A bird that’s breaking the tree of life | Hacker News Reader

A bird that’s breaking the tree of life

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111 pointsSirLJ39 comments

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

To picture the more complex “rings” I am mentally creating a paper snowflake with large chunks cut out of it, and then unfolding it

Neat, has this been reproduced in laboratory?

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.

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.

The whole point of a "ring species" is that the ring isn't closed, and the individuals at its ends are not compatible mates.

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.

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?

It's an analogy to help understand evolution over time in a lineage.

The Wikipedia entry quotes Dawkins:

The evolutionary biologist Richard Dawkins remarks that ring species "are only showing us in the spatial dimension something that must always happen in the time dimension".

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.

Interesting in that in population spread, expanding rings aren't entirely improbable - if a population has a tendency to exhaust resources when it expands into an area, its spread could naturally form loops around the edge of depleted, unpopulated areas. It would be interesting if there could be cases where a species expanded like that in the past, and evolved under that kind of closed ring pressure. Even if later that ring broke, how would that ancestry show up in the surviving species' taxonomy?

Isn’t the human species a ring species?

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.

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.

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

I have a feeling it's the simple fact that most bird species can fly and many of those species migrate incredible distances. This means (1) bird populations spread out and (2) they face survival pressure across multiple ecosystems.

Caveat emptor, that's just my layperson's "makes sense to me" hunch. No credentials or citations.

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.

Definitely has a prehistoric look. I could imagine it sharing the Cretaceous forests with Quetzalcoatlus and other pterosaurs

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

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

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.

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!

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

"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.

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.

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.

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

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.

> 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.

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.

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.

Z/w sex chromosome elements.

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.

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.

aberrant mating would depend on compatible chromosome layouts?

Viruses DNA can be added into animal DNA. Maybe a virus infected a bird, then a mammal that later evolved into the platypus.

> 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

| 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.

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