[HN Gopher] A bird that's breaking the tree of life
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A bird that's breaking the tree of life
Author : SirLJ
Score : 59 points
Date : 2022-07-22 12:32 UTC (10 hours ago)
(HTM) web link (www.newyorker.com)
(TXT) w3m dump (www.newyorker.com)
| xipho wrote:
| "Genome" is used so loosely here (it always is in Science/Nature
| + Phylogeny papers), it's not the full totality of RNA/DNA in the
| organism the that is being compared. Similar sequences are
| aligned into "genes", with much data being excluded along the
| way. The repeatability of the overal analysis from start to
| finish is notoriously impossible, as there are so many parameters
| at different stages to keep track of, including versions of
| software used, etc. There is little to now
| appreciation/understanding of what CI, virtualization, etc. might
| add to this process yet, but it shoudl come. This isn't to say
| the methods are fundamentally flawed, it is to say we have long
| way to grow to truly incrementally build on the results of prior
| giants in a more robust way.
|
| Long-branches, like the bird in question, happen in pretty much
| all clades of life from what I've seen. I suspect we will need a
| richer phylogentic model that takes into account things like epi-
| genetics, protein-folding, gene-rearangement etc. if we are to
| reach a higher level of resolution (or understanding) of the far-
| off-corners of the TOL.
| not2b wrote:
| The point of the article is that the tree you come up with
| changes depending on which set of genes you look at, meaning
| that there's no one correct tree: each gene is inherited at
| least partially independently, meaning that a simple branching
| tree is the wrong data structure to use.
| acomjean wrote:
| Its a hard problem. My understanding is the phylogenic trees
| isn't as an exact science as you would think. Its "NP hard" so
| they use heuristics to get a good estimate.
|
| https://en.wikipedia.org/wiki/Phylogenetic_tree#Construction
|
| Its a hard problem. Its like using genetics as a road map to
| look back in time, but the previous species don't exist.
| incogitomode wrote:
| I had the good luck to see several of these in the wild in
| Ecuador, along the Napo River, about 15 years ago. The guide said
| they called them the "stinky turkey", which gave me a chuckle. I
| could also swear he said they had purple blood, but I haven't
| been able to verify that detail.
| cratermoon wrote:
| Christopher Alexander wrote "A City is Not a Tree" in 19651[1].
| Software consultant and author of _97 Things Every Programmer
| Should Know_ Kevlin Henney has a talk titled "A System is Not a
| Tree"[2]. Microbiologists have known for a long time that
| bacteria exchange DNA in multiple ways, and their evolution is
| not at all neat.
|
| It makes sense that the strict "tree" model is too simple for
| life, but something like a semi-lattice better describes the
| interaction of hybridization and other forms of gene transfer.
|
| 1 https://www.patternlanguage.com/archive/cityisnotatree.html
|
| 2 https://www.slideshare.net/Kevlin/a-system-is-not-a-tree
| axlprose wrote:
| Reminds me of the SICP lecture[0] where Hal Abelson introduces
| the concept of linguistic abstraction (or Stratified Design[1])
| as an alternative to the approach of decomposing a program into
| a tree of well-specified sub-components/tasks, which ultimately
| fails to capture the essence of the problem being solved.
|
| [0] https://youtu.be/2QgZVYI3tDs?t=3349
|
| [1] https://dspace.mit.edu/handle/1721.1/6064
| throwawaymaths wrote:
| Nobody has yet explained to me how platypuses can be a "missing
| link" (I'm aware that that's not a real concept) when the last
| common ancestor between birds and mammals is so far back -- I
| continue to believe that monotremata are the result of a very
| aberrant mating.
| masklinn wrote:
| Why would the platypus be a missing link _to birds_? Monotremes
| are rather obviously a very early mammalian offshoot, having
| retained significant original character (and a lot of
| weirdnesses) compared to therians.
|
| And the platypus' bill is convergent, if you look at a platypus
| skull it doesn't look like a duck's.
| throwawaymaths wrote:
| Z/w sex chromosome elements.
| [deleted]
| masklinn wrote:
| Z/w is not exclusive to birds, and is present in a number
| of reptiles (as well as fishes and crustaceans).
|
| So it could be a recurring sex determination scheme, or it
| could be a common amniote trait. Either would make a lot
| more sense than the idea that platypuses would be
| descendants of birds or whatever.
| thaumasiotes wrote:
| I assume throwawaymaths is talking about this paper:
| https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2413164/
|
| (or maybe to one of the papers this paper refers to as
| false?)
|
| It finds that platypuses have five sex chromosomes which
| arrange themselves in a fixed order, that these five
| chromosomes do not share homologous material with the
| ancestral therian X chromosome, and that several of them
| (possibly all?) do share homologous material with the
| (single) chicken Z chromosome.
|
| It says that earlier findings indicated (erroneously) that
| one end of the platypus sex chromosome sequence shared
| homology with the therian X, and the other end shared
| homology with the bird Z, and that this was taken as evidence
| contradicting the established view that the bird and mammal
| sex determination systems evolved independently of each
| other. But it goes on to contradict those earlier findings,
| which would seem to leave the even earlier view of
| independent evolution of sex determination systems in place.
|
| It is not clear why this would make the platypus a missing
| link between mammals and birds. The focus seems to be pretty
| squarely on the evolution of the standard mammalian X
| chromosome, not on mammals generally.
| jjtheblunt wrote:
| aberrant mating would depend on compatible chromosome layouts?
| loonster wrote:
| Viruses DNA can be added into animal DNA. Maybe a virus
| infected a bird, then a mammal that later evolved into the
| platypus.
| joshuaissac wrote:
| I thought this article would also mention ring species, which is
| a species where geographically adjacent members can mate with
| each other, but sufficiently far-away members cannot. The "ring"
| occurs when the habitat goes around the globe and two
| "incompatible" populations meet. In isolation, they would be
| separate species, but considering the existence of the ring
| connecting them, they are deemed to be a single species. Gene
| flow can happen between the two incompatible populations through
| the ring connecting them.
|
| Of course, there is nothing preventing such a ring from having
| more than two ends, so there could potentially even be ring
| species with branches or further sub-rings coming off them.
|
| https://en.wikipedia.org/w/index.php?title=Ring_species
| [deleted]
| ErikCorry wrote:
| I wonder if there is something special about birds in the
| immediate post-Chicxulub period that makes the bird species
| hard to arrange in a tree. You might expect that the few
| surviving birds were rapidly diversifying into ecological
| niches that were vacant after the asteroid. The sorts of
| genetic changes that make interbreeding impossible might lag
| behind (Eg changes in numbers of chromosomes) since the
| frequency of such species-bifurcating events would be based on
| other mechanisms not related to available ecological niches.
|
| So perhaps there's a period in which birds that look completely
| different can still interbreed to a larger extent than now? It
| would be like ring species, but taken to an absurd degree. I'm
| kinda riffing without really knowing what I'm talking about,
| but imagine a world where birds of all shapes and sizes can
| interbreed and occasionally do so.
| 7952 wrote:
| Maybe certain genes facilitate a particular strategy to
| evolution. And part of an organisms phenotype makes the
| species evolve in a particular way that gives genes an
| advantage over successive species. Adapting to the
| evolutionary environment. And naively birds are different.
| They can fly great distances in a single lifetime and cross
| many different habitats. In the time dimension that is very
| different to a plant or a small mammal. Not sure if that
| actually makes a difference though over such long timescale.
| An insect family can spread across the world just like a bird
| can.
| cwmma wrote:
| Sounds like "push of the past" [1] basically successful
| species often stem from a highly successful adaption so show
| intense diversification early on, like birds when they are
| suddenly the only flying species.
|
| 1. https://en.wikipedia.org/wiki/Push_of_the_past?wprov=sfla1
| tantalor wrote:
| Neat, has this been reproduced in laboratory?
| pklausler wrote:
| Observed in the wild (Larus gulls) as a ring species around
| (almost!) the Arctic.
|
| You can also make a good case that most species are "ring
| species" in the time dimension.
| alanbernstein wrote:
| E: ignore this
|
| I think that would require a modern species to be
| compatible with a direct ancestor from the distant past,
| with generations of incompatible beings in between.
| Otherwise there is no "ring". But that seems 1) unlikely,
| 2) untestable.
| pklausler wrote:
| The whole point of a "ring species" is that the ring
| isn't closed, and the individuals at its ends are not
| compatible mates.
| dragonwriter wrote:
| While the term applies more broadly, it's called a "ring"
| from geographic examples where the ring is closed
| _geographically_ , with adjacent/overlapping incompatible
| populations, but where there is a literal ring of
| geography wherein adjacent populations interbreed
| continuously _except_ the two adjacent incompatible ends.
| alanbernstein wrote:
| Whoops, I guess you're right. I read about ring species
| long ago and I definitely misunderstood the concept, so
| I'm glad you corrected that. I was thinking all neighbors
| are compatible, but incompatible with the opposite side.
|
| However, because of the impossibility of contact between
| the two temporal ends, I'm not sure what the value would
| be in thinking about a temporal ring species?
| joshuaissac wrote:
| The kind of ring species you refer to would also be
| possible, although far less likely.
|
| The ancestor species could form a geographical ring, and
| if the members are not too populous, nor too migratory,
| then mutations that cause local incompatibility would be
| selected out (because it makes it much harder to find a
| mate) whereas mutations that cause non-local
| incompatibility may persist (if the species is largely
| non-migratory, so non-local compatibility is not as
| valuable). Over time, the non-local incompatibilities can
| build up and create a ring species like the one you
| describe.
|
| But something like this is far less likely than a ring
| species with incompatible ends. Because such "complete"
| rings can decay into incomplete rings through the
| extinction of a connecting subspecies, and similarly,
| incomplete rings can segment further, and then grow again
| as two separate ring species. But a complete ring, once
| broken, is very unlikely to re-form.
| pklausler wrote:
| It's an analogy to help understand evolution over time in
| a lineage.
| hammock wrote:
| To picture the more complex "rings" I am mentally creating a
| paper snowflake with large chunks cut out of it, and then
| unfolding it
| jacquesm wrote:
| So many subtle reminders that the whole idea of a species is an
| arbitrary line that is defined by what is observed as the end
| result of the bulk of that tree disappearing and only some of the
| leafs and branches remaining.
|
| The book 'The Ancestors Tale' is a really nice read if this stuff
| interests you.
|
| https://en.wikipedia.org/wiki/The_Ancestor%27s_Tale
| dvh wrote:
| divbzero wrote:
| > _This strange-sounding state of affairs is not unique to the
| hoatzin; we see it in our own DNA. Human beings share their most
| recent common ancestor with chimpanzees and bonobos, but more
| than ten per cent of the human genome is actually more closely
| related to the gorilla genome. Another tiny fraction of the human
| genome also seems to be most closely shared with an even more
| distant relative: the orangutan. "This implies that there is no
| such thing as a unique evolutionary history of the human genome,"
| a team of molecular biologists wrote in 2007. "Rather, it
| resembles a patchwork of individual regions following their own
| genealogy."_
|
| Is horizontal gene transfer [1] the right term for this
| phenomenon? Are we talking about transfer of individual genes
| that could occur via transposons, or transfer of entire genomic
| regions that occur via a different mechanism?
|
| [1]: https://en.wikipedia.org/wiki/Horizontal_gene_transfer
| mmmrtl wrote:
| | Is horizontal gene transfer [1] the right term for this
| phenomenon?
|
| This is "incomplete lineage sorting". There's no need to invoke
| anything more exotic than standard vertical inheritance, but
| the existence of genetic diversity within populations after
| they split/speciate (i.e. it's not a single Adam & Eve that
| give rise to a new species) produces counter-intuitive patterns
| of relatedness like this.
| swayvil wrote:
| Scrolling scrolling... Where's a pic of the actual bird??
|
| https://upload.wikimedia.org/wikipedia/commons/e/e7/Hoatzin_...
|
| (From wikipedia)
|
| The hoatzin or hoactzin, also known as the reptile bird, skunk
| bird, stinkbird, or Canje pheasant, is a species of tropical bird
| found in swamps, riparian forests, and mangroves of the Amazon
| and the Orinoco basins in South America. It is notable for having
| chicks that have claws on two of their wing digits.
| cratermoon wrote:
| Definitely has a prehistoric look. I could imagine it sharing
| the Cretaceous forests with Quetzalcoatlus and other pterosaurs
| [deleted]
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