Phylogeny and the Tree of Life


Hey it’s Professor Dave, I wanna tell you
about the tree of life. By now we know a lot about natural selection
and the ways that populations of organisms can change dramatically over long periods
of time, just like slow geological processes that create mountains and canyons. Over the half-billion years since the Cambrian
explosion, an unbelievable array of organisms has come to be, most of which are gone, but
plenty of which are still here. We can explore the world and find strange
creatures in the jungle and at the bottom of the ocean, and we can look at fossils to
see what once was. So how do we keep track of all these different
kinds of life? Which creatures are more closely related,
and which are more distant? To stay organized, we use something called
the tree of life. We can think of the trunk of this tree as
the unicellular common ancestor of every living thing in history. Of course this is long extinct, but it produced
other organisms, which are represented by different branches, and these in turn produced
other organisms, and so on, until millions of years later, here we are, along with whales
and birds and porcupines and bears. The process by which one species produces
a new species is called speciation, and this is the bridge between microevolution, which
looks at changes in allele frequencies, and macroevolution, which is a broad pattern that
produces new organisms that look totally different from pre-existing ones. We have a way of classifying an organism that
tells us exactly how it is related to everything else, how recently or distantly, and every
organism belongs to a particular species. These are groups of populations that have
sufficiently similar genetic material such that they are capable of breeding to generate
viable, fertile offspring. If two organisms can do this, they are of
the same species. If not, they aren’t. But before we start with the trunk of the
tree of life, let’s quickly recall exactly what happened in the early history of life
on earth. We’ve already talked about the origin of
life, but let’s review a few points to put things in perspective. From the famous Miller-Urey experiment we
saw how conditions on the early earth, just after it cooled enough for liquid water to
exist, were such that amino acids and nitrogenous bases could form spontaneously. These were able to polymerize to form long
chains, and when some of these were by chance encapsulated in a self-generating membrane,
like the way soap micelles form, the first proto-cell was born. Once nucleic acids became self-replicating,
the concept of inheritance took hold. We also discussed how multicellular life arose
from unicellular life, which resulted in an even greater variety of organisms. This is admittedly a speculative series of
events, and one could go into much greater detail on any individual step, but it is rooted
in firm science and testable hypotheses, so let’s move to the time period where an extensive
fossil record begins. We can look at fossils to learn about living
organisms that existed at any point over the past several billion years, which gives us
incredible insight into the history of the earth. We divide this history into different eons,
beginning with the Hadean eon, where the earth was still a hot ball of molten rock. In the Archaean eon, prokaryotic life arose,
living alone for a billion and a half years. This is when the earth became covered in oxygen,
as the product of photosynthesis. In the Proterozoic eon, eukaryotic life evolved
through endosymbiosis, and eventually multicellular eukaryotic life, through cell specialization. This eon ends with the Cambrian explosion. And lastly, the Phanerozoic eon starts a little
after animals show up on the scene, and is divided into the Paleozoic, Mesozoic, and
Cenozoic eras. This whole eon is around half a billion years
long, starting just before animals make it onto dry land. Dinosaurs dominate the Mesozoic era, and humans
show up only in the last sliver of the Cenozoic era. The boundaries between these eras and eons
mark huge extinction events that can be seen in the fossil record, and we continue to examine
fossils to learn about life from all periods of biological history. Now that we are up to speed with the history
of life, we want to know about the phylogeny of various species. This is their evolutionary history, or ancestry,
and the discipline of taxonomy is what we use to classify every species in the context
of its ancestry. For greater context, we look at the tree of
life. This tree has many branches, where different
species evolved from a common ancestor. The more recently two species converge as
you go down, the more recent their common history, and the more closely related they
are. As you continue to go down the tree, species
become less and less related, so humans and chimpanzees, whose branches are very close
to one another, diverged from a common ancestor only a couple million years ago, whereas humans
and jellyfish are much more distantly related, having diverged hundreds of millions of years
ago, when all life was in the sea. If we get all the way to the bottom, the trunk
of this tree marks the beginning of life on earth, a single-celled organism that everything
alive today is descended from. Since we don’t know precisely what that
was, we start with what we know, and at the most basic level, we consider three domains
of life. These are bacteria, archaea, and eukarya. Bacteria and archaea are the unicellular prokaryotes
we talked about, and eukarya is all eukaryotes. This means unicellular protists as well as
all multicellular life on earth, including every plant and animal there is. Within the domain eukarya, there are several
kingdoms. Animalia contains all animals, plantae contains
all plants, fungi contains all mushrooms and molds, and protista contains all the rest,
though many biologists don’t recognize this as a valid kingdom any longer. Within each kingdom there are several phyla. Within the animal kingdom there are nine major
ones. There is the phylum arthropoda, which contains
all kinds of bugs and lobsters and creepy crawlies, mollusca, which contains octopi
and snails and other such things, and most notably there is chordata. This phylum includes any animal with a spinal
cord, and the divergence of vertebrates and invertebrates was a major step in evolution. Within each phylum we can find different classes
of organisms. Chordata contains the class reptilia, which
are reptiles like crocs and snakes and lizards; amphibia, which are amphibians like toads
and frogs; and mammalia, which are all the mammals, from kangaroos to elephants. Humans belong to mammalia, and within this
class there a number of orders. The order cetacea contains all the whales
and dolphins. Carnivora contains things like bears and weasels. Then there are the primates. That’s got everything from orangutans to
lemurs, and humans are in there too. Within the order of primates, there are several
families. The family hominidae contains all the great
apes, so that’s us again. Within hominidae every organism belongs to
a particular genus, and that’s where we diverge from the apes. Our genus is called homo, which means man
in latin. Within a genus there are several species,
and all the species within the genus homo are now extinct except for homo sapiens, and
that’s us. The species that came before us, homo erectus,
homo habilis, and many others, are all gone, and homo sapiens, which means wise man, sits
at the very top of the tree, the only species to have evolved an intelligence that spawned
complex civilizations and information storage, first as written language and eventually the
omnipresent internet, which you’re using right now. So every species can be classified, and there
are mnemonic devices that can help us remember the different tiers of categorization. Do kangaroos prefer cake or frosting, generally
speaking? Or, did King Phillip come over from great
Spain? You can even make up your own. To review, we humans are collectively the
species homo sapiens. We belong to the genus homo, the family hominidae,
the order primates, the class mammalia, the phylum chordata, the kingdom animalia, and
the domain eukarya. We can trace a path from the tip of our branch
all the way to the trunk, and every organism on earth will converge with our path at some
point, whether very recent, or very distant, which means that every living thing is related
in some way. To see precisely how related two species are,
we could use sophisticated techniques like ribosomal RNA sequencing, or we can simply
examine homologies. These are similarities between organisms,
be they genotypic or phenotypic, and they typically suggest common ancestry, as an organism’s
evolutionary history is documented in its genome. But to get into these details for specific
animals, we will have to wait until the zoology course, and a discussion of everything that’s
inside a human will have to wait for the anatomy and physiology course, both of which will
come in the future. For now, let’s move forward and wrap things
up with a quick survey of biotechnology, so we can see what humans have been able to do
with all of this powerful biological knowledge.

22 Comments

Add a Comment

Your email address will not be published. Required fields are marked *