Scott H Mullins
Jun-07-93 08:10AM
Protein and amino acid sequences
Organization: Purdue University Engineering Computer Network
From: smullins@author.ecn.purdue.edu (Scott H Mullins)
Message-ID:
Newsgroups: talk.origins
A creationist with whom I am debating has recently brought up supposed
problems with protein sequences. He has cited the following evidence:
In cytochrome-C sequences the following percentage of divergence
(measured as a percentage of difference between the sequences in the
total number of amino acid sites) are found between the species given
in line A and each of the species in line B:
A: Rhodospirillum rubrum (a bacterium)
B: human (66%), pig (64%), turtle (64%), tuna (66%), sunflower (69%)
silkworm (65%), lamprey (66%), wheat (66%), Baker's yeast (69%)
A: screw-worm fly
B: kangaroo (22), lamprey (26), penguin (22), dog(19),
pekin [sic] duck (20)
A: baker's yeast
B: horse (42), dog (41), pigeon (41), tuna (43), lamprey (45),
sunflower (43) castor bean (42)
A: carp
B: horse (13), rabbit (13), chicken (14), turtle (13), frog (13)
Now for hemoglobin (I don't know if it is alpha or beta hemo)
A: snail
B: lamprey (85), carp (87), frog (87), chicken (85), kangaroo (85)
The first, third, and fourth sets of sequence data make sense to me
because the last ancestor for all those in group B with the the
species in A is the same (I am not entirely sure for yeast in the
third data set). My problem is that I don't know where the lamprey
falls in the classification scheme or really exactly where the fly
or yeast goes either. Is the lamprey a vertebrate? From the data it
is hard to tell if it is a fish or what.
Another question: Is the degree of divergence among frogs as great
as that among mammals? Why might this be?
He has also given the following data on "relaxin" (I don't even
know what that is) again in percent variation:
A: human
B: pig (46), rat (46), shark (46), skate (34)
A: pig
B: rat (54), shark (50), skate (31)
A: shark
B: pig (50), rat (37), skate (42)
This data looks extremely odd to me so I have requested his references.
My request to t.o'ers. Does anyone out there know the answers to these
question and/or have good references that I should look at? These are
specific questions from a creationist (what a surprise) and I would
love to be able to expand on my previous answer to him but I simply
don't have the background for it.
Thanks for any help you can provide.
Scott
smullins@ecn.purdue.edu
==================================================================
Loren I. Petrich
Jun-07-93 12:24PM
Protein and amino acid sequences
Organization: LLNL
From: lip@s1.gov (Loren I. Petrich)
Message-ID: <1v085j$e9h@s1.gov>
Newsgroups: talk.origins
: A creationist with whom I am debating has recently brought up supposed
: problmes with protein sequences. He has cited the following evidence:
Well, I'm sure that L.A. Moran or Stan Friesen might know more
about molecular evolution than I do, but that's one of my amateurish
interests, so I'll take it on.
: In cytochrome-C sequences the following percentage of divergence (measured as
: a percentage of difference between the sequences in the total number of amino
: acid sites) are found between the species given in line A and each of the
: species in line B:
:
: A:Rhodospirillum rubrum (a bacterium)
: B: human (66%), pig (64%), turtle (64%), tuna (66%), sunflower (69%)
: silkworm (65%), lamprey (66%), wheat (66%), Baker's yeast (69%)
:
: A: screw-worm fly
: B: kangaroo (22), lamprey (26), penguin (22), dog(19), pekin [sic] duck (20)
:
: A: baker's yeast
: B: horse (42), dog (41), pigeon (41), tuna (43), lamprey (45), sunflower (43)
: castor bean (42)
:
: A: carp
: B: horse (13), rabbit (13), chicken (14), turtle (13), frog (13)
:
: Now for hemoglobin (I don't know if it is alpha or beta hemo)
I may add that sequences have been found for both alpha and
beta; they appear to be descended from a common ancestral molecule.
: A: snail
: B: lamprey (85), carp (87), frog (87), chicken (85), kangaroo (85)
:
: The first, third, and fourth sets of sequence data make sense to me
: because the last ancestor for all those in group B with the the species
: in A is the same (I am not entirely sure for yeast in the third data set).
: My problem is that I don't know where the lamprey falls in the classification
: scheme or really exactly where the fly or yeast goes either. Is the lamprey
: a vertebrate? From the data it is hard to tell if it is a fish or
: what.
A lamprey is indeed a vertebrate: it is a jawless fish, like
the first fish to appear on this planet. Jaws are derived from the
first gill bars.
As to where yeast would fall, it appears that
molecular-evolution studies like this one are able to answer this
question, extrapolating from their success where independent evidence
is available.
What one really wants is a table of _all_ the values, not just
"one vs. the others" as shown here.
Here is a family tree, from various sources of data:
_Rhodospirillum rubrum_: a purple bacterium
Mitochondria of:
Animals:
Insects:
screwworm fly
silkworm moth
Vertebrates:
Jawless fish:
lamprey
Bony fish:
carp
tuna
Land ones:
frog
turtle
Birds:
pigeon
chicken
duck
penguin
Mammals:
kangaroo
rabbit
pig
horse
dog
human
Plants:
sunflower
castor bean
wheat
Fungi:
yeast
: Another question: Is the degree of divergence among frogs as great as that
: among mammals? Why might this be?
Why are all the divergences approximately the same? That's one
of the key results of molecular evolution, the "neutral theory", which
states that much of molecular-level evolution is driven by genetic
drift between equally-capable possibilities. This means that, aside
from alteration by natural selection and statistical effects, one will
see the same molecular distance between all pairs of species sharing
the same youngest common ancestor. "Stage of evolution" is totally
irrelevant.
Indeed, it is interesting to see a revival of the 19th-cy.
concept of orthogenesis in the form of the statistics of molecular
evolution.
: He has also given the following data on "relaxin" (I don't even know what
: that is) again in percent variation:
:
: A: human
: B: pig (46), rat (46), shark (46), skate (34)
:
: A: pig
: B: rat (54), shark (50), skate (31)
:
: A: shark
: B: pig (50), rat (37), skate (42)
:
: This data looks extremely odd to me so I have requested his references.
It may be that this protein is under so little selective
constraint that its non-critical parts are effectively randomized. Or
else these may be molecules with two different ancestries serving the
same function in different species.
The family tree:
Cartilaginous fish:
shark
skate
Mammals:
rat
pig
human
: My request to t.o'ers. Does anyone out there know the answers to these
: question and/or have good references that I should look at? These are
: specific questions from a creationist (what a surprise) and I would
: love to be able to expand on my previous answer to him but I simply don't
: have the background for it.
:
: Thanks for any help you can provide.
--
/Loren Petrich, the Master Blaster
/lip@s1.gov
From: Loren I. Petrich
To: All Msg #80, Jun-07-93 02:58PM
Subject: Re: Protein and amino acid sequences
Organization: LLNL
From: lip@s1.gov (Loren I. Petrich)
Message-ID: <1v0h5s$h1l@s1.gov>
Newsgroups: talk.origins
In article smullins@author.ecn.purdue.edu
(Scott H Mullins) writes:
[a lot of stuff...]
I forgot to present estimated divergence dates. Here is the
family tree and the dates:
[Format: Parent, then all the branches, then the date;
unfortunately, I cannot draw family trees very well in text form]
Purple bacteria / mitochondria:
_Rhodospirillum rubrum_ (a purple photosynthetic bacterium)
Eukaryotic mitochondria in ancestral protists
1500 my [Proterozoic]
Ancestral protists:
Animals
Plants
Fungi (yeast)
1000 my [Proterozoic]
Animals:
Insects
Mollusks (snail)
Vertebrates
600 my [Base of Cambrian]
Insects (with pupa phase):
silkworm moth
screwworm fly
100-200 my [Mesozoic]
Vertebrates:
Jawless Fish (lamprey)
Jawed Fish
500 my [early Paleozoic]
Jawed Fish:
Elasmobranchs
Bony Fish
Land Vertebrates
400 my [mid-Paleozoic]
Elasmobranchs:
shark
skate
[I don't know for sure]
Bony fish (teleosts here):
carp
tuna
100 my [Late Mesozoic?]
Land Vertebrates:
Amphibians (frog)
Reptiles
350 my [Late Paleozoic]
Reptiles:
Turtles
Birds
Mammals
250 my [Permian]
Birds:
duck
chicken
penguin
pigeon
65 my [late Mesozoic / early Cenozoic]
Mammals:
Marsupials (kangaroo)
Placentals
100 my [late Mesozoic]
Placentals:
pig
horse
dog
rabbit
rat
human
65 my [late Mesozoic / early Cenozoic]
Plants (flowering):
Dicots
Monocots (wheat):
100-150 my [late Mesozoic]
Dicots:
sunflower
castor bean
50-150 my [late Mesozoic / early Cenozoic]
===============================================================
Cornelius Krasel
Jun-08-93 12:47AM
Protein and amino acid sequences
Organization: InterNetNews at ZDV Uni-Tuebingen
From: zxmkr08@studserv.zdv.uni-tuebingen.de (Cornelius Krasel)
Message-ID:
Newsgroups: talk.origins
I am not very familiar with sequence analysis (yet), but I will give
it a try...
In smullins@author.ecn.purdue.edu (Scott H
Mullins) writes:
>A creationist with whom I am debating has recently brought up supposed
>problmes with protein sequences. He has cited the following evidence:
[Cytochrome C will be considered in a later post]
>He has also given the following data on "relaxin" (I don't even know what
>that is) again in percent variation:
This is from the SwissProt entry RELX_PIG (which contains the sequence
for pig relaxin):
FUNCTION: RELAXIN IS AN OVARIAN HORMONE THAT ACTS WITH ESTROGEN
TO PRODUCE DILATATION OF THE BIRTH CANAL IN MANY MAMMALS.
It is (with this definition) surprising that sharks and skates
also have relaxins, but as far as I can remember at least
sharks have live offspring (so it's not so surprising any more).
Relaxin has also been found in the spiny dogfish (squalus
acanthias) which is oviparous. Hence, its function there
is not known.
Relaxins usually consist of two amino acid chains which are
connected by disulfide bonds. The B chain is about 30-40 amino
acids long, the A chain seems to be a bit shorter. Relaxins
are made as preprohormones, that is, when synthesized, the
chains are connected by a peptide on which selective pressure
is probably quite low. This peptide is cut out during processing.
There is also a leader peptide which channels preprorelaxin
into the secretory pathway. These leader peptides are quite
similar for all secreted proteins since they fulfil a common
signaling function (namely, marking the protein for secretion).
Generally, short proteins are very unsuitable for constructing
evolutionary trees if they have a function because most
of the amino acids cannot be replace d without loss of
function. This is assumed to be a smaller problem with
bigger proteins (with hundreds of amino acids). For
example, the A chain of whale relaxin is identical to the
A chain of pig relaxin.
If you nevertheless make a cluster analysis with the GCG
program PILEUP with the A and B chains just concatenated,
you get the following picture:
(approximately ASCII figure)
---------------------------
! !
------- !
! ! ---------------------------
! ! ! !
! ! ---------- !
! ! ! ! !
! ! ! ! --------------------
! ! ! ! ! !
! ! ! ------- ! !
! ------ ! ! ! ! !
! ! ! ! ! ! ! ----------------
! ! ! ! ! ! ! ! !
! ! ! ! ! ! ! ! -----------
! ! ! ! ! ! ! ! ! !
A B C D E F G H I J
A: Raja Erinacea (Little Skate)
B: Squalus Acanthias (Spiny dogfish)
C: Odontaspis Taurus (Sand tiger shark)
D: Rat
E: Rhesus monkey
F: Human
G: Horse
H: Balaenoptera acutorostrata (Minke whale)
I: Pig
J: Balaenoptera edeni (Bryde's whale)
Although the near relationship between Bryde's whale and pig is not
really convincing :-) the rough relations between groups are
not that wrong...
(Data were taken from SWISSPROT Release 24.0 and aligned with
PILEUP by UWGCG. Connecting and leader peptides were removed before
aligning in the human, the monkey, the pig and the rat
sequence.)
BTW: does anybody know of a good introductory text
into evolutionary analysis of sequences?
--Cornelius.
