Genome analysis of the platypus reveals unique signatures of evolution

https://www.nature.com/articles/nature06936

Abstract
We present a draft genome sequence of the platypus, Ornithorhynchus anatinus. This monotreme exhibits a fascinating combination of reptilian and mammalian characters. For example, platypuses have a coat of fur adapted to an aquatic lifestyle; platypus females lactate, yet lay eggs; and males are equipped with venom similar to that of reptiles. Analysis of the first monotreme genome aligned these features with genetic innovations. We find that reptile and platypus venom proteins have been co-opted independently from the same gene families; milk protein genes are conserved despite platypuses laying eggs; and immune gene family expansions are directly related to platypus biology. Expansions of protein, non-protein-coding RNA and microRNA families, as well as repeat elements, are identified. Sequencing of this genome now provides a valuable resource for deep mammalian comparative analyses, as well as for monotreme biology and conservation.

The platypus genome, as well as the animal, is an amalgam of ancestral reptilian and derived mammalian characteristics. The platypus karyotype comprises 52 chromosomes in both sexes14,15, with a few large and many small chromosomes, reminiscent of reptilian macro- and microchromosomes. Platypuses have multiple sex chromosomes with some homology to the bird Z chromosome16. Males have five X and five Y chromosomes, which form a chain at meiosis and segregate into 5X and 5Y sperm17,18. Sex determination and sex chromosome dosage compensation remain unclear.

On 1/12/24 9:38 AM, Ruben Safir wrote:
> Genome analysis of the platypus reveals unique signatures of evolution
>
> https://www.nature.com/articles/nature06936
>
> Abstract
> We present a draft genome sequence of the platypus, Ornithorhynchus anatinus. This monotreme exhibits a fascinating combination of reptilian and mammalian characters. For example, platypuses have a coat of fur adapted to an aquatic lifestyle; platypus females lactate, yet lay eggs; and males are equipped with venom similar to that of reptiles. Analysis of the first monotreme genome aligned these features with genetic innovations. We find that reptile and platypus venom proteins have been co-opted independently from the same gene families; milk protein genes are conserved despite platypuses laying eggs; and immune gene family expansions are directly related to platypus biology. Expansions of protein, non-protein-coding RNA and microRNA families, as well as repeat elements, are identified. Sequencing of this genome now provides a valuable resource for deep mammalian comparative analyses, as well as for monotreme biology and conservation.
>
>
>
> The platypus genome, as well as the animal, is an amalgam of ancestral reptilian and derived mammalian characteristics. The platypus karyotype comprises 52 chromosomes in both sexes14,15, with a few large and many small chromosomes, reminiscent of reptilian macro- and microchromosomes. Platypuses have multiple sex chromosomes with some homology to the bird Z chromosome16. Males have five X and five Y chromosomes, which form a chain at meiosis and segregate into 5X and 5Y sperm17,18. Sex determination and sex chromosome dosage compensation remain unclear.
>
>
You can't draw that conclusion from the study you cite. If you want, you
could coin a term "reptile-like mammal", but that isn't any more use
than the now-deprecated "mammal-like reptile". I'm surprised the nature
article uses it at all.

>>
> You can't draw that conclusion from the study you cite. If you want, you
> could coin a term "reptile-like mammal", but that isn't any more use
> than the now-deprecated "mammal-like reptile".  I'm surprised the nature
> article uses it at all.

You know I am just armchair speculating, but the evidence shows that it
has broken from all mainstream mammals maybe even before the Placental
split? That is pretty amazing and puts the platapus into its own
classification.

It would be like a last surviving non-Avian therapod making it to the
present?

On 1/13/24 7:48 PM, Popping Mad wrote:
>>>
>> You can't draw that conclusion from the study you cite. If you want, you
>> could coin a term "reptile-like mammal", but that isn't any more use
>> than the now-deprecated "mammal-like reptile".  I'm surprised the nature
>> article uses it at all.
>
>
> You know I am just armchair speculating, but the evidence shows that it
> has broken from all mainstream mammals maybe even before the Placental
> split? That is pretty amazing and puts the platapus into its own
> classification.

This is not a surprise. Monotremes are not placentals and never have
been considered placentals. They're not therians either. But they're
still mammals. Nothing in that study is surprising.

> It would be like a last surviving non-Avian therapod making it to the
> present?

No, it would be like paleognaths surviving to the present, while you
make the claim that only neognaths are really birds.

On 1/13/24 7:48 PM, Popping Mad wrote:
>>>
>> You can't draw that conclusion from the study you cite. If you want, you
>> could coin a term "reptile-like mammal", but that isn't any more use
>> than the now-deprecated "mammal-like reptile".  I'm surprised the nature
>> article uses it at all.
>
>
> You know I am just armchair speculating, but the evidence shows that it
> has broken from all mainstream mammals maybe even before the Placental
> split? That is pretty amazing and puts the platapus into its own
> classification.
>
> It would be like a last surviving non-Avian therapod making it to the
> present?
>
>
It definitely split off before placentals, the sister is theria

On Monday, January 15, 2024 at 11:24:37 AM UTC-5, erik simpson wrote:
> On 1/13/24 7:48 PM, Popping Mad wrote:
> >>>
> >> You can't draw that conclusion from the study you cite. If you want, you
> >> could coin a term "reptile-like mammal", but that isn't any more use
> >> than the now-deprecated "mammal-like reptile". I'm surprised the nature
> >> article uses it at all.

"now-deprecated" is a highly subjective term that accepts Newspeak
from the dominant clique in taxonomy without murmur.

Popping Mad has the late Isaac Asimov on his side: he wanted desperately for
monotremes to be non-mammalian therapsids.
> >
> >
> > You know I am just armchair speculating, but the evidence shows that it
> > has broken from all mainstream mammals maybe even before the Placental
> > split? That is pretty amazing and puts the platapus into its own
> > classification.
> >
> > It would be like a last surviving non-Avian therapod making it to the
> > present?
> >
> >
> It definitely split off before placentals, the sister is theria

That's only among extant mammals. The sister group among
all mammals, extinct or extant, is very hard to pin down.

It's more fruitful to look for the sister group of therians,
the sister group of the clade the two determine, and repeat the process
an indeterminate number of times. Before you get close to monotremes,
you encounter multituberculates and, further away from therians,
a tantalizing Miocene mammal from Patagonia, *Necrolestes*.

I would be enthralled if it turned out that a descendant survived there.
Patagonia is sufficiently sparsely populated that a small burrowing
mammal might have escaped notice.

Peter Nyikos
Professor, Dept. of Mathematics -- standard disclaimer--
University of South Carolina
https://people.math.sc.edu/nyikos

On 1/15/24 21:58, Peter Nyikos wrote:
> opping Mad has the late Isaac Asimov on his side: he wanted desperately for
> monotremes to be non-mammalian therapsids.

If I am reading the genetics hear correctly, Platpus is not related to
any modern monotremes.

On 1/16/24 6:25 PM, Popping Mad wrote:
> On 1/15/24 21:58, Peter Nyikos wrote:
>> opping Mad has the late Isaac Asimov on his side: he wanted desperately for
>> monotremes to be non-mammalian therapsids.
>
>
> If I am reading the genetics hear correctly, Platpus is not related to
> any modern monotremes.

You are not reading the genetics correctly. The platypus *is* a modern
monotreme, and its closest relatives are the other modern monotremes,
echidnas.