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  • Decoding Animal Evolution: Insights from Chromosome-Scale Genomes

    For over a century, biologists have been fascinated by the origins of the earliest animals that emerged in the ancient oceans more than half a billion years ago. After extensive investigation into the most primitive-looking animals alive today, scientists have narrowed down the options to two groups: sponges and comb jellies.

    In a new study published in Nature, researchers have used a novel approach based on chromosome structure to definitively identify comb jellies, also known as ctenophores, as the first lineage to branch off from the animal tree of life. Sponges followed as the next branch, with all other animals, including the lineage leading to humans, diversifying afterward.

    Although both ctenophores and sponges have continued to evolve from their common ancestor, evolutionary biologists believe that these groups still retain characteristics of the earliest animals. By studying these early branches of the animal tree of life, scientists hope to gain insights into the emergence and evolution of animals, shedding light on the diversity of species we observe today.

    The researchers relied on an unexpected feature—chromosome structure—to determine whether sponges or ctenophores represented the earliest animal branch. Each species possesses a characteristic chromosome number and gene distribution along the chromosomes. Previous studies by the same researchers had revealed that sponges, jellyfish, and other invertebrates carried similar sets of genes on their chromosomes, despite millions of years of independent evolution. This finding suggested that animal chromosomes evolve slowly, allowing the team to computationally reconstruct the chromosomes of the common ancestor of these diverse animals.

    The chromosome structure of ctenophores remained unknown until 2021 when Darrin Schultz, then a graduate student at UC Santa Cruz, and his co-advisers Richard Green and Steven Haddock, determined the chromosome structure of the ctenophore Hormiphora californiensis. The ctenophore chromosomes appeared distinctly different from those of other animals, raising questions about their evolutionary placement.

    To resolve the controversy over the order in which sponges and ctenophores branched off from the animal tree of life, the researchers sequenced the genomes of another comb jelly and sponge, along with three non-animal organisms. By comparing the chromosomes of these diverse organisms, they made a remarkable discovery. Ctenophores and non-animal organisms shared specific gene-chromosome combinations, while sponges and other animals displayed distinct rearrangements.

    The findings provide strong evidence that ctenophores branched off first, prior to the rearrangements observed in sponges and other animals. The ancient chromosomal signal discovered in the genomes of animals hundreds of millions of years later supports the "ctenophore-branched-first" scenario. The alternative hypothesis, suggesting sponges as the earliest branch, would require multiple convergent rearrangements in both sponges and non-ctenophore animals, which is highly unlikely.

    Understanding the relationships among different animal lineages is crucial for comprehending the evolution of key features such as the nervous system, muscles, and digestive tract. By studying the early branches of the animal tree of life, scientists can gain valuable insights into the fundamental functions shared by all animals, including how they sense their environment, eat, and move.

    This groundbreaking research lays the foundation for a deeper understanding of the origins and evolution of animal life. The scientists involved in the study have developed an innovative way to explore the origins of animals, providing the scientific community with a powerful tool to unravel the mysteries of animal evolution.

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