Hello and welcome.
My name is Betül Kaçar.
Today we will be talking about phylogenetics
and how to make sense of phylogenetic trees.
Before we get started - what is a phylogenetic tree?
Consider these very different organisms:
a flower, bacteria, an elephant, a giraffe, an orange, a human being.
As different as they are...
what do all these species have in common?
They all contain DNA
and they share a genetic code that programs for the different types
and arrangements of molecules that make up their bodies.
Biologists have found a way to utilize this information
in order to understand the relationship between species.
As different as all of these organisms are,
and as varied as all of their genes may be,
all of Earth's known organisms
share a small group of genes that encode for molecules
that have the same basic functions in each of their cells.
These genes are critical for cell replication,
meaning that the cells cannot persist without these molecules.
So, it is important that the sequences remain functional.
As a result, these genes tend to have
similar but not identical sequences across different organisms.
Scientists can compare how similar or how different
these similar sequences are to create an ancestral tree
that demonstrates whether organisms are more or less related to one another.
This is what is referred to as a "phylogenetic tree."
Phylogenetic trees are hypotheses - they are not definitive facts.
The branching pattern in the phylogenetic tree
illustrates how organisms are evolved from a list of common ancestors.
If organisms are located near one another on the tree,
it is very likely that those organisms are more closely related to one another
or that they inherited those genes from a similar ancestor.
In a very broad sense,
a phylogenetic tree that surveys relatedness
across many diverse groups of organisms
may be thought of as a tree of life - a map that indicates
how every single organism might be related to one another
going back billions of years to the first ancestors of all life on Earth.
But, just because the origin of this tree goes back billions of years,
it doesn't means that we have all the information that is needed
to solve difficult problems regarding life's origins and evolution.
Organisms that leave recognizable fossils
are most from a group called the "eukaryotes."
And, while millions of the these organisms have been genetically cataloged,
over 99 percent of all species that have ever lived on our planet
are estimated to have gone extinct -
meaning that our ability to extrapolate backwards into the past is quite limited.
The limitations of sampling in our available genetic and fossil records
severely limits our ability to make inferences
about past relationships of organisms,
and genes... and genomes to one another.
Nevertheless, the high degrees of sequence similarities
across similar genes found in all organisms
gives us ways in which we can reconstruct the sequences
that were likely found in our ancestors.
Let's take down to another level a simple example of a phylogenetic tree.
The specific branching pattern indicates the degree to which
current genes may resemble genes that were found
in the common ancestors' shared evolutionary history.
The genes that we can study in extant organisms
are located near the ends of the branches and are called "leaves" or "tips."
These are connected with branches back to internal nodes
that represent the likely states of shared ancestors.
The oldest node may be referred to as a "root" of the tree.
We can step sequentially backwards
through the different nodes to investigate
what sequences or attributes have been inherited from ancestors
or to estimate the timing for the emergence
of newly evolved sequences or attributes.
From this, we can begin to develop and investigate more specific questions
about the relatedness of specific groups of organisms
or to estimate how ancestral traits may have been modified
to yield the traits of certain organisms today.
In examining even a simple tree,
there are many possible combinations of sequence changes along the branches
that would fit the observed distribution of sequences in existing organisms.
But, generally speaking,
in the lack of compelling evidence to the contrary,
the simplest ways of gaining and losing attributes -
such as requiring the fewest number of genes, losses, additions -
that with the tree will probably be the most accurate.
The steps that we use in this process are straightforward.
First - sequences of the same genes from different organisms are collected.
Next - these genes are aligned
so that the key functional portions of each gene
match up in the same column with one another.
And, keep in mind that we can do this process for genomes as well.
With more advanced programs,
you can do this with multiple genes at once
to get a more complete picture of how organisms might be related.
Finally - trees are constructed using these genes.
There are usually many different tree shapes
or topologies that are possible using the same data set.
So, different analyses are run to see
which topologies require the fewest assumptions,
or which best match up with the fossil record.
It is only after a rigorous analysis of many different possible trees
that phylogenies can be prudently interpreted
and applied to evolutionary questions.
Though we have only run through a quick survey
of how to construct phylogenetic trees, there are many different applications
beyond just comparing the relatedness of organisms to one another.
These applications look at many different levels of biology,
from whole populations down to individual proteins
and how they change over time.
Perhaps the most fundamental contribution to origins studies
was the discovery that all organisms on Earth
fall into one of three major groups -
bacteria, archaea and eukaryotes.
Before this magnificent discovery by Carl Woese and George Fox in 1977,
organisms were classified into groupings - mostly based on morphology.
And, there was almost no definitive way
to distinguish archaea from bacteria at all
since they are both predominantly small and single-celled.
This fundamental view has helped to organize a focus
on the attributes and timing of the last universal common ancestor -
or LUCA -
and has opened new questions concerning the extent to which
LUCA's emergence may actually be pretty far removed from life's origins.
Based on the attributes of all of its descendants,
it seems clear that LUCA was already a very sophisticated organism
and many open questions remain as to what must have been
an extensive pre-LUCA history of emergence and evolutionary innovation.
This has been a quick survey of phylogenetics.
For more details, these papers will serve as a good starting point
for further reading into many of the topics we've covered.
And, thank you for your time.