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L04v03_-_2015
[00:00:00.00]
[00:00:01.32] PROFESSOR: Hi. In this video, we'll touch on a few basics of evolution. This
video is a little longer than the rest, but there's a lot of great stuff at the end, so I hope you can
stick through it. We'll talk about the mechanism of evolution, that some sort of variation exists,
that the variation is heritable, and that organisms with the variation have differential success at
reproduction, which is at the heart of natural selection.
[00:00:25.76] We'll discuss how evolutionary relationships can be deduced from DNA sequence,
in addition to the better known fossil record. And then we'll end with a few facts about human
evolution. The fact that primates diverged from other mammals about 65 million years ago. That
humans diverged from other apes around 7 or 8 million years ago. And that modern behavioral
all humans appeared about 60,000 years ago.
[00:00:52.57] To put things in the big perspective, Earth formed maybe about 5 billion years ago.
And somewhere around 3.6 billion years ago, the first living cells occurred. The first milestone
after that was the development of photosynthetic cells.
[00:01:08.06] Now, cells can create molecules from sunlight and carbon dioxide. Whereas
before, they had to scavenge them from the environment. At this time, the earth has a heavily
reducing atmosphere with a lot of energy-rich molecules present.
[00:01:23.59] But the photosynthetic cells developed the ability to split water, releasing oxygen.
After about a billion years, oxygen starts to accumulate in the environment. Up until this time,
the oxygen that had been produced was absorbed by the environment.
[00:01:39.99] As oxygen accumulates, respiration starts to be a viable strategy. It becomes
prevalent. And eukaryotes appear approximately 1.6 billion years ago, multicellular organisms
about 800,000 years ago, and primates about 65 million years ago. So we are very recent history.
[00:02:01.75] And this is what 3.6 billion years of evolution has produced. Prokaryotes, the
bacteria and the archaea, and the eukaryotes. This common ancestor cell was the cell that
appeared about 3.6 billion years ago. And the distances here are related to evolutionary times.
[00:02:20.27] Notice how close plants, humans, and single-celled baker's yeast are in this tree of
life, compared to bacteria such as E. coli. It's really remarkable to think about how three such
very different forms of life are very closely related in evolutionary terms. On this slide, I just
wanted to highlight one of the big differences between prokaryotes, the bacteria, and archaea
bacteria, from eukaryotes.
[00:02:49.70] And that's the presence of a nucleus, in which the genetic material is held. There
are many other differences between them, and we'll discuss those in future lectures. In this slide,
we see the mechanism of evolution. There is variation that exists in the beetles.
[00:03:07.21] In this case, it's the color of the beetles. The implication is that the color difference
is based on genetic difference. That doesn't always have to be the case, but that's the assumption
here. And then, here's the example of a predator, which has a preference for green beetles,
meaning that the brown beetles are able to reproduce more effectively.
[00:03:28.60] When they do reproduce, they inherit the genes that are responsible for the brown
color. And over time, you have an evolutionary result that the green beetles have become extinct,
at least in this local environment. A couple of points.
[00:03:44.22] The genetic variation or the mutations that originally produced the color changes
are random. We don't genetically vary towards a particular end. However, natural selection is the
result of the environmental pressure, which in this case is the predator, and so that is directed.
Therefore, certain traits become more dominant in a population, and the genes that are
responsible for those traits become present in increased amounts over time.
[00:04:15.50] One thing that we can discuss more in class is the concept of fitness for modern
humans. Fitness is really only reproductive success. It's not how successful one is at business,
life, or creativity. It's just the number of offspring you have. Later on, when we talk about
genetic engineering, we'll also consider why you as an engineer might be able to evolve humans
who are far superior to that produced by nature, that are not well adapted to our current
environment, because the changes in our environment have occurred so rapidly, recently.
[00:04:49.74] The last 200 years, we have seen tremendous changes, which we have not been
able to yet genetically adapt. For instance, even 100 years ago, a broken bone could easily lead to
death. That, fortunately, does not happen much anymore.
[00:05:05.82] Here are a number of ways in which changes in DNA can lead to evolution.
Mutations producing changes in amino acids or proteins are perhaps the most obvious. I would
like to highlight here the instance of gene duplications in which one copy of a gene is duplicated
into two copies. This gives evolution the opportunity to be creative in terms of developing
modified functions for the two genes. Please recall this, as we have a slide at the end of the
lecture that's going to talk about how gene duplication leads to evolution.
[00:05:41.57] As to the heritability of genetic variation, this slide makes the point that only
mutations that occur in the germ line cells, the sperm and eggs, get passed on to your offspring
and are relevant for evolution. Mutations might occur in your somatic cells, which is all the rest
of your body. And those can affect you, and have quite negative consequences. But they will not
affect your offspring directly. But they may affect your offspring indirectly, such as you not
being around to teach them or support for them.
[00:06:11.46] Most evolutionary relationships are indicated by phylogenetic trees. And we'll
describe a little bit how those trees are constructed. However, the point I want to make on this
slide is that the degree of sequence relatedness is proportional to the time that has elapsed since
divergence. So our closest genetic relatives are chimpanzees, and the gorillas are next.
[00:06:33.36] So we'll have slightly more numbers of DNA differences with gorillas than we
have with chimps. There are two types of chimps, but they split off after the last common
ancestor occurred. So all chimps and bonobos have roughly the same genetic similarity to
humans.
[00:06:53.51] Here we've just been talking about a small branch of primates. At the bottom here,
we show again, we see those three big kingdoms of the tree of life. Eukaryotes, archaea, and
bacteria. There are sequence similarities between humans and Methanococcus, and humans and
E. coli. So these sequence similarities have persisted over 3.6 billion years ago, which is a much
richer record of evolution than the fossil record.
[00:07:24.94] This is an example of a phylogenetic tree based on sequence differences in the
protein, cytochrome c oxidase. And here you can see that the differences in sequence between
humans and another mammal, pig, a bird, a reptile, and a cartilaginous fish, an insect, and a
single-cell organism, generally reproduce what you would expect, based on your intuition about
evolution. But this tree is created solely by sequence differences.
[00:07:57.12] Now, before DNA was around, and people could compare the sequence
differences, people constructed these evolutionary relationships based on shared anatomical
characteristics. This example highlights the anatomical features that are shared in common that
relates different species. For instance, having forelimbs relates amphibians, primates, and
rodents, and so on.
[00:08:23.99] Some interesting cases arise when the classifications done by DNA sequence and
the classification done by anatomical features do not agree. While I'm no expert in evolution, my
gut tells me to go with the relationships deduced by sequence relationships rather than the
anatomical relationship. On this slide, we wish to explain a little bit more about phylogenetic
trees.
[00:08:50.97] Here there are four different types of species that are present in current time. In the
past, there's a distant ancestor for all four of these species. At each node, there's a speciation
event. And we see here that species B has a unique period. And that species B and C share a
history going back to the very beginning. And we can define unique ancestors of various species,
and common ancestors, which are not specifically related to either of the two species that
emerged from this ancestor, but it's sort of an average.
[00:09:27.60] Now, for evolution, not all DNA sequence changes are equally informative. And
that's because some changes are neutral or don't lead to differential reproductive success. And
some have had a big impact, based on the selective pressures exerted on the changed proteins.
[00:09:45.11] Here we can see a portion of a gene, the cystic fibrosis gene, and that there is a
great deal of evolutionarily relationship amongst mammals. And for birds and fish, there's only a
small portion is conserved to any great amount, as indicated by the green lines. We can see that
the positions that have been conserved are the exon regions, those regions that code for the
protein.
[00:10:09.50] These stay more related, because there's more important function based upon those
sequences, where there is less selective pressure on the intron sequences. You can change most
of those sequences readily, without deleterious consequences for function, most of the time. Now
here we see the evolution of mammals. The last common ancestor of all mammals is several
hundred million years ago.
[00:10:39.01] The last common ancestor between mice and humans occurred around 100 million
years ago. Primates diverged from the other mammals about 65 million years ago. At the time,
dinosaurs became extinct due to the impact of the meteorite off the Yucatan Peninsula in
Mexico. Rats and mice appear more evolved in this depiction. That's because there have been a
greater number of generations following the speciation events that have occurred in the past.
[00:11:11.13] When we talk about sequence relationships between the genomes of organisms, it's
not just the sequences within genes, but larger chunks of chromosomes. Here you can see
relationships over a large genetic region between human and mice. And what's varying here
mostly, is the intervening space of junk DNA, or introns, or intergenic regions.
[00:11:34.50] If you took the human set of chromosomes and chopped it up into about 200
pieces, you could do a good job of assembling mouse chromosomes. So the genomes are very
related, not only at the sequence level or at the gene level, but at the chromosomal organizational
level as well. Here we see some details of primate evolution at 65 million years ago.
[00:11:57.99] Prosimians, which I believe lemurs are an example, were the first to break off from
the common ancestor, about 55 million years ago. Old world monkeys in Africa and new world
monkeys in the Americas break off around 45 million years ago. And then lesser apes diverge
around 25 million years ago, leaving the great apes, orangutans, humans, chimpanzees, and
gorillas.
[00:12:23.21] On this slide, the gorillas diverged about 10 million years ago. And the chimps,
well, according to the picture, it looks about 4 or 5 million years ago. But it's generally more
accepted to be 7 or 8 million years ago when we diverged from the chimps, our closest genetic
relatives.
[00:12:40.97] In the human line, there are many different species, of which here there are a few
examples of four skull structures. Neanderthals existed over a million years ago, but probably
only became extinct about 40,000 years ago. And it's speculated that some Neanderthal genes are
mixed in with Homo sapien genes. Modern anatomical humans, based on the shape of the skull,
which we can recognize as similar to our own, appear about 200,000 years ago.
[00:13:11.85] But as has been described, that even 100,000 years ago, we're still basically
nothing more than smart monkeys. Our brain is about four times bigger than monkeys, and we
have about four times more intelligence, but we are not fundamentally behaviorally different.
Sometime around 60,000 years ago, we made what's referred to as the Great Leap Forward. All
of a sudden, you see lots of behavioral changes, and now we are definitely something different
than smart monkeys.
[00:13:42.70] Changes include finer tool making, religious practices, respect for ancestors, even
leading to artwork, maybe 40,000 years ago. So the question, what changed so suddenly? We are
very different, but it can't be due to lots of genetic changes, because the rate of evolution did not
all of a sudden speed up that dramatically.
[00:14:04.09] Not that many genetic changes could have occurred in the 40,000 years between
100,000 years ago and 60,000 years ago, for humans to change so significantly. It's thought that
perhaps the biggest evolutionary drivers were a few genetic changes in the larynx and the vocal
cords, so that we could develop sophisticated language. This enables us to communicate with
other members of our species. It allows for the accumulation of knowledge and wisdom, and the
ability to organize groups into specialized labor.
[00:14:34.02] Then, more recently, we have the development of agriculture, about 10,000 years
ago. And the appearance of civilizations about 3,000 years ago. If you're interested in evolution
in general, on the very first page, I linked to an awesome website about evolution.
[00:14:47.53] If you're interested in the relationship between man and apes, I would recommend
the book, The Third Chimpanzee, by Jared Diamond. Or if you're interested in more recent
human history, I recommend Guns, Germs, and Steel, also by Jared Diamond, a fascinating
account about the development of humans and modern civilization. Of course, whole courses are
given on the topic of evolution, but we only have a short amount of time to devote to the basics.
Which again, is genetic variation exists, it can be inherited, and there's differential reproductive
success of the variation.
[00:15:21.81] Now to conclude this discussion on evolution, we have to think back to slide six,
where we first talked about the instance of gene duplication. This slide will explain why gene
duplication is so important for the development of evolved new function. Let's consider the
ancestral globin gene right here.
[00:15:42.39] Globins are genes that carry oxygen in the cells. When there's only a single copy
of the globin gene, it needs to be a jack of all trades. It needs to be able to carry oxygen
reasonably well over a wide variety of conditions. Once you have a gene duplication event, now
you have two copies of the gene, and they can start to specialize.
[00:16:03.55] Now you can have one copy of the gene, perhaps the alpha, that can be optimized
for carrying oxygen at low oxygen abundances, and perhaps the beta would be optimized for
high oxygen tensions. A graph should help. Here we graph oxygen tension. The word tension
basically means, how much oxygen is available in the immediate environment.
[00:16:25.43] On the y-axis we'll plot how well the protein will bind the oxygen. The original
gene, the ancestral gene, has its function as sort of an average. And then when you have a gene
duplication event, initially, the duplicated gene has the same profile. But then the two copies can
evolve differently.
[00:16:44.30] The alpha might evolve for functioning at lower oxygen tensions, and the beta
form could evolve to function at higher oxygen tensions. So from an average oxygen carrying
protein, you can now have specialization. New functional capabilities in terms of transporting
oxygen within cells and organisms. This is a theme we'll see over and over again.
[00:17:05.35] If you think about light sensing pigments, we have rods and cones. This is clearly
the result of multiple gene duplication events, where one protein is good for seeing in black and
white, and then we started developing color vision. Nearly all proteins based on similar sequence
which we're allowed to evolve over time develop new functional capabilities after being
duplicated. OK, please make sure you're familiar with the important concepts we've covered
today. Thanks for listening.