MSGID: 1:317/3 6465a9ea   
   PID: hpt/lnx 1.9.0-cur 2019-01-08   
   TID: hpt/lnx 1.9.0-cur 2019-01-08   
    What did the earliest animals look like?    
    Chromosome analysis resolves debate about sister group of all animals.   
   It's comb jellies, not sponges    
      
     Date:   
         May 17, 2023   
     Source:   
         University of California - Berkeley   
     Summary:   
         Surprisingly, genome comparisons have failed to resolve a   
         major question in animal evolution: Which living animals are   
         the descendants of the earliest animals to evolve in the world's   
         oceans? Scientists performed a detailed chromosomal analysis that   
         comes down definitively in favor of comb jellies, or ctenophores,   
         as the most recent common ancestor of all animals, or the sister   
         taxa to all animals. Sponges evolved later.   
      
      
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   For more than a century, biologists have wondered what the earliest   
   animals were like when they first arose in the ancient oceans over half   
   a billion years ago.   
      
   Searching among today's most primitive-looking animals for the earliest   
   branch of the animal tree of life, scientists gradually narrowed the   
   possibilities down to two groups: sponges, which spend their entire   
   adult lives in one spot, filtering food from seawater; and comb jellies,   
   voracious predators that oar their way through the world's oceans in   
   search of food.   
      
   In a new study published this week in the journal Nature, researchers   
   use a novel approach based on chromosome structure to come up with a   
   definitive answer: Comb jellies, or ctenophores (teen'-a-fores), were   
   the first lineage to branch off from the animal tree. Sponges were next,   
   followed by the diversification of all other animals, including the   
   lineage leading to humans.   
      
   Although the researchers determined that the ctenophore lineage branched   
   off before sponges, both groups of animals have continued to evolve from   
   their common ancestor. Nevertheless, evolutionary biologists believe   
   that these groups still share characteristics with the earliest animals,   
   and that studying these early branches of the animal tree of life can   
   shed light on how animals arose and evolved to the diversity of species   
   we see around us today.   
      
   "The most recent common ancestor of all animals probably lived 600 or 700   
   million years ago. It's hard to know what they were like because they   
   were soft-bodied animals and didn't leave a direct fossil record. But   
   we can use comparisons across living animals to learn about our common   
   ancestors," said Daniel Rokhsar, University of California, Berkeley   
   professor of molecular and cell biology and co-corresponding author of   
   the paper along with Darrin Schultz and Oleg Simakov of the University   
   of Vienna. "It's exciting -- we're looking back deep in time where   
   we have no hope of getting fossils, but by comparing genomes, we're   
   learning things about these very early ancestors."  Understanding the   
   relationships among animal lineages will help scientists understand how   
   key features of animal biology, such as the nervous system, muscles and   
   digestive tract, evolved over time, the researchers say.   
      
   "We developed a new way to take one of the deepest glimpses possible   
   into the origins of animal life," said Schultz, the lead author and a   
   former UC Santa Cruz graduate student and researcher at the Monterey Bay   
   Aquarium Research Institute (MBARI) who is now a postdoctoral researcher   
   at the University of Vienna. "This finding will lay the foundation for   
   the scientific community to begin to develop a better understanding of   
   how animals have evolved."  What's an animal?  Most familiar animals,   
   including worms, flies, mollusks, sea stars and vertebrates -- and   
   including humans -- have a head with a centralized brain, a gut running   
   from mouth to anus, muscles and other shared features that had already   
   evolved by the time of the famed "Cambrian Explosion" around 500 million   
   years ago. Together, these animals are called bilaterians.   
      
   Other bona fide animals, however, such as jellyfish, sea anemones,   
   sponges and ctenophores, have simpler body plans. These creatures lack   
   many bilaterian features -- for example, they lack a defined brain   
   and may not even have a nervous system or muscles -- but still share   
   the hallmarks of animal life, notably the development of multicellular   
   bodies from a fertilized egg.   
      
   The evolutionary relationships among these diverse creatures --   
   specifically, the order in which each of the lineages branched off from   
   the main trunk of the animal tree of life -- has been controversial.   
      
   With the rise of DNA sequencing, biologists were able to compare the   
   sequences of genes shared by animals to construct a family tree that   
   illustrates how animals and their genes evolved over time since the   
   earliest animals arose in the Precambrian Period.   
      
   But these phylogenetic methods based on gene sequences failed to resolve   
   the controversy over whether sponges or comb jellies were the earliest   
   branch of the animal tree, in part because of the deep antiquity of   
   their divergence, Rokhsar said.   
      
   "The results of sophisticated sequence-based studies were basically   
   split," he said. "Some researchers did well-designed analyses and found   
   that sponges branched first. Others did equally complex and justifiable   
   studies and got ctenophores. There hasn't really been any convergence   
   to a definitive answer."  Just looking at them, sponges seem quite   
   primitive. After their free-swimming larval stage, they settle down   
   and generally remain in one place, gently sweeping water through their   
   pores to capture small food particles dissolved in sea water. They have   
   no nerves or muscles, though their hard parts make nice scrubbers in   
   the bath.   
      
   "Traditionally, sponges have been widely considered to be the earliest   
   surviving branch of the animal tree, because sponges don't have a   
   nervous system, they don't have muscles, and they look a little bit like   
   colonial versions of some unicellular protozoans," Rokhsar said. "And so,   
   it was a nice story: First came the unicellular protozoans, and then   
   sponge-like multicellular consortia of such cells evolved and became   
   the ancestor of all of today's animal diversity. In this scenario,   
   the sponge lineage preserves many features of the animal ancestor on   
   the branch leading to all other animals, including us. Specializations   
   evolved that led to neurons, nerves and muscles and guts and all those   
   things that we know and love as the defining features of the rest of   
   animal life. Sponges appear to be primitive, since they lack those   
   features."  The other candidate for earliest animal lineage is the   
   group of comb jellies, popular animals in many aquariums. While they   
   look superficially like jellyfish -- they often have a bell-like shape,   
   although with two lobes, unlike jellyfish, and usually tentacles -- they   
   are only distantly related. And while jellyfish squirt their way through   
   the water, ctenophores propel themselves with eight rows of beating   
   cilia arranged down their sides like combs. Along the California coast,   
   a common ctenophore is the 1-inch-diameter sea gooseberry.   
      
   Chromosomes to the rescue To learn whether sponges or ctenophores were   
   the earliest branch of animals, the new study relied on an unlikely   
   feature: the organization of genes into chromosomes. Each species has   
   a characteristic chromosome number -- humans have 23 pairs -- and a   
   characteristic distribution of genes along chromosomes.   
      
   Rokhsar, Simakov and collaborators had previously shown that the   
   chromosomes of sponges, jellyfish and many other invertebrates carry   
   similar sets of genes, despite more than half a billion years of   
   independent evolution. This discovery suggested that chromosomes of many   
   animals evolve slowly, and allowed the team to computationally reconstruct   
   the chromosomes of the common ancestor of these diverse animals.   
      
   But the chromosome structure of ctenophores was unknown until 2021,   
   when Schultz -- then a graduate student at UC Santa Cruz -- and his   
   co-advisers, Richard Green of UCSC and Steven Haddock of MBARI and   
   UCSC, determined the chromosome structure of the ctenophore Hormiphora   
   californiensis. It looked very different from those of other animals,   
   which posed a puzzle, Rokhsar said.   
      
   "At first, we couldn't tell if ctenophore chromosomes were different   
   from those of other animals simply because they'd just changed a lot   
   over hundreds of millions of years," Rokhsar explained. "Alternatively,   
   they could be different because they branched off first, before all other   
   animal lineages appeared. We needed to figure it out."  The researchers   
   joined forces to sequence the genomes of another comb jelly and sponge,   
   as well as three single-celled creatures that are outside the animal   
   lineage: a choanoflagellate, a filasterean amoeba and a fish parasite   
   called an ichthyosporean. Rough genome sequences of these non-animals   
   already existed, but they did not contain the critical information needed   
   for chromosome-scale gene linkage: where they sit on the chromosome.   
      
   A smoking gun Remarkably, when the team compared the chromosomes of   
   these diverse animals and non-animals, they found that ctenophores and   
   non-animals shared particular gene-chromosome combinations, while the   
   chromosomes of sponges and other animals were rearranged in a distinctly   
   different manner.   
      
   "That was the smoking gun -- we found a handful of rearrangements shared   
   by sponges and non-ctenophore animals. In contrast, ctenophores resembled   
   the non- animals. The simplest explanation is that ctenophores branched   
   off before the rearrangements occurred," he said.   
      
   "The fingerprints of this ancient evolutionary event are still present   
   in the genomes of animals hundreds of millions of years later," Schultz   
   said. "This research ... gives us context for understanding what makes   
   animals animals.   
      
   This work will help us understand the basic functions we all share,   
   like how they sense their surroundings, how they eat and how they move."   
   Rokhsar emphasized that the team's conclusions are robustly based on   
   five sets of gene-chromosome combinations.   
      
   "We found a relic of a very ancient chromosomal signal," he said. "It   
   took some statistical detective work to convince ourselves that this   
   really is a clear signal and not just random noise, because we're dealing   
   with relatively small groups of genes and perhaps a billion years of   
   divergence between the animals and non-animals. But the signal is there   
   and strongly supports the 'ctenophore- branched-first' scenario. The   
   only way the alternative sponge-first hypothesis could be true would   
   be if multiple convergent rearrangements happened in both sponges and   
   non-ctenophore animals, which is very unlikely."  Jessen Bredeson of UC   
   Berkeley also contributed to this work.   
      
   Funding for this research was provided by the David and Lucile Packard   
   Foundation, MBARI, the National Science Foundation (GRFP DGE 1339067 and   
   DEB- 1542679), the European Research Council's Horizon 2020: European   
   Union Research and Innovation Programme (grant No. 945026), internal   
   funds of the Okinawa Institute of Science and Technology Molecular   
   Genetics Unit, the Chan Zuckerberg Biohub Network and the Marthella   
   Foskett Brown Chair in Biological Sciences.For more than a century,   
   biologists have wondered what the earliest animals were like when they   
   first arose in the ancient oceans over half a billion years ago.   
      
   Searching among today's most primitive-looking animals for the earliest   
   branch of the animal tree of life, scientists gradually narrowed the   
   possibilities down to two groups: sponges, which spend their entire   
   adult lives in one spot, filtering food from seawater; and comb jellies,   
   voracious predators that oar their way through the world's oceans in   
   search of food.   
      
   In a new study published this week in the journal Nature, researchers   
   use a novel approach based on chromosome structure to come up with a   
   definitive answer: Comb jellies, or ctenophores (teen'-a-fores), were   
   the first lineage to branch off from the animal tree. Sponges were next,   
   followed by the diversification of all other animals, including the   
   lineage leading to humans.   
      
   Although the researchers determined that the ctenophore lineage branched   
   off before sponges, both groups of animals have continued to evolve from   
   their common ancestor. Nevertheless, evolutionary biologists believe   
   that these groups still share characteristics with the earliest animals,   
   and that studying these early branches of the animal tree of life can   
   shed light on how animals arose and evolved to the diversity of species   
   we see around us today.   
      
   "The most recent common ancestor of all animals probably lived 600 or 700   
   million years ago. It's hard to know what they were like because they   
   were soft-bodied animals and didn't leave a direct fossil record. But   
   we can use comparisons across living animals to learn about our common   
   ancestors," said Daniel Rokhsar, University of California, Berkeley   
   professor of molecular and cell biology and co-corresponding author of   
   the paper along with Darrin Schultz and Oleg Simakov of the University   
   of Vienna. "It's exciting -- we're looking back deep in time where   
   we have no hope of getting fossils, but by comparing genomes, we're   
   learning things about these very early ancestors."  Understanding the   
   relationships among animal lineages will help scientists understand how   
   key features of animal biology, such as the nervous system, muscles and   
   digestive tract, evolved over time, the researchers say.   
      
   "We developed a new way to take one of the deepest glimpses possible   
   into the origins of animal life," said Schultz, the lead author and a   
   former UC Santa Cruz graduate student and researcher at the Monterey Bay   
   Aquarium Research Institute (MBARI) who is now a postdoctoral researcher   
   at the University of Vienna. "This finding will lay the foundation for   
   the scientific community to begin to develop a better understanding of   
   how animals have evolved."  What's an animal?  Most familiar animals,   
   including worms, flies, mollusks, sea stars and vertebrates -- and   
   including humans -- have a head with a centralized brain, a gut running   
   from mouth to anus, muscles and other shared features that had already   
   evolved by the time of the famed "Cambrian Explosion" around 500 million   
   years ago. Together, these animals are called bilaterians.   
      
   Other bona fide animals, however, such as jellyfish, sea anemones,   
   sponges and ctenophores, have simpler body plans. These creatures lack   
   many bilaterian features -- for example, they lack a defined brain   
   and may not even have a nervous system or muscles -- but still share   
   the hallmarks of animal life, notably the development of multicellular   
   bodies from a fertilized egg.   
      
   The evolutionary relationships among these diverse creatures --   
   specifically, the order in which each of the lineages branched off from   
   the main trunk of the animal tree of life -- has been controversial.   
      
   With the rise of DNA sequencing, biologists were able to compare the   
   sequences of genes shared by animals to construct a family tree that   
   illustrates how animals and their genes evolved over time since the   
   earliest animals arose in the Precambrian Period.   
      
   But these phylogenetic methods based on gene sequences failed to resolve   
   the controversy over whether sponges or comb jellies were the earliest   
   branch of the animal tree, in part because of the deep antiquity of   
   their divergence, Rokhsar said.   
      
   "The results of sophisticated sequence-based studies were basically   
   split," he said. "Some researchers did well-designed analyses and found   
   that sponges branched first. Others did equally complex and justifiable   
   studies and got ctenophores. There hasn't really been any convergence   
   to a definitive answer."  Just looking at them, sponges seem quite   
   primitive. After their free-swimming larval stage, they settle down   
   and generally remain in one place, gently sweeping water through their   
   pores to capture small food particles dissolved in sea water. They have   
   no nerves or muscles, though their hard parts make nice scrubbers in   
   the bath.   
      
   "Traditionally, sponges have been widely considered to be the earliest   
   surviving branch of the animal tree, because sponges don't have a   
   nervous system, they don't have muscles, and they look a little bit like   
   colonial versions of some unicellular protozoans," Rokhsar said. "And so,   
   it was a nice story: First came the unicellular protozoans, and then   
   sponge-like multicellular consortia of such cells evolved and became   
   the ancestor of all of today's animal diversity. In this scenario,   
   the sponge lineage preserves many features of the animal ancestor on   
   the branch leading to all other animals, including us. Specializations   
   evolved that led to neurons, nerves and muscles and guts and all those   
   things that we know and love as the defining features of the rest of   
   animal life. Sponges appear to be primitive, since they lack those   
   features."  The other candidate for earliest animal lineage is the   
   group of comb jellies, popular animals in many aquariums. While they   
   look superficially like jellyfish -- they often have a bell-like shape,   
   although with two lobes, unlike jellyfish, and usually tentacles -- they   
   are only distantly related. And while jellyfish squirt their way through   
   the water, ctenophores propel themselves with eight rows of beating   
   cilia arranged down their sides like combs. Along the California coast,   
   a common ctenophore is the 1-inch-diameter sea gooseberry.   
      
   Chromosomes to the rescue To learn whether sponges or ctenophores were   
   the earliest branch of animals, the new study relied on an unlikely   
   feature: the organization of genes into chromosomes. Each species has   
   a characteristic chromosome number -- humans have 23 pairs -- and a   
   characteristic distribution of genes along chromosomes.   
      
   Rokhsar, Simakov and collaborators had previously shown that the   
   chromosomes of sponges, jellyfish and many other invertebrates carry   
   similar sets of genes, despite more than half a billion years of   
   independent evolution. This discovery suggested that chromosomes of many   
   animals evolve slowly, and allowed the team to computationally reconstruct   
   the chromosomes of the common ancestor of these diverse animals.   
      
   But the chromosome structure of ctenophores was unknown until 2021,   
   when Schultz -- then a graduate student at UC Santa Cruz -- and his   
   co-advisers, Richard Green of UCSC and Steven Haddock of MBARI and   
   UCSC, determined the chromosome structure of the ctenophore Hormiphora   
   californiensis. It looked very different from those of other animals,   
   which posed a puzzle, Rokhsar said.   
      
   "At first, we couldn't tell if ctenophore chromosomes were different   
   from those of other animals simply because they'd just changed a lot   
   over hundreds of millions of years," Rokhsar explained. "Alternatively,   
   they could be different because they branched off first, before all other   
   animal lineages appeared. We needed to figure it out."  The researchers   
   joined forces to sequence the genomes of another comb jelly and sponge,   
   as well as three single-celled creatures that are outside the animal   
   lineage: a choanoflagellate, a filasterean amoeba and a fish parasite   
   called an ichthyosporean. Rough genome sequences of these non-animals   
   already existed, but they did not contain the critical information needed   
   for chromosome-scale gene linkage: where they sit on the chromosome.   
      
   A smoking gun Remarkably, when the team compared the chromosomes of   
   these diverse animals and non-animals, they found that ctenophores and   
   non-animals shared particular gene-chromosome combinations, while the   
   chromosomes of sponges and other animals were rearranged in a distinctly   
   different manner.   
      
   "That was the smoking gun -- we found a handful of rearrangements shared   
   by sponges and non-ctenophore animals. In contrast, ctenophores resembled   
   the non- animals. The simplest explanation is that ctenophores branched   
   off before the rearrangements occurred," he said.   
      
   "The fingerprints of this ancient evolutionary event are still present   
   in the genomes of animals hundreds of millions of years later," Schultz   
   said. "This research ... gives us context for understanding what makes   
   animals animals.   
      
   This work will help us understand the basic functions we all share,   
   like how they sense their surroundings, how they eat and how they move."   
   Rokhsar emphasized that the team's conclusions are robustly based on   
   five sets of gene-chromosome combinations.   
      
   "We found a relic of a very ancient chromosomal signal," he said. "It   
   took some statistical detective work to convince ourselves that this   
   really is a clear signal and not just random noise, because we're dealing   
   with relatively small groups of genes and perhaps a billion years of   
   divergence between the animals and non-animals. But the signal is there   
   and strongly supports the 'ctenophore- branched-first' scenario. The   
   only way the alternative sponge-first hypothesis could be true would   
   be if multiple convergent rearrangements happened in both sponges and   
   non-ctenophore animals, which is very unlikely."  Jessen Bredeson of UC   
   Berkeley also contributed to this work.   
      
   Funding for this research was provided by the David and Lucile Packard   
   Foundation, MBARI, the National Science Foundation (GRFP DGE 1339067 and   
   DEB- 1542679), the European Research Council's Horizon 2020: European   
   Union Research and Innovation Programme (grant No. 945026), internal   
   funds of the Okinawa Institute of Science and Technology Molecular   
   Genetics Unit, the Chan Zuckerberg Biohub Network and the Marthella   
   Foskett Brown Chair in Biological Sciences.   
      
       * RELATED_TOPICS   
             o Plants_&_Animals   
                   # Life_Sciences # Wild_Animals # Animals   
             o Earth_&_Climate   
                   # Rainforests # Exotic_Species # Environmental_Awareness   
             o Fossils_&_Ruins   
                   # Origin_of_Life # Evolution # Early_Humans   
       * RELATED_TERMS   
             o Sponge o Germ_layer o Convergent_evolution o Roundworm o   
             Evolution_of_cetaceans o Animal o Herbivore o Animal_rights   
      
   ==========================================================================   
   Story Source: Materials provided by   
   University_of_California_-_Berkeley. Original written by Robert   
   Sanders. Note: Content may be edited for style and length.   
      
      
   ==========================================================================   
   Related Multimedia:   
       * Comb_jellies_and_sponges   
   ==========================================================================   
   Journal Reference:   
      1. Schultz, D.T., Haddock, S.H.D., Bredeson, J.V. et al. Ancient gene   
         linkages support ctenophores as sister to other animals. Nature,   
         2023 DOI: 10.1038/s41586-023-05936-6   
   ==========================================================================   
      
   Link to news story:   
   https://www.sciencedaily.com/releases/2023/05/230517122111.htm   
      
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