Ask someone to think of an animal, and they’ll likely come up with one of our mammalian relatives. A few people would go so far as to mention other vertebrates, such as birds and fish. But these barely scratch the surface of animal diversity, with things like cephalopods, insects, and echinoderms having distinct features.
And that’s before you get to the really weird stuff, like radially symmetric hollow objects, or sponges that lack muscles and nerve cells. Or the comb jellies, which move around by spinning lots of thread-like cilia. or the Oddity is a really strange statureDisk-like creatures that have two sides but no interior and digest things on their surface.
For people who tend to think that evolution involves adding greater complexity to organisms, it’s tempting to imagine that an animal’s family tree arose by incrementally adding more things, like nerve cells and muscles. But there has been a steady stream of genetic studies indicating that there are two separate lineages that ended up with neurons. The results of these studies depended little on the genes and species chosen for analysis. But a new study that does not rely on individual genes now firmly positions sponges as more closely related to humans than some other animals with nervous systems.
rearranges the chromosomes
Most of the early studies in this field involved identifying related genes present in all animals and learning how these genes were linked. It is assumed that the organisms themselves are related in the same way. This can be very useful in many situations, but the analysis tends to get confusing when a lot of species diverge in a short period of time, or when individual genes change a lot due to evolutionary pressures. Therefore, the exact answer you get can sometimes depend on which genes you choose to look at.
The new study attempts to avoid confusion by looking at how genes are arranged on chromosomes. It turns out that individual genes tend to stay in the same place on the chromosome for long periods of time. It is estimated that it takes 40 million years for just one percent of the genes in a typical animal genome to be transferred to a new chromosome. So odds are that if four genes are next to each other now, they were next to each other in the ancestors of today’s mammals that would have had to avoid being eaten by dinosaurs.
This does not mean that these ancestors had exactly the same number and arrangement of chromosomes. Large-scale rearrangements occur, such as the fusion or splitting of chromosomes, or the swapping of a large segment from one to the other. But these large rearrangements keep nearly all nearby genes next to each other, even if the entire assembly ends up on a different chromosome (swaps can involve a single break in a DNA molecule).
This means that breaking down the linear arrangement of a group of genes – is called technical synthetic– very rare in the evolutionary history of animals. And by tracking changes in gene order across different species, we can learn where previous gene combinations in an organism broke apart, and which other species inherited the same rearrangement. And that can tell us which organisms are most closely related to us.
Reorder tracking
To do this type of analysis, you need to know how the genes are arranged on the chromosomes. We have recently developed a technology that allows us to sequence very long pieces of DNA — often tens of thousands of bases stretching out — making it much easier to put chromosomes back together. The researchers drew on as many animal genomes as this was done and completed a few of their own for the study. In addition, they reconstructed the chromosomes of single-celled organisms thought to be closely related to animals to provide a baseline for their starting arrangements.
It is believed that the origin of animals occurred approximately 800 million years ago. Therefore, although the break-up of gene clusters is rare, this is sufficient time for this to occur across a large part of the genome. The researchers were only able to identify just under 300 genes that were in clusters that extended to relatives of single-celled animals, with the largest group comprising 29 genes. When the researchers ran 10 million simulations that randomly pieced together genes at the rates expected over 800 million years, they never ended up with a group as large as eight genes, so most of these are likely true ancestral cases.
By tracking the rearrangements, the researchers were able to identify eight rearrangements common to right- and left-sided animals like us vertebrates, and things like jellyfish (Cnidaria) and sponges (Porifera). None of these have been seen in comb jellies (Ctenophora). Again, they ran 100 million random simulations and never saw this pattern of inheritance, so it appears to be real.
This means that animals like us as vertebrates, along with everything else that has a left and right side, are more closely associated with sponges than we are with jellies. This is despite the fact that sponges do not have muscles or a nervous system, while comb jellies share us all together.
How could this be true?
Aside from their lack of nerves and muscles, sponges are unusual in that many of them have an internal mineral structure that looks a bit like a skeleton. A lot of them use calcium carbonate to make this, but some types make it out of silica, which is chemically very different from anything we two-legged make. It also lacks anything like an internal digestive system.
But if these look like strange relatives, Placozoans are the Festers uncle of the animal family. These exist as a two-sided disk that moves in a coordinated manner across the surfaces. When they scoot through food, they simply form a small sac on the underside of the disc and digest it in place. All of this occurs without any obvious neurons or muscles, although there are reports that they experience spikes in electrical activity, which, in other animals, are the hallmarks of neurons.
Again, these clusters appear to be more closely related to us than comb jellies, which contain nerve networks and muscle cells.
There are two possible explanations for this, and it’s impossible to tell them apart at this point. The first is that the ancestors of sponges and placozoans also had muscles and nerve cells, but they lost them during evolution, which radically facilitated the plans of their bodies over hundreds of millions of years. This goes against how most people would expect evolution to work, but there are plenty of organisms that have thrived with streamlined body plans (many of them are parasites). Sponges have thrived in the niche they occupy. Placozoans may also be thriving, but they’re small and easy to overlook, so we don’t have a solid understanding of that.
The alternative is that things like muscles and nerve cells evolved twice. This may seem impossible, but there are a few things that point in this direction. One is that there appear to be significant differences between the neurons and muscles of comb jellies and those of right- and left-sided animals. Placozoans, as mentioned above, appear to have neuron-like behavior even if they lack neurons. Many of the protein compounds needed for nerve cell function are produced by sponges. So it could be that the ancestors of all of these animals had pieces in place that allowed neurons to develop with fewer changes than would otherwise be needed.
Distinguishing between these possibilities would be a serious challenge, and it is not likely that simply collecting more genome sequences will provide us with an answer. Instead, perhaps we need to start working on culturing comb jellies in the lab, so we can get a closer look at neurons and muscles.
Nature, 2023. DOI: 10.1038 / s41586-023-05936-6 (about DOIs).