Vertebrate

The big breakthrough of the vertebrates appears to be the ability to swim around in a straight line and eat smaller species that are floating about.

Bones appear to help that a lot!

It is likely the most efficient design to travel long distances. Be thin and wiggle your tail around.

Perhaps smaller animals can skip the bone thing. Maybe a notable example are the lancelets, which look a bit like small fish. But they only go up to 8 cm.

Vertebrates minus tetrapods.

This paraphyletic subgroup is easy to form the "acquatic only" (fishes) vs "things that come out of water" (tetrapods). Though mudfish make that distinction harder.

Which kind of makes sense, why would you want for limbs unless you are going to stay out of water!

Once Ciro joked in a twenty questions-like game that humans are animals.

But counting humans a fish would have been a stroke of genius.

Includes:

The exact relationships between those clades is not very clear as there's a bunch of extinct species in the middle we are not sure exactly where they go exactly, some hypothesis are listed at: en.wikipedia.org/w/index.php?title=Tetrapod&oldid=1053601110#Temnospondyl_hypothesis_(TH)

But at least it seems rock solid that those three are actually clades.

Name origin: amnion, a pellicle that covers embryos of both eggs and also during pregnancy.

Includes:

Does not include amphibians. If you include them, you have the tetrapods.

This being a class is bullshit because it is not a clade, notably birds are not considered reptiles, but they are clearly in the clade.

Mammals and a bunch of extinct animals that look more like mammals than reptiles.

TODO name: Wikipedia says "being with a fused arch" but what does that mean???

Good phylogenetic tree: en.wikipedia.org/w/index.php?title=Mammal&oldid=1052295685#Molecular_classification_of_placentals

The weirdest mammal clade: they lay fucking eggs. Only 5 known species alive as of 2020.

Eggs are basal: they simply didn't evolve out of what other reptiles do. From which we conclude that milk came before eggs stopped.

So this is the most basal subclade of mammals.

Etymology: means "single hole" in Greek, because like other reptiles it has a single hole for shit, pee and fucking: the cloaca.

Every mammal except the weird monotremes, i.e. marsupials and the placentalia.

The name is completely random, "wild beast". Are platypuses not "wild beasts"? They have a freaking poison!!

They split up from the rest of the mammals after the monotremes.

Every other mammal has a placenta.

This baby in pouch thing just feels like a pre-placenta stage.

As of 2020, account for about 20% of the known mammal species!!! www.sciencefocus.com/nature/why-are-there-so-many-species-of-bat/ mentions some reasons:

Mice, rabbits and primates.

Since rat and mouse are not scientifically specific names, we'll just use them interchangeably.

When one specific species is implied, we will mean Mus musculus by default.

Exciting... sometimes cruel. But too exciting not to do:

Databases and projects:

Databases and projects:

This is the level at which human and all extinct siblings lie, with no other extant species, all others were killed or fucked to death: Section "Interbreeding between archaic and modern humans".

Good cladogram: en.wikipedia.org/w/index.php?title=Homo&oldid=1155900663#Phylogeny

Genome:

wget ftp://ftp.ncbi.nlm.nih.gov/refseq/H_sapiens/annotation/GRCh38_latest/refseq_identifiers/GRCh38_latest_genomic.fna.gz
gunzip --keep GRCh38_latest_genomic.fna.gz

The key cladograms:

Frozen and cut on Microtome at 1mm intervals.

They actually use fingerprint minutiae, not raw images, which is cool.

Bibliography:

Bibliography:

Bibliography:

Possibly not made not possible from userland due to privacy issues. Apparently not even kernelland can see it, only

Bibliography:

The point of these is that they are good for transfection apparently.

20k genes, 3 billion base pairs. We can handle this!!!

This is really cool. Ciro Santilli would be tempted to participate, but his wife is not a fan, in part due to the loss of privacy of children. Maybe she is right...

Someone should implement a version of that where you can upload your privately sequenced genome and get analytics for free.

This was the first large part of the genome that was sequenced, in 1981: Cambridge Reference Sequence. Presumably they picked it because it is short and does not undergo crossover.

About 16.6 kbp:

TODO: many places say "exactly" 16,569, it seems that variable number tandem repeat are either rare or don't occur!

By Fred Sanger's group.

Published as: sequence and organization of the human mitochondrial genome by Sanger et al. (1981).

As mentioned by Craig Venter in 100 Greatest Discoveries by the Discovery Channel (2004-2005), the main outcomes of the project were:

Important predecessors:

This was one of the first notable country-led large scale sequencing efforts of the world.

Sample paper: www.nature.com/articles/ng.3247

UniProt human: www.uniprot.org/uniprot/Q9BYF1 It is interesting to see in the Mutagenesis how many known mutations can increase or decrease SARS-CoV-2 S protein binding affinity.

Receptor in SARS-CoV-2 cell entry.

Receptor in SARS-CoV-2 cell entry.

Carnivores, ungulates, hedgehogs.