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Biology

In the evolution of walking, the hip bone connected to the rib bones – EurekAlert

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New reconstruction of the skeleton of the 375-million-year-old fossil fish, Tiktaalik roseae. In a new study, researchers used Micro-CT to reveal vertebrae and ribs of the fish that were previously hidden beneath rock. The new reconstruction shows that the fishs ribs likely attached to its pelvis, an innovation thought to be crucial to supporting the body and for the eventual evolution of walking.

Credit: Thomas Stewart, Penn State

UNIVERSITY PARK, Pa. Before the evolution of legs from fins, the axial skeleton including the bones of the head, neck, back and ribs was already going through changes that would eventually help our ancestors support their bodies to walk on land. A research team including a Penn State biologist completed a new reconstruction of the skeleton of Tiktaalik, the 375-million-year-old fossil fish that is one of the closest relatives to limbed vertebrates. The new reconstruction shows that the fishs ribs likely attached to its pelvis, an innovation thought to be crucial to supporting the body and for the eventual evolution of walking.

A paper describing the new reconstruction, which used microcomputed tomography (micro-CT) to scan the fossil and reveal vertebrae and ribs of the fish that were previously hidden beneath rock, appeared April 2 in the journal Proceedings of the National Academy of Sciences.

Tiktaalik was discovered in 2004, but key parts of its skeleton were unknown, said Tom Stewart, assistant professor of biology in the Eberly College of Science at Penn State and one of the leaders of the research team. These new high-resolution micro-CT scans show us the vertebrae and ribs of Tiktaalik and allow us to make a full reconstruction of its skeleton, which is vital to understanding how it moved through the world.

Unlike most fish, which have vertebrae and ribs that are the same along the length of the trunk, the axial skeletons of limbed vertebrates show dramatic differences in the vertebrae and ribs from the head region to the tail region. The evolution of this regionalization allowed the performance of specialized functions, one of which was a mechanical linkage between ribs in the sacral region to the pelvis that enabled support of the body by the hind limbs.

The pelvic fins of fish are evolutionarily related to hind limbs in tetrapods four-limbed vertebrates, including humans. In fish, the pelvic fins and bones of the pelvic girdle are relatively small and float freely in the body. For the evolution of walking, the researchers explained, the hind limbs and pelvis became much larger and formed a connection to the vertebral column as a way of bracing the forces related to supporting the body.

Tiktaalik is remarkable because it gives us glimpses into this major evolutionary transition, Stewart said. Across its whole skeleton, we see a combination of traits that are typical of fish and life in water as well as traits that are seen in land-dwelling animals.

The original description of Tiktaalik focused on the front portion of the skeleton. Fossils were meticulously prepared to remove the surrounding matrix of rock and expose the skull, shoulder girdle and pectoral fins. The ribs in this area were large and expanded, suggesting that they may have supported the body in some way, but it was unclear exactly how they would have functioned. In 2014, the fishs pelvis, discovered in the same location as the rest of the skeleton, was also cleaned of matrix and described.

From past studies, we knew that the pelvis was large, and we had a sense that the hind fins were large too, but until now couldnt say if or how the pelvis interacted with the axial skeleton, Stewart said. This reconstruction shows, for the first-time, how it all fit together and gives us clues about how walking might have first evolved.

The researchers explained that, unlike our own hips where our bones fit tightly together, the connection between the pelvis and axial skeleton of Tiktaalik was likely a soft-tissue connection made of ligaments.

Tiktaalik had specialized ribs that would have connected to the pelvis by a ligament, Stewart said. Its astonishing really. This creature has so many traits large pair of hind appendages, large pelvis, and connection between the pelvis and axial skeleton that were key to the origin of walking. And while Tiktaalik probably wasnt walking across land, it was definitely doing something new. This was a fish that could likely prop itself up and push with its hind fin.

The new reconstruction of the skeleton also sheds light on specializations for head mobility in Tiktaalik and new details of the fishs pelvic fin anatomy.

"It's incredible to see the skeleton of Tiktaalik captured in such vivid detail, said Neil Shubin, Robert R. Bensley Distinguished Service Professor of Organismal Biology and Anatomy at the University of Chicago and one of the authors of the paper. This study sets the stage for ones that explore how the animal moved about and interacted with its environment 375 million years ago."

In addition to Stewart and Shubin, the research team includes Justin B. Lemberg, Emily J. Hillan, and Isaac Magallanes at The University of Chicago, and Edward B. Daeschler at Academy of Natural Sciences of Drexel University.

Support from the Brinson Foundation, the Biological Sciences Division of The University of Chicago, an anonymous donor to the Academy of Natural Sciences of Drexel University, and the U.S. National Science Foundation funded this research. Fieldwork was made possible by the Polar Continental Shelf Project of Natural Resources, Canada; the Department of Heritage and Culture, Nunavut; the hamlets of Resolute Bay and Grise Fiord of Nunavut; and the Iviq Hunters and Trappers of Grise Fiord.

Proceedings of the National Academy of Sciences

The axial skeleton of Tiktaalik roseae

The authors declare no competing interest.

Disclaimer: AAAS and EurekAlert! are not responsible for the accuracy of news releases posted to EurekAlert! by contributing institutions or for the use of any information through the EurekAlert system.

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In the evolution of walking, the hip bone connected to the rib bones - EurekAlert

Biology

Synaptic ribbon dynamics after noise exposure in the hearing cochlea | Communications Biology – Nature.com

Pre-synaptic ribbons are electron-dense structures in the retina, inner ear and pinealocytes that dock synaptic vesicles, facilitating sustained vesicle release in pre-synaptic active zones. In the cochlea, overexposure to moderate levels of sound leads to cochlear synaptopathy loss of synaptic connections between sensory IHCs and afferent SGNs and auditory functional disability. Using a RIBEYE-tagRFP transgenic mouse, we performed live imaging in cochlear explants to visualize the dynamic behavior of pre-synaptic ribbons in live hair cells in real time and three dimensions, and demonstrate that chemical overstimulation and noise exposure induce random, as well as directional movement of subpopulations of pre-synaptic ribbons.

Prior studies in mammalian cochleaehave always used immunohistochemistry to examine ribbon synapses in fixed tissue at a single timepoint. Although these studies have revealed immense amounts of knowledge about pre- and post- synaptic structures, they are unable to provide dynamic spatiotemporal information, precluding direct investigation of the effect of noise and other ototoxic insults on ribbon dynamics. In contrast, the genetically encoded model of RFP-tagged RIBEYE allows monitoring of movement of pre-synaptic ribbons in real time in live cochlear innerhair cells.

We identified pre-synaptic ribbons using endogenous RIBEYE-tagRFP signals, while IHCs were delineated using FM1-43; this enabled us to normalize the reference frame around the stable 3D framework of FM1-43 signal and isolate ribbon movement relative to the hair cells. Similar to prior studies of live-cell speed in tumor-associated macrophages46, we utilized the Spots function in Imaris to identify and render individual RIBEYE puncta. This strategy proved to be ideal for detecting the small RIBEYE puncta and assign a globular-like shape to each. As the first measure during image analysis, we used the Quality filter in Imaris47. If the threshold value is too low, erroneous spots are picked; alternatively, if the value is too high only the brightest puncta are picked. Together with Quality, the Intensity Threshold parameter needed to be optimized separately for neonatal and adult imaging, and it was necessary to perform contemporaneous control measurements with age-matched mice to ensure experimental rigor.

In the current study, we performed live imaging in neonatal cultures as well as an explant preparation of the mature, hearing cochlea in juvenile, 710-week-old mice. In the case of neonatal cochlear cultures, this imaging enabled investigation of ribbon properties and behavior at multiple timepoints before and after experimental manipulation, including chemical excitotoxicity using KA, in the same specimen. In juvenile, mature-hearing cochlear explants, inability to maintain healthy tissue ex vivo greater than 30min precluded similar prolonged ex vivo investigation; however, this model was uniquely able to provide direct insight into ribbon behavior after physiologically relevant acoustic noise exposure known to cause cochlear synaptopathy.

We first validated our live imaging and processing model against standard immunohistochemical methods, demonstrating our ability to accurately detect pre-synaptic ribbons in real time. We then evaluated the effect of overstimulation on pre-synaptic ribbons in an established KA model for glutamate excitotoxicity in neonatal cochlear cultures as well as synaptopathic 98-dB SPL noise exposure in a juvenile, mature-hearing cochlear explant model.

At baseline, compared with neonatal cochlea, synaptic ribbons from mature hearing cochlea were less numerous, larger, and less mobile. The difference in ribbon volume, in particular, was large, with the mean (SEM) volume of puncta in juvenile cochleae (0.460.01m3) nearly 20-fold greater than in neonatal cochleae (0.0260.001m3; Fig.4c). In a previous study using focused ion beam-scanning electron microscopy (FIB-SEM) to quantity ribbon volume during development from P9-P34, ribbon size was found to increase approximately 2-fold (0.003440.00099 versus 0.005680.00045m3)40. Measurements in P49 mice (more comparable in age to the juvenile mice used in our study) were larger still, ranging from 0.0080.14m3 and 0.010.15m3 in two studies using serial block-face electron microscopy48,49. The absolute volumes measured in our study, using live fluorescent imaging, are not comparable to the much smaller structural measurements using electron microscopy; however, the trend towards larger ribbons in older cochleae is consistent. The much larger difference that we observed compared to previous studies may be related to differences in imaging and processing that were necessary between the neonatal and juvenile cochlear preparations, and is reflected in the significantly lower mean intensity of the punctal signals in juvenile animals (Fig.4e).

After a 2-h exposure of neonatal cochleae to KA, which induces glutamate excitotoxicity, or exposure of mature hearing mice to 98dB SPL, which induces cochlear synaptopathy, immediate physiological changes were observed. Neither chemical overstimulation nor noise exposure affected the number of pre-synaptic ribbons; however, noise exposure was associated with an immediate increase in synaptic ribbon volume in the mature hearing cochlea that was even more substantial 2 weeks later. The close correlation between the size and mean brightness of pre-synaptic puncta raises the possibility that observed changes in size may be related to changes in endogenous signal intensity, rather than actual volume increase; however, overall these findings on ribbon number and size corroborate previous observations from fixed specimens37,38,40. The ability from this live-imaging model to observe dynamic behavior of ribbon synapses revealed that both chemical overstimulation and noise exposure induces increased movement of pre-synaptic ribbons. Ribbons in KA-stimulated neonatal cochlea and noise-stimulated mature hearing cochlea both exhibited increased speed of ribbon movement. These initial increases in ribbon speed persisted, albeit to a lesser degree, 2 weeks after noise exposure. Ribbon speed in both neonatal and juvenile mouse cochlea was significantly slower than that observed in zebrafish using a similar transgenic system. In zebrafish, despite small spatial displacements over extended periods, short-term instability and high mobility of the ribbons underlying structure was observed, challenging traditional views of ribbon physical rigidity and proposing a fluid mosaic model for the ribbon surface33. Further study in the mammalian system is required, especially improvement in temporal resolution, to further investigate whether these differences truly reflect species-specific differences in ribbon stability.

When the entire aggregate population of ribbons was examined together, there was no consistent directionality to the KA- or noise-induced ribbon displacement; overall, displacement vectors appeared to be randomly distributed. RIBEYE proteins are dynamic in nature but become stabilized in ribbon synapses50. The increased speed in the KA-treated and noise-exposed ribbons might be due to induction of instability in the ribbon synapses in the pre-synaptic zone. The lack of overall directionality suggests that ribbons are becoming unanchored; that is, RIBEYE anchorage is disrupted but without subsequent directed transport. In ribbon synapses, Bassoon anchors RIBEYE at the active zone of the presynaptic membrane. Although both Bassoon-deficient and wild-type IHCs have large RIBEYE spots at afferent synapses, Bassoon-deficient IHCs were also shown to possess unanchored and floating ribbons close to the synapses51. Furthermore, physical interaction between Bassoon and RIBEYE is thought to be present at the cytomatrix active zone in retina photoreceptors, maintaining the integrity of the ribbon complex52.

Though, overall, ribbons did not have a concerted vector of displacement, a subgroup of ribbons in the mature hearing cochlea closest to the basal pole of the hair cells exhibited clear directionality. Compared to all ribbons in control, non-noise exposed animals as well as apical ribbons in noise-exposed animals, which exhibited no directionality of movement, basal ribbons moved towards the apex immediately after noise exposure. While it is possible that these basal ribbons in juvenile, noise-exposed mice are moving apically simply because they have no other direction to go after being unanchored by noise exposure, we did not observe this directionality in basal ribbons either in unexposed juvenile cochlea or in neonatal cochleae after KA exposure, suggesting that this directional movement is specific to noise-exposed mature hearing cochleae. This initial apical movement of the basal-most ribbons towards the hair-cell nucleus was followed by movement back towards the base of the hair cell, which may reflect re-attachment. These findings provide direct visual evidence of dynamic, directional movement of basal synaptic ribbons after noise exposure in the mature hearing cochlea.

Prior reports showed that synaptopathy occurs rapidly during noise exposure, with limited subsequent recovery24, though strain-specific differences have been observed53. Synapses around the IHC are arranged based on fiber characteristics; large ribbons are associated with small receptor patches on the modiolar side, and small ribbons are linked to large receptor patches on the pillar side54. These gradients underlie variation in cochlear nerve response, reflecting a low-spontaneous discharge rate (SR) to high-SR gradient55. Following noise exposure, synapses are preferentially lost on the modiolar side of the IHC, and more orphan ribbons are found near the habenular end. These orphan ribbons appeared to recover eventually rather than degenerate. These conclusions, however, were all inferred from fixed imaging; it could not be determined or observed directly whether ribbons were migrating to and from the receptor patches, or whether they were being dissolved and reformed.

Our current study provides complementary evidence to directly show how ribbons are moving immediately after noise exposure. Though the overall population of ribbons appear to be moving in random directions, suggesting unanchoring, the basalmost subgroup of puncta migrated apically towards the nucleus and then returned to the cell membrane, suggesting that ribbons are recycled rather than immediately degraded and then reformed. Further refinement and study of this live imaging model may reveal further subgroups of ribbons that have characteristic behaviors after acoustic overstimulation that can be targeted for treatment of cochlear synaptopathy.

This study was limited by the spatial and temporal resolution of the imaging technique. Adequate 3D imaging of puncta required high-spatial-resolution laser-scanning confocal microscopy across the entire synaptic region, with each z-stack requiring 5min to acquire on average, thus limiting temporal resolution. For large movements or rapidly drifting preparations, this might result in a systemic underestimation or overestimation of the punctal speed even after adjusting for the reference frame, if the imaged punctum was captured within a significantly different imaging plane from one frame to another. However, the preparations were quite stable, with minimal movement of the reference frame (Supplementary Fig.S1), and the punctal movements were small; therefore, it is likely that despite the prolonged acquisition time, the measured speeds are likely to be accurate at the 5-min time resolution limit. We are unable to make conclusions, however, about movement occurring faster than this limit; future studies restricting imaging to small volumetric regions of interest to enable faster image acquisition are needed to evaluate faster synaptic movement.

We relied on Imaris software to track puncta from one frame to the next; over a 20-min recording period with 6 serial images, less than half of puncta could be tracked across all images. These vanished puncta were not interpreted to represent actual loss of puncta over that time period, and the number of vanished puncta was not different between control and noise-exposed animals; however, it illustrates the challenges inherent to the imaging technique.

We observed other changes that occurred during routine culture and imaging: even in untreated cochleae the number of puncta detected in neonatal cultures decreased after 24h in culture, and the speed of punctal movement decreased over the first 20min of serial imaging, (Fig.3a, e). The reasons for these changes are unknown, but may reflect either a phototoxic response to the initial imaging itself or simply evolution of synapses in explant cultures that had previously been undetectable without serial imaging of the same preparation. These finding illustrate the necessity for consistency of culture duration and inclusion of rigorous control conditions in any study using neonatal cochlear cultures, whether using live or fixed imaging techniques.

While imaging of neonatal cochlear cultures enabled observation of ribbon dynamics during chemical overstimulation with KA, this is not a physiological perturbation; conversely, while we were able to examine ribbon dynamics after a physiologically relevant stimulus (noise exposure) in the mature hearing cochlea, we could not acoustically stimulate the explanted juvenile cochlea and directly observe the effect of sound stimulation, as was done previously in a limited fashion in the gerbil cochlear explant56. In future studies, further refinement of the imaging technique and mature hearing explant model can advance understanding of ribbon dynamics after noise exposure.

In summary, our findings suggest that noise exposure induces synapses to become more loosely anchored, and that a subpopulation of the basalmost synapses migrate apically, towards the nucleus. Within 20min, some of these ribbons then migrate back towards the synaptic terminals, likely to re-form paired synapses. These insights suggest that further investigation of ribbon anchoring may uncover molecular targets for intervention to prevent this initial noise-induced ribbon dissociation or promote re-targeting in the early moments after noise exposure, thereby preventing permanent synaptopathy.

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Synaptic ribbon dynamics after noise exposure in the hearing cochlea | Communications Biology - Nature.com

Biology

Biologist Beth Shapiro on the ‘de-extinction’ of woolly mammoths – STAT

Humans have long tinkered with the evolutionary trajectories of other species. Thousands of years ago we tamed wolves into dogs and transformed a wild grass into the agricultural wonder wheat. Within the past few centuries, we exterminated the Tasmanian tiger and doomed the dodo bird to oblivion. Now, we stand on the brink of an ambitious new era in how humans may transfigure life around us: by pursuing the science of de-extinction, or the resurrection of species once lost to this world.

Beth Shapiro is an evolutionary biologist, an ancient DNA adventurer who has collected fossilized bison bones from Arctic permafrost, and a titan in the de-extinction movement. She co-led the Paleogenomics Lab at the University of California, Santa Cruz, was a Howard Hughes Medical Institute investigator and a MacArthur Fellow, and is the author of the books How to Clone a Mammoth: The Science of De-Extinction and Life as We Made It: How 50,000 Years of Human Innovation Refinedand RedefinedNature. In 2022 she announced that her team sequenced the genome of the dodo bird.

Recently, Shapiro was named chief scientific officer of Colossal Biosciences, a biotech company with its sights set on bringing back such fallen fauna as the woolly mammoth, dodo bird and Tasmanian tiger, or thylacine. Shapiro spoke with STAT about CRISPR, conservation, and her recent move from academia to biotech. She also discussed how the scientific journey to reviving extinct species may provide insight into better protecting and preserving ecosystems in the present day. This interview has been edited for length and clarity.

How did your interest in de-extinction start?

I have worked in ancient DNA for my whole graduate career since 1999, when I joined Alan Coopers group in Oxford. I was fascinated by this combination of paleontology, evolutionary biology, and molecular biology. At that time, it was just beginning. It was crazy to think that we could actually recover DNA sequences from things that had been dead for tens of thousands of years, and then use that to try to better understand how species, populations, communities, and entire ecosystems shift and change over evolutionarily significant time scales.

Whenever we would publish one of these papers, often we got a lot of media attention, and it was very exciting to think about mammoth DNA, ancient bison, or extinct horses. But really, the question that they were most interested in asking us was, What does this mean about bringing extinct species back to life? At first it was disappointing. I really wanted to talk about the cool stuff that were learning, and all they wanted to talk about is Jurassic Park or Pleistocene Park. But then, you start to understand its that type of question that engages people with the science.

Gradually over my career, Ive just gotten more and more engaged with what [de-extinction] would actually look like. Ive really begun to appreciate how the technologies one would need in order to bring back something similar to a mammoth are exactly the types of technologies we need to be able to protect and preserve species that are still alive today but in danger of becoming extinct like the mammoth did. That is where my pure excitement about this technology lives, in this whole wealth of new biotechnologies that we have at our fingertips that we should be able to use for endangered species preservation.

Are you sick and tired of the Jurassic Park comparisons at this point? Especially now that youre working for Colossal full-time as their chief scientific officer?

Not at all. In the very beginning when it was the only question that I got, I got tired of hearing this question. But now I realize that this is why kids are paying attention. This is why my mother is paying attention. Mostly science is in the noise for people who arent actively working in science. But the extinction crisis shouldnt be in the noise. And if it takes people thinking to themselves, Oh, my goodness, theres a real company out there doing Jurassic Park which were not I better read up on this and find something out, then weve won. There are a bunch of people who wouldnt have cared at all about extinction who now are thinking about it.

What does the jump from academia to biotech look like for you?

Its a big jump right now. I am a little bit terrified, but really excited. I think academics are not very good at risk-taking. This is certainly a risky move, but this is a combination of all of the hardest problems in biology.

I think that is where I started in ancient DNA: Its really hard to get DNA out of old things, and that was exciting. Its not actually so hard to do that anymore now. Then it was really hard to figure out exactly how we were going to use that to learn about population history. And now we kind of got that. But now the big hard thing is how do we translate these genome sequences of extinct species into better understanding why these species looked and acted the way that they did, so that we can use that information to learn about preservation of species today. That is now, I think, one of the hardest problems in biology. It is definitely not something that I can tackle on my own in my academic lab.

So what is de-extinction?

When most people hear the word de-extinction, what comes to mind immediately is cloning something. Im going to clone a mammoth. But in order to clone a mammoth, you need a living cell. You need an intact nuclear genome of a mammoth, and that just doesnt exist anymore. Once an organism dies, the DNA in all of its cells starts to get broken down into smaller and smaller pieces, until eventually theres nothing left. Our job as ancient DNA scientists is to try to figure out how to pull those tiny, broken pieces of DNA out of these cells. But that is not the same thing as having an intact cell, an intact nucleus.

What we actually mean when we talk about de-extinction now is using the tools of genome engineering to resurrect the core traits of these species that used to be there. Were not creating a mammoth. Were taking an Asian elephant and helping it to become something that is more similar to a mammoth by resurrecting the capacity to live in colder climates. One thing thats cool about this is it means we have to understand what it is that made a mammoth able to live in colder climates. We start to learn about how these sorts of traits evolve, and what is it in the genome that drives cold tolerance? A hard question, but we need to know that if were going to drive those traits into an Asian elephant. When I think of de-extinction, I think of resurrecting these core phenotypes, these core traits.

What role does CRISPR play in de-extinction and bringing back the mammoth?

What we have now is the genome sequences of several dozen, maybe more, mammoth genomes lined up against each other on a computer. And we have a bunch of sequences of Asian elephants and African elephants also on a computer. We line them up next to each other, and we can look at these sequences and ask, Where in the genome are all the mammoths like each other but different from the elephants? This gives us an idea of potentially where some mammoth-specific mutations might be in the genome.

Where does CRISPR come in? We dont have a living cell that is a mammoth. We have our elephant cell, and in that elephant cell we have the elephant genome. And we know very specific places in that genome where we want to tweak the DNA sequence to make that sequence more mammoth-like. We know which parts we want to change because weve compared all the mammoth and elephant genomes and identified the mutations we want to make. That is where we need to use the tools of genome engineering like CRISPR. We will use CRISPR to genetically modify that elephant genome sequence so it looks increasingly more mammoth-like.

Where is Colossal right now on its journey to de-extincting a mammoth?

Eriona [Hysolli]s team the mammoth team they understand that we have all of the core technologies that we would need to create a mammoth, but what we need to do is, tune them, tweak them, and make them all apply to elephant cells. They are able to genetically modify the genome sequence of elephants in elephant cells growing in a dish in a lab. They have the capacity to be able to make those edits. Theyre working on new tools like multiplex genome editing, because we know that there are a lot of edits that we have to make. At the same time, she has an embryology team thats really focused on taking those genetically modified cells and pushing them toward that next step.

Speaking about embryology, Colossal made an announcement last month about taking skin cells from elephants and turning them into stem cells. Could you tell me more about that?

One of the tools that would make it much simpler to work with elephants is if we could take elephant cells and make them into stem cells. If you had elephant stem cells, you can actually use that to make elephant egg cells and then we dont have to actually ask for elephant egg cells from elephants. Instead, we can just make them in the lab. That is a huge advance both technologically and ethically. The announcement that the team had succeeded in making elephant stem cells for the first time really speaks to some of the innovations that are going on at Colossal.

Lets get into the ethics of this work. Shouldnt something thats extinct stay extinct?

Extinction and speciation are important processes in evolution. But what we know right now is that the rate of extinction today is somewhere on the order of 1,000 to 10,000 times faster than the average across the fossil record. Much of this is because of things that people are doing. In many cases, the pace of change is too fast for evolution by natural selection to keep up.

A lot of people see this as two choices: We either choose to intervene or we choose not to intervene. But by making that choice, the choice not to intervene, we are still choosing to do something. In this case, we are choosing to watch all of these species become extinct. And that is also a choice.

I get what success would look like: bringing back a woolly mammoth. But what would failure look like in this case? At what point would you say we cant de-extinct a mammoth?

Im really not worried about failure in this case. To me, I think there are so many successes that come on the path toward de-extinction that will have immediate application for conservation of living species. Elephant iPSCs [induced pluripotent stem cells] are not only good for mammoth de-extinction, theyre also good for work that people want to do with elephants. We want to be able to help elephants thrive in habitats of today and tomorrow, including habitats that include diseases that have been introduced by people. This provides the capacity to do that.

The multiplex genome editing technologies that are being developed, the artificial womb technologies that are being developed, these all have applications outside of mammoth de-extinction, including to help people. There are so many successes along the path that I would find it hard to see a place where there is failure.

What is it that Colossal is doing that can actually impact me as a human?

Along the path to mammoth or dodo or thylacine, Colossal will be developing technologies that have immediate application outside of those specific applications. There are millions of evolutionary differences between an Asian elephant and a mammoth, and its unlikely that making one or two small changes is going to create the mammoth phenotype in an Asian elephants genetic background. We need tools for multiplex genome editing, for introducing large fragments of DNA, all of which will have application to using CRISPR gene editing technologies in humans and other species.

How might this work provide us with better insight into human health?

One of the hardest problems in biology right now is understanding how the long stretches of As and Cs and Gs and Ts that make up the genome translate into the way a person or an organism looks and acts, and that includes disease manifestations. We have hundreds of thousands of human genomes, and we still cant pinpoint with precision what gene means what phenotype. One of the ways that were going to get there is through comparative genomics, and that includes species outside of our own. So if we are building these resources where we have genomes from across the tree of life, and more complete understanding of how DNA translates into the way something looks or acts, we will be able to apply this to making more informed decisions or hypotheses that will drive future experiments to understand the link between genotype and disease.

Beyond the charismatic creatures that we often think about when it comes to de-extinction, like the mammoth, the dodo, the thylacine, what animal would you like to de-extinct?

I have my conservation biologist hat on. What other groups of organisms are most in danger of becoming extinct that pushing this technology toward might help them to survive? Insects are highly endangered. Should we be thinking about developing tools and technologies to do CRISPR gene editing in insects?

I think we choose the charismatic animals because its exciting. How do we excite other people about an insect? Well, theres the Xerces blue butterfly [which human activity drove to extinction in the 1940s in the San Francisco Bay] thats beautiful and charismatic. Should we think about that as a mechanism of developing tools that might be applicable across the order of insects that are out there?

Why should a biotech company be thinking about conservation? Why is de-extinction the best allocation of those resources as opposed to more traditional approaches to conservation?

I think conservation is everybodys responsibility, and I know that there are many of the investors in Colossal who have invested in more traditional aspects of conservation as well. My answer is often, yes, we should invest this much money in traditional approaches to conservation, but we also should be investing this money into developing new tools for conservation. Because while traditional approaches to conservation are great and have had some successes, we still have this exceptionally high rate of extinction. We should be thinking about how to grow our conservation toolkit as we move forward.

Whats the biggest barrier to doing de-extinction work right now? Is it ethics, public sentiment, research funding, or just people thinking that genetically modified animals are scary?

All of these are barriers to some extent, but theyre all also surmountable. I think as scientists, we need to do a better job making sure that were reaching out and communicating with people about what it is that we are doing and what it is that were not doing. I think theres a lot of noise out there that is imagining that were doing something crazier than we actually are doing. I think there are technological barriers that are different for every one of the species that are there, ethical, ecological, theyre all the same.

You said your colleagues Eriona Hysolli and George Church think that maybe in 2028 we could see the first live mammoths. What happens next?

That is way earlier than theyll ever be out in the wild wandering around, which means that we have a lot of time to engage with people.

The goal that Eriona and George and Colossal have set up is to reintroduce these animals into the wild. I know that Ben [Lamm, co-founder and CEO of Colossal] has been having conversations with local governments and Indigenous groups in Alaska and elsewhere about where would these animals go or what we need to do in preparation for this. But this is a long way in the future, and, I think exactly what happens to them really needs to be the decision made by the Indigenous groups and the local people that are on the ground.

You have the mammoth team. You have the thylacine team. You have the dodo bird team. Will there ever be a Neanderthal de-extinction team?

Neanderthals were people, and if youre going to work on people, you need to get informed consent. I dont know how you would get informed consent from a Neanderthal that you wanted to bring back to life. But I will say, from a scientific perspective and not from a classical perspective, we have somewhere between 1% and 4% Neanderthal in our DNA. Less well known is that its not the same 1% to 4%. If you go around the planet and you collect all the bits of Neanderthal DNA that survive in people who are alive today, we can put together around 93% of the Neanderthal genome. So Ill just end this by asking you if 93% of their genome exists today, are they really extinct?

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Biologist Beth Shapiro on the 'de-extinction' of woolly mammoths - STAT

Biology

MCC students inducted into new honor society geared toward biology – Mohave Valley News

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MCC students inducted into new honor society geared toward biology - Mohave Valley News

Biology

FRIDAY FACULTY FEATURE: Boente’s Biology Background the Rock Online – The Rock Online

Bee-o-int-te, Bo-int, Boe-net. All three different ways to say her name, but all are incorrect.

Boente, pronounced Bent-te, is one of the eighteen science teachers within the school department.

Boente went to the University of Iowa for two years before transferring to the University of Illinois for the last two years of her undergraduate degree. Boente began teaching after graduating from Illinois, starting as a substitute teacher at Lincoln Park High School, where she eventually became a teacher for two years.

She then moved to Colorado and began teaching in the Aurora Public Schools District at Vista Peak High School. After the principal of her last school left, she began looking for a different career path. Boente applied for a position at Rock Canyon.

[Rock Canyon is] definitely the best school Ive taught at, Im definitely the happiest here, Boente said. I do miss parts of the other schools. I miss the diversity, the different points of views and things like that, people from different backgrounds.

Growing up, Boente never really had a dream career but can always remember looking at teaching and thinking of a career in it.

I think that I just always wanted to be one, Boente said. I remember in first grade, when we dressed up as what we wanted to be when were older. I [dressed] up as a teacher and I think its just what I like to picture myself as.

Boente is currently in year five as a Jag and year 10 of teaching total.

My degree is I majored in Integrative Biology, and I minored in chemistry at U of I, and then I went to DePaul in Chicago and I got my masters in secondary science education, Boente said.

Even though teaching has always been something Boente has had an interest in and loved doing, if she could have a dream job, she would be a genetic counselor.

I teach genetics. Its obviously something that I find really interesting, Boente said. That field allows you to really kind of combine the science piece and also the working with people piece. So I do get that in teaching but its just kind of a completely different application to things. I just find it super interesting.

The application of science combined with helping people is what makes the job so interesting to her.

I think that [genetic counseling is] something thats always going to have a need for jobs, Boente said. Theres a lot of need for that position because we have lots of different technologies. A lot of the time, its used when people are trying to have children, and now that we have lots of technology as far as in vitro fertilization and that kind of stuff, theres just definitely going to be a need for it and just the whole field of genetics.

Boente teaches regular Biology, a class mostly taken by sophomores, and also teaches Genetics, an elective that any student can take.

While Boente currently only teaches science, she grew up playing volleyball and coached volleyball for a few seasons.

I played [for] like my whole life before that and I used to coach [at Rock Canyon] so its definitely one of my favorite things, Boente said. I volunteered my first year, so that was 2019 [to] 2020 but I wasnt really like a coach that year. So I would say from 2020 to 2022 [I coached]. So I think I did it for three seasons.

She was the sophomore girls volleyball coach for two years and then was the head JV boys volleyball coach for the 2020 season. The team only had one game due to COVID-19 interrupting the season.

We won [that game], Boente said. And then we didnt have a season after that. So we technically went undefeated.

While Boente does not coach anymore, she spends her free time with her daughter Mackie and also enjoys kickboxing.

I have a heavy bag in my basement, but I just dont use it very often, Boente said.

Before having her daughter, Boente would find herself up in the mountains skiing almost every weekend with her husband when they moved from Illinois to Colorado.

Skiing is something [that I enjoy], thats like one of the main reasons that we moved out here is because we both love to ski and we both love the mountains, Boente said.

Boente spends her time in room 9200 throughout the day, helping students and teaching.

[Rock Canyon] is definitely the best school Ive taught at, Boente said. Thats why Ive stayed here.

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FRIDAY FACULTY FEATURE: Boente's Biology Background the Rock Online - The Rock Online

Biology

Measuring the Intelligence of a Cell – University of California San Diego

What is Quantitative Biology and Why Does it Matter? As explained by Pradipta Ghosh

Our group is fascinated with molecules inside the cell popularly referred to as switches, because they control the flow of information inside a cell and between the cell and its external environment. A long-held belief was that one class of switch solely senses the outside environment, such as lower oxygen availability, while another class of switch solely coordinates communication within the cell, such as telling the genes to produce different proteins. Finding out whether the two types of switches interact has been elusive.

This is because cells are tiny, and the switches even tinier! There are many compelling mysteries that we biologists are still chipping away at, aided by technological advances with each passing decade.

Through these advances, we have recently discovered a circuit that combines both types of switches and allows the cell to sense its environment and mount a fitting response to it. To investigate how this circuit works in commanding a cells behavior, we now need to approach it as engineers, i.e., by building it as an electrical circuit in a virtual cell model.

To do so, we must use quantitative biology to gather measurements from the real world and feed those measurements to inform the model. Such a model, if built right, can have predictive power to ask questions that have never been possible before, and further our insights into how cells behave as intelligent machines that adapt to changing environments.

The scientists who build the modelsmathematicians, computational biologists, systems engineersneed numbers. At what second does the switch turn on? For how long? To answer their questions, we need assays that get precise measurements of whats happening in the cells interior. Thats the type of technology well have at the Agilent Center of Excellence for Cellular Intelligence.

Once the model is built, it becomes a virtual cell that we can tinker with, visualizing its behavior if we lower the oxygen supply or put it into chemotherapy. In this way, predictive models allow us to create an intervention and ask how it changes the cells behavior. If, for instance, I add a drug that will take out one of the switches, can I prevent a tumor cell from metastasizing?

This is how quantitative biology, advanced technology, and multidisciplinary research synergize to save peoples lives.

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Measuring the Intelligence of a Cell - University of California San Diego

Biology

Shy sea anemones are more likely to survive heatwaves – EurekAlert

image:

Sea anemones that live on the rocky coasts of the Atlantic are exposed to large differences in water temperature. Depending on the individual's personality, they cope with the heat differently.

Credit: Jack Thomson

Even in nature, pride can prevail. A study with researchers from the University of Gothenburg shows that sea anemones that react more slowly to change can survive a heatwave better than individuals that change their behaviour quickly.

Along the Atlantic coasts of Europe, many species are exposed to abrupt shifts in habitat. Tides, storms and rapid temperature changes are commonplace for the marine species that live there. With climate change, heatwaves are expected to become more frequent, and researchers wanted to find out how coastal marine species cope with extreme water temperatures. They chose to study the sea anemone species Actinia equina, a species that exhibits individual behaviours.

Brave or shy

We call them animal personalities. They are different behavioural life strategies found in the same species. The anemones we studied have two personality traits, bold and shy, and in extreme heat waves the shy anemones do better, says Lynne Sneddon, a zoophysiologist at the University of Gothenburg and co-author of the study published in the Journal of Experimental Biology.

Being a shy or bold anemone describes the individual's risk-taking. Both behaviours have advantages that have made them winners in evolution, otherwise they would not exist. A bold anemone reacts more quickly to changes in the environment than a shy anemone does. This means that the bold ones are quicker than the shy ones to open their tentacles to forage after a change. The bold anemones can trap more of the nutrients in the water, and this gives them a competitive advantage. On the other hand, they become more vulnerable in extreme conditions, such as heat waves. The researchers' study shows that being a shy individual is a better survival strategy when the water is extremely hot.

We measured the metabolism of the anemones and could see that when the water temperature was high, the metabolism of the bold anemones skyrocketed. This meant that they had to increase their nutrient intake so much that they risked dying. The shy anemones' metabolism increased less, so they were better able to cope with the heat stress, says Lynne Sneddon.

Rapid warming at low tide

In coasts with large tidal differences, water collects in rock pools that warm up quickly on the ebb tide before the next flood washes in with colder seawater. Anemones living in these pools are therefore particularly vulnerable to large temperature differences.

Heat waves will become more common in the future and cold-blooded animals may find it difficult to cope. We studied anemones, but we have reason to believe that the phenomenon applies to other species as well. If the animals can't cope, there will be a disruption in the ecosystems and this could have implications for the whole food web, says Lynne Sneddon.

Journal of Experimental Biology

Experimental study

Animals

Differential metabolic responses in bold and shy sea anemones during a simulated heatwave

7-Feb-2024

Disclaimer: AAAS and EurekAlert! are not responsible for the accuracy of news releases posted to EurekAlert! by contributing institutions or for the use of any information through the EurekAlert system.

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Shy sea anemones are more likely to survive heatwaves - EurekAlert

Biology

Akoya Biosciences Showcases Spatial Biology 2.0 Solutions at AACR Annual Meeting with Case Studies … – GlobeNewswire

MARLBOROUGH, Mass., April 05, 2024 (GLOBE NEWSWIRE) -- Akoya Biosciences, Inc., (Nasdaq: AKYA), The Spatial Biology Company, today announced it will highlight case studies featuring its Spatial Biology 2.0 Solutions that enable unprecedented speed and scale for spatial biology studies at the American Association for Cancer Research (AACR) 2024 Annual Meeting in San Diego, April 5 to 10. In addition, the company will showcase new applications of its PhenoCode Signature Panels and preliminary data from the Thermo Fisher ViewRNA assays on Akoyas platforms.

Presentations Showcase the Power of Spatial Biology 2.0

Industry-leading capabilities of the companys spatial biology platforms will be presented during Akoyas Spotlight Theater, titled Spatial Biology 2.0: Spatial Insights and Precision Medicine at Unprecedented Scale on Monday, April 8 at 3 PM (PST). The event will describe how researchers are revealing new insights into the tumor microenvironment, elucidating the mechanisms of cancer treatment response, and paving the way for spatial biology to impact patient outcomes. Deployment of Akoyas PhenoCycler-Fusion 2.0, PhenoImager HT 2.0, and PhenoCode Panels across the research continuum, from ultrahigh-plex discoveries to actionable signatures, will be described by the presenters:

Dr. Kulasinghe will also present a talk entitled Ultra high-plex profiling of the tumor microenvironment on April 6 from 12:36 PM - 12:54 PM PT in Session MW14 - Choosing and Using Antibodies for Spatial Informed Protein Expression. He will discuss the development of ultrahigh-plex antibody panels for the comprehensive characterization of the tumor microenvironment.

Spatial Biology 2.0 Solutions Displayed at Booth #247

Akoya Biosciences will demonstrate new uses of its PhenoCode Signature Panels for accelerating discovery and validation of spatial biomarkers using the PhenoImager HT 2.0 platform. The company will also present initial findings from the Thermo Fisher Scientific ViewRNA assays on the PhenoCycler-Fusion 2.0.

Poster Presentations

Several studies featuring Akoyas Spatial Biology platforms will be described in the following posters:

Monday, April 8: 9:00 AM 12:30 PM

Poster 1525: Integration of high-plex tumor-Immune phenotyping and checkpoint interactions for deeper spatial characterization of human cancer tissues. S. Bodbin, Navinci Diagnostics et al.

Monday, April 8: 1:30 PM 5:00 PM

Poster 3623: Quantifying pharmacodynamic markers of radioligand therapies in tumor by multiplex immunofluorescence and automated quantitative analysis (AQUA) algorithms. J. Santos, Navigate BioPharma Services, Inc. et al.

Poster 3651: Mutational analysis and spatial phenotyping to decipher racial disparities in pancreatic adenocarcinoma; D. J. Salas-Escabillas, University of Michigan et al.

Poster 3763: Comparative spatial analyses of the tumor immune landscape in different mouse models of glioblastoma; D. Klymyshyn, Akoya Biosciences et al.

Tuesday, April 9: 9:00 AM 12:30 PM

Poster 3988: Deep spatial immunophenotyping of lymphoid aggregates in pancreatic cancer using multi-omic integration of ultra high-plex proteomics and transcriptomics; D. Gong, Massachusetts Institute of Technology (MIT) et al.

Poster 5503: Ultrahigh-plex spatial phenotyping of head and neck cancer tissue uncovers multiomic signatures of immunotherapy response; A. Pratapa, Akoya Biosciences et al.

Poster 5504: Integrating ultrahigh-plex spatial phenotyping: From discovery to clinical applications, A. Pratapa; Akoya Biosciences et al.

Tuesday, April 9: 1:30 PM 5:00 PM

Poster 5507: High-resolution spatial atlas reveals insight into spatial landscape of lung cancer and chronic lung diseases; R. Nandigama, Justus Liebig University et al.

Poster 5508: Single-cell spatial landscape of the mutation-specific human lung tumor immune microenvironment; R. Nandigama, Justus Liebig University et al.

Wednesday, April 10: 9:00 AM 12:30 PM

Poster 6738: Overlapping and distinct mechanisms of effective neoantigen cancer vaccines and immune checkpoint therapy; S. Keshari, UT MD Anderson Cancer Center et al.

Poster 6872: A spatio-temporal approach to mapping the dynamics of cutaneous squamous cell carcinoma progression and immunotherapy response: A journey through TiME; N. Jhaveri, Akoya Biosciences et al.

Network of CROs Providing Spatial Biology Services Continues to Grow

Thirteen of Akoyas twenty qualifiedCRO service providerswill also be exhibiting at AACR. Akoyas CRO network continues to grow rapidly, reflecting the demand for spatial phenotyping solutions across the biopharmaceutical industry. Offering biomarker testing services, these CROs enable drug developers and academic research institutions to accelerate the discovery and development of new immuno-therapies.

Full details about Akoyas AACR activities and poster presentations can be found here.

Forward Looking Statements

This press release contains forward-looking statements that are based on managements beliefs and assumptions and on information currently available to management. All statements contained in this release other than statements of historical fact are forward-looking statements, including statements regarding our expectations about the potential and utility of our products and services, the market demand for spatial phenotyping solutions and predictions regarding the future impact of spatial biology.

In some cases, you can identify forward-looking statements by the words may, will, could, would, should, expect, intend, plan, anticipate, believe, estimate, predict, project, potential, continue, ongoing or the negative of these terms or other comparable terminology, although not all forward-looking statements contain these words. These statements involve risks, uncertainties and other factors that may cause actual results, levels of activity, performance, or achievements to be materially different from the information expressed or implied by these forward-looking statements. These risks, uncertainties and other factors are described under "Risk Factors," "Management's Discussion and Analysis of Financial Condition and Results of Operations" and elsewhere in the documents we file with the Securities and Exchange Commission from time to time. We caution you that forward-looking statements are based on a combination of facts and factors currently known by us and our projections of the future, about which we cannot be certain. As a result, the forward-looking statements may not prove to be accurate. The forward-looking statements in this press release represent our views as of the date hereof. We undertake no obligation to update any forward-looking statements for any reason, except as required by law.

About Akoya Biosciences

As The Spatial Biology Company, Akoya Biosciences mission is to bring context to the world of biology and human health through the power of spatial phenotyping. The Company offers comprehensive single-cell imaging solutions that allow researchers to phenotype cells with spatial context and visualize how they organize and interact to influence disease progression and response to therapy. Akoya offers a full continuum of spatial phenotyping solutions to serve the diverse needs of researchers across discovery, translational and clinical research: PhenoCode Panels and PhenoCycler, PhenoImager Fusion and PhenoImager HT Instruments. To learn more about Akoya, visitwww.akoyabio.com.

Investor Contact:

Priyam Shah Sr. Director, Investor Relations Akoya Biosciences investors@akoyabio.com

Media Contact:

Christine Quern 617-650-8497 media@akoyabio.com

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Akoya Biosciences Showcases Spatial Biology 2.0 Solutions at AACR Annual Meeting with Case Studies ... - GlobeNewswire

Biology

BD Increases Access to Cutting-Edge Image-Enabled, Spectral Cell Sorters – BioSpace

New BD FACSDiscover S8 Cell Sorters to Enable More Researchers to Push the Boundaries of Discovery

FRANKLIN LAKES, N.J., April 5, 2024 /PRNewswire/ -- BD (Becton, Dickinson and Company) (NYSE: BDX), a leading global medical technology company, today announced the global commercial release of new cell sorters that will enable more researchers in a broader range of fields, including cell biology, cancer research and immunology, to reveal insights that were previously invisible in traditional flow cytometry experiments.

The new BD FACSDiscover S8 Cell Sorters feature BD CellView Image Technology, profiled on the cover of the journal Science in 2022, and BD SpectralFX Technology bringing to market breakthrough innovations in real-time imaging and spectral flow cytometry. The three- and four-laser additions to the BD FACSDiscover S8 Cell Sorter family complement the five-laser instrument launched last year and provide scientists greater access, options, and flexibility to incorporate real-time imaging and spectral cell sorting technology in their labs.

"For my research in cellular biology, the instrument was perfectly configured when it came to number of lasers and imaging capabilities," said Daniel Schraivogel, Ph.D., a research staff scientist at EMBL, who estimates he had 600 hours working on the three-laser prototype. "It has the same sorting speed and software capabilities as the five-laser unit, making experiments extremely scalable on an easy-to-use instrument."

Using the FACSDiscover S8 Cell Sorters, researchers can confirm complex biological and spatial insights in real time, obtain individual cell images and isolate desired cells based on visual characteristics at high speeds, all within a simplified and easy to use workflow. BD CellView Image Technology improves sort and sample quality, bringing confidence to biological results and saving researchers time and cost in their downstream applications. This expedited time to insight expands capabilities for researchers to transform research and cell-based therapeutic development across numerous fields in drug discovery, immuno-oncology and genomics.

"In flow cytometry, there are often 'suspect' populations where cells are dead or dying, and doublets and cellular debris that can impact the integrity of experiments," Schraivogel continued. "In addition to the added value of spatial information that is needed for many projects in cell biology, infection biology and functional genomic screening, the imaging sorter allows us to better explore our cell populations and is used to validate true single-cell gating and sorting, to deliver better-quality cells and biological outputs."

The family of BD FACSDiscover Cell Sorters will be featured at upcoming conferences beginning with the American Association for Cancer Research (AACR) Annual Meeting, April 5-10, and is now available to order through local sales representatives. More information is available at bdbiosciences.com/S8.

About BD BD is one of the largest global medical technology companies in the world and is advancing the world of health by improving medical discovery, diagnostics and the delivery of care. The company supports the heroes on the frontlines of health care by developing innovative technology, services and solutions that help advance both clinical therapy for patients and clinical process for health care providers. BD and its more than 70,000 employees have a passion and commitment to help enhance the safety and efficiency of clinicians' care delivery process, enable laboratory scientists to accurately detect disease and advance researchers' capabilities to develop the next generation of diagnostics and therapeutics. BD has a presence in virtually every country and partners with organizations around the world to address some of the most challenging global health issues. By working in close collaboration with customers, BD can help enhance outcomes, lower costs, increase efficiencies, improve safety and expand access to health care. For more information on BD, please visit bd.com or connect with us on LinkedIn at http://www.linkedin.com/company/bd1/, X (formerly Twitter) @BDandCo or Instagram @becton_dickinson.

View original content to download multimedia:https://www.prnewswire.com/news-releases/bd-increases-access-to-cutting-edge-image-enabled-spectral-cell-sorters-302108936.html

SOURCE BD (Becton, Dickinson and Company)

Company Codes: NYSE:BDX

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BD Increases Access to Cutting-Edge Image-Enabled, Spectral Cell Sorters - BioSpace

Biology

We’ve had bird evolution all wrong – EurekAlert

image:

A greater flamingo in Mallorca, Spain. Unraveling a genetic mystery revealed that flamingos and doves are more distantly related than previously thought.

Credit: Daniel J. Field

An enormous meteor spelled doom for most dinosaurs 65 million years ago. But not all. In the aftermath of the extinction event, birds technically dinosaurs themselves flourished.

Scientists have spent centuries trying to organize and sort some 10,000 species of birds into one clear family tree to understand how the last surviving dinosaurs filled the skies. Cheap DNA sequencing should have made this simple, as it has for countless other species.

But birds were prepared to deceive us.

In a pair of new research papers released today, April 1, scientists reveal that another event 65 million years ago misled them about the true family history of birds. They discovered that a section of one chromosome spent millions of years frozen in time, and it refused to mix together with nearby DNA as it should have.

This section, just two percent of the bird genome, convinced scientists that most birds could be grouped into two major categories, with flamingos and doves as evolutionary cousins. The more accurate family tree, which accounts for the misleading section of the genome, identifies four main groups and identifies flamingos and doves as more distantly related.

My lab has been chipping away at this problem of bird evolution for longer than I want to think about, said Edward Braun, Ph.D., the senior author of the paper published in the Proceedings of the National Academy of Sciences and a professor of biology at the University of Florida. We had no idea there would be a big chunk of the genome that behaved unusually. We kind of stumbled onto it.

Braun supervised an international team of collaborators led by Siavash Mirarab, a professor of computer engineering at the University of California San Diego, to publish their evidence that this sticky chunk of DNA muddied the true history of bird evolution. Mirarab and Braun also contributed to a companion paper published in Nature that outlines the updated bird family tree, which was led by Josefin Stiller at the University of Copenhagen.

Both papers are part of the B10K avian genomics project led by Guojie Zhang of Zhejiang University, Erich Jarvis of Rockefeller University, and Tom Gilbert of the University of Copenhagen.

Ten years ago, Braun and his collaborators pieced together a family tree for the Neoaves, a group that includes the vast majority of bird species. Based on the genomes of 48 species, they split the Neoaves into two big categories: doves and flamingos in one group, all the rest in the other. When repeating a similar analysis this year using 363 species, a different family tree emerged that split up doves and flamingos into two distinct groups.

With two mutually exclusive family trees in hand, the scientists went hunting for explanations that could tell them which tree was correct.

When we looked at the individual genes and what tree they supported, all of a sudden it popped out that all the genes that support the older tree, theyre all in one spot. Thats what started the whole thing, Braun said.

Investigating this spot, Brauns team noticed it was not as mixed together as it should have been over millions of years of sexual reproduction. Like humans, birds combine genes from a father and a mother into the next generation. But birds and humans alike first mix the genes they inherited from their parents when creating sperm and eggs. This process is called recombination, and it maximizes a species genetic diversity by making sure no two siblings are quite the same.

Brauns team found evidence that one section of one bird chromosome had suppressed this recombination process for a few million years around the time the dinosaurs disappeared. Whether the extinction event and the genomic anomalies are related is unclear.

The result was that the flamingos and doves looked similar to one another in this chunk of frozen DNA. But taking into account the full genome, it became clear that the two groups are more distantly related. Whats surprising is that this period of suppressed recombination could mislead the analysis, Braun said. And because it could mislead the analysis, it was actually detectable more than 60 million years in the future. That's the cool part.

Such a mystery could be lurking in the genomes of other organisms as well.

We discovered this misleading region in birds because we put a lot of energy into sequencing birds genomes, Braun said. I think there are cases like this out there for other species that are just not known right now.

This work was supported in part by the National Science Foundation.

Proceedings of the National Academy of Sciences

Data/statistical analysis

Not applicable

A region of suppressed recombination misleads neoavian phylogenomics

1-Apr-2024

Disclaimer: AAAS and EurekAlert! are not responsible for the accuracy of news releases posted to EurekAlert! by contributing institutions or for the use of any information through the EurekAlert system.

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We've had bird evolution all wrong - EurekAlert