Lecture notes for Evolution II
David Nelson
For Dec. 19, 2001
Last revised Dec. 19, 2001 8:15 AM
SOME FEATURES THAT ARE NOT CONSERVED AMONG THE
THREE DOMAINS
One feature that is not well conserved in all three domains is ribonucleotide reductase.
Each domain of life has a very different enzyme that uses different cofactors to catalyze
this important reaction. The reaction is the removal of the 2' OH group from
ribonucleotides. The absence of a conserved protein sequence for this function suggested
that this reaction was being catalyzed by an RNA ribozyme in the last common ancestor. The
argument follows that this ribozyme has since been replaced, but independently in all three
lineages. This argument is now known to be untrue. Sequence similarity has been shown
between the class I and class II enzymes (recently sequenced in a genome project from an
Archaea). The crystal structure for a class III enzyme has been solved and the fold is a 10
stranded beta/alpha barrel as in the class I enzyme, even though the sequences are very
different. (Science 283, 1499-1504 1999) The class III enzyme has a glycyl radical instead
of a tyrosine radical and it is poisoned by oxygen (it actually cuts off its own tail). The
thought now is that the class I and class II forms evolved after oxygen arose in the
atmosphere to make an oxygen stable radical that would not self destruct. The fact that
there are de novo pathways for ribonucleotides but not for deoxyribonucleotides (they are only
made from ribonucleotides) suggests that DNA came after RNA in evolution.
A related issue is the question of which came first DNA or protein. In an article discussing
this (Science 286, issue of 22 Oct. 1999, pp. 690-692) RNA is assumed to be first before DNA
or protein, but which came next? The answer seems to be that protein came next because
protein catalysts are apparently necessary to make ribonucleotide reduction possible and this
had to happen before DNA was ever made. The mechanism is a rare and energetically costly one
and it looks like it may be the only possible way to do this reaction, since no other enzyme
type has been found to do it. The possibility that RNA could catalyze a free radical
reaction seems unlikely, therefore protein was needed before ribonucleotide reductase could
exist and therefore before DNA could be made.
The lipids of modern archaea are ether linked lipids, while bacteria and eukarya have ester
linked lipids. The archaea with the highest heat tolerance have ether linked lipids that are
covalently coupled across the bilayer. This adds to their membrane stability at high
temperatures. Christian de Duve suggests that the common ancestor was an ether linked
species that had to switch to ester linkages to survive a drop in temperature. The present
day archaea have some members that can grow at 110 degrees, but the most thermophilic
bacteria can only stand about 80 degrees. He suggests this is related to lipid composition.
If the common model of branching is correct, then the transition to ester linked lipids had
to occur twice, once in the bacteria and again in the eukarya. If the chimeric model of
eukarya is correct, the gram negative bacteria that fused with archaea could have brought the
ester linked lipid biosynthetic genes along.
Murein is only found in bacteria not archaea. It is a cell wall component made of sugars
and D and L amino acids. The presence of both D and L amino acids suggests an ancient
origin for this material. Archaea may have lost the ability to make murein, however, it is
possible that the synthesis of murein evolved after bacteria and archaea split.
Cholesterol is a eukaryotic lipid. Not all eukaryotes make it. Yeast make ergosterol
instead and plants make cycloartenol derivatives, though palms do make cholesterol. There
are reports that three bacteria can make partially demethylated lanosterol products, on the
way to cholesterol. But, for the most part cholesterol biosynthesis seems to be a eukaryotic
phenomenon.
DEVELOPMENT OF PHOTOSYNTHESIS AND THE OXYGEN CRISIS
Life in the early earth was anaerobic. In the history of photosynthesis, photosystem I must
have developed first. PSI cannot split water to make O2, so the first source of electrons for
this pathway had to be mineral compounds. Eventually, PSII evolved from PSI and the
ability to split water and form O2 changed the planet. Here is a quote "The cr4eation of a
photosynthetic apparatus capable of splitting water into oxygen, protons and electrons was the
pivotal innovation in the evolution of life on Earth. This event literally changed the face of
the Earth." (Dismukes, G.C. et al. Theorigin of atmospheric oxygen on Earth: The innovation of
oxygenic photosynthesis. PNAS 98, 2170-2175 2001) O2 is the source of many toxic oxygen
compounds such as superoxide anion, hydrogen peroxide and hydroxyl radical. These are known as
reactive oxygen species (ROS). Cells had to protect themselves from these oxygen byproducts of
photosynthesis. Of course, the cells that produced these compounds had to protect themselves
first. This required the evolution of free radical scavengers like vitamins C and E, and
enzymes like superoxide dismutase and catalase.
Oxygen released to the environment by photosynthesizing cyanobacteria would react with
any oxidizable substance. The early oceans were believed to contain a lot of Fe2+ that
could react with oxygen to form rust. There is evidence from 3.75 billion year old
sedimentary deposits called banded-iron formations, that Fe2+ served as an oxygen sink.
These deposits formed from 3.75 billion years to about 1.7 billion years. As these deposits
began to lessen, oxygen began to appear in the atmosphere, starting about 2 billion years
ago. It has remained pretty constant since 1.5 billion years ago. The inference is that iron
in the oceans served as an oxygen trap for almost 2 billion years until it was all oxidized.
As the iron became depleted, oxygen concentrations in the atmosphere could rise.
Organisms that were not O2 producers either had to hide from O2 or adapt. There are still
anaerobes that hid from the toxic effects of O2. The other organisms adapted and
developed protections from oxygen. These organisms eventually learned how to exploit
O2 as the ultimate electron acceptor of their electron transport chains and gained a great
advantage in the amount of energy that could be recovered in the form of ATP.
The presence of oxygen also opened up the possibilities of oxygen chemistry that were not
available before. Note that none of the amino acid biosynthesis pathways requires
molecular oxygen, but many of the breakdown pathways do. You should also be aware
that cholesterol biosynthesis requires oxygen to remove a 14 alpha methyl group from the
cholesterol ring structure. This is needed to make cholesterol planar, which is an important
feature of this critical eukaryotic lipid. Cholesterol cannot be made without oxygen and the
cytochrome P450 CYP51 (lanosterol 14 alpha demethylase).
THE ACQUISITION OF MITOCHONDRIA AND CHLOROPLASTS BY
EUKARYOTES. HYDROGENOSOMES PROVIDE CLUES
It is thought that the earliest eukaryotes had no mitochondria or chloroplasts, but they
acquired these organelles by endosymbiosis. Today the most ancient branches on the
eukaryotic tree all represent groups without mitochondria. The earliest eukaryotes seem to
be the Archaezoans diplomonads (includes Giardia), and the trichomonads. The
evidence is very strong that mitochondria were taken in as endosymbionts of the alpha
proteobacteria. Phylogenetic trees of the rRNAs from bacteria and mitochondria show this
plainly. A paper published in Nature (Nature 396, 133-143 1998) shows the
Rickettsia are the closest living relatives of mitochondria. A similar case is made for the
chloroplast's origin among cyanobacteria. Hydrogenosomes and peroxisomes may also be
endosymbionts, but they do not contain a genome of their own today.
Note on microsporidians: Sequences of the largest subunit of RNA polymerase II show
that microsporidians are really related to fungi. Their deep branching on rRNA trees is
artifactual. PNAS 96, 580-585, 1999 Microsporidia are related to Fungi:Evidence from the
largest subunit of RNA polymerase II and other proteins. Microsporidians also contain a
characteristic insertion in their EF1 alpha protein that is only seen in the fungal and animal
clade (Opisthokonta). This strongly suggests they must belong to this clade.
An article published in Science 275, 790 1997 strongly suggests that the
amitochondriate eukaryotes mentioned above actually did have mitochondria, but they lost
them, or they became hydrogenosomes. Mitochondrial-like heat shock protein genes are
found in the genomes of these organisms. Because of this, the use of Giardia as a model
of the primitive eukaryote before mitochondria were acquired is no longer viable. In fact,
there is no living model for the earliest eukaryote that existed before mitochondria.
Recent work has shown that Giardia are part of a very early branch on the eukaryotic tree
All eukaryotic alanyl tRNA synthetases in eukaryotes have been replaced by a bacterial version
probably from the mitochondrial endosymbionts genome. This did not happen in Giardia where the
synthetase is like an archaeal gene. The authors of this paper say that Giardia did not
complete the transition to mitochondria, but lost the mitochondria before this key event took
place (Origin of mitochondria in relation to evolutionary history of eukaryotic
alanyl-tRNA synthetase PNAS 97, 12153-12157 2000 (Oct. 24 issue). Since this is the only
organism with this property, they (diplomonads) must be the first branch on the eukaryotic line.
Hydrogenosomes are organelles found only in eukaryotes that do not have mitochondria.
These organelles are surrounded by a double membrane like mitochondria. They are the site
of pyruvate fermentation to produce acetate, CO2 and H2. ATP is formed by substrate level
phosphorylation, so these organelles resemble mitochondria in that they produce ATP.
They do not have pyruvate dehydrogenase. Instead they use an enzyme called pyruvate
ferredoxin oxidoreductase, and they have hydrogenase. These enzymes are not found in
mitochondria, but they are seen in anaerobic bacteria. Hydrogenosomes do not have an
electron transport chain and F1F0 ATPase. They do not perform oxidative
phosphorylation. But they do have an ADP/ATP carrier to exchange ATP and ADP with the cytosol.
Recently a ciliate (Nyctotherus ovalis) was found with a hydrogenosome that still has a genome
of its own (Nature 396, 527-528 and commentary on 517-519 1998). The small subunit rRNA gene
was PCRed out and found to match with other mitochondrial versions of this gene.
One set of proteins found in hydrogenosomes are the heat shock proteins Hsp70, Hsp60
and Hsp10. These are ideal sequences to use for phylogenetic analysis. As we saw in the
first evolution lecture, Gupta And Golding used them to argue for a hybrid eukaryote
genome. A sequence analysis of the hydrogenosome Hsp70 and Hsp60 proteins showed a
signature sequence characteristic of these proteins in mitochondria and gram negative
purple bacteria. Trees made with other available sequences of all three Hsp proteins placed
each of them in the mitochondrial Hsp group. Since this happened in all three cases, the
hydrogenosome Hsps and the mitochondrial Hsps appear to have a common bacterial
ancestor. In anaerobic environments where these organisms live, it was not useful to retain
the OXPHOS genes encoded in the mitochondrial genome, which may explain why most
hydrogenosomes have no genome of their own. These organelles are apparently a
degenerate version of the mitochondrial ancestor.
Before the eukaryotic ancestor could engulf these bacteria, it would have to evolve into a
phagocytic cell, with the ability to take a whole living bacterium inside itself. This is
not possible with a rigid cell wall. Therefore, the precursor of the eukaryote host had to
lose the ancestral cell wall.
An example of symbiosis between amebas and a bacterium has been documented in the lab.
Kwang Jeon of our own UT (at Knoxville) was studying amebas when he noticed a
bacterial infection had killed most of the cells in one of his cultures. He isolated the
bacterium and tested it on another group of amebas. Again it killed most of them, but some
survived and had 40,000 bacteria living inside the ameba cells. He cultured the amebas for
many generations and then tried an experiment where he removed the nucleus from these
infected amebas and transplanted it to the original uninfected strain. The amebas died
unless he "infected" them with the bacteria. In other words, the host had become
dependent on the bacteria and needed them to survive.
LINK TO AN ENDOSYMBIOSIS PAGE
An interesting twist to this idea comes from William Martin of Braunschweig Technical
University in Germany and Miklos Mueller of Rockefeller University. They suggest that the
first eukaryote evolved from a methanogen, a microbe that uses hydrogen and
carbon dioxide and produces methane and a bacterium that made hydrogen and carbon dioxide as
waste products. These would be natural allies that would want to get close together, so
close that it makes sense they would form a symbiosis. (Nature 392, 37-41 1998 The hydrogen
hypothesis for the first eukaryote.)
INTRONS LATE OR INTRONS EARLY
(see PNAS 92, 8507-8511 1995)
Introns are found in eukaryotic genes (Nature 271, 501 1978). There are two opposing
views on what the origin of introns might be. In one view, introns are ancient and were
present in all genes. The amino acid coding regions of genes were made of small pieces of
15-20 codons each and these were all spliced together by removal of the introns. In this
model, genetic diversity was assured by exon shuffling, that combined different exons to
make a very large collection of proteins. This is the exon theory of genes. Since these
types of introns are not in bacteria, the theory goes that bacteria are streamlined and have
lost all their introns. Furthermore, the exons in this theory are supposed to code for units
of protein structure, such as helices and beta strands.
The "introns late" theory says that the original common ancestor did not have introns and
they only evolved in the eukaryote branch of the tree of life. This theory suggests that
introns are placed pretty much at random into genes, and exons do not necessarily
correspond to protein structural elements like helices and strands.
Triose phosphate isomerase is an enzyme that was used to support the introns early
hypothesis, because the chicken TPI gene has six introns and they all occur between
structural elements in the protein. When additional sequences from a plant and a fungus
were determined, additional introns were found. Five were in the same place in plants and
animals suggesting they existed in the common ancestor to plants and animals. The total
number of presumed introns was now 11, with different lineages losing different introns
over time. One of the new exons was big and did not fit well with the theory that compact
modules of protein were encoded in the exons. Walter Gilbert predicted that another
sequence would have an intron that would break this exon in two. This was found in a
mosquito.
The issue was not solved yet, because more sequences were done from another insect,
another fungi and C. elegans (nematode). These identified seven new intron positions, for
a total of 21 introns and an average exon size of 11.2 codons. 12 introns only occur in one
sequence, suggesting that all other lineages lost that intron. The exon theory then is
getting to be very cumbersome. Additional sequences from more insects showed that a close
relative of the Culex mosquito (Aedes mosquitoes) had the intron, but more distant relatives
(Anopheles mosquitoes, flies and moths) did not(PNAS 92, 8503-8506 1995). This is
consistent with late insertion of the intron in an ancestor of the Culex and Aedes
mosquitoes. Since 19 species are missing this intron, at least 10 independent losses of this
intron would be required to fit the introns early model. Therefore, the introns early model
seems to be wrong.
Walter Gilbert continues to defend the introns early theory. Based on a statistical analysis
of the intron exon boundaries, he claims now that the ancient introns were phase 0 introns
(introns that do not interrupt a codon) [Proc Natl Acad Sci U S A 95, 5094-9 1998]. This
seems like an attempt to salvage a failing idea. As more data come in, the introns late model
seems more believable. A recent review shows evidence supporting the recent insertion of
several introns in Drosophila xanthine dehydrogenase (Curr Biol 8, R560-3 1998) which
supports the introns late model.
Sidney Brenner who is responsible for C. elegans as a model organism has used introns as a
tool to follow evolution. If intron insertion or loss is a rare event, then the presence or
absence of introns in a lineage should correlate with a single historic event when the intron
was inserted (or lost). He has looked at seven introns from genes in the fugu fish but without
the intron in man as a test case.(PNAS 96, 10267-10271, August 31, 1999 Late changes in
spliceosomal introns define clades in vertebrate evolution). By sampling many different
species from all the major groups of fishes, he could see when the introns were inserted or
lost. This is much better than looking at average numbers like percent sequence identity
between genes, since those numbers reflect many individual mutations, that can occur at the
same site more than once and can back mutate. There is probably no noise to the signal from
intron insertion or loss.
SIMILARITIES AND DIFFERENCES BETWEEN ARCHAEA AND EUKARYA.
Archaea and eukarya share some distinctive features, including N-linked glycoproteins,
absence of N-formylmethionine and introns in their tRNAs(see PNAS 92, 5761-5764
1995). N-linked glycoproteins are made in eukaryotes in the endoplasmic reticulum and the
golgi. They are initially formed using a dolichol carrier lipid intermediate. Their presence
in archaea suggests that dolichol is there and some membrane bound system similar to the
N-linked biosynthetic machinery of the ER is also present. Bacteria use N-
formylmethionine at the beginning of all their proteins. There is a special tRNA for this
amino acid. Eukarya and archaea do not have N-formylmethionine. Some eukaryotic
tRNA genes have introns. In yeast, there are 262 tRNA genes, and about one third contain
introns. Archaea also have introns in some of their tRNAs. Methanococcus jannaschii has
37 tRNA genes, with introns in a met and trp tRNA. The transcriptional apparatus of
archaea is much more eukaryote-like than bacteria-like. This may reflect similarities in how
DNA is packaged in the two domains. Methanococcus jannaschii has five histone genes,
so the DNA may be packaged in nucleosomes as in eukaryotes. This may require a more
complex transcription machinery to get at the DNA. Bacteria don't have histones and they
have a much simpler transcriptional apparatus.
Archaea and bacteria both have polycistronic operons, and some of these have the genes
arranged in a similar order in both lineages. This implies that the operons existed in the
common ancestor. Recently, there has been some evidence that C. elegans, a model
organism for genome sequencing also has operons. This was unheard of in animals before
these C. elegans operons were described.
HOMEOBOX GENES AND MACROEVOLUTION
(see Molecular Biology of the Cell, chapter 21)
Humans, worms and flies don't look very similar and they do not go through the same
developmental stages. Yet the genes that control their body shape and organization are
related in sequence. These genes all share a common sequence called the homeobox. This
180 nucleotide sequence codes for 60 amino acids found in these proteins. The rest of the
proteins may be very different, but this 60 amino acid piece is crucial for their function.
The homeodomain is a helix turn helix DNA binding domain that recognizes a specific
DNA sequence. The homeodomain targets the remainder of the protein to regulate the gene
expression of any genes with the appropriate recognition sequence in their control regions.
There are at least 50 homeobox genes in Drosophila. They fall into two main divisions, the
complex superclass and the dispersed superclass. Those in the complex group are found in
clusters, the dispersed group are solo genes.
One subset of these genes are called homeotic selector genes. In Drosophila, there are 8
genes arranged in a series along 650,000 base pairs of DNA. This whole region is called
the HOM complex. There are two smaller subsets of these genes in the HOM complex,
the antennapedia complex (5 genes) and the bithorax complex (3 genes). Other insects
have these genes all in one complex, so it looks as though the HOM complex became split
in Drosophila.
Mutations in the 8 genes of the HOM complex cause large scale mutations in flies. A
mutation in bithorax causes a fly to have an extra set of wings. Mutation in antennapedia
causes a leg to grow where an antenna should be. These genes are not master switches for
making wings or legs, but they specify position in the fly's body. The order of the genes
on the chromosome is the same as the order of segments in the fly's body where they are
expressed. The left most gene is expressed in the head, the right most gene is expressed in
the abdomen. When a gene is deleted or mutated, the segment where it is normally
expressed cannot tell where it is because its position clue is gone, so it behaves like the
closest segment to it. That is why a bithorax mutation causes an extra set of wings. The
segments adjacent to the bithorax segment dictated what should be made.
An amazing fact is that these HOM genes have clear homologs in vertebrates. These are
called hox gene clusters. Mice have four hox gene clusters on four different chromosomes.
These are called HoxA ,B, C and D. HoxB has all the same genes as HOM plus one more.
They are in exactly the same order. The other three segments are missing some of the
HOM genes, but they have some extra homeobox genes not in the HOM cluster.
The HOM cluster seems to have arisen by gene duplication of a single homeobox gene long
ago. This cluster then was duplicated in total four times in the lineage of vertebrates .
Some additional gene duplication and deletion resulted in the present day set of Hox genes
in mammals. These genes specify position in mouse embryos, just like they did in flies.
They seem to have a similar function to the HOM cluster in flies, except it is more
complicated in mammals because there are four clusters. Two sets of hox gene clusters are
expressed in limb buds in perpendicular directions. The gene products from one cluster are
expressed along a left to right axis in the limb bud(HoxD) and the other gene cluster is
expressed top to bottom in the same bud(HoxA). This creates a checkerboard pattern that
makes each position in the limb bud unique, like the elements of a mathematical array that
are described by x, y and z coordinates. If a single gradient in the fly can specify the
development of different symmetrical segments, like head, thorax and abdomen, then a
dual gradient in the limb bud can specify the development of asymmetry in the limbs,
things like the bones and muscles of the hand, the layout of nerves and blood vessels, what
is to be skin and fingernails.
The HoxA cluster in mouse has 11 genes, Drosophila has eight genes in the HOM cluster.
HoxA has added three extra genes. Probably, if one looks back at simpler organisms there
will be some that have fewer homeotic genes in these clusters, or fewer clusters. The
Annual Review of Biochemistry 1994 has an article on homeodomain proteins (Vol. 63,
487-526). There, evidence is cited for one hox cluster in acorn worms (a hemichordate),
two hox clusters in amphioxus (a cephalochordate) and three (or 4) in lamprey (a primitive
vertebrate). More recent work shows three probable clusters in a fresh water lamprey
(Sharman AC, Holland PW Estimation of Hox gene cluster number in lampreys. Int J Dev
Biol 42,617-20 1998)
Another paper shows one Hox cluster in ribbon worms PNAS 95, 3030
1998, that are more primitive invertebrate animals. One hox cluster is seen in sea urchins.
It is tempting to extrapolate that gain of hox genes in a cluster increases the
complexity of an organism by allowing additional segments to be specified. Initially these
would be just like adjacent segments, but there would be opportunity to evolve into more
specialized functions. For example, if there are three sets of legs in insects, could another
set of legs be added just by duplicating a hox gene that specified a leg segment of the body?
What do the hox gene clusters of spiders, centipedes and millipedes look like? Are there
dozens of duplicated hox genes that specify many identical segments? This provides the
possibility of macroevolution. Duplication of hox genes, or whole hox gene clusters,
followed by deletion and mutation might alter a species very dramatically in a short time
period.
Note added in 1997: The International Society of Developmental Biologists and the
Society for Developmental Biology met in July 1997 at Alta, Utah. Researchers reported
that centipedes and onychophorans, primitive, wormlike creatures believed to be the closest
living relatives of the organisms that gave rise to the arthropods, including insects, have the
same eight homeobox (Hox) genes as insects themselves. This indicates that the diverse
body segments of insects did not evolve as a result of Hox gene duplication as previously
thought, but may instead have arisen as a result of changes in Hox gene regulation.
(Science 277, 639 1997). This is very exciting, because it offers many opportunities to
evolve by changing the regulation of the hox genes and not the number of these genes.
Note added in 1998: The 21 August issue of Science p. 1119 says that there are seven Hox
clusters in zebrafish on seven different chromosomes. There are two copies of Hoxa,
Hoxb and Hoxc with only one copy of Hoxd. The interpretation is that the whole fish
genome duplicated to give eight Hox clusters and one Hoxd cluster was lost.
In Mol Phylogenet Evol 9, 375-381 1998, Hox genes in the simplest known animal
Trichoplax adhaerens are discussed. At least 5 Hox genes in sea anemone were detected
by PCR Biol Bull 193, 62-76 1997.
Another homeobox gene in Drosophila is eyeless. This gene appears to be a master switch
gene that turns on eye formation(see Science 267, 1766-1767 and 1788-1792 1995). If
eyeless is expressed in tissues where it normally would not be active, whole functional
eyes form. These may be on the end of antenna, on the wings or on the legs. This gene
has homologs in mouse (small eye, Pax-6) and man (aniridia) that also affect the formation
of eyes. In fact, the mouse gene can substitute in Drosophila for the eyeless gene. This
means that eye formation is controlled by a gene that evolved before eyes evolved.
(invertebrates and vertebrates diverged 600 million years ago). The common ancestor
apparently had a light sensitive tissue that later evolved into different types of eyes in
insects and vertebrates. Eyeless controlled the development of that light sensitive tissue
and it has continued in that role for at least 600 million years.
A recently discovered gene called Manx is not a homeobox gene, but it is a zinc-finger
transcription factor and it is another candidate for a master switch gene. (see Science Nov.
15, 1996, p. 1205 and news section) The Manx gene is found in tunicates, a type of
primitive chordate. These organisms start life as a tadpole like creature with a tail and
notochord. During maturation, they lose their tail and become sessile on the sea bottom.
Manx is the gene that controls the tail formation. If it is mutated, the tail never forms.
This was demonstrated by William Jeffery and Billie J. Swalla, who found two closely
related tunicates, one with a tail and one without. They bred the two and the hybrid had a
small tail, suggesting that a single gene was responsible and one functional copy could turn
on the pathway. The gene was identified and its expression was blocked by antisense
RNA in the hybrid embryo. When this was done, the tail did not form. They are now
looking for homologs in more complex vertebrates. Manx is similar to eyeless, in that it
turns on a whole developmental program to form a tail. Of course the hunt is on to see
what gene might control Manx and which genes lie downstream of Manx to effect tail
development.
A second way to bring about macroevolution is polyploidy. Xenopus laevis has twice the
DNA of Xenopus tropicalis, by a genome duplication. This gives Xenopus laevis a lot of
DNA to experiment with and try out new functions for old duplicated genes. One
consequence of doubling the number of genes is an increase in size. Xenopus laevis is
much larger than Xenopus tropicalis, perhaps due to a gene dosage effect. As we
mentioned above, the fish seem to have undergone a genome duplication also. Plants are
often tetraploid or hexaploid, again giving evolution a lot of material to work with.
SOLVING THE MAMMALIAN RADIATION
The Oct. 97 Trends in Genetics has an article on mapping the cat genome. A genetic map of
the cat is being made along with other mammalian species, such as cattle and mouse.
When the maps are compared, there are regions that have the same order of genes in
different species. These regions are called syntenic regions. The regions are descended
from the mammalian ancestor without rearrangement caused by chromosome
translocations, breaks, fusions or inversions. Surprisingly, the whole X chromosome and
chromosome 11 seems to be retained intact in cats and humans, though chromosome 11
does seem to have an internal rearrangement in it. Between cats and humans there are 32
recognizable syntenic blocks. This number is about 200 for mouse and human and about
50 for cattle and humans, though the maps are not completed yet. By using these blocks to
compare genomes of the mammals, it will be possible to decide the evolutionary history of
mammals. This is not easily done using protein sequences because there was a rapid
evolution of mammals after the dinosaurs became extinct about 65 million years ago. This
has been called the mammalian radiation. This makes the percent differences between the
gene sequences very similar, so conventional trees do not work to make the determination.
The mapping of mammalian genomes to identify unique chromosomal breaks and
rearrangements do not suffer from this same problem, so the order of branching on the
mammalian tree should be firmly established by comparative genome mapping.
Comparative genomics was the subject of a major article and Genome Map X in the 1999 Science
genome issue (15 Oct.). This article carried forward the concept of comparative mapping to
decide the history of the mammalian radiation. The chromosome rearrangements are similar to
intron insertions or losses in that they are exceedingly rare events. Therefore thay can act
as evolutionary tags saying this only happened once. For example, the comparison of primates
suggests that all large scale differences between chromosomes can be explained by only 7
translocation events in the past 60 million years. Cats and humans have only 13 events that
can explain the differences in their chromosomes. One very significant event in human evolution
was the fusion of two ape chromosomes (12 and 13) to form human chromosome 2. All other great
apes have 24 sets of chromosomes and humans have 23. This is a defining event in our history.
(Genome, the autobiography of a species in 23 chapters Matt Ridley Harper Collins, New York,
1999 p. 24)
THE PLANT, ANIMAL, FUNGI TRICHOTOMY
The use of unique evolutionary events can resolve other difficult branchings on the tree of
life. One good example is the order of branching of plants, animals and fungi. Gene trees
based on single genes from these Kingdoms can support all 3 possible branch patterns.
However, EF-1alpha has a 12 amino acid insertion that is only seen in fungi and animals,
but not plants or protists. Proc. Natl. Acad. Sci. USA 90, 11558-11562 (1993). These
rare events can clarify evolutionary events in the history of life. In this case plants are
shown to branch before fungi and animals. This has been supported by other evidence.
MITOCHONDRIAL EVE
Mitochondrial DNA mutates at a rate that is about 17 times greater than nuclear DNA. This
is probably due to lack of effective repair mechanisms. Because this DNA changes so
rapidly, it can be used as a monitor of evolution on a time scale of a few hundred thousand
years rather than millions or billions of years. It is a fast molecular clock. In addition,
mitochondria are inherited maternally, so there is no genetic recombination to account for.
The line of descent is direct from mother to mother, because fathers do not contribute
mitochondria to the egg on fertilization. By comparing DNA from people from around the
world and especially in Africa, it is possible to build a tree showing the divergence of
human mtDNA over time. This tree can be rooted by using chimpanzee mitochondrial DNA as an
outgroup sequence, and the time of the last common ancestor can be estimated. This was
first done in 1987 (Nature 325, p. 31), but it was criticized for inadequate sampling of
populations and weak methods for making the tree. The process was repeated with DNA
sequence from 189 people (121 from Africa) using a hypervariable region of mitochondrial
DNA. (Science 253, 1503-1507 1991). The results were similar in both cases, though the
critics could not find as much to fault in the second paper.
The results were, that the 14 deepest branches on the tree were all of African origin. This
implies that modern humans evolved in Africa. The time of the last common ancestor of all
human mitochondrial DNA types is 166,000 to 249,000 years ago assuming that
chimpanzees and humans diverged from 4-6 million years ago.
A new study has completely sequenced 53 human mitochondrial genomes (Nature Dec 7, 2000) with
similar results but with better statistics.
One inference from this conclusion is that there was one woman whose mitochondria gave
rise to all present human mitochondrial genomes. This is the concept of a mitochondrial
Eve. This idea was immediately misunderstood to mean that there was only one woman
alive at this time. The result does not suggest that. Such a finding would create a
tremendous genetic bottleneck in human history. What the evidence does say is that the
present population of human mitochondrial DNA did have one founder mother. She was
the lucky one whose mitochondria have survived 200,000 years. All her contemporaries
have had their mtDNA lineages fizzle, by not having children, or not having female children
to be more specific. There could have been a large population of humans 200,000 years ago, in
fact the next thing we will discuss is exactly how big was this population.
The newest data comes from an Australian skeleton called Mungo Man 62000 years old. This DNA does not fit with any modern mtDNA, but matches best to a mtDNA insert on human chromosome 11.
It seems to be an extinct sequence with no modern relatives. This is causing some controversy.
PNAS 98 537-542 2001
POLYMORPHISMS AND THE SIZE OF HUMAN POPULATIONS.
Polymorphisms are fixed sequence differences in a population that make up more than 1%
of the population. The HLA locus in humans corresponds to the MHC locus in mice and
other vertebrates. This is a highly polymorphic region with about 100 genes. One of these
genes is the DRB1 gene. 59 alleles exist in humans and 60 non-human primate sequences
have been determined. A tree of these sequences gives an estimate of the time for a last
common ancestor of about 60 million years. (see Science 270, 1930-1936 1995) It is
important to point out here, that these 59 alleles are different sequence variants of the same
gene in humans. These do not represent different genes.
To carry that many polymorphisms in a population, the absolute minimum number of
individuals would be 30, one diploid person for every two alleles, and they would all have
to be heterozygotes, each with a different allele. This situation is very unlikely. Six
million years ago, there were 32 lineages of the DRB1 gene, with a minimum population to
carry this number of alleles being 16. Again the actual population would have to be much
greater than that. There is a theory dealing with polymorphisms and population size. This
is called coalescence theory. If the time of coalescence is known, and the number of genes
is known, then this theory will predict what the population size must be for this to happen.
The results of simulations show that for 60 alleles to persist for 1.7 million years (time of
humans as Homo sapiens) the population size would have to be about 100,000. If it was
less, many of the alleles would become lost over that many generations.
The numbers are not incompatible with a mitochondrial Eve hypothesis, because
mitochondrial Eve is only considering the inheritance of one small piece of DNA,
equivalent to a single gene. It must be true that a single woman of about 200,000 years ago
is the mother of all of our mitochondrial DNA, but it is not true that she is the mother of all
our other genes.
Y CHROMOSOME ADAM
Males do not have to be left out of this analysis. Portions of the Y chromosome are unique
to males and are inherited paternally. As long as a region of the Y chromosome is out of
the pseudoautosomal region, it cannot recombine with other alleles and so it is very
analogous to mitochondrial DNA, except it evolves at a much slower rate. To do these
same types of calculations with Y chromosome DNA, a 729bp fragment of the ZFY gene
has been sequenced from 38 men. There was no difference found. The numbers of
samples is too small yet, or perhaps a more variable region should be used, like an intron.
Even with no differences detected, the divergence of the ZFY gene between humans and
great apes can give a rate that is usable with coalescence theory. In this case the number of
alleles is two, one in humans and one in apes. The estimate for the time of the last human
common ancestor ZFY gene from these assumptions is 270,000 years (later estimates are
considerably younger).
It seems unreasonable that an estimate can be made when there were no differences found
in the 38 sequences. The project has been continued and in 1997 advances were
made in finding polymorphisms on the Y chromosome. At least 93 polymorphic sites
have now been identified in 900 men scanned (Science 278, 804-805 1997). One of these
is an A in non-human primates and a few African men. 15% of the Khoisan people have
A, 5-10% of Ethiopians and Sudanese have A. All peoples from outside Africa have T and
most Africans also have T. The interpretation is that this A-T mutation occurred very early
in human evolution after humans split from apes. The majority of living humans now have
the T allele. The Khoisan may be the closest living relatives to the Y chromosome Adam.
The interpretation is that humans evolved in Africa between 100,000 to 200,000 years ago.
The most recent data Dec. 7 2000 Nature gives an even younger age (about 59,000 years ago)
This fits with the mitochondrial Eve data. A second group of researchers found a similar
result in studying 1544 men (Mol Biol Evol 15, 427-41 1998). They found an A present in
chimpanzees and only a few Africans. Most modern humans have G at this site. The
Khosian people also had the highest frequency of the A polymorphism. They estimated an
African origin for humans between 150,000 and 200,000 years ago.
The newest data on Y chromosome Adam can be found in Nature Genetics 26, 358-61 2000. This
study looks at 160 polymorphic markers on 1062 men from around the world and concludes a more
recent origin for modern humans of about 59,000 years in Africa. A related study done on 1007
European men shows migration patterns in Europe over the last 40,000 years (Science Nov. 10,
news article 1080 research article on 1155, 2000).
HOW MANY GENES DOES IT TAKE TO MAKE A LIVING CELL?
The sequences of 72 genomes are now complete and many more are in progress.
Go to TIGR Genome Projects Page
Go to Magpie Genome Projects Page
Mycoplasma genitalium is the smallest known genome that is not a virus. It codes for 468
proteins, that have been called the minimal set for life. This is not strictly true, since there
are probably some genes in this set that are specific for M. genitalium and won't be found
in other unrelated genomes. Mushegian and Koonin compared the M. genitalium genome
with the H. influenza genome (1703 protein coding genes)to identify those genes common
to both.(see PNAS 93, 10268-10273 1996) These are gram positive and gram negative
organisms, so they diverged about 1.5 billion years ago. Any homologous genes are
probably essential. They found 240 genes. Some essential genes were missing, because
the same function in some pathways was performed by different non-orthologous genes in
the two organisms, so these missing genes had to be accounted for. That added back 22
genes. Then they looked for redundant functions and parasite specific genes, since both
organisms are parasites, and subtracted 6 more genes to get a total of 256 protein coding
genes as the minimal set. Later gene knockout experiments showed about 15% of these genes could
be knocked out of Mycoplasma genitalium and the cells survived, so the number is closer to 220
genes. (Koonin, How many genes can make a cell: The minimal-gene-set concept. Annu. Rev.
Genomics and Hum. Genet. 1, 99-116 2000).
The authors point out that parasites import metabolic intermediates, but they do not import
proteins, so the minimum number of genes illustrates what must be done after all possible
intermediates are imported from a rich environment.
A LINK TO A PAGE ON THE ORIGINS AND EVOLUTION OF THE PROTISTS