The study, published in Science Advances, suggests that animal genomes do not evolve through an unlimited number of possible routes. Instead, chromosome changes tend to move along a restricted set of irreversible pathways that the researchers describe as “evolutionary highways.” The findings may also provide a valuable foundation for efforts to understand and conserve animal biodiversity.

Tracing More Than 600 Million Years of Genome Evolution

Every living animal ultimately descends from a common ancestor that existed more than 600 million years ago. Since that time, chromosomes have repeatedly fused, separated, and been rearranged as new animal lineages emerged.

Thousands of animal genomes have now been sequenced, but comparing their long-term evolution has remained difficult. In this study, an international team led by University of Vienna researchers brought thousands of genomes together in a single large-scale comparison.

“Understanding these rules of evolution doesn’t just tell us about the past,” said Oleg Simakov, a professor at the University of Vienna who co-led the study. “It also lets us ask where genome evolution might go next and enables us to identify key measures for the conservation of animal biodiversity.”

Many sequenced genomes remain “drafts.” They can reveal which genes an animal possesses without showing exactly where those genes are positioned along its chromosomes. Chromosome-scale assemblies provide much more detail by arranging genes in their proper order across complete chromosomes. Producing these assemblies is considerably more difficult, and only recently have enough species been analyzed at this level to make a broad comparison across the animal kingdom possible.

Largest Chromosome Comparison Across the Animal Tree of Life

The researchers examined more than 5,800 publicly available chromosome-scale genomes representing 4,454 species from 19 animal phyla. According to the team, this is the largest comparison of its kind across the animal tree of life.

To organize such a vast amount of information, the scientists created a framework called evolutionary genome topology. It places the enormous variety of animal genome structures onto a single map.

That map revealed an important pattern. Genome architecture does not appear to change randomly. Instead, animal lineages tend to move along “evolutionary highways.” Evidence from hundreds of living species shows that different groups traveled along these routes or departed from them at different times and at different rates.

“For the first time, we can see thousands of genomes on a single map and trace the unique paths along which animals’ DNA evolved. Viewing the map as a whole gives us a picture of the patterns by which animal genomes have changed over time,” said Darrin Schultz, who led the work as a postdoctoral researcher at the University of Vienna and is now an Assistant Professor at Lehigh University and Lehigh Oceans. “And if we fold the map up in a different way, we can compare how different groups of animals took different paths from each other after splitting onto different evolutionary paths.”

Irreversible Chromosome Mixing Leaves a Genetic Record

A major force behind these patterns is a process the researchers previously named “fusion-with-mixing.” It occurs when two chromosomes join, and their genes become intermixed. Once this happens, the original arrangement cannot be restored.

That irreversibility makes such chromosome changes especially useful for reconstructing evolutionary history. Each event leaves a lasting genomic record that can serve as a marker of shared ancestry. Researchers have already used this type of evidence to help identify the sibling group to all other animals.

The team found that differences in chromosome numbers among animal groups can arise in two main ways. Ancestral chromosomes can combine, or they can separate. In either case, fusion-with-mixing can push different lineages onto very different evolutionary trajectories.

Animal Groups Occupy Distinct Genome Architecture Regions

Because the process cannot be reversed, a major chromosome detour can permanently influence where a lineage ends up in what researchers describe as “genome-architecture space.”

Once such a change (“fusion with mixing”) takes place, major animal groups can be shifted into distinct regions of this genomic landscape. As chromosome mixing accumulates over time, lineages continue to diverge. These changes can leave long-lasting effects across many genes, including important genes involved in controlling development.

Evolutionary genome topology focuses on the arrangement and structure of genomes rather than relying only on DNA sequences. This gives researchers a shared coordinate system for comparing the rapidly growing number of chromosome-scale animal genomes.

The framework could make it easier to identify unusual evolutionary lineages that deserve closer study. It may also help scientists investigate whether changes in chromosome structure are connected to differences in gene regulation, development, or biodiversity.

Identifying Some of the Most Distinctive Animal Genomes

The potential applications extend beyond reconstructing evolutionary history. Some clades occupy highly isolated parts of the genome map because their chromosome architecture has few close parallels.

Mosquitoes, glass sponges, and earthworms are among the lineages that stand out in this way. By highlighting groups with especially distinctive genome organization, the framework could help researchers identify evolutionarily unusual animals that may warrant greater scientific or conservation attention.

The system can also simulate possible future directions of genome evolution. That could give scientists a way to explore how animal genomes and biodiversity might continue to change over time.

Summary

• Researchers created the first unified “map” of animal genome organization by comparing more than 5,800 chromosome-scale genomes from 4,454 species across 19 major animal groups. It represents the largest analysis of its kind so far.
• The results suggest that animal genomes move along a limited set of “evolutionary highways.” Chromosome mergers and separations can produce changes that cannot be reversed, preventing genomes from simply returning to earlier arrangements.
• The new map reveals which animal lineages have particularly unusual genome architectures and can also be used to simulate possible future directions of genome evolution.
• Researchers may use the framework to identify unusual lineages for additional study and to test whether chromosome changes are associated with differences in gene regulation, development, or biodiversity.
• The findings may also provide an important scientific basis for conserving animal biodiversity.

Funding for this research was provided by the European Research Council (Horizon 2020 / European Union Research and Innovation Programme, grant No. 945026), the Austrian Science Fund (FWF, grant P32190), and the Rupert Riedl Prize of the Vienna Haus des Meeres Verein.

The findings suggest that a person’s prescription history may help explain differences in the gut microbiome years later. The gut microbiome includes the vast community of bacteria and other microorganisms that live in the digestive tract and can influence digestion, metabolism, immune function, and other aspects of health.

Drug Effects May Persist for Years

Researchers analyzed stool samples and prescription records from more than 2,500 participants in the Estonian Biobank who were part of the Estonian Microbiome cohort. They found that most of the medications examined were associated with differences in the gut microbiome.

For a substantial number of drugs, those differences could still be detected years after people had stopped taking the medication.

The lasting effects were not limited to antibiotics, which are already well known for their ability to disrupt populations of gut bacteria. Antidepressants, beta-blockers, proton pump inhibitors, and benzodiazepines were also associated with distinctive microbial “fingerprints.”

Beta-blockers are commonly used to treat conditions such as high blood pressure and certain heart problems. Proton pump inhibitors reduce stomach acid and are often prescribed for acid reflux and related conditions. Benzodiazepines are medications commonly used for anxiety and other disorders.

“Most microbiome studies only consider current medications, but our results show that past drug use can be just as important as it is a surprisingly strong factor in explaining individual microbiome differences,” said Dr. Oliver Aasmets, lead author.

The finding suggests that researchers studying connections between the microbiome and disease may need to look beyond the medications a person is currently taking. Drugs used months or even years earlier could still influence the microbial patterns seen in a stool sample.

Anxiety Drugs Show Surprisingly Strong Effects

One particularly striking finding involved benzodiazepines, which are commonly prescribed for anxiety. Their associations with the gut microbiome were comparable to those seen with broad-spectrum antibiotics.

Broad-spectrum antibiotics are designed to act against many different types of bacteria, which is why they can produce substantial changes in the gut microbial community.

The study also found that medications belonging to the same drug class did not necessarily affect the microbiome in the same way. Drugs that may be prescribed for similar conditions, such as diazepam and alprazolam, differed in how strongly they appeared to disrupt gut microbes.

That distinction could be important because medications are often grouped together in microbiome research based on their drug class. The new results suggest that individual drugs may need to be considered separately.

Follow-Up Samples Reveal Predictable Changes

Researchers also examined follow-up stool samples from a smaller group of participants. These samples allowed them to observe what happened when people started or stopped certain medications.

Those changes were accompanied by predictable shifts in gut microbes, providing evidence that the medications themselves may be responsible for at least some of the observed differences.

Although the second time-point analysis involved a relatively small number of participants, researchers were able to confirm persistent effects linked to proton pump inhibitors, selective serotonin reuptake inhibitors and antibiotics, such as penicillins in combination and macrolides.

Selective serotonin reuptake inhibitors are a widely used class of antidepressants. Macrolides are a group of antibiotics that includes drugs used to treat a range of bacterial infections.

Medication History Could Matter in Microbiome Research

The results add to growing evidence that the gut microbiome reflects more than a person’s current diet, lifestyle, health, and medication use. Past treatments may leave biological traces that remain detectable long after the prescription has ended.

“This is a comprehensive systematic evaluation of long-term medication effects on the microbiome using real-world medical health records,” said Professor Elin Org, corresponding author. “We hope this encourages researchers and clinicians to factor in medication history when interpreting microbiome data.”

Accounting for that history could help scientists more accurately distinguish microbiome changes associated with disease from changes caused by medications taken in the past.

However, this practice could act as a superspreader event – where a disease infects an unusually high number of people or animals – of the H5N1 virus. This deadly strain of bird flu has already decimated wild bird and mammal populations worldwide. It is now spreading across Australia, most recently killing more than 1,000 crested terns and a long-nosed fur seal, the first detection in a mainland mammal.

Although many Australians feed wild birds, the practice is controversial. This is mainly due to concerns about people offering unsuitable foods and birds becoming dependent on humans.

So why is backyard bird feeding such a problem when it comes to bird flu? And can we do it safely?

Not just a hobby

People feed wild birds for various reasons, including to provide food during tough times or simply enjoy their presence. Most care deeply about their avian companions and believe feeding them is helpful.

However, they may not realize the danger this creates for the birds they love.

Feeding wild birds heightens the risk of disease transmission at feeding locations. When we offer supplementary food, such as seeds or meat scraps, this attracts birds of many different species in a combination and number that would not happen in nature. They may carry deadly diseases, such as the H5N1 virus, and potentially spread them to other birds.

This can create a transmission hotspot right on our back deck. And catching bird flu can push our most threatened species, such as the orange-bellied parrot, to the brink of extinction.

The fatal effects of H5N1 are not only contained to birds. Scavenger animals such as possums, red foxes and crows can be exposed to the virus while devouring the carcasses of infected birds. Humans in close contact with infected wildlife, such as wildlife carers and veterinarians, can contract H5N1. However, human infection is rare and typically only causes mild symptoms.

Stopping the spread

Backyard bird feeding may seem like a harmless hobby. But given how many people do it, and the risks it poses to both birds and people, bird feeding activities could lead to many more wildlife deaths.

So if you feed birds in your backyard, how can you do so safely?

The most effective strategy is to stop feeding birds altogether. If you don’t offer food to wild birds, they will be less likely to congregate in your backyard or garden. And they will be fine without your help. Our previous research found most birds that visit feeders obtain most of their nutrition from natural sources, such as insects and worms. So the food we provide is a snack, not an essential meal.

But if you do continue feeding wild birds, here are three precautions to take:

Offer less food

Having feeders full of seeds and leftover meat will attract more birds. So to discourage them from congregating, simply provide less food. Much like COVID-era social distancing rules, this will lower the risk of H5N1 transmission by keeping birds separate.

Avoid hand-feeding

Having a bird swoop down to snatch food from your hand is one of the most intimate interactions we can have with wildlife. But in the era of bird flu, this must stop. While humans are unlikely to contract H5N1, close physical contact with birds through hand-feeding is simply not worth the risk.

Keep everything clean

If you keep feeding wild birds, it’s vital to regularly clean all feeding surfaces and equipment using domestic bleach. If you’re not prepared to do this, you shouldn’t be feeding them at all.

Backyard bird feeding could worsen Australia’s current H5N1 crisis. Indeed, your avian visitors may complain if you give them fewer tasty treats or stop feeding them altogether. But these measures will protect both you and them from this deadly disease.

Please do not touch sick or dead birds or marine mammals. Record the location, take photographs from a safe distance, keep pets away and report the sighting to the Emergency Animal Disease Hotline on 1800 675 888 (Australia).

“Previous studies have found that sleep is largely linked to aging and the pathological burden of the brain. Our study goes further and shows that too little and too much sleep are associated with faster aging in nearly every organ, supporting the idea that sleep is important in maintaining organ health within a coordinated brain-body network, including metabolic balance and a healthy immune system,” says study leader Junhao Wen, assistant professor of radiology at Columbia University Vagelos College of Physicians and Surgeons.

The research was published in Nature.

Biological Clocks Reveal How Organs Age

Scientists are increasingly using aging clocks to estimate whether a person is aging biologically faster or slower than their chronological age. These tools rely on machine learning and biological information (e.g., proteins from a minimally invasive blood test) to calculate patterns associated with aging.

Many aging clocks provide a single measure for the entire body. However, different organs can age at different speeds. One familiar example is the decline in ovarian function that contributes to the biological clock associated with female fertility.

Wen and his colleagues have been developing aging clocks that focus on individual organs. The goal is to provide more detailed and potentially more personalized information about a person’s health.

“Everyone is excited by these aging clocks and their ability to predict disease and mortality risk,” Wen says. “But to me, the more exciting question is, can we link aging clocks to a lifestyle factor that can be modified in time to slow aging?”

Finding a Sleep Sweet Spot

Sleep offered researchers an ideal way to explore that question because mounting evidence suggests that sleep plays an important role in health. Wen also had a personal interest in the issue.

“I’m also a light sleeper and was getting worried about the effects on myself,” says Wen.

To create the aging clocks, Wen used information from about half a million participants in the UK Biobank. Machine learning was applied to identify biological signatures associated with aging in different organs.

The researchers built clocks using several types of information, including structural measurements from medical imaging, proteins associated with specific organs, and molecules detected in the blood.

“In the liver, for example, we have an aging clock built with protein data, an aging clock of metabolic data, and an aging clock of imaging data,” Wen says. “This allows us to see whether sleep is distinctively associated with aging clocks derived from multiple omics and molecular layers.”

The team then compared sleep duration (as reported by each Biobank participant) with biological age estimates from 23 aging clocks covering 17 organ systems.

Too Little and Too Much Sleep Linked to Faster Aging

A clear U-shaped pattern appeared across the body. People reporting short sleep (fewer than 6 hours) and long sleep (greater than 8 hours) tended to show faster biological aging.

The lowest levels of aging were seen among people who reported sleeping between 6.4 and 7.8 hours each day.

Importantly, the findings do not show that sleep duration by itself causes organs to age faster or slower. Instead, they suggest that sleeping either too little or too much could be a sign of poorer health throughout the body.

Sleep Duration Tied to Diseases Across the Body

The results also point to a broad connection between sleep, the brain, and the rest of the body.

Short sleep was significantly associated with depressive episodes and anxiety disorders, consistent with earlier research connecting insufficient sleep with mental health problems.

It was also associated with obesity, type 2 diabetes, hypertension, ischemic heart disease, and heart arrhythmias.

Both short and long sleep were linked to chronic obstructive pulmonary disease and asthma. They were also associated with several digestive disorders, including gastritis and gastroesophageal reflux disease.

Wen says, “The broad brain-body pattern is important because it tells us that sleep duration is a deeply embedded part of our entire physiology, with far-reaching implications across the body.”

Sleep, Aging, and Late Life Depression

The organ-specific aging clocks may also help scientists understand how sleep is connected to individual diseases. Wen and his colleagues explored this possibility by examining late life depression.

The researchers could not establish whether differences in sleep duration caused late life depression or whether depression itself changed how long people slept.

To investigate further, the team used “mediation analysis” to examine whether biological aging might help explain the relationship between short or long sleep and late life depression.

The results suggested that short sleep may be more directly connected with the burden of late-life depression. Long sleep, in contrast, may influence depression through pathways reflected in aging clocks for the brain and adipose tissue.

“This has a strong implication for future sleep management and future therapeutics,” Wen says. “Our study suggests there may be different biological pathways between long and short sleepers that lead to the same outcome, late-life depression, and we shouldn’t treat them the same way.”