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.

The scientific community has long sought to understand the enigmatic origins of consciousness. A recent landmark experiment has taken us one step closer to unraveling this mystery. Conducted by researchers from the Allen Institute, this collaborative effort brought together 256 human subjects and two prominent theories: Integrated Information Theory (IIT) and Global Neuronal Workspace Theory (GNWT).

According to IIT, consciousness emerges when information inside a system (like the brain) is highly connected and unified. In contrast, GNWT suggests that consciousness arises from a network of brain areas spotlighting important pieces of information in the brain, broadcasting it widely when it enters consciousness.

The findings of this experiment de-emphasize the importance of the prefrontal cortex in consciousness, suggesting that while it’s crucial for reasoning and planning, consciousness itself may be linked with sensory processing and perception. This discovery has significant implications for our understanding of consciousness and may shed light on disorders such as comas or vegetative states.

The study involved a highly collaborative approach, bringing together researchers from diverse backgrounds to test these two competing theories in a critical environment aimed at reducing confirmation bias and accelerating scientific progress. While neither theory emerged victorious, the findings remain valuable, providing new insights into both theories and the brain’s processing of visual experience.

As Christof Koch, Ph.D., meritorious investigator at the Allen Institute, noted, “Unravelling this mystery is the passion of my entire life.” This experiment marks a pivotal moment in our pursuit to understand the elusive origins of consciousness, and its implications will undoubtedly continue to shape our understanding of human perception and thought.

The discovery of ancient flying reptiles, known as pterosaurs, has long fascinated scientists and the general public alike. However, recent research at the University of Leicester has shed new light on these awe-inspiring creatures by linking fossilized footprints to specific types of pterosaurs.

Using advanced 3D modeling, detailed analysis, and comparisons with pterosaur skeletons, a team of researchers led by Robert Smyth successfully identified three distinct types of tracks that matched up with different groups of flying reptiles. These findings provide a unique opportunity to study how these creatures lived, moved, and evolved in their natural environment.

One group of pterosaurs, the neoazhdarchians (including Quetzalcoatlus), was found to be frequent ground dwellers, inhabiting coastal and inland areas around the world. Their footprints were discovered in rock layers that date back 160 million years ago, during the middle part of the Age of Dinosaurs. These long-legged creatures dominated both the skies and the ground, with some tracks present right up until the asteroid impact event that led to their extinction.

Another group, the ctenochasmatoids, left behind tracks most commonly found in coastal deposits. These animals likely waded along muddy shores or in shallow lagoons, using their specialized feeding strategies to catch small fish or floating prey. The abundance of these tracks suggests that these coastal pterosaurs were far more common in these environments than their rare bodily remains indicate.

The third type of footprint was discovered in rock layers that also preserve the fossilized skeletons of the same pterosaurs, known as dsungaripterids. These pterosaurs had powerful limbs and jaws, with toothless, curved beak tips designed for prising out prey, while large, rounded teeth at the back of their jaws were perfect for crushing shellfish and other tough food items.

Smyth explains that tracks are often overlooked when studying pterosaurs, but they provide a wealth of information about how these creatures moved, behaved, and interacted with their environments. By closely examining footprints, scientists can now discover things about the biology and ecology of pterosaurs that would be impossible to learn anywhere else.

The discovery of these ground-breaking habits in ancient flying reptiles not only expands our understanding of these fascinating creatures but also highlights the importance of interdisciplinary research in uncovering hidden secrets from the past.