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• Phylogenetics: the art of reconstruction of Lifeís History, and of building the 'Tree of Life'
• Homology
• Convergence

Drawing the Tree of Life:

• Pre-Darwinian: ascending complexity, Scala Naturae 'from amoeba to man'
• Post-Darwinian: tree of life represents ancestor-descendent relationships

Phylogenetic Systematics: reconstruction of the true tree of life, relationships between all organisms.We concentrate on Eukaryote animals.

How are phylogenies (tree of lives), or cladograms (plots of ancestor-descendant relationships) constructed?

Use characters of organisms. Example: many Phyla of animals share that their bodies are made up of three layers of cells (triploblastic), bilateral symmetry; most common exceptions: Sponges (Porifera) and Cnidaria (corals, jellyfish). These triploblastic, bilaterally symmetrical animals are divided into protostomates (which in their turn are divided into Ecdysozoa and Lophotrochozoa), and deuterostomates, using a character in their embryological development (see lecture 3).

Characters used to subdivide animals:

• Morphology (Embryological development, Fossil Record)
• Physiology
• Behavior
• Molecular evidence (include. Protein and DNA structure)

There are various different ways to characterize animals; in phylogeny one must select characters important to evolutionary relationships

What gives a character phylogenetic significance? It must reflect common ancestry, not adaptation to a similar mode of life or habitat.

Example:

A figure like that shown above (a cladogram) represents relationships:

1. organisms sharing a branching point are more closely related to each other than to any other organisms shown in the plot
2. all organisms share a common ancestor

Whales, baboons, gorilla and humans are shown to be more closely related to each other than to anyone else. Shared characters: warm blooded, have hair, suckle young (mammalian characters). IF we look at body shape only, whales would plot with sharks and skates. If whales were more closely related to sharks/skates than to mammals, all mammalian characters (listed above) would have evolved twice, independently: in whales, and in other mammals. It is more parsimonious (simpler) to assume that such specific and complex characters evolved once only and that body shape does not indicate relationships.

In order to choose characters reflecting relationships we must separate analogy and homology, as first defined by Sir Richard Owen (1843, i.e., pre Darwin).

• Homology: the same organ in different organisms under every variety of form and function is said to be homologous. Classic example: fore limbs in vertebrates, such as arms in human, wings in bats, birds, pterosaurs are homologous, made up of the same bones (one upper bone, two lower bones, small wrists bones, digits of fingers), inherited from common ancestor. Wings are constructed differently in each group: birds use feathers, have 3 fingers grown together; bats have long finger bones in membrane, pterosaurs have 1 finger bone in membrane. Arm bones from common ancestor, but ancestor did not have wings: these developed in a different pattern in each group, independently.
• Analogy: a part of organ in one animal which has the same function as another part or organ in a different animal.

Owen was no evolutionist; he thought each group of organisms was shaped according to an 'archetype' (made by creator). The word archetype can be replaced by the word ancestor to make sense in evolution.

Difficulties: in many cases difficult to decide whether something is homologous or analogous. Great similarities in shape may not reflect common ancestry. Example: placental and marsupial mammals, separated more than 85 million year ago (Ma); common ancestor was small, rodent-like looking animal (mouse-rat sized). Placental and marsupial wolves, placental and marsupial mice, placental and marsupial moles resemble each other in shape, but are not closely related. This similarity is due to convergence.

Flamingo has feathers as all birds do. A character shared by all organisms in a group (feathers in  birds, hair in mammals) is called ëprimitiveí, i.e., inherited from common ancestor. What defines a flamingo as different from all other birds?

Its large beak, used for filtering micro-organisms from salty waters while holding head upside down. Has lamellae through which water is pumped.

Analog of beak: mouth of baleen whales, which also filter micro-organisms from water. Not homolog, and evolved separately in birds and mammals.

• Where do flamingos fit within birds? Mostly grouped with either Ciconiiformes (storks, herons, ibises) or with Ansiformes (ducks, geese, swans). Flamingoes share with Ciconiiformes overall body plan (long legs, necks), with Ansiformes bill for filter feeding (although different structured), webbed feet, embryological similarity, similarity of its parasites, honking sound.
• Which characters are primitive, which derived within group?

New data from molecular information: DNA-DNA hybridization.

• Double strand DNA on heating melts into single strands, on cooling two strands combine again (anneal). Add flamingo DNA to DNA from duck-group and stork-group. The better the match between the base pairs in the two different types of DNA, the higher the melting point and annealing point. The higher the melting point, the closer related the organisms are. The more different the DNA, the longer ago did the ancestors of the two organisms evolve separately.
• Method places flamingoes with storks.
• Assumption: rate of change in base pairs of DNA is fixed over time in all groups considered.

Are molecules always right? Maybe molecular convergence is possible. Appears to be so in case of cytochrome C, involved in respiration. Analysis of cytochrome C places Echinoderms (deuterostomes) in one group with worms (Annelida) and Molluscs, which are both protostomes.

People: DNA-DNA hybridization places humans much closer to chimpanzees than either of them is to the other apeas (humans ? chimpanzees ~99% identical, as close as sister species of fruit flies). Note that molecular rates of changes thus differ from morphological rates of change: chimps resemble other apes more in morphology than they resemble humans.