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Researchers use genomes of 241 species to redefine mammalian tree of life
- fastaguy88 3y agoBuilding evolutionary trees from genomes is challenging, in part because of the difficulties inferring trees when different parts of the genome may be evolving at very different rates, but also because of the wide dynamic range of genome quality. Human and mouse genomes have far fewer errors (missing regions) than rat and cow, and many of the other several hundred genomes will be of much much lower quality. At this scale, it is difficult to know whether surprising results reflect biology or inaccuracy.
- inciampati 3y agoA flip side of constraint is constrained diversity. Does a tree always work? Where are the genomes in ILS? Those will be very interesting regions.
- inciampati 3y agoFrom the abstract: "However, because these approaches infer a single best tree, they mask signatures of phylogenetic conflict that result from incomplete lineage sorting and historical hybridization." So it can't be avoided, and the solution of making more trees from different stuff is somewhat unsatisfying. They have to work with the methods they have today.
- f6v 3y agoThey used maximum likelihood tree building. In Bayesian approach it’s possible to sample from a distribution of trees which can help with the uncertainty. Anyway, I only have very limited knowledge on this from my evolutionary biology course.
- runeblaze 3y agoReading the paper I think they used both SVDquartets (coalescence-based explicitly for ILS) and concatenation + maximum likelihood, which is a very sane combination for the analysis. Not contradicting you here, but at their scale it is unlikely any Bayesian approach will converge, so they had to settle with whatever they had to quantify uncertainty (branch supports and others). Edit: and also the Bayesian approaches might have model mismatch, for example I am not sure what's an accurate Bayesian method that models hybridization and ILS
- sandworm101 3y agoTrees are tricky. They assume solid splits between species. While that may work well across millions/billions of years it does not work well when describing the specifics of split points. There is no bright line when one generation is suddenly a different species than the last. Genetics describes the slow accumulation of changes. Translating that into a tree of lines connected by points will always require compromise.
- Myrmornis 3y agohttps://www.science.org/doi/10.1126/science.abl8189 https://www.science.org/doi/10.1126/science.abl8189 It looks like they looked at a larger amount of the genome, and still found that relationships at the level of Order and below were hard to be sure about, since different genomic regions disagreed. They then speculate that this is related to different geological / tectonic / geomorphological processes occurring at that point in history, compared to the time of the earlier divergences. It’s a frustrating area of science; we’ve learned that the reality is that some aspects of evolutionary history are very hard to be sure about, but scientific publishing and careers require more interesting claims.
- vrglvrglvrgl 3y ago[dead]
- mkl 3y agoSo horses are closer to lions than to antelopes? The pictures on phys.org and in the Science article preview are frustratingly unclear; most leaves of the tree are unlabelled.
- akiselev 3y agoSort of - it's more accurate to say that the order Perissodactyla (containing horses) shares a common ancestor with the order carnivora labeled #4 in the picture. Both of them share a common ancestor with artiodactyla (even toed ungulates like antelope) labeled #3. They all differentiated over 60 million years ago, though, which was enough time for mammals to split into herbivores and carnivores and evolve back into sea animals like whales and dolphins. With converging and diverging evolution over that kind of time span, saying an animal is "closer to" another over simplifies a lot of detail. One species' genetics might resemble one order while the slowly evolving genes used to identify evolutionary relationships place it in a second order.
- cjbgkagh 3y agoI think the layout is optimized for showing branches event and not relative difference between species, though as a side effect of showing branching it does somewhat approximate relative difference.
- thriftwy 3y agoEuarchontoglira would be a way less researched and relevant branch of life have it not produced us humans. Same thing that if sentient birds were to appear, they will consider dinosaur epoch never ended, just had a setback and useful bottleneck.
- sandworm101 3y ago>> way less researched and relevant branch of life have it not produced us humans. I doubt that any branch would have been even studied in any way had not euarchontoglira produced us humans. I doubt many other animals are even aware of evolution as a concept.
- AtlasBarfed 3y ago>> sentient birds have you seen the problem solving of crows? edit: vid: https://www.youtube.com/watch?v=Gui3IswQ0DI https://www.youtube.com/watch?v=Gui3IswQ0DI
- jjtheblunt 3y agoAre African Greys sentient bird examples?
- thriftwy 3y agoDid they manage to build and publish an evolution tree?