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Biology

Unlocking the Genetic Code of Adaptation: How Stick Insects Evolved to Avoid Predation

Scientists report adaptive divergence in cryptic color pattern is underlain by two distinct, complex chromosomal rearrangements, where millions of bases of DNA were flipped backwards and moved from one part of a chromosome to another, independently in populations of stick insects on different mountains.

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The study of adaptive evolution has been a long-standing goal in biology, dating back to Charles Darwin’s time. Recent debates have centered on whether adaptive evolution relies on numerous small mutations or one or few major changes that significantly impact traits. To shed light on this question, researchers have turned to the analysis of chromosomal rearrangements – large-scale “macromutations” that can reshape an organism’s genetic makeup.

Stick insects (Timema cristinae), found in coastal chaparral habitats near Santa Barbara, California, provide a fascinating example of adaptive evolution. These wingless, plant-feeding insects have developed distinct color patterns to blend in with their surroundings and avoid predation. Specifically, some populations display a green pattern that allows them to remain undetected among the California lilac, while others feature a thin white stripe on their back that makes them nearly invisible amidst the needle-like leaves of the chamise shrub.

A recent study published in Science has revealed that this adaptive difference in color pattern is almost entirely explained by two distinct complex chromosomal rearrangements. These rearrangements involve millions of bases of DNA being flipped backwards and moved from one part of a chromosome to another, independently in populations on different mountains.

Using newer, molecular and computational approaches that generate phased genome assemblies – where the two copies of each chromosome are assembled separately – researchers have been able to directly demonstrate how these complex chromosomal rearrangements have enabled stick insects to adapt by being cryptic on different host plants.

The study’s lead author, Zachariah Gompert, an evolutionary biologist at Utah State University, emphasizes that the new phased genomic assembly technology used in this study was a critical piece in helping them examine how color pattern evolved in these insects. “Our findings suggest chromosomal rearrangements might be more widespread and more complex than we previously thought,” he says.

Gompert’s research suggests that structural variation – rather than being rare – may regularly prompt evolution. “Chromosomal rearrangements can be difficult to detect and characterize using standard approaches,” Gompert notes. “We’re essentially exploring the ‘dark matter’ of the genome.”

This study offers a significant contribution to our understanding of adaptive evolution, shedding light on the complex genetic basis of this process in stick insects. By examining chromosomal rearrangements and their role in evolution, researchers may uncover new insights into how organisms adapt to their environments and respond to selection pressures.

Ultimately, the discovery that chromosomal rearrangements can drive major changes in traits opens up exciting avenues for further research. As Gompert puts it, “We’re just scratching the surface.”

Behavioral Science

Echidna Pseudo-Pouch Microbiome Shifts During Lactation Helps Young Thrive

Research shows microbial communities in echidna pseudo-pouches undergo dramatic changes while the animal is lactating, which could help in creating an environment for their young, known as puggles, to thrive.

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Echidnas, the only mammals that lay eggs, have an unusual reproductive system that includes a pseudo-pouch where their young, called puggles, grow and develop during lactation. Researchers from the University of Adelaide have made a fascinating discovery about the microbiome in these pseudo-pouches, which changes significantly while the mother is nursing her young.

The study, published in FEMS Microbiology Ecology, reveals that the microbial communities in echidna pseudo-pouches undergo dramatic changes during lactation, creating an environment that’s conducive to the health and well-being of their puggles. This is particularly important since puggles hatch at a very early developmental stage, lacking a functional immune system.

“We know that the reproductive microbiome is crucial for infant health in many species, including humans,” says Isabella Wilson, lead researcher on the study. “However, little was known about how it functions in egg-laying monotremes like echidnas.”

One of the key findings of this research is that during lactation, the pseudo-pouch microbial communities show significant differences in composition compared to samples taken outside of breeding season or during courtship and mating. This suggests that the echidna pseudo-pouch environment changes during lactation to accommodate young that lack a functional adaptive immune system.

The way puggles suckle may contribute to this shift in microbes. Unlike other species, echidnas don’t have nipples; instead, their young rub their beaks against a part of the pseudo-pouch called the milk patch, causing milk to come out of the skin, similar to a sweat or oil gland.

Compounds within the milk and from the skin probably contribute to the changes seen in the pseudo-pouch microbiota during lactation. This study highlights the importance of understanding these unique reproductive dynamics for conservation efforts and breeding programs for echidnas.

The research also sheds light on previous findings that showed big differences in the gut microbiome between echidnas in zoos and those in the wild. Surprisingly, no major difference was found in the pseudo-pouch microbiota between zoo-managed and wild animals. This suggests that the milk, rather than external environmental factors like captivity, is what primarily shapes the bacterial landscape of the pseudo-pouch.

For conservation efforts and breeding programs, it’s essential to learn more about the bacteria found in echidna pseudo-pouches and how they affect echidna health. This knowledge will help ensure the well-being of these unique animals and their young, ultimately contributing to the preservation of this fascinating species.

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Biochemistry Research

A More Realistic Look at DNA in Action: Researchers Shed Light on the Mechanical Forces Behind Strand Separation

By creating a more true-to-life representation of DNA’s environment, researchers have discovered that strand separation may take more mechanical force than the field previously believed.

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The way we study DNA has long been a topic of discussion among researchers. Traditionally, biochemistry labs isolate DNA within a water-based solution that allows scientists to manipulate it without interacting with other molecules. However, this approach can be misleading, as it doesn’t reflect the true environment of a living cell. In fact, the interior of a cell is “super crowded” with molecules, which can significantly impact the behavior of DNA.

Researchers at Northwestern University have taken a more realistic approach to studying DNA by creating an environment that mimics the conditions within a living cell. Led by Professor John Marko, the team used microscopic magnetic tweezers to separate DNA and then carefully attach strands of it to surfaces on one end, and tiny magnetic particles on the other. This allowed them to conduct high-tech imaging and investigate how different types of molecules interact with DNA.

The researchers found that strand separation, a crucial process for initiating replication or making repairs, may require more mechanical force than previously believed. They introduced three types of molecules to the solution holding DNA, mimicking proteins and investigating interactions among glycerol, ethylene glycol, and polyethylene glycol (each approximately the size of one DNA double helix, two or three nanometers).

“We wanted to have a wide variety of molecules where some cause dehydration, destabilizing DNA mechanically, and then others that stabilize DNA,” said Northwestern post-doctoral researcher Parth Desai. “It’s not exactly analogous to things found in cells, but you could imagine that other competing proteins in cells will have a similar effect.”
The team wrote a paper on their findings, which will be published on June 17 in the Biophysical Journal. Marko and Desai hope to run more experiments that incorporate multiple crowding agents and move closer to a true representation of a cell.

“If this affects DNA strand separation, all protein interactions with DNA are also going to be affected,” said Marko. “For example, the tendency for proteins to stick to specific sites on DNA and to control specific processes — this is also going to be altered by crowding.”

Their research has significant implications for understanding fundamental biochemical processes and may lead to new medical advances. The team hopes to study how interactions between enzymes and DNA are impacted by crowding in a living cell, which could have far-reaching consequences for our understanding of cellular biology.

This work was supported by the National Institutes of Health (grant R01-GM105847) and by subcontract to the University of Massachusetts Center for 3D Structure and Physics of the Genome (under NIH grant UM1-HG011536).

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Animals

A “Roadmap” to Understanding the Fruit Fly Brain: Breakthrough Study Reveals Comprehensive Insights into Entire Nervous System

Researchers have gained comprehensive insights into the entire nervous system of the fruit fly (Drosophila melanogaster). The study describes in detail the neurons that span the entire nervous system of the adult fruit fly. The researchers also compared the complete set of neural connections (the connectome) in a female and a male specimen — and identified differences.

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The fruit fly (Drosophila melanogaster) has long been a model organism for scientists studying genetics, development, and behavior. However, despite its importance, the intricacies of the fruit fly’s nervous system have remained somewhat of a mystery – until now. Researchers at Leipzig University and other institutions have made a groundbreaking discovery, publishing a study in Nature that provides comprehensive insights into the entire nervous system of the adult fruit fly.

For the first time, scientists have mapped out the neural connections (the connectome) in a female and a male specimen, revealing differences between the two sexes. This breakthrough is a significant step forward in understanding the complex interactions within the fruit fly’s brain and nervous system.

The study, led by Dr. Katharina Eichler from Leipzig University, involved analyzing three connectomes: one female brain data set and two nerve cord data sets (one male, one female). The researchers used light microscopy to identify all neurons in the neck of the fruit fly that could be visualized using this technique.

This allowed them to analyze the circuits formed by these cells in their entirety. When comparing male and female neurons, the scientists identified sex-specific differences for the first time. They found previously unknown cells that exist only in one sex and are absent in the other.

One notable example is a descending neuron known as aSP22, which communicates with neurons present only in females. This finding provides an explanation for the behavioral differences observed when this neuron is active: female flies extend their abdomen to lay eggs, while males curl theirs forward to mate.

The study’s findings are significant not only because they provide a comprehensive overview of the fruit fly connectome but also because they offer a “roadmap” for future research. By understanding the intricate connections within the nervous system, scientists can design more intelligent experiments to investigate the function of individual neurons or entire circuits – saving time and resources.

As Eichler notes, now that the technical challenges in analyzing the fruit fly’s nervous system have been overcome, her research group is working on two new data sets covering the entire central nervous system of both a female and a male specimen. This continued research will undoubtedly shed more light on the complexities of the fruit fly brain and its implications for our understanding of nervous systems in general.

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