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Early Humans

Revolutionizing Species Tree Inference with ROADIES

Engineers are making it easier for researchers from a broad range of backgrounds to understand how different species are evolutionarily related, and support the transformative biological and medical applications that rely on these species trees. The researchers developed a scalable, automated and user-friendly tool called ROADIES that allows scientists to infer species trees directly from raw genome data, with less reliance on the domain expertise and computational resources currently required.

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Revolutionizing Species Tree Inference with ROADIES

A team of engineers at the University of California San Diego has made it easier for researchers from various backgrounds to understand how different species are evolutionarily related. The researchers developed a scalable, automated, and user-friendly tool called ROADIES that allows scientists to infer species trees directly from raw genome data, reducing reliance on domain expertise and computational resources currently required.

Species trees are crucial in solidifying our understanding of how species evolved on a broad scale. They can also help find functional regions of the genome that could serve as drug targets, link physical traits to genomic changes, predict and respond to zoonotic outbreaks, and guide conservation efforts.

In a recent paper published in the journal Proceedings of the National Academy of Sciences (PNAS), the researchers demonstrated that ROADIES infers species trees comparable in quality with state-of-the-art studies but requires significantly less time and effort. This study focused on four diverse life forms: placental mammals, pomace flies, birds, and budding yeasts.

“Rapid advances in high-throughput sequencing and computational tools have enabled genome assemblies to be produced at scale,” said Anshu Gupta, a computer science PhD student at the Jacobs School of Engineering and the study’s first author. “However, accurately inferring species trees is still beyond the reach of many researchers.”

The innovation behind ROADIES lies in its completely automated pipeline that produces highly accurate results without the need for predefined genomic regions or orthology inference.

“ROADIES is a timely and transformative solution to this problem,” said Yatish Turakhia, the electrical and computer engineering professor leading the study. “With its speed, accuracy, and automation, ROADIES has the potential to vastly simplify species tree inference, making it accessible to a broader range of scientists and applications.”

The researchers are continuing to improve the capability of ROADIES, including the placement of new taxa on existing species trees and the potential use of GPUs to allow for the processing of tens of thousands of genomes. Large-scale initiatives are underway to sequence thousands of species, and the team wants to ensure that ROADIES is ready to meet this scale.

This work is supported by an Amazon Research Award (Fall 2022 Call for Proposals), NIH grant 1R35GM142725, and funding from the Hellman Fellowship. The development of ROADIES has the potential to revolutionize species tree inference, making it easier for researchers to understand evolutionary relationships between different species.

Early Humans

The Hidden Legacy of the Denisovans: Uncovering the Secrets of Human Evolution

Denisovans, a mysterious human relative, left behind far more than a handful of fossils—they left genetic fingerprints in modern humans across the globe. Multiple interbreeding events with distinct Denisovan populations helped shape traits like high-altitude survival in Tibetans, cold-weather adaptation in Inuits, and enhanced immunity. Their influence spanned from Siberia to South America, and scientists are now uncovering how these genetic gifts transformed human evolution, even with such limited physical remains.

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The discovery of the Denisovans has revolutionized our understanding of human evolution. In 2010, scientists uncovered the first draft of the Neanderthal genome, confirming that early humans had interbred with these extinct relatives. Just months later, a finger bone found in Denisova Cave revealed the presence of another unknown hominin group, the Denisovans. Like their Neanderthal counterparts, researchers have found evidence of interbreeding between modern humans and Denisovans.

According to Dr. Linda Ongaro, Postdoctoral Researcher at Trinity College Dublin’s School of Genetics and Microbiology, this phenomenon is not unique to a single event but rather the result of multiple interbreeding episodes that shaped the course of human history. “It’s a common misconception that humans evolved suddenly and neatly from one common ancestor,” she notes. “The more we learn, the more we realize interbreeding with different hominins occurred and helped shape the people we are today.”

Despite the limited Denisovan fossil record, scientists have managed to uncover significant evidence of their genetic legacy. By leveraging surviving segments in modern human genomes, researchers have identified at least three past events where genes from distinct Denisovan populations were incorporated into the genetic signatures of humans.

These events reveal varying degrees of genetic similarity to the Denisovan remains found in the Altai region, suggesting a complex relationship among these closely related groups. In their review, Dr. Ongaro and Professor Emilia Huerta-Sanchez highlight evidence that Denisovans lived across a vast territory stretching from Siberia to Southeast Asia and from Oceania to South America. Different groups appear to have been adapted to their own specific environments.

Moreover, scientists have detailed several Denisovan-derived genes that provided survival advantages in different parts of the world. For example, one genetic locus confers tolerance to hypoxia (low oxygen conditions), which makes sense in Tibetan populations; multiple genes confer heightened immunity; and one gene impacts lipid metabolism, providing heat when stimulated by cold, giving an advantage to Inuit populations in the Arctic.

Dr. Ongaro emphasizes that there are numerous future directions for research that will help tell a more complete story of how the Denisovans impacted modern humans. These include more detailed genetic analyses in understudied populations and integrating more genetic data with archaeological information, which could reveal currently hidden traces of Denisovan ancestry.

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Early Humans

A Tiny Dinosaur Bone Rewrites the Origin of Bird Flight

A tiny, overlooked wrist bone called the pisiform may have played a pivotal role in bird flight and it turns out it evolved far earlier than scientists thought. Fossils from bird-like dinosaurs in Mongolia reveal that this bone, once thought to vanish and reappear, was actually hiding in plain sight. Thanks to pristine preservation and 3D scans, researchers connected the dots between ancient theropods and modern birds, uncovering a deeper, more intricate story of how dinosaurs evolved the tools for powered flight.

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The evolution from dinosaurs to birds included significant anatomical modifications. One crucial change was the development of a tiny wrist bone called the pisiform that helped stabilize wings in flight. A new study suggests that this bone appeared in bird ancestors millions of years earlier than first thought.

Paleontologists at Yale and Stony Brook University led a research team that made the discovery after examining fossils from two species of bird-like dinosaurs found in the Gobi Desert in Mongolia. The findings were published in the journal Nature.

“We were fortunate to have two immaculately preserved theropod wrists for this,” said Alex Ruebenstahl, a student at Yale’s Graduate School of Arts and Sciences. Both Ruebenstahl and his colleague Bhart-Anjan Bhullar noticed that the wrist bones were small and had shifted during decay and preservation.

The evolution of theropod dinosaurs into birds included significant anatomical modifications, such as changes in the pelvis and its surrounding musculature – and a transformation of the dinosaur forelimbs. One key change was the replacement of the ulnare with the pisiform bone in birds. In living birds, the pisiform is an unusual wrist bone that forms within a muscle tendon.

“This integration is particularly important for stabilizing the wing during flight,” said Bhullar. The discovery suggests that the integrated pisiform evolved prior to modern avian flight, and was diminutive in these near-bird dinosaurs, which is consistent with their limited flight capabilities.

The research continues a rich Yale tradition of advancing understanding of bird evolution from dinosaurs. In the 1960s, Yale paleontologist John Ostrom identified another wrist bone found in both meat-eating dinosaurs and modern birds. In the 1980s, Yale paleontologist Jacques Gauthier definitively showed that this wrist bone linked dinosaurs to birds.

The study’s lead author, James Napoli, of Stony Brook University, collaborated with Ruebenstahl and Bhullar to re-identify wrist bones in other dinosaurs as pisiforms. Further analysis showed the unidentified bones were indeed pisiform bones. The researchers then expanded their efforts to study the development of some of the flight muscles associated with the pisiform.

The research was conducted by a team including co-authors Matteo Fabbri, Jimgmai O’Connor, and Mark Norell, and furthered understanding of bird evolution from dinosaurs.

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Ancient Civilizations

Unraveling a 130-Year-Old Literary Mystery: The Song of Wade Finally Solved

After baffling scholars for over a century, Cambridge researchers have reinterpreted the long-lost Song of Wade, revealing it to be a chivalric romance rather than a monster-filled myth. The twist came when “elves” in a medieval sermon were correctly identified as “wolves,” dramatically altering the legend’s tone and context.

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In this groundbreaking study, two scholars from Girton College, Cambridge, present their findings on the Humiliamini sermon, which contains the enigmatic reference to Wade. By analyzing the writing style and arguments presented in the sermon, they conclude that it was likely written by Alexander Neckam or an acolyte familiar with his work.

The sermon’s focus on humility as a lesson in the face of human vices is strikingly relevant today. The researchers highlight the use of vivid animal imagery to convey these themes, including powerful men becoming like wolves and cunning individuals imitating serpents.

Their study sheds new light on the Song of Wade, a medieval literary mystery that has puzzled scholars for over a century. By uncovering its true meaning, this research contributes significantly to our understanding of medieval literature, history, and theology.

As one scholar notes, “This sermon still resonates today… It warns that it’s us, humans, who pose the biggest threat, not monsters.” The retranslation of the Song of Wade offers a powerful reminder of the importance of humility in our daily lives.

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