Introduction to Phylogenetics part 2

From the Stearns and Hoekstra book Evolution 2nd edition, chapter 13 Phylogenetics and systemantics

Phylogeny refers to the history and relations of organisms.

From the Greek phyl- meaning tribe and gen- origin or descent.

The goal of phylogeny is to map the relationships of all organisms that we have evidence to have existed.

The phylogenetic tree has three main branches: Bacteria, Archaea, and Eukaryota

Bacteria: single-celled or noncellular spherical or spiral or rod-shaped organisms lacking chlorophyll that reproduce by fission; important as pathogens and for biochemical properties; taxonomy is difficult; often considered to be plants Ref: Princeton

Archaea: Single-celled organisms similar to bacteria as they do not have their genetic material enclosed within a nucleus. Archaea are prokaryotic but genetically similar to eukaryotes so are placed in a separate kingdom 'the archaea'. Ref: Australian Academy of Science

Eukaryota: The domain comprised of eukaryotes or organisms whose cells contain a true nucleus. Ref: Biology Online

Any complete branch of the phylogenetic tree is called a clade. A group of organisms that share a recent common ancestor.

At the largest scale the phylogenetic tree is dominated by bacteria and the phylogenetic tree spans 3.7 billion years. From mitochondrial eve to present day organisms.

Figure 1: From Darwin's Origin of Species (1859) The lowest ancestors A, B, C, D, E and descendants. Only A and E have descendants that reach the time of study.

Figure 2: From Evolution 2nd edition. A more complete phylogenetic tree.

It should be noted that the ability for Eukaryotes gained the ability to use chlorophyll and breathe comes from a symbiotic relationship with Bacteria.

The vast majority of the phylogenetic tree is dedicated to single cell organisms

There are three main types of multicellular organisms: Plants, Fungi, and Animals. They share a common ancestor approximately .8-1 billion years ago.

Figure 3: The phylogenetic tree for multicellular organisms from about 800 million years ago to present day. Source Evolution 2nd edition

Phylogenetic relationships are not obvious, they must be discovered. Related organisms are similar in important ways and the more distantly related organisms are different in other important ways.

Early biologists could only use morphological data to determine how organisms are related but now biologists can use molecular traits to quickly identify relationships through DNA inheritance. Using DNA can specify relationships back in time allowing for correct ancestor relationships.

Some modern phylogenetic relationships are surprising, such as the fact that the closest relative to a whale is a hippopotamus. Since whales are highly adapted to life in water using morphological data is difficult to classify them in relation to land animals so molecular data must be used.


Figure 4: some of the surprising relationships illuminated by modern phylogenetics. Source Evolution 2nd edition.

Another surprise is that giant pandas and lesser pandas are not closely related. The giant panda is related to bears and the lesser panda is related to weasels and raccoons.

Monophyletic groups are a group where the most recent common ancestor is not the ancestor of any other group. The dog clade is an example of a monophyletic group.

A paraphyletic group is an unnatural group that does not include all the descendants of the most recent common ancestor. Lizards are a good examle, since the lizard group does not include birds or mammals that also descend from the most recent common ancestor.

A polyphyletic group is one that descends from a number of ancestors. Worms are a good example of a polyphyletic group as the different species (flat worms, earth worms) descend from different ancestors.

Figure 5: An example of a monophyletic group versus a paraphyletic group, source Evolution 2nd edition

Adaptive convergence is where differing species adapt to similar conditions gaining similar morphological traits, such as a dolphin and a tuna having similar slimline shapes in order to swim faster than a non-slimline shape without having a recent common ancestor. Adaptive convergence can confuse phylogenetic taxonomy when species are grouped by morphological data.

Divergence is the opposite of convergence, it is when a species adapts in a new way to a new or changing environment in a different way to close relatives. This is the cause of speciation, but it can also confuse phylogenetic taxonomy as some species have wildly divergent morphology while still being the same species.

Taken together convergence and divergence can really confuse the attempt to build a phylogenetic tree as shared traits (morphological and molecular) must be traced to a common ancestor.

To be continued in part 3