Microchromosomes

[erik simpson]

The articles I reference here aren't really paleontology, and this post might actually be more appropriate for talk.origins, but i'm putting it here because
talk.origins is pretty thoroughly corrupted these days.

The article that caught my eye in the "semi-popular" press is

"'Useless Specks of Dust' Turn Out to Be Building Blocks of All Vertebrate Genomes "

https://www.sciencealert.com/useless-specks-of-dust-turn-out-to-be-ancient-building-blocks-of-all-vertebrate-genomes

The useless specks are microchromosomes, and the scientific publication
is

"Microchromosomes are building blocks of bird, reptile, and mammal chromosomes"

https://www.pnas.org/content/118/45/e2112494118

One of the things that really caught my attention was the result that amphioxus (the lancelet) turns out to be less closely related to vertebrates
than tunicates, with a branching date of 684 Mya. I can't find where this
remarkably precise number comes from as the closest reference to the
early divergence seems to be

"Deeply conserved synteny resolves early events in vertebrate evolution"

https://www.nature.com/articles/s41559-020-1156-z

which doesn't provide the number. Anyway, a fascinating subject which I
can't easily digest with my primitive understanding of genetics.

[John Harshman]

Very interesting review. This incidental bit was new to me: "Comparison
of the amphioxus sequence with those of garfish and chicken revealed two
genome doublings: an autotetraploidization in the Cambrian ∼500 Ma and
allotetraploidy by fusion of genomes that had diverged in a fish
ancestor ∼460 Ma, followed by extensive loss of duplicate genes."

I presume we all know about the two successive genome doublings in
vertebrates, but the fact that the first was autopolyploid and the
second allopolyploid was news to me.

One annoying bit: the pigeon is out of place in Fig. 1. And considering
that there are upwards of 40 published avian genomes, I would have hopes
for more analysis there.

[Glenn]

On Wednesday, November 3, 2021 at 10:10:51 PM UTC-7, erik simpson wrote:
> The articles I reference here aren't really paleontology, and this post might actually be more appropriate for talk.origins, but i'm putting it here because
> talk.origins is pretty thoroughly corrupted these days.
>
> The article that caught my eye in the "semi-popular" press is
>
> "'Useless Specks of Dust' Turn Out to Be Building Blocks of All Vertebrate Genomes "

""Even more astonishingly, they were the same as the tiny chromosomes of Amphioxus – a little fish-like animal with no backbone that last shared a common ancestor with vertebrates 684 million years ago."
>
> https://www.sciencealert.com/useless-specks-of-dust-turn-out-to-be-ancient-building-blocks-of-all-vertebrate-genomes

"Scientists have discovered that tiny ‘microchromosomes’ in birds and reptiles are the same as the tiny chromosomes in a spineless fish-like ancestor that lived 684 million years ago.

https://newsroom.unsw.edu.au/news/science-tech/dust-specks-which-are-actually-building-blocks-our-genome

Um, no, they "suggest" that. Were chromosomes found intact after 684 million years, they wouldn't need to .

[erik simpson]

Um, no, the scientists didn't say that. You should read the primary sources instead of news releases.

[Glenn]

So the scientists didn't 'suggest'. Got it. Maybe you should read...oh, never mind.

[erik simpson]

Exactly. Never mind.

[John Harshman]

There's really no point in trying to talk to Glenn.

[Glenn]

At least on some level you realize that doing so spoils your fantasy world.

[jillery]

On Wed, 3 Nov 2021 22:10:50 -0700 (PDT), erik simpson
<eastsi...@gmail.com> wrote:

>The articles I reference here aren't really paleontology, and this post might actually be more appropriate for talk.origins, but i'm putting it here because
>talk.origins is pretty thoroughly corrupted these days.

You sound jealous. Just wait for Glenn and the peter to redirect
their attentions back here. I promise I have no problem sharing them
with you.

>The article that caught my eye in the "semi-popular" press is
>
>"'Useless Specks of Dust' Turn Out to Be Building Blocks of All Vertebrate Genomes "
>
>https://www.sciencealert.com/useless-specks-of-dust-turn-out-to-be-ancient-building-blocks-of-all-vertebrate-genomes
>
>The useless specks are microchromosomes, and the scientific publication
> is
>
>"Microchromosomes are building blocks of bird, reptile, and mammal chromosomes"
>
>https://www.pnas.org/content/118/45/e2112494118

from the "significance" section:
*********************************
Many microchromosomes have been lost independently in turtles, snakes,
and lizards as they have fused with each other or with larger
chromosomes. In mammals they have completely disappeared
*********************************
I don't understand what the article means by "lost", "fused", and
"disappeared". Does the article mean the genes within the
microchromosomes are lost, or does it mean the genes have become
distributed throughout a chromosome and are no longer organized
together?

[Oxyaena]

Molecular clock dates, especially of such a distant time period, must be
taken with a hefty grain of salt. The molecular clock works best when
calibrated with fossil evidence, but we don't have fossils of chordates
that far back. Admittedly, fossilization is a rare process, and the
further back in time we go the luckier we are to have *any* fossils at
all, so this may just be an error of taphonomy.

[John Harshman]

By "disappeared" he means no longer in existence as separate entities.
Some of the genes have been lost, as genes are regularly lost. Some of
the genes have been maintained as synteny groups in the chromosomes they
have become part of through chromosomal fusion. And some such groups
have been further broken up and distrbiuted in separate parts of
different chromosomes. But the number of pieces maintaining synteny
and/or remaining as separate chromosomes is surprising.

[erik simpson]

It's different in Synapsids and Sauropsids. The latter retained the micros as separate specks, but
somewhere along the line of Synapsids (some of) the micro stuff got incorporated into longer chromosomes.
There are lots more crown taxa representing ancient lineages among sauropsids than there sre of
synapsids in the critical early divergence. The oldest monotreme fossil ( a playpoid) is from the
Cretaceous, while Rhynchocephalians date back to the early Triassic. Why the differences between
the genetic histories are so different is a good question that's going to be hard to answer.

[erik simpson]

Amen! said the congregation. There are no bilaterian fossils known earlier than ~560 Mya,
and they are too small to say much about. The LCA of lancelets (pikaia?, middle cambrian)
and crainiates was obviously much earlier, but molecular clocks work best when calibrated
by fossils bracketing the thing being dated, rather than extrpolating. 684 is over-precise.
maybe "Ediacaran or even earlier" would be better. Even pre-Ediacaran metazoan fossils are
rare and controversial.

[erik simpson]

On Saturday, November 6, 2021 at 6:42:04 PM UTC-7, 69jp...@gmail.com wrote:

> On Wed, 3 Nov 2021 22:10:50 -0700 (PDT), erik simpson
> <eastsi...@gmail.com> wrote:
>
> >The articles I reference here aren't really paleontology, and this post might actually be more appropriate for talk.origins, but i'm putting it here because
> >talk.origins is pretty thoroughly corrupted these days.
> You sound jealous. Just wait for Glenn and the peter to redirect
> their attentions back here. I promise I have no problem sharing them
> with you.

Glenn has already appeared, but has apparently abandoned. That's fine with me. Peter
appears very busy with other pressing issues. That's also fine.

[erik simpson]

Well, that was confused. My only defense is the approach of the end of DST rattled me. We actually
have lots of crown taxa whose origins antedate the separation of lancelets from vertebrates; protostomes,
cnidarians, placozoans, sponges, ctenophorans. The 684 Mya number seems much too large.

[jillery]

On Sat, 6 Nov 2021 20:39:10 -0700 (PDT), erik simpson

Thanks for your reply, but could you be more precise? You say
Sauropsids retained the micros as separate specks? Do you mean
physically floating separately and duplicating separately within their
nuclei? Or do you mean they retained their composition within a
larger chromosome? If the former, how do microsomes sort evenly
during meiosis? Given how small they are, I would be surprised if
they have their own centromeres.

When you say Synapsids incorporated them into longer chromosomes, do
you mean the microsomes retained their composition within larger
chromosomes? If so, what does the article mean when it says
microsomes "completely disappeared" in mammals? What evidence is
there microsomes ever existed in mammals?

[erik simpson]

I'm apprehensive about answering definitively, but I'd reply "yes" to both your questions.
The abstract from the PNAS citation:

"Microchromosomes, once considered unimportant shreds of the chicken genome, are gene-rich elements with a high GC content and few transposable elements. Their origin has been debated for decades. We used cytological and whole-genome sequence comparisons, and chromosome conformation capture, to trace their origin and fate in genomes of reptiles, birds, and mammals. We find that microchromosomes as well as macrochromosomes are highly conserved across birds and share synteny with single small chromosomes of the chordate amphioxus, attesting to their origin as elements of an ancient animal genome. Turtles and squamates (snakes and lizards) share different subsets of ancestral microchro- mosomes, having independently lost microchromosomes by fusion with other microchromosomes or macrochromosomes. Patterns of fusions were quite different in different lineages. Cytological observations show that microchromosomes in all lineages are spatially separated into a central compartment at interphase and during mitosis and meiosis. This reflects higher interaction between microchromosomes than with macrochromosomes, as observed by chromosome conformation capture, and suggests some functional coherence. In highly rearranged genomes fused microchromo- somes retain most ancestral characteristics, but these may erode over evolutionary time; surprisingly, de novo microchromosomes have rapidly adopted high interaction. Some chromosomes of early-branching monotreme mammals align to several bird micro- chromosomes, suggesting multiple microchromosome fusions in a mammalian ancestor. Subsequently, multiple rearrangements fueled the extraordinary karyotypic diversity of therian mammals. Thus, microchromosomes, far from being aberrant genetic elements, represent fundamental building blocks of amniote chromosomes, and it is mammals, rather than reptiles and birds, that are atypical."

[jillery]

On Sun, 7 Nov 2021 10:16:28 -0800 (PST), erik simpson

I read the abstract from the PNAS citation before I posted my
questions. If simply reading it answered my questions, I would not
have asked them. They are not "yes/no" type questions. I regret if
you think my questions are out of line.

[erik simpson]

I didn't mean to imply that your questions are out of line. As I pointed out in the original post,
I consider my proficiency with genetic terminology inadequate to give an answer without some
possibility that I read it wrong. Platypoids are mammals, and some of the microchromosomes present in
the earliest synapsids are still to be seen tin their heir genome, but incorporated in longer chromosomes. The fact
that the paper doesn't mention any idntification of microchromasomes in the genome of more derived
mammals would seem to suggest that they've disappeared, or have been modified beyond recognition.

[Oxyaena]

Indeed, which is why, as I pointed out earlier, the molecular clock is
best taken with a grain of salt without fossil evidence to calibrate the
results. According to Wikipedia, there are potential trace fossils of
metazoan activity as far back as 1.1 Ga, but it also notes that "their
uneven width and tapering ends make a biological origin so difficult to
defend that even the original author no longer believes they are authentic."

- https://en.wikipedia.org/wiki/Trace_fossil#Evolution

Make of that what you will.

[John Harshman]

Mammals do not have microchromosomes, but they have regions of their
macrochromosomes that are homologous to some of the microchromosomes
present in sauropsids.

[erik simpson]

Are the homologous regions been identified in mammals other than monotremes? If so, I
missed that. I'm also curious to know how deep in the tree microchromosomes go. I haven't
found any reference for their presence in Ambulacraria or other more basal deuterostomes.

[erik simpson]

Owe grammar! "Have the homologous..."

[John Harshman]

I don't know either. I had previously been aware of microchromosomes
only in birds.

[John Harshman]

"The most prominent exception is a microchromosome in all other bird
lineages that aligns to chicken chromosome 4p, as previously noted (8,
12), and is significant because it also has homology to the conserved
region of the mammalian X chromosome (34)."

and

"To explore the fate of ancient microchromosomes in therian mammals
(eutherian and marsupial mammals), we compared the genomes of emu with
those of koala (a marsupial) and human (eutherian) (Fig. 3H). We
observed regions with some homology to bird microchromosomes, though
these were weak and dispersed. There was one region of the human genome
(chromosome 17) and two regions of the koala genome that had homology to
two or more microchromosomes but no evidence that microchromosomes are
retained intact in either species."