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https://www.smithsonianmag.com/smart-news/female-elephants-are-evolving-to-go-tuskless-but-may-be-killing-males-180978938/

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Scientists have linked heavy ivory poaching to an increase of tuskless African female elephants in Mozambique at the Gorongosa National Park, reports Maite Fernández Simon for the Washington Post. The East African country underwent a nearly two decade civil war that decimated 90 percent of the Grongosa elephant population because both sides engaged in animal poaching. This activity may have set off an evolutionary response that favored tuskless elephants as population numbers recovered. While no longer having ivory tusks may save elephants from poaching, the genetic mutation responsible for eliminating tusks is lethal to male elephants, reports Elizabeth Preston for the New York Times. Details of the study were published this month in the research journal .

Ivory tusks are massive teeth or incisors that elephants use to dig for water, strip trees of bark for food, lift objects, protect their trunks, and defend themselves, reports Christina Larson for the Associated Press. The large teeth are highly sought after for their value. One pound of ivory is worth $1,500, and tusks can weigh up to 250 pounds.

Poaching was amplified during the Mozambican Civil War between 1977 to 1992 to finance the war efforts. Elephant population numbers dropped from 2,500 individuals to around 200 in the early 2000s, reports Nicola Jones for . However, many female elephants that survived poaching during wartime were overlooked because they were already naturally tuskless. So, after the war ended, female elephants that naturally lacked tusks were more likely to pass down genes coding for tusklessness, per the New York Times.

To see how the ivory trade and poaching pressures may have amplified natural selection towards tuskless elephants, researchers started collecting data on the elephants at Gorongosa National Park. However, they noticed that the elephants with no incisors were usually female. The park has never seen a tuskless male, suggesting the trait related to tusklessness is sex-linked.

This find suggests the mutation for tusklessness may kill male elephants, per the New York Times. The team calculated that 18.5 percent of female elephants did not have tusks before the war began. After the war, 33 percent of 91 female elephants born were naturally tuskless, per Nature. Half of the female elephants at Gorongosa are tuskless, suggesting that poaching survivors passed the trait down to their daughters.

If a female elephant had one copy of the tuskless mutation, they would have no tusks. So, when the elephant reproduces, half of their daughters will have tusks, and the others will not have tusks at all. Half of the males will have tusks if their offspring is male, and the other half will die, possibly even before birth, per the New York Times.

"When mothers pass it on, we think the sons likely die early in development, a miscarriage," says study co-author Brian Arnold, a Princeton evolutionary biologist, to the Associated Press.

By sequencing the genomes of seven females with tusks and 11 females without tusks, the research team identified two genes responsible for helping build tusks that may be causing tuskless females and death in tuskless males. One of the genes, called AMELX, is exclusively located on the X chromosome, and the other is called MEP1a, Nature reports. In mammals, these genes code for the development of incisor teeth.

AMELX is located near critical genes that can kill males if they are not present in the X chromosome, per the New York Times. Scientists are still not sure which changes are causing a loss of tusks in either of the genes, whichthey plan to evaluate in future research.

"They have this very compelling genomic data," Chris Darimont, a conservation expert at the University of Victoria, Canada, tells Nature. "This is a wake-up call in terms of coming to grips with humans as a dominant evolutionary force on the planet."

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Female Elephants Are Evolving Without Tusks in Mozambique

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Scientists have linked heavy ivory poaching to an increase of tuskless African female elephants in Mozambique at the Gorongosa National Park, reports Maite Fernández Simon for the Washington Post . The East African country underwent a nearly two decade civil war that decimated 90 percent of the Grongosa elephant population because both sides engaged in animal poaching.

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https://www.science.org/content/article/humans-are-still-evolving-and-we-can-watch-it-happen

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Many people think evolution requires thousands or millions of years, but biologists know it can happen fast. Now, thanks to the genomic revolution, researchers can actually track the population-level genetic shifts that mark evolution in action-and they're doing this in humans. Two studies presented at the Biology of Genomes meeting here last week show how our genomes have changed over centuries or decades, charting how since Roman times the British have evolved to be taller and fairer, and how just in the last generation the effect of a gene that favors cigarette smoking has dwindled in some groups.

"Being able to look at selection in action is exciting," says Molly Przeworski, an evolutionary biologist at Columbia University. The studies show how the human genome quickly responds to new conditions in subtle but meaningful ways, she says. "It's a game-changer in terms of understanding evolution."

Evolutionary biologists have long concentrated on the role of new mutations in generating new traits. But once a new mutation has arisen, it must spread through a population. Every person carries two copies of each gene, but the copies can vary slightly within and between individuals. Mutations in one copy might increase height; those in another copy, or allele, might decrease it. If changing conditions favor, say, tallness, then tall people will have more offspring, and more copies of variants that code for tallness will circulate in the population.

With the help of giant genomic data sets, scientists can now track these evolutionary shifts in allele frequencies over short timescales. Jonathan Pritchard of Stanford University in Palo Alto, California, and his postdoc Yair Field did so by counting unique single-base changes, which are found in every genome. Such rare individual changes, or singletons, are likely recent, because they haven't had time to spread through the population. Because alleles carry neighboring DNA with them as they circulate, the number of singletons on nearby DNA can be used as a rough molecular clock, indicating how quickly that allele has changed in frequency.

Pritchard's team analyzed 3000 genomes collected as part of the UK10K sequencing project in the United Kingdom. For each allele of interest in each genome, Field calculated a "singleton density score" based on the density of nearby single, unique mutations. The more intense the selection on an allele, the faster it spreads, and the less time there is for singletons to accumulate near it. The approach can reveal selection over the past 100 generations, or about 2000 years.

Stanford graduate students Natalie Telis and Evan Boyle and postdoc Ziyue Gao found relatively few singletons near alleles that confer lactose tolerance-a trait that enables adults to digest milk-and that code for particular immune system receptors. Among the British, these alleles have evidently been highly selected and have spread rapidly. The team also found fewer singletons near alleles for blond hair and blue eyes, indicating that these traits, too, have rapidly spread over the past 2000 years, Field reported in his talk and on 7 May in the preprint server bioRxiv.org. One evolutionary driver may have been Britain's gloomy skies: Genes for fair hair also cause lighter skin color, which allows the body to make more vitamin D in conditions of scarce sunlight. Or sexual selection could have been at work, driven by a preference for blond mates.

Other researchers praise the new technique. "This approach seems to allow much more subtle and much more common signals of selection to be detected," says evolutionary geneticist Svante Pääbo of the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany.

In a sign of the method's power, Pritchard's team also detected selection in traits controlled not by a single gene, but by tiny changes in hundreds of genes. Among them are height, head circumference in infants, and hip size in females-crucial for giving birth to those infants. By looking at the density of singletons flanking more than 4 million DNA differences, Pritchard's team discovered that selection for all three traits occurred across the genome in recent millennia.

Joseph Pickrell, an evolutionary geneticist at New York Genome Center in New York City, has used a different strategy to put selection under an even keener microscope, detecting signs of evolution on the scale of a human lifetime. He and Przeworski took a close look at the genomes of 60,000 people of European ancestry who had been genotyped by Kaiser Permanente in Northern California, and 150,000 people from a massive U.K. sequencing effort called the UK Biobank. They wanted to know whether genetic variants change frequency across individuals of different ages, revealing selection at work within a generation or two. The biobank included relatively few old people, but it did have information about participants' parents, so the team also looked for connections between parental death and allele frequencies in their children.

In the parents' generation, for example, the researchers saw a correlation between early death in men and the presence in their children (and therefore presumably in the parents) of a nicotine receptor allele that makes it harder to quit smoking. Many of the men who died young had reached adulthood in the United Kingdom in the 1950s, a time when many British men had a pack-a-day habit. In contrast, the allele's frequency in women and in people from Northern California did not vary with age, presumably because fewer in these groups smoked heavily and the allele did not affect their survival. As smoking habits have changed, the pressure to weed out the allele has ceased, and its frequency is unchanged in younger men, Pickrell explains. "My guess is we are going to discover a lot of these gene-by-environment effects," Przeworski says.

Indeed, Pickrell's team detected other shifts. A set of gene variants associated with late-onset menstruation was more common in longer-lived women, suggesting it might help delay death. Pickrell also reported that the frequency of the ApoE4 allele, which is associated with Alzheimer's disease, drops in older people because carriers died early. "We can detect selection on the shortest timeframe possible, an individual's life span," he says.

Signs of selection on short timescales will always be prey to statistical fluctuations. But together the two projects "point to the power of large studies to understand what factors determine survival and reproduction in humans in present-day societies," Pääbo says.

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Humans are still evolving-and we can watch it happen

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Many people think evolution requires thousands or millions of years, but biologists know it can happen fast. Now, thanks to the genomic revolution, researchers can actually track the population-level genetic shifts that mark evolution in action-and they're doing this in humans.

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https://www.science.org/content/article/dopamine-may-have-given-humans-our-social-edge-over-other-apes

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Dopamine may have given humans our social edge over other apes

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The neurotransmitter might have helped spur the evolution of social intelligence

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https://www.sciencedaily.com/releases/2022/09/220921093000.htm

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It may be the most baffling quirk of COVID: What manifests as minor, flu-like symptoms in some individuals spirals into severe disease, disability, and even death in others. A new paper published in Nature may explain the genetic underpinnings of this dichotomy.

The researchers demonstrated that mice with gene variants previously linked to Alzheimer's disease were at greater risk of dying when infected with COVID. And a retrospective analysis suggests that patients with those same gene variants were more likely to have died of COVID throughout the pandemic. Because three percent of the world population possesses these gene variants, the findings may have implications for hundreds of millions of individuals globally.

"It is clear that age, sex, and certain preconditions such as diabetes increase the risk of detrimental outcomes, but these factors don't fully explain the spectrum of COVID outcomes," says Sohail Tavazoie, the Leon Hess Professor at The Rockefeller University. "This is the first time that we've seen such a common genetic variant associated with COVID mortality."
A closer look at APOE
In previous work, Tavazoie's lab studied a gene called APOE that plays a role in cancer metastasis. After demonstrating that the gene suppresses the spread of melanoma and regulates anti-tumor immune responses, he and his team began looking at its different forms, or alleles, more closely. Most people have a form called APOE3, but 40 percent of the population carries at least one copy of the APOE2 or APOE4 variant. Individuals with APOE2 or APOE4 produce proteins that differ from APOE3 protein by one or two amino acids.

One or two amino acids make a difference. Individuals with APOE4 are at greater risk of developing Alzheimer's and atherosclerosis, and Tavazoie and Benjamin Ostendorf, a postdoctoral fellow in his lab, have demonstrated that APOE4 and APOE2 impact the immune response against melanoma. As the pandemic progressed, Tavazoie and Ostendorf began to wonder whether APOE variants might impact COVID outcomes, too. "We had looked only at non-infectious diseases," he says. "But what if APOE variants also made people vulnerable to an infectious agent, like SARS-CoV-2? Could they cause different immune responses against a virus?"

To find out, Tavazoie and colleagues first exposed more than 300 mice engineered to carry human APOE to a mouse-adapted version of SARS-CoV-2 produced by colleagues Hans-Heinrich Hoffmann and Charles M. Rice. They found that mice with APOE4 and APOE2 were more likely to die than those with the more common APOE3 allele. "The results were striking," says Ostendorf, lead author on the study. "A difference in just one or two amino acids in the APOE gene was sufficient to cause major differences in the survival of mice exhibiting COVID."

Mice with APOE2 and APOE4 also had more virus replicating in their lungs, and more signs of inflammation and tissue damage. At the cellular level, the researchers found that APOE3 appeared to reduce the amount of virus entering the cell, while animals with the other variants had less potent immune responses to the virus. "Taken together, these results suggest that the APOE genotype impacts COVID outcomes in two ways," Ostendorf says, "by modulating the immune response and by preventing SARS-CoV-2 from infecting cells."
Toward clinical practice
The lab then turned to retrospective human studies. In an analysis of 13,000 patients in the UK Biobank, the researchers found that individuals with two copies of either APOE4 or APOE2 were more likely to have died of COVID than those with two copies of APOE3. (Roughly three percent of individuals have two copies of APOE2 or APOE4, representing an estimated 230 million people worldwide.)

Tavazoie emphasizes that there is no evidence that the 40 percent of individuals carrying only one of these alleles are at increased risk. Moreover, he says those with two APOE2 or APOE4 alleles are likely at lower risk today than the data indicates. "Vaccination changes the picture," he explains. "Data in UK Biobank spans the length of the pandemic, and many of the individuals who died early on would likely have been protected had they been vaccinated."

Moving forward, Tavazoie hopes to see prospective studies on the link between APOE and distinct COVID outcomes. "We've taken the first step," he says. "But to be clinically useful, these results will need to be assessed in prospective human trials that test individuals for their APOE genotypes and account for the availability of vaccination, something that wasn't available early in the pandemic and would improve COVID outcomes across APOE genotypes."

If future studies do confirm a link between APOE and COVID outcomes, clinicians might recommend that individuals with APOE4 or APOE2 be prioritized for vaccinations, boosters, and antiviral therapies. Screening for APOE is fairly routine and inexpensive, and many individuals already know their APOE variants because commercial genetic tests such as 23andMe use it to gauge Alzheimer's risk. At the same time, Tavazoie cautions that screening for a gene variant linked to Alzheimer's is not without ethical hurdles, given that many people would rather not know whether they are predisposed to an incurable neurodegenerative disease.

For his part, Tavazoie plans to also take a closer look at how APOE interacts with various biological systems. The link between APOE4, Alzheimer's, and COVID, for instance, raises the possibility that this gene may play a role in the neurocognitive complications that arise in some COVID patients. "We want to better understand the function of APOE by studying how it shapes the behavior of cells in these disparate contexts of cancer, dementia and now viral infection," he says.

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diseases and conditions; immune system; gene therapy; alzheimer's research; human biology; personalized medicine; infectious diseases; genes

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Common gene variant linked to COVID mortality

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It may be the most baffling quirk of COVID: What manifests as minor, flu-like symptoms in some individuals spirals into severe disease, disability, and even death in others. A new paper published in Nature may explain the genetic underpinnings of this dichotomy.

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https://www.sciencedaily.com/releases/2022/09/220928094821.htm

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An international team has reconstructed the genome organization of the earliest common ancestor of all mammals. The reconstructed ancestral genome could help in understanding the evolution of mammals and in conservation of modern animals. The earliest mammal ancestor likely looked like the fossil animal "Morganucodon" which lived about 200 million years ago. The work is published the scientific journal Proceedings of the National Academy of Sciences.

Every modern mammal, from a platypus to a blue whale, is descended from a common ancestor that lived about 180 million years ago. We don't know a great deal about this animal, but the organization of its genome has now been computationally reconstructed by an international team of scientists.

"Our results have important implications for understanding the evolution of mammals and for conservation efforts," says Harris Lewin, distinguished professor of evolution and ecology at the University of California, Davis, and senior author on the paper.

The scientists drew on high-quality genome sequences from 32 living species representing 23 of the 26 known orders of mammals. They included humans and chimps, wombats and rabbits, manatees, domestic cattle, rhinos, bats and pangolins. The analysis also included the chicken and Chinese alligator genomes as comparison groups. Some of these genomes are being produced as part of the Earth BioGenome Project and other large-scale biodiversity genome sequencing efforts. Lewin chairs the Working Group for the Earth BioGenome Project.

The reconstruction shows that the mammal ancestor had 19 autosomal chromosomes, which control the inheritance of an organism's characteristics outside of those controlled by sex-linked chromosomes, (these are paired in most cells, making 38 in total) plus two sex chromosomes, said Joana Damas, first author on the study and a postdoctoral scientist at the UC Davis Genome Center. The team identified 1,215 blocks of genes that consistently occur on the same chromosome in the same order across all 32 genomes. These building blocks of all mammal genomes contain genes that are critical to developing a normal embryo.
Chromosomes stable over 300 million years
The scientists found nine whole chromosomes, or chromosome fragments in the mammal ancestor whose order of genes is the same in modern birds' chromosomes.

"This remarkable finding shows the evolutionary stability of the order and orientation of genes on chromosomes over an extended evolutionary timeframe of more than 320 million years," Lewin says. In contrast, regions between these conserved blocks contained more repetitive sequences and were more prone to breakages, rearrangements and sequence duplications, which are major drivers of genome evolution.

"Ancestral genome reconstructions are critical to interpreting where and why selective pressures vary across genomes. This study establishes a clear relationship between chromatin architecture, gene regulation and linkage conservation," says Professor William Murphy, Texas A&M University, who was not an author on the paper. "This provides the foundation for assessing the role of natural selection in chromosome evolution across the mammalian tree of life."

The scientists were able to follow the ancestral chromosomes forward in time from the common ancestor. They found that the rate of chromosome rearrangement differed between mammal lineages. For example, in the ruminant lineage (leading to modern cattle, sheep and deer) there was an acceleration in rearrangement 66 million years ago, when an asteroid impact killed off the dinosaurs and led to the rise of mammals.

"The results will help understanding the genetics behind adaptations that have allowed mammals to flourish on a changing planet over the last 180 million years," explains co-author Dr Camilla Mazzoni, head of "Evolutionary and conservation genetics" at Berlin Center for Genomics in Biodiversity Research and Research Group Leader in Evolutionary and Conservation Genomics at the Department of Evolutionary Genetics at Leibniz-IZW.

Journal Reference:

Joana Damas, Marco Corbo, Jaebum Kim, Jason Turner-Maier, Marta Farré, Denis M. Larkin, Oliver A. Ryder, Cynthia Steiner, Marlys L. Houck, Shaune Hall, Lily Shiue, Stephen Thomas, Thomas Swale, Mark Daly, Jonas Korlach, Marcela Uliano-Silva, Camila J. Mazzoni, Bruce W. Birren, Diane P. Genereux, Jeremy Johnson, Kerstin Lindblad-Toh, Elinor K. Karlsson, Martin T. Nweeia, Rebecca N. Johnson, Harris A. Lewin, Gregory Andrews, Joel C. Armstrong, Matteo Bianchi, Bruce W. Birren, Kevin R. Bredemeyer, Ana M. Breit, Matthew J. Christmas, Hiram Clawson, Joana Damas, Federica Di Palma, Mark Diekhans, Michael X. Dong, Eduardo Eizirik, Kaili Fan, Cornelia Fanter, Nicole M. Foley, Karin Forsberg-Nilsson, Carlos J. Garcia, John Gatesy, Steven Gazal, Diane P. Genereux, Linda Goodman, Jenna Grimshaw, Michaela K. Halsey, Andrew J. Harris, Glenn Hickey, Michael Hiller, Allyson G. Hindle, Robert M. Hubley, Graham M. Hughes, Jeremy Johnson, David Juan, Irene M. Kaplow, Elinor K. Karlsson, Kathleen C. Keough, Bogdan Kirilenko, Klaus-Peter Koepfli, Jennifer M. Korstian, Amanda Kowalczyk, Sergey V. Kozyrev, Alyssa J. Lawler, Colleen Lawless, Thomas Lehmann, Danielle L. Levesque, Harris A. Lewin, Xue Li, Abigail Lind, Kerstin Lindblad-Toh, Ava Mackay-Smith, Voichita D. Marinescu, Tomas Marques-Bonet, Victor C. Mason, Jennifer R. S. Meadows, Wynn K. Meyer, Jill E. Moore, Lucas R. Moreira, Diana D. Moreno-Santillan, Kathleen M. Morrill, Gerard Muntané, William J. Murphy, Arcadi Navarro, Martin Nweeia, Sylvia Ortmann, Austin Osmanski, Benedict Paten, Nicole S. Paulat, Andreas R. Pfenning, BaDoi N. Phan, Katherine S. Pollard, Henry E. Pratt, David A. Ray, Steven K. Reilly, Jeb R. Rosen, Irina Ruf, Louise Ryan, Oliver A. Ryder, Pardis C. Sabeti, Daniel E. Schäffer, Aitor Serres, Beth Shapiro, Arian F. A. Smit, Mark Springer, Chaitanya Srinivasan, Cynthia Steiner, Jessica M. Storer, Kevin A. M. Sullivan, Patrick F. Sullivan, Elisabeth Sundström, Megan A. Supple, Ross Swofford, Joy-El Talbot, Emma Teeling, Jason Turner-Maier, Alejandro Valenzuela, Franziska Wagner, Ola Wallerman, Chao Wang, Juehan Wang, Zhiping Weng, Aryn P. Wilder, Morgan E. Wirthlin, James R. Xue, Xiaomeng Zhang. Evolution of the ancestral mammalian karyotype and syntenic regions. Proceedings of the National Academy of Sciences, 2022; 119 (40) DOI: 10.1073/pnas.2209139119

Cite This Page:

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evolutionary biology; genetics; nature; environmental policy; ecology; biodiversity; evolution; early humans; origin of life

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Revealing the genome of the common ancestor of all mammals

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An international team has reconstructed the genome organization of the earliest common ancestor of all mammals. The reconstructed ancestral genome could help in understanding the evolution of mammals and in conservation of modern animals. The earliest mammal ancestor likely looked like the fossil animal 'Morganucodon' which lived about 200 million years ago.

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Blue-eyed humans have a single, common ancestor

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New research shows that people with blue eyes have a single, common ancestor. Scientists have tracked down a genetic mutation which took place 6,000-10,000 years ago and is the cause of the eye color of all blue-eyed humans alive on the planet today.