Phylogeny, speciation and extinction

A phylogenetic tree (or cladogram) is a hypothesis about how groups are related. The tips are groups; each branch point, or node, stands for the most recent common ancestor of every group beyond it. Two groups are more closely related the more recent the node they share. Turning branches around a node does not change the relationships, and a tree does not show one living species turning into another.

Trees are built from shared derived characters: traits that arose in an ancestor and are shared by its descendants. An outgroup, a group known to have branched off earlier, shows which traits are ancestral. Molecular data work the same way: the fewer differences two groups have in a DNA or protein sequence, the more recently they shared an ancestor. When the rate of change is fairly steady, the number of differences can estimate how long ago two groups split. New evidence can revise a tree.

Under the biological species concept, a species is a group whose members can interbreed in nature and produce fertile offspring. It cannot be used for fossils or for organisms that reproduce only asexually, so biologists also use body form and DNA.

A new species forms when reproductive isolation arises. Prezygotic barriers stop mating or fertilization: different habitats, different breeding times, different courtship, body parts that do not fit, or gametes that cannot fuse. Postzygotic barriers act after fertilization: hybrids die, are sterile, or their offspring fail.

In allopatric speciation, a physical barrier splits a population. With no gene flow, the two groups change apart by mutation, selection and drift. In sympatric speciation, a new species forms in the same area; in plants this often happens through polyploidy, an error that doubles the chromosome sets. Change can be slow and steady (gradualism) or come in short bursts between long quiet periods (punctuated equilibrium). One ancestor can give rise to many species that fill different roles, an adaptive radiation, often after a mass extinction frees up resources.

Extinction is the end of a lineage. Small populations, low genetic variation, a narrow range and slow reproduction all raise the risk, and fast environmental change raises extinction rates.

To build a tree from a trait table, count how many derived traits each group has. The trait shared by every group except the outgroup arose first and sits nearest the root. Each later trait marks a node that joins only the groups that have it. The groups that share the most derived traits branch from the most recent node.

To explain how one population becomes two species, give three links: something stops gene flow; the separated groups change differently; enough differences build up that they can no longer interbreed and produce fertile offspring.