On Monday, November 8, 2021 at 8:17:38 AM UTC-8, erik simpson wrote:
> On Sunday, November 7, 2021 at 4:56:02 PM UTC-8, John Harshman wrote:
> > On 11/7/21 2:26 PM, erik simpson wrote:
> > > On Sunday, November 7, 2021 at 12:26:45 PM UTC-8, 69jp...@gmail.com wrote:
> > >> On Sun, 7 Nov 2021 10:16:28 -0800 (PST), erik simpson
> > >> <eastsi...@gmail.com> wrote:
> > >>
> > >>> On Sunday, November 7, 2021 at 9:22:27 AM UTC-8, 69jp...@gmail.com wrote:
> > >>>> On Sat, 6 Nov 2021 20:39:10 -0700 (PDT), erik simpson
> > >>>> <eastsi...@gmail.com> wrote:
> > >>>>
> > >>>>> 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.
> > >>>>>>> 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?
> > >>>>>>> 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..
> > >>>>>
> > >>>>> 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.
> > >>>> 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?
> > >>>
> > >>> 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."
> > >> 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.
> > >
> > > 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.
> > >
> > Mammals do not have microchromosomes, but they have regions of their
> > macrochromosomes that are homologous to some of the microchromosomes
> > present in sauropsids.
> 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.

Owe grammar! "Have the homologous..."