The pag below is from http://evolution.berkeley.edu/evolibrary/article/0_0_0/evo_05
Understanding a phylogeny is a lot like reading a family tree.
The root of the tree represents the ancestral lineage, and the tips of the branches represent the descendants of that ancestor.
As you move from the root to the tips, you are moving forward in time.
When a lineage splits (speciation), it is represented as branching on a phylogeny.
When a speciation event occurs, a single ancestral lineage gives rise to two or more daughter lineages.
Phylogenies trace patterns of shared ancestry between lineages.
Each lineage has a part of its history that is unique to it alone and parts that are shared with other lineages.
Similarly, each lineage has ancestors that are unique to that lineage and ancestors that are shared with other lineages — common ancestors.
A clade is a grouping that includes a common ancestor and all the descendants (living and extinct) of that ancestor.
Using a phylogeny, it is easy to tell if a group of lineages forms a clade.
Imagine clipping a single branch off the phylogeny — all of the organisms on that pruned branch make up a clade.
Clades are nested within one another — they form a nested hierarchy. A clade may include many thousands of species or just a few.
Some examples of clades at different levels are marked on the phylogenies below. Notice how clades are nested within larger clades.
So far, we’ve said that the tips of a phylogeny represent descendant lineages. Depending on how many branches of the tree you are including however, the descendants at the tips might be different populations of a species, different species, or different clades, each composed of many species.
Are there higher or lower forms of life?
Several times in the past, biologists have committed themselves to the erroneous idea that life can be organized on a ladder of lower to higher organisms. This idea lies at the heart of Aristotle’s Great Chain of Being.
Here is the 1579 drawing of the Great Chain of Being from the Franciscan missionary Didacus Valades, titled Rhetorica Christiana.
Here is another artist’s conception of the great chain (with English translation)
Similarly, it’s easy to misinterpret phylogenies as implying that some organisms are more “advanced” than others.
Here’s a phylogeny showing the relationship of mosses to other land plants. In this simplified phylogeny, a speciation event occurred resulting in two lineages.
One led to the mosses of today; the other led to the fern, pine, and rose.
Since that speciation event, both lineages have had an equal amount of time to evolve.
Although mosses branch off early on the tree of life, and share many features with the ancestor of all land plants, living moss species are not ancestral to other land plants.
Nor are they more primitive. Mosses are the cousins of other land plants.
Keep three things in mind:
Evolution produces a pattern of relationships among lineages that is tree-like, not ladder-like.
Just because we read phylogenies from left to right, there is no correlation with level of “advancement.”
For any speciation event on a phylogeny, the choice of which lineage goes to the right and which goes to the left is arbitrary.
The following phylogenies are equivalent:
Biologists often put the clade they are most interested in (whether that is bats, bedbugs, or bacteria) on the right side of the phylogeny.
Humans did not evolve from chimpanzees
Humans and chimpanzees are evolutionary cousins and share a recent common ancestor that was neither chimpanzee nor human.
Humans are not “higher” or “more evolved” than other living lineages. Since our lineages split, humans and chimpanzees have each evolved traits unique to their own lineages.
Building the tree
Like family trees, phylogenetic trees represent patterns of ancestry. However, while families have the opportunity to record their own history as it happens, evolutionary lineages do not — species in nature do not come with pieces of paper showing their family histories. Instead, biologists must reconstruct those histories by collecting and analyzing evidence, which they use to form a hypothesis about how the organisms are related — a phylogeny.
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Using DNA analysis to make a clade including whales
Lindell Bromham, Australian National University, writes:
The origins of the whale lineage, this fully aquatic mammal – so different from its terrestrial relatives – puzzled biologists. Darwin was famously puzzled by the origin of whales because he needed to be able to explain how you could get such a remarkably different animal from a series of small modifications, each of which would be beneficial. He did not know what the whale’s closest relatives were. For example, he hypothesised that they might have been changed from something like a bear.
But now we can take the DNA from whales and compare it to other mammals to see which ones they are most similar to. The answer was quite surprising: whales are most closely related to hippos.
This initially startling idea, which came to be known as the ‘whippo hypothesis’, was generated by DNA sequence analysis, but it has now been widely corroborated. I think Darwin would probably quite like this because it gives a picture of a possible semiaquatic stage between fully terrestrial mammals and the fully aquatic ones.