6 ms·

A bird that’s breaking the tree of life

111 points by SirLJ 4y ago

deleted 4y ago
[deleted]
cratermoon 4y ago
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 https://www.patternlanguage.com/archive/cityisnotatree.html 2 https://www.slideshare.net/Kevlin/a-system-is-not-a-tree https://www.slideshare.net/Kevlin/a-system-is-not-a-tree
- axlprose 4y ago
  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 https://youtu.be/2QgZVYI3tDs?t=3349 [1] https://dspace.mit.edu/handle/1721.1/6064 https://dspace.mit.edu/handle/1721.1/6064
- jakzurr 4y ago
  Pretty amazing - near the end of the article they discuss just that, "Although tree-thinking biologists used to think that hybridization was extremely rare, genetic studies have shown that it actually happens all the time. Human DNA indicates that early Homo sapiens interbred with Neanderthals and other extinct hominins. Conservative estimates suggest that at least ten per cent of birds hybridize; among South America’s largest group of birds, that number is thirty-eight per cent, according to one recent study." "Semi-lattice", networks; I guess it's a lot more complicated than I ever imagined.
dvh 4y ago
throwawaymaths 4y ago
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 4y ago
  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 4y ago
    Z/w sex chromosome elements.
    - deleted 4y ago
      [deleted]
    - masklinn 4y ago
      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 4y ago
    I assume throwawaymaths is talking about this paper: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2413164/ 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.
joshuaissac 4y ago
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 https://en.wikipedia.org/w/index.php?title=Ring_species
- hammock 4y ago
  To picture the more complex “rings” I am mentally creating a paper snowflake with large chunks cut out of it, and then unfolding it
- tantalor 4y ago
  Neat, has this been reproduced in laboratory?
  - pklausler 4y ago
    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 4y ago
      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 4y ago
xipho 4y ago
"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 4y ago
  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 4y ago
  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 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.
swayvil 4y ago
Scrolling scrolling... Where's a pic of the actual bird?? https://upload.wikimedia.org/wikipedia/commons/e/e7/Hoatzin_-_Manu_NP_-_Per%C3%B9_9203_%2815525812066%29.jpg 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 4y ago
  Definitely has a prehistoric look. I could imagine it sharing the Cretaceous forests with Quetzalcoatlus and other pterosaurs
incogitomode 4y ago
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.
- chmod775 4y ago
  > I could also swear he said they had purple blood, but I haven't been able to verify that detail. That would mean they likely don't use cells containing lots of iron to transport oxygen in their blood. That... exists. Not all animals have red blood.
jacquesm 4y ago
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 https://en.wikipedia.org/wiki/The_Ancestor%27s_Tale
divbzero 4y ago
> 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 https://en.wikipedia.org/wiki/Horizontal_gene_transfer
- mmmrtl 4y ago
  | 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.
codeflo 4y ago
So there seem to be three separate issues with the concept of "species" as used in (pop?) biology, speaking as a non-biologist CS type of person: * The "interbreeds with" relation isn't transitive: population A may interbreed with B, B with C, but A not with C. Examples are observed in nature today, and must have existed many many times historically. This makes any attempt at building tree arrangement of species inherently logically suspect, purely from a data structure point of view. * There are some cultural expectations around the term "species" that seem to thwart attempts at coming up with a clear definition. For example, we really seem to want to classify dogs as a species distinct from wolves, whether that logically make sense or not. This seems similar to people really wanting to classify Europe as a continent, regardless of plate tectonics or land masses or any other objective criterion. For a counter-example, the physics community at some point went "fuck historical precedent, we need a precise definition of 'planet'" and excluded Pluto. * We also want to use the term "species" for organisms that don't sexually breed at all, necessitating different definitions for these cases. All of this leads to Wikipedia defining the word "species" in this hilarious way: "A species is often defined as the largest group of organisms in which any two individuals of the appropriate sexes or mating types can produce fertile offspring, typically by sexual reproduction. Other ways of defining species include their karyotype, DNA sequence, morphology, behaviour or ecological niche. In addition, paleontologists use the concept of the chronospecies since fossil reproduction cannot be examined." That's all fine, but with definitions like that, apparent contradictions shouldn't be a surprise, and formulations like "breaking the tree of life" are clear hyperbole. PS: I'd love for actual biologists to correct any misunderstandings I might have!
- culi 4y ago
  The truth is that the definition of "species" even within published science can vary widely between different parts of the ~~tree~~ network of life If botanists really tried to maintain the idea that different species can't interbreed with each other then we'd have a LOT less species of plants. In some discussions, such as with the taxonomy of oaks which are notoriously difficult to classify into species, definitions can even vary from author to author and can be based on morphology, phylogeny, distribution, or, most often, some blend of elements from all of the above

111 points by SirLJ 4y ago

deleted 4y ago

[deleted]

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 https://www.patternlanguage.com/archive/cityisnotatree.html 2 https://www.slideshare.net/Kevlin/a-system-is-not-a-tree https://www.slideshare.net/Kevlin/a-system-is-not-a-tree

axlprose 4y ago
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 https://youtu.be/2QgZVYI3tDs?t=3349 [1] https://dspace.mit.edu/handle/1721.1/6064 https://dspace.mit.edu/handle/1721.1/6064
jakzurr 4y ago
Pretty amazing - near the end of the article they discuss just that, "Although tree-thinking biologists used to think that hybridization was extremely rare, genetic studies have shown that it actually happens all the time. Human DNA indicates that early Homo sapiens interbred with Neanderthals and other extinct hominins. Conservative estimates suggest that at least ten per cent of birds hybridize; among South America’s largest group of birds, that number is thirty-eight per cent, according to one recent study." "Semi-lattice", networks; I guess it's a lot more complicated than I ever imagined.

dvh 4y ago

throwawaymaths 4y ago

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 4y ago
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 4y ago
  Z/w sex chromosome elements.
  - deleted 4y ago
    [deleted]
  - masklinn 4y ago
    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 4y ago
  I assume throwawaymaths is talking about this paper: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2413164/ 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.

joshuaissac 4y ago

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 https://en.wikipedia.org/w/index.php?title=Ring_species

hammock 4y ago
To picture the more complex “rings” I am mentally creating a paper snowflake with large chunks cut out of it, and then unfolding it
tantalor 4y ago
Neat, has this been reproduced in laboratory?
- pklausler 4y ago
  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 4y ago
    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 4y ago

xipho 4y ago

"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 4y ago
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 4y ago
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 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.

swayvil 4y ago

Scrolling scrolling... Where's a pic of the actual bird?? https://upload.wikimedia.org/wikipedia/commons/e/e7/Hoatzin_-_Manu_NP_-_Per%C3%B9_9203_%2815525812066%29.jpg 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 4y ago
Definitely has a prehistoric look. I could imagine it sharing the Cretaceous forests with Quetzalcoatlus and other pterosaurs

incogitomode 4y ago

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.

chmod775 4y ago
> I could also swear he said they had purple blood, but I haven't been able to verify that detail. That would mean they likely don't use cells containing lots of iron to transport oxygen in their blood. That... exists. Not all animals have red blood.

jacquesm 4y ago

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 https://en.wikipedia.org/wiki/The_Ancestor%27s_Tale

divbzero 4y ago

> 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 https://en.wikipedia.org/wiki/Horizontal_gene_transfer

mmmrtl 4y ago
| 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.

codeflo 4y ago

So there seem to be three separate issues with the concept of "species" as used in (pop?) biology, speaking as a non-biologist CS type of person: * The "interbreeds with" relation isn't transitive: population A may interbreed with B, B with C, but A not with C. Examples are observed in nature today, and must have existed many many times historically. This makes any attempt at building tree arrangement of species inherently logically suspect, purely from a data structure point of view. * There are some cultural expectations around the term "species" that seem to thwart attempts at coming up with a clear definition. For example, we really seem to want to classify dogs as a species distinct from wolves, whether that logically make sense or not. This seems similar to people really wanting to classify Europe as a continent, regardless of plate tectonics or land masses or any other objective criterion. For a counter-example, the physics community at some point went "fuck historical precedent, we need a precise definition of 'planet'" and excluded Pluto. * We also want to use the term "species" for organisms that don't sexually breed at all, necessitating different definitions for these cases. All of this leads to Wikipedia defining the word "species" in this hilarious way: "A species is often defined as the largest group of organisms in which any two individuals of the appropriate sexes or mating types can produce fertile offspring, typically by sexual reproduction. Other ways of defining species include their karyotype, DNA sequence, morphology, behaviour or ecological niche. In addition, paleontologists use the concept of the chronospecies since fossil reproduction cannot be examined." That's all fine, but with definitions like that, apparent contradictions shouldn't be a surprise, and formulations like "breaking the tree of life" are clear hyperbole. PS: I'd love for actual biologists to correct any misunderstandings I might have!

culi 4y ago
The truth is that the definition of "species" even within published science can vary widely between different parts of the ~~tree~~ network of life If botanists really tried to maintain the idea that different species can't interbreed with each other then we'd have a LOT less species of plants. In some discussions, such as with the taxonomy of oaks which are notoriously difficult to classify into species, definitions can even vary from author to author and can be based on morphology, phylogeny, distribution, or, most often, some blend of elements from all of the above