percent had Y-chromosomes of native origin, even though most Panamanians are of female indigenous ancestry.
Everyone has a pair of sex chromosomes that determine their gender. Females have two X-chromosomes, while males have one X and one Y, the latter inherited from their father. These chromosomes are found in each cell's nucleus. Another genetic component called mitochondrial DNA (mtDNA) is found in cells outside the nucleus. Both males and females inherit their mtDNA from their mother alone. Over time, small mutations accumulate in both mtDNA and Y-chromosomes, allowing scientists to trace their history.
A team of geneticists from the University of Pavia including Antonio Torroni found that among the 408 Panamanian men whose genetics were analyzed, 60 percent had Y-chromosomes that originated in West Eurasia and North Africa (probably mostly from Europe). About 22 percent were of Native American origin, 6 percent from sub-Saharan Africa and 2 percent from South Asia (probably China or the Indian sub-continent). In contrast, a large majority of this group--including nearly all those with Native American, African and Asian Y-chromosomes--had mtDNA of indigenous origin. Among men with Eurasian Y-chromosomes, 13 percent had mtDNA from sub-Saharan Africa and only a very few had European mtDNA.
Climate change can influence everything from pine beetle outbreaks in the Rocky Mountains to rising sea levels in Papua New Guinea. In the face of a rapidly changing earth, plants and animals are forced to quickly deal with new challenges if they hope to survive. According to a recent paper by Jason Fridley, associate professor of biology in Syracuse University's College of Arts and Sciences, recently minted SU Ph.D. Catherine Ravenscroft, and University of Liverpool professor Raj Whitlock some species may be able to handle environmental changes better than others.
Fridley explains that species have a couple options to deal with stress associated with environmental change: they can pick up and move to more favorable areas, or they can stick it out and adapt to the new challenges. This ability to adapt to climate changes was the main focus of the researcher's study
Ribwort plantain and sheep fescue, two plants common in the study site, show signs of being able to respond to induced climate challenges. "There is evidence of genetic differentiation with a long term climate treatment," says Ravenscroft, explaining that genetic difference have built up between climate-treated versus untreated plants in the study site.
What's more, the gene-level changes have happened remarkably fast. Because these grasses are perennial species, meaning they live and reproduce for multiple growing seasons, Fridley estimates there have only been around 10 generations of plants over the 15-year experiment. While that may sound like a lot of generations if you think back to your great-great-great-great-great-great-great-great-grandparent, genetic splits happen on an evolutionary timescale - think in terms of hundreds or thousands of years.
Centenarians show successful aging as they remain active and alert at very old ages. Scientists at Stanford University and the University of Bologna have begun to unravel the basis for longevity by finding genetic loci associated with extreme longevity.
Previous work indicated that centenarians have health and diet habits similar to the average person, suggesting that factors in their genetic make-up could contribute to successful aging. However, prior genetic studies have identified only a single gene (APOE, known to be involved in Alzheimer's disease) that was different in centenarians versus normal agers. The results from the current study indicate that several disease variants may be absent in centenarians versus the general population.
Many human gene variants have evolved specifically to protect older adults against neurodegenerative and cardiovascular diseases, thus preserving their contributions to society, report University of California, San Diego School of Medicine researchers in the November 30 issue of Proceedings of the National Academy of Sciences.
"We unexpectedly discovered that humans have evolved gene variants that can help protect the elderly from dementia," said Ajit Varki, MD, Distinguished Professor of Medicine and Cellular and Molecular Medicine at UC San Diego School of Medicine, adjunct professor at the Salk Institute for Biological Studies and co-director of the UC San Diego/Salk Center for Academic Research and Training in Anthropogeny (CARTA). "Such genes likely evolved to preserve valuable and wise grandmothers and other elders, as well as to delay or prevent the emergence of dependent individuals who could divert resources and effort away from the care of the young." Varki led the study, along with Pascal Gagneux, PhD, associate professor of pathology and associate director of CARTA.
The standard model of natural selection predicts that once the age of reproduction ends, individuals die. That's because selection early in life strongly favors variants that benefit reproductive success, even at the cost of negative consequences late in life -- one major reason we age. This is indeed the case in almost all vertebrates. Humans (and certain whales) are an exception to this rule, living decades beyond reproductive age. Such elders contribute to the fitness of younger individuals by caring for grandchildren and also by passing down important cultural knowledge. Age-related cognitive decline compromises these benefits, and eventually burdens the group with the need to care for dependent older members.
In this first-of-its kind discovery, Varki, Gagneux and their teams initially focused on the gene that encodes the CD33 protein. CD33 is a receptor that projects from the surface of immune cells, where it keeps immune reactions in check, preventing "self" attack and curtailing unwanted inflammation. Previous studies suggested that a certain form of CD33 suppresses amyloid beta peptide accumulation in the brain. Amyloid beta accumulation is thought to contribute to late-onset Alzheimer's disease, a post-reproductive condition that uniquely affects humans and is aggravated by inflammation and cerebral vascular disease.
The researchers compared CD33 regulation in humans and our closest living relatives, chimpanzees. They found that levels of the CD33 variant that protects against Alzheimer's are four-fold higher in humans than chimpanzees.
Using some ancient DNA detective work, a new study led by University of California Berkeley postdoctoral researcher Mike D. Martin and University of Copenhagen professor Tom Gilbert has linked the culprit behind the 19th-century Irish potato famine, which was transported to Europe in the 1840s, to a fungus-like organism that originated in South America.
Just how the pathogen, called Phytophthora infestans, made the transatlantic leap to destroy potato crops on a global scale is a "Guns, Germs, and Steel"-like tale of New World exploration and devastation published in the advanced online edition of Molecular Biology and Evolution.
The authors used genome sequences from 71 modern and historical samples of the microbial pathogen, a unique collection culled from worldwide private archives, to construct the ancestral tree of the pathogen. The origin of the species dates back to 1558 AD, the age when the first Europeans explored South America.
The research team further observed that the species was first introduced to 19th-century Europe shortly after it evolved and diversified. They found a close connection between a present-day sister species, P. andina (found only in the highlands of Ecuador and Peru) and the ancient P. infestans that triggered the first global outbreak in 1845 and the catastrophic Irish potato famine.
The authors speculate that after being found in South America, the pathogen either spread from South America directly to the U.S., or was simultaneously introduced from Mexico into South America and the U.S. prior to its infestation of Europe. "We think early European activities in the New World led to the origin of this devastating pathogen. Countless improbable events led to the introduction of this species to Europe in 1845, but our work narrows down the evolutionary possibilities to exactly two," said Martin.
If you have diabetes, or cancer or even heart problems, maybe you should blame it on your dad's behaviour or environment. Or even your grandfather's. That's because, in recent years, scientists have shown that, before his offspring are even conceived, a father's life experiences involving food, drugs, exposure to toxic products and even stress can affect the development and health not only of his children, but even of his grandchildren.
But, despite a decade of work in the area, scientists haven't been able to understand much about how this transmission of environmental memories over several generations takes place. McGill researchers and their Swiss collaborators think that they have now found a key part of the molecular puzzle. They have discovered that proteins known as histones, which have attracted relatively little attention until now, may play a crucial role in the process.
They believe that this finding, which they describe in a paper just published in Science, has the potential to profoundly change our understanding of how we inherit things. That's because the researchers show that there is something apart from DNA that plays an important role in inheritance in general, and could determine whether a father's children and grandchildren will be healthy or not.
Evolutionary Genomics and Conservation of the Endangered Przewalski’s Horse
Authors:
Der Sarkissian et al
Abstract:
Przewalski’s horses (PHs, Equus ferus ssp. przewalskii) were discovered in the Asian steppes in the 1870s and represent the last remaining true wild horses. PHs became extinct in the wild in the 1960s but survived in captivity, thanks to major conservation efforts. The current population is still endangered, with just 2,109 individuals, one-quarter of which are in Chinese and Mongolian reintroduction reserves [ 1 ]. These horses descend from a founding population of 12 wild-caught PHs and possibly up to four domesticated individuals [ 2–4 ]. With a stocky build, an erect mane, and stripped and short legs, they are phenotypically and behaviorally distinct from domesticated horses (DHs, Equus caballus). Here, we sequenced the complete genomes of 11 PHs, representing all founding lineages, and five historical specimens dated to 1878–1929 CE, including the Holotype. These were compared to the hitherto-most-extensive genome dataset characterized for horses, comprising 21 new genomes. We found that loci showing the most genetic differentiation with DHs were enriched in genes involved in metabolism, cardiac disorders, muscle contraction, reproduction, behavior, and signaling pathways. We also show that DH and PH populations split ∼45,000 years ago and have remained connected by gene-flow thereafter. Finally, we monitor the genomic impact of ∼110 years of captivity, revealing reduced heterozygosity, increased inbreeding, and variable introgression of domestic alleles, ranging from non-detectable to as much as 31.1%. This, together with the identification of ancestry informative markers and corrections to the International Studbook, establishes a framework for evaluating the persistence of genetic variation in future reintroduced populations.
If you go back far enough, all people share a common ancestry. But some populations are more closely related than others based on events in the past that brought them together. Now, researchers reporting in the Cell Press journal Current Biology on September 17 have shown that it's possible to use DNA evidence as a means to reconstruct and date those significant past events. The findings suggest that evidence in our genomes can help to recover lost bits of history.
"We now have the statistical machinery to uncover which historical events have produced the mosaic genomes of people in Europe today," says George Busby of the University of Oxford. "The successful reconstruct ion of the genetic history of a region of the world that has been well investigated both archaeologically and historically suggests that these approaches have the potential to be applied to areas where history has not been so well recorded and where genetics might be the only way of recovering history."
Busby and his colleagues applied a new method they've developed to compare single genetic variants among populations, taking into account the relationships among those markers based on their physical proximity along the chromosomes. That information can be used to infer subtle relationships among populations, including those that are genetically very similar, as well as the history of a continent.
The new work shows that all European populations have mixed over time as people picked up and moved from one place to another. Usually this mixing has involved nearby groups, but sometimes populations bear the mark of invading populations from more distant locations.
A group of scientists from Okinawa Institute of Science and Technology Graduate University (OIST), Nagoya University, and the University of Tokyo decoded the first lingulid brachiopod genome, from Lingula anatina collected at Amami Island, Japan. The paper published in Nature Communications presents the results of their analysis of over 34,000 genes comprising the L. anatina genome and shows that despite Lingula's reputation as a "living fossil" its genome is actively evolving.
