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Date: Fri, 22 Oct 2004 13:38:55 +0200
From: [unknown]
To: PML <phylocode@ouvaxa.cats.ohiou.edu>
Subject: Highly imprecise name uses in a neontological paper
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--Boundary_(ID_DCjwsYMvozGajF3yTHcI0Q)
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Here is a recent article about genetics. Let's see if it uses anythin=
g =3D
similar to the crown convention. Quotes in Times New Roman.
Reference phylogeny (all taxa are extant):
Osteichthyes (bony vertebrates)
|--Actinopterygii (ray-finned fishes)
| `--Teleostei
| |--Brachydanio rerio (zebrafish)
| `--+--Tetraodon nigroviridis (see below)
| `--Takifugu rubripes (fugu)
`--Sarcopterygii (lobe-finned... fishes)
|--Latimeria
`--+--lungfish
`--Tetrapoda (apomorphy or crown -- doesn't matter here)
Olivier Jaillon et omnes: Genome duplication in the teleost fish =
=3D
Tetraodon nigroviridis reveals the early vertebrate proto-karyotype, =
=3D
Nature 431, 946 -- 957 (21 October 2004)
The article itself makes clear that not Vertebrata but just Osteichth=
yes =3D
is meant by "vertebrate". It says nothing about hagfish, lampreys or =
=3D
cartilaginous fishes.
Tetraodon nigroviridis is a freshwater puffer fish with the smallest =
=3D
known vertebrate genome. Here, we report a draft genome sequence with=
=3D
long-range linkage and substantial anchoring to the 21 Tetraodon =
=3D
chromosomes. Genome analysis provides a greatly improved fish gene =
=3D
catalogue, including identifying key genes previously thought to be =
=3D
absent in fish.
In... fish? What does that mean? In percomorphs? Teleosts? =3D
Actinopterygians? Vertebrates except tetrapods? Vertebrates except =
=3D
mammals?
Comparison with other vertebrates and a urochordate indicates that fi=
sh =3D
proteins have diverged markedly faster than their mammalian homologue=
s.
Interesting dichotomy: fish vs mammals. Clearly, "fish" means =3D
Actinopterygii... and "mammals" means anything from Sarcopterygii to =
=3D
(Homo + Mus).
Comparison with the human genome suggests ~ 900 previously unannotate=
d =3D
human genes. Analysis of the Tetraodon and human genomes shows that =
=3D
whole-genome duplication occurred in the teleost fish lineage, =3D
subsequent to its divergence from mammals.
Teleostei vs Mammalia... yet another peculiar dichotomy. Did it occur=
at =3D
the origin of Teleostei, or somewhere between there and the origin of=
=3D
Actinopterygii? Most but not all living ray-finned fishes belong to =
=3D
Teleostei, so I'm not talking about the genes of fossils here.
The analysis also makes it possible to infer the basic structure of t=
he =3D
ancestral bony vertebrate genome, which was composed of 12 chromosome=
s, =3D
and to reconstruct much of the evolutionary history of ancient and =
=3D
recent chromosome rearrangements leading to the modern human karyotyp=
e.
There has been a vigorous and unresolved debate as to whether a =3D
whole-genome duplication (WGD) occurred in the ray-finned fish =3D
(actinopterygians) lineage after its separation from tetrapods.
=46rom Sarcopterygii.
We annotated 18 distinct families in Tetraodon based on similarities =
=3D
with the 19 protein families known in eukaryotes, and discovered a ne=
w =3D
selenoprotein that seems to be restricted to the actinopterygians amo=
ng =3D
vertebrates and does not have a Cys counterpart in mammals. We also =
=3D
catalogued type I helical cytokines and their receptors (HCRI), a gro=
up =3D
of genes that were not found in the Takifugu genome because of their =
=3D
poor sequence conservation, leading to the hypothesis that fish may n=
ot =3D
possess this large family that includes hormones and interleukins.
Sequenced "fish" so far: Tetraodon nigroviridis, Takifugu rubripes, =
=3D
Brachydanio rerio. Hm. All three are quite closely related. They belo=
ng =3D
to Percomorpha, a small part of Teleostei... so is its presence an =
=3D
apomorphy that occurred somewhere along the sarcopterygian line, or i=
s =3D
its absence an apomorphy that occurred somewhere along the =3D
actinopterygian line, which is what "fish" probably means here?
[...] the analysis here shows that Tetraodon is the descendant of an =
=3D
ancient WGD that most probably affected all teleosts.
The explosion of transposable elements in the mammalian lineage, =
=3D
subsequent to divergence from the teleost lineage, may have provided =
the =3D
conditions for increased interchromosomal rearrangements in mammals; =
in =3D
contrast, the Tetraodon genome underwent much less interchromosomal =
=3D
rearrangement.
Again a dichotomy Teleostei-Mammalia instead of =3D
Actinopterygii-Sarcopterygii.
With the availability of additional vertebrate genomes (dog, marsupia=
l, =3D
chicken, medaka, zebrafish and frog are underway), it will be possibl=
e =3D
to explore intermediate nodes such as the last common ancestor of =
=3D
amniotes, of sarcopterygians and of actinopterygians, and to gain an =
=3D
increasingly clearer picture of the early vertebrate ancestor.
The medaka is again a teleost, as these pictures =3D
http://biol1.bio.nagoya-u.ac.jp:8000/980818.html show. The first 140 =
of =3D
43,600 Google results seemed to be incapable of telling me where insi=
de =3D
Teleostei it belongs... two searches later I had it: =3D
http://www.fmnh.helsinki.fi/users/haaramo/Metazoa/Deuterostoma/Chorda=
ta/A=3D
ctinopterygii/Eurypterygii.htm -- it belongs to the sistergroup of =
=3D
Percomorpha, as the zebrafish seems to do. (The crown-group of Teleos=
tei =3D
is 3 pages away, the conventional meaning of the name even 4.) Means,=
=3D
all four "fish" that will have been sequenced in the near future belo=
ng =3D
to a clade of highly derived teleosts. That "early vertebrate ancesto=
r" =3D
belongs to Osteichthyes. Vertebrata as a whole is far, far away.
And which "marsupial" and which "frog" are meant here???
I conclude that this article uses all names very, very sloppily. Not =
=3D
only doesn't it care about the difference between crown-groups and ot=
her =3D
clades, it doesn't care about the difference between small but famous=
=3D
and larger but less famous crown clades! It is completely useless in =
an =3D
argument about the crown convention. It doesn't use enough tree-think=
ing =3D
-- by far.=3D
--Boundary_(ID_DCjwsYMvozGajF3yTHcI0Q)
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<BODY bgColor=3D3D#ffffff>
<DIV><FONT face=3D3DArial><FONT size=3D3D2>Here is a recent article a=
bout =3D
genetics.=3D20
Let's see if it uses anything similar to the crown convention. Quotes=
in =3D
Times=3D20
New Roman.</FONT></FONT></DIV>
<DIV><FONT face=3D3DArial size=3D3D2></FONT> </DIV>
<DIV><FONT face=3D3DArial><FONT size=3D3D2>Reference phylogeny (all t=
axa are =3D
extant):</FONT></FONT></DIV>
<DIV><FONT face=3D3DArial size=3D3D2></FONT> </DIV>
<DIV><FONT face=3D3DArial><FONT size=3D3D2>Osteichthyes (bony=3D20
vertebrates)</FONT></FONT></DIV>
<DIV><FONT face=3D3DArial><FONT size=3D3D2> |--Actinopterygii =
=3D
(ray-finned=3D20
fishes)</FONT></FONT></DIV>
<DIV><FONT face=3D3DArial><FONT size=3D3D2> | =
=3D20
`--Teleostei</FONT></FONT></DIV>
<DIV><FONT face=3D3DArial><FONT size=3D3D2> =3D20
| |--<EM>Brachydanio =
=3D
rerio</EM>=3D20
(zebrafish)</FONT></FONT></DIV>
<DIV><FONT face=3D3DArial><FONT size=3D3D2> |=3D20
`--+--<EM>Tetraodon =3D
nigroviridis</EM>=3D20
(see below)</FONT></FONT></DIV>
<DIV><FONT face=3D3DArial><FONT size=3D3D2> =3D20
| &n=
bsp;=3D
`--<EM>Takifugu=3D20
rubripes</EM> (fugu)</FONT></FONT></DIV>
<DIV><FONT face=3D3DArial><FONT size=3D3D2> `--Sarcopterygii =
=3D
(lobe-finned...=3D20
fishes)</FONT></FONT></DIV>
<DIV><FONT face=3D3DArial><FONT=3D20
size=3D3D2> |--<EM>Latimeria</EM><=
/FONT>=3D
</FONT></DIV>
<DIV><FONT face=3D3DArial><FONT=3D20
size=3D3D2> `--+--lungfish</FONT><=
/FONT>=3D
</DIV>
<DIV><FONT face=3D3DArial><FONT=3D20
size=3D3D2> =
=3D
`--Tetrapoda=3D20
(apomorphy or crown -- doesn't matter here)</DIV>
<DIV> </DIV></FONT></FONT>
<DIV><FONT face=3D3DArial size=3D3D2>Olivier Jaillon et omnes: =3D
<STRONG>Genome=3D20
duplication in the teleost fish <EM>Tetraodon nigroviridis</EM> revea=
ls =3D
the=3D20
early vertebrate proto-karyotype</STRONG>, Nature <STRONG>431</STRONG=
>, =3D
946 --=3D20
957 (21 October 2004)</FONT></DIV>
<DIV><FONT face=3D3DArial size=3D3D2></FONT> </DIV>
<DIV><FONT face=3D3DArial size=3D3D2>The article itself makes clear t=
hat not =3D
Vertebrata=3D20
but just Osteichthyes is meant by "vertebrate". It says nothing about=
=3D
hagfish,=3D20
lampreys or cartilaginous fishes.</FONT></DIV>
<DIV><FONT face=3D3DArial size=3D3D2></FONT> </DIV>
<DIV><EM>Tetraodon nigroviridis</EM> is a freshwater puffer fish with=
=3D
the=3D20
smallest known vertebrate genome. Here, we report a draft genome =
=3D
sequence with=3D20
long-range linkage and substantial anchoring to the 21 <I>Tetraodon</=
I>=3D20
chromosomes. Genome analysis provides a greatly improved fish gene =
=3D
catalogue,=3D20
including identifying key genes previously thought to be absent in =
=3D
fish.</DIV>
<DIV> </DIV>
<DIV><FONT face=3D3DArial size=3D3D2>In... fish? What does that mean?=
In =3D
percomorphs?=3D20
Teleosts? Actinopterygians? Vertebrates except tetrapods? Vertebrates=
=3D
except=3D20
mammals?</FONT></DIV>
<DIV><FONT face=3D3DArial size=3D3D2></FONT> </DIV>
<DIV>Comparison with other vertebrates and a urochordate indicates th=
at =3D
fish=3D20
proteins have diverged markedly faster than their mammalian =3D
homologues.</DIV>
<DIV> </DIV>
<DIV><FONT face=3D3DArial size=3D3D2>Interesting dichotomy: fish vs m=
ammals. =3D
Clearly,=3D20
"fish" means Actinopterygii... and "mammals" means anything from =
=3D
Sarcopterygii=3D20
to (<EM>Homo</EM> + <EM>Mus</EM>).</FONT></DIV>
<DIV><FONT face=3D3DArial size=3D3D2></FONT> </DIV>
<DIV>Comparison with the human genome suggests ~ 900 previously =3D
unannotated=3D20
human genes. Analysis of the <I>Tetraodon</I> and human genomes shows=
=3D
that=3D20
whole-genome duplication occurred in the teleost fish lineage, =3D
subsequent to its=3D20
divergence from mammals.</DIV>
<DIV> </DIV>
<DIV><FONT face=3D3DArial size=3D3D2>Teleostei vs Mammalia... yet ano=
ther =3D
peculiar=3D20
dichotomy. Did it occur at the origin of Teleostei, or somewhere betw=
een =3D
there=3D20
and the origin of Actinopterygii? Most but not all living ray-finned =
=3D
fishes=3D20
belong to Teleostei, so I'm not talking about the genes of fossils=
=3D20
here.</FONT></DIV>
<DIV><FONT face=3D3DArial size=3D3D2></FONT> </DIV>
<DIV>The analysis also makes it possible to infer the basic structure=
of =3D
the=3D20
ancestral bony vertebrate genome, which was composed of 12 chromosome=
s, =3D
and to=3D20
reconstruct much of the evolutionary history of ancient and recent =
=3D
chromosome=3D20
rearrangements leading to the modern human karyotype.</DIV>
<DIV><FONT face=3D3DArial size=3D3D2></FONT> </DIV>
<DIV>There has been a vigorous and unresolved debate as to whether a=
=3D20
whole-genome duplication (WGD) occurred in the ray-finned fish=3D20
(actinopterygians) lineage after its separation from tetrapods.</DIV>
<DIV><FONT face=3D3DArial size=3D3D2></FONT> </DIV>
<DIV><FONT face=3D3DArial size=3D3D2>From Sarcopterygii.</FONT></DIV>
<DIV><FONT face=3D3DArial size=3D3D2></FONT> </DIV>
<DIV>We annotated 18 distinct families in <I>Tetraodon</I> based on =
=3D
similarities=3D20
with the 19 protein families known in eukaryotes, and discovered a ne=
w=3D20
selenoprotein that seems to be restricted to the actinopterygians amo=
ng=3D20
vertebrates and does not have a Cys counterpart in mammals. We also =
=3D
catalogued=3D20
type I helical cytokines and their receptors (HCRI), a group of genes=
=3D
that were=3D20
not found in the <I>Takifugu</I> genome because of their poor sequenc=
e=3D20
conservation, leading to the hypothesis that fish may not possess thi=
s =3D
large=3D20
family that includes hormones and interleukins.</DIV>
<DIV><FONT face=3D3DArial size=3D3D2></FONT> </DIV>
<DIV><FONT face=3D3DArial size=3D3D2>Sequenced "fish" so far: <EM>Tet=
raodon=3D20
nigroviridis</EM>, <EM>Takifugu rubripes</EM>, <EM>Brachydanio =3D
rerio</EM>. Hm.=3D20
All three are quite closely related. They belong to Percomorpha, a sm=
all =3D
part of=3D20
Teleostei... so is its presence an apomorphy that occurred somewhere =
=3D
along the=3D20
sarcopterygian line, or is its absence an apomorphy that occurred =
=3D
somewhere=3D20
along the actinopterygian line, which is what "fish" probably means=
=3D20
here?</FONT></DIV>
<DIV><FONT face=3D3DArial size=3D3D2></FONT> </DIV>
<DIV>[...] the analysis here shows that <I>Tetraodon</I> is the =3D
descendant of an=3D20
ancient WGD that most probably affected all teleosts.</DIV>
<DIV> </DIV>
<DIV>The explosion of transposable elements in the mammalian lineage,=
=3D
subsequent=3D20
to divergence from the teleost lineage, may have provided the conditi=
ons =3D
for=3D20
increased interchromosomal rearrangements in mammals; in contrast, th=
e=3D20
<I>Tetraodon</I> genome underwent much less interchromosomal=3D20
rearrangement.</DIV>
<DIV><FONT face=3D3DArial size=3D3D2></FONT> </DIV>
<DIV><FONT face=3D3DArial size=3D3D2>Again a dichotomy Teleostei-Mamm=
alia =3D
instead of=3D20
Actinopterygii-Sarcopterygii.</FONT></DIV>
<DIV><FONT face=3D3DArial size=3D3D2></FONT> </DIV>
<DIV>With the availability of additional vertebrate genomes (dog, =
=3D
marsupial,=3D20
chicken, medaka, zebrafish and frog are underway), it will be possibl=
e =3D
to=3D20
explore intermediate nodes such as the last common ancestor of amniot=
es, =3D
of=3D20
sarcopterygians and of actinopterygians, and to gain an increasingly =
=3D
clearer=3D20
picture of the early vertebrate ancestor.</DIV>
<DIV><FONT face=3D3DArial size=3D3D2></FONT> </DIV>
<DIV><FONT face=3D3DArial size=3D3D2>The medaka is again a teleost, a=
s these =3D
pictures=3D20
</FONT><FONT face=3D3DArial size=3D3D2><A=3D20
href=3D3D"http://biol1.bio.nagoya-u.ac.jp:8000/980818.html">http://bi=
ol1.bi=3D
o.nagoya-u.ac.jp:8000/980818.html</A> show.=3D20
</FONT><FONT face=3D3DArial size=3D3D2>The first 140 of 43,600 Google=
=3D
results seemed to=3D20
be incapable of telling me where inside Teleostei it belongs... two =
=3D
searches=3D20
later I had it: <A=3D20
href=3D3D"http://www.fmnh.helsinki.fi/users/haaramo/Metazoa/Deuterost=
oma/Ch=3D
ordata/Actinopterygii/Eurypterygii.htm">http://www.fmnh.helsinki.fi/u=
sers=3D
/haaramo/Metazoa/Deuterostoma/Chordata/Actinopterygii/Eurypterygii.ht=
m</A=3D
> --=3D20
it belongs to the sistergroup of Percomorpha, as the zebrafish seems =
to =3D
do. (The=3D20
crown-group of Teleostei is 3 pages away, the conventional meani=
ng =3D
of the=3D20
name even 4.) Means, all four "fish" that will have been =
=3D
sequenced in=3D20
the near future belong to a clade of highly derived teleosts. Th=
at =3D
"early=3D20
vertebrate ancestor" belongs to Osteichthyes. Vertebrata as a whole i=
s =3D
far, far=3D20
away.</FONT></DIV>
<DIV><FONT face=3D3DArial size=3D3D2></FONT> </DIV>
<DIV><FONT face=3D3DArial size=3D3D2>And which "marsupial" and which =
=3D
"frog" are=3D20
meant here???</FONT></DIV>
<DIV><FONT face=3D3DArial size=3D3D2></FONT> </DIV>
<DIV><FONT face=3D3DArial size=3D3D2>I conclude that this article use=
s all =3D
names very,=3D20
very sloppily. Not only doesn't it care about the difference between=
=3D20
crown-groups and other clades, it doesn't care about the difference =
=3D
between=3D20
small but famous and larger but less famous crown clades! It is =3D
completely=3D20
useless in an argument about the crown convention. It doesn't use eno=
ugh =3D
tree-thinking -- by far.</FONT></DIV></BODY></HTML>
--Boundary_(ID_DCjwsYMvozGajF3yTHcI0Q)--