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Jon Stone

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Phylogenies and the History of Life
Key Concepts
Phylogenies and the fossil record are major tools that biologists use to study the history of life.
The Cambrian explosion was the rapid morphological and ecological diversification of animals that occurred during the
Cambrian period.
Adaptive radiations are a major pattern in the history of life. They are instances of rapid diversification associated with new
ecological opportunities and new morphological innovations.
Mass extinctions have occurred repeatedly throughout the history of life. They rapidly eliminate most of the species alive in a
relatively unbiased manner.
In biology we must consider profound changes in the nature of life on Earth over immense periods of time. (Now looking at
macro evolutionary process).
Let’s first look at two major analytical tools that biologists use to reconstruct the history of life: phylogenetic tress and the
fossil record.
Tools for Studying History: Phylogenetic Trees
The evolutionary history of a group of organisms is called o phylogeny.
A phylogenetic tree shows ancestor-descendants relationships among populations or species.
o The diagram provides an extremely effective way to summarise data (according to criteria such as distance,
parsimony, likelihood, Bayesianism) and may be interpreted as depicting the evolutionary history for the group.
An ancestor and its descendants from a monophyletic group (also called a clade or lineage).
Bio skills 2: Reading a Phylogenetic Tree
Branches: represent groups through time. Adjacent branches are sister taxa. (a taxon is any named group of organisms).
Tips: are the tree’s endpoints and represent living groups or a group’s end in extinction.
The names at the tips can represent populations or higher taxa.
Nodes: occur where an ancestral group split into two or more descendant groups (an inference)
Polytomy: is a node where more than two descendant groups branch off (an inference)
In rooted phylogenies the most ancient node of the tree is shown at the bottom (an inference)
The location of this node is determined using an out-group, a taxonomic group that is diverged before the rest of the taxa
being studied.
How Do Researchers Estimate Phylogenies?
Phylogenetic trees are an extremely effective way of summarizing data on the evolutionary history group of organisms.
Researchers analyze morphological and/or genetic characteristics to infer phylogenetic relationships among species. (Other
traits may be used).
For example, to reconstruct relationships among fossil species of humans, scientists analyze toot, jaw. And skull structures.
There are two general strategies for using data to estimate trees: the phonetic and the cladistics approaches.
o Actually 4: distance, parsimony, likelihood, Bayesianism
The phenetic approach is based on computing a statistic that summarizes the overall similarity among populations.
For example, researchers might use gene sequences to compute an overall “genetic distance” between two populations. A
genetic distance summarizes the average percentage of bases in a DNA sequence that differs between two populations.
A computer program then compares the statistics for different populations and builds a tree that clusters the most similar
populations and places more divergent populations on more distant branches.
The cladistics approach to inferring trees focuses on synapomorphies, the shared derived characters of the species under
o A synapomorphy is a trait that certain groups of organisms have that exists in no others. Synapomorphies allow
biologists to recognize monophyletic groups.
For example, fur and lactation are synapomorphies that identify mammals as a monophyletic group.
When many such traits have been measured, traits unique to each monophyletic group are identified and the groups are placed
on a tree in the appropriate relationship to one another.
Distinguishing Homology from Homoplasy
Homology (same-source): occurs when traits are similar due to shared ancestry.
Problems can arise with both phonetic and cladistics analyses because similar traits can evolve independently in two distant
species rather than from a trait present in a common ancestor.
o For example, Species 2 is not at all related to species. Its ancestors may have had the sequence TAT GGT AGT,
which happened to change to AAC GCT ACT, due to mutation, selection, and drift that took place independently of
the changes that took place in the ancestors of species 1.
Homoplasy (same-form): occurs when traits are similar for reasons other than common ancestry. Figure 27.2a shows an
example comparing the similar traits of dolphins and extinct marine reptiles called ichthyosaurs.
Many other animals,
Phylogenies and the History of Life
Parsimony: is a principle of logic stating that the most likely explanation or pattern is the one that implies the least amount of
Convergent evolution and other causes of homoplasy should be rare compared with similarity due to shared descent, so the
tree that implies the fewest overall evolutionary changes should be the one that most accurately reflects what happened during
o Inferring process from pattern.
Convergent evolution occurs when natural selection favours similar solutions to the problems posed by a similar way of life,
as shown by the dolphin and ichthyosaur.
o Dolphins and ichthyosaur both need to live in an aquatic environment.
Convergent evolution is a common cause of Homoplasy.
Whale Evolution: A Case History
Traditionally, cladogram based on morphological data placed whales outside of the artiodactyls-mammals that have hooves,
an even number of toes, and an unusual pulley-shaped ankle bone (astragalus).
DNA sequence data; however, suggest a close relationship between whales and hippos. This cladogram would require two
changes to the astragalus trait.
o Beta-casein (a protein in milk) sequence data.
More recently obtained and analysed data on gene sequences called short interspersed nuclear elements (SINEs) show that
whales and hippos share several SINE genes that are absent in other artiodactyl groups.
These SINEs are shared derived traits (synapomorphies) and support the hypothesis that whales and hippos are indeed closely
Tools for Studying History: The Fossil Record
A fossil is the physical trace left by an organism that lived in the past.
The fossil record is the total collection of fossils that have been found throughout the world.
The fossil record provided the only direct evidence about what organisms that lived in the past looked like, where they lived,
and when they existed.
o Fossils proved minimum ages for groups
How do Fossils Form?
Most fossils form when an organism is buried in sediment before decomposition occurs.
Four types of fossils are intact fossils, compression fossils, cast fossils, and permineralized fossils.
Fossilization is an extremely rare event.
(Figure 27.6)
Limitations of the Fossil Record
There are several limitations of the fossil record that need to be recognized: habitat bias, taxonomic bias, temporal bias, and
abundance bias.
Habitat bias: occurs because organisms that live in areas where sediment are actively being deposited are more likely to form
fossils than are organisms that live in other habitats.
Taxonomic bias: is due to the fact that some organisms (e.g. those with bones) are more likely to decay slowly and leave
fossil evidence.
Temporal bias: occurs because more recent fossils are more common than ancient fossils.
Abundance bias: occurs because organisms that are abundant widespread, and present on Earth for a long time leave evidence
much more often than do species that are rare, local, or short-lived.
Palaeontologists: scientists who study fossils-recognize that they are limited to studying tiny and scattered segments on the
tree of life, yet they also know that this is the only way to get a glimpse of what extinct life was like.
Lifes Timeline
Major events in the history of life are marked on the timeline shown in Figure 27.8 which has been broken into four segments.\
The Precambrian encompasses the Haden, Achaean, and Proterozoic eons. This period spans from the formation of the Earth
to the appearance of most animal groups about 542 m.y.a.
In the Precambrian super eon, almost all life was unicellular and hardly any oxygen was present.
o O2 levels rose at approximately 2.4 b,y,a, and 600 m,y,a, The cause of the oxygen level to rise 2.4. b.y.a. is due to
The interval between 542 m.y.a. and the present is called the Phanerozoic eon and is divided into three eras: the Palaeozoic,
the Mesozoic, and the Cenozoic. These eras are further divided into periods.
The Palaeozoic era covers the interval from 542 to 541 m.y.a,
Many groups-including fungi, land plants, and land animals-appeared in the Palaeozoic era. This era with the obliteration of
almost all multicellular life-forms at the end of the Permian period.
o Cause of that was still undetermined
The Mesozoic era covers the interval from 251 to 65.5 m.y.a.
This era is also known as the Age of Reptiles because it saw the rise and dominance of the dinosaurs. This era ended with the
extinction of the dinosaurs, except birds.
The Cenozoic era included the interval from 65.5 m.y.a. to the present.
Phylogenies and the History of Life
The Cenozoic era is known as the Age of Mammals, since during this time the mammals diversified after the disappearance of
the dinosaurs.
Events that occur today are considered to be part of the Cenozoic era.
The Cambrian Explosion
The first animals-sponges, jellyfish, and simple “worms”-appear in the fossil record around 565 m,y,a, at the end of the
Proterozoic eon (about 565 million years ago).
Soon after that in geologic time, by about 50 million years later, animals had diversified into almost all the major groups living
This diversification is known as the Cambrian explosion. This period was arguably the most evolutionary change in this
history of life.
Cambrian Fossils: An Overview
The Cambrian explosion is documented by three major fossil assemblages, called Doushantuo, Ediacaran, and Burgess Shale
The presence of these exceptionally rich deposits before, during, and after the Cambrian explosion makes the fossil record for
this event extraordinarily complete.
These three assemblages all break one of the cardinal rules of fossil preservation. Soft-bodied animals, which usually do not
fossilize efficiently, are well represented in all three groups.
The Doushantuo Microfossils
From the Doushantuo formation in China, researchers identified microfossils (tiny fossils) of sponges, cyanobacteria, and
multicellular algae in samples date 570-580 m.y.a. They also found what they concluded were animal embryos in early stages.
These were example of the first type of animals on Earth..
Scattered among other organisms in the Doushantuo formation were sponges and possibly other tiny creatures that probably
made their living by filtering
The Ediacaran Faunas
In the Ediacaran Hills in Australia, palaeontologists identified fossils of sponges, jellyfish, comb jellies, and traces of other
animals dated 544-565 m,y,a,
These were small, soft-bodies animals that burrowed in sediments, sat immobile on the sea floor, or floated in the water.
There is no evidence that they had structures associated with actively hunting and capturing food. Instead, they most likely
filtered or absorbed material from their surroundings..
The Burgess Shale Faunas
Virtually every major living animal group is represented in the Burgess Shale fossils from British Columbia, Canada, which
date to 515-525 m,y,a,
These fossils indicate a tremendous increase in the size and morphological complexity of animals accompanied by
diversification in how they made a living.
The Cambrian seas were filled with animals that had eyes, mouths, limbs and shells. They swam, burrowed, walked, ran,
slithered, clung, or floated; there were predators, scavengers, filter feeders, and grazers.
This diversification filled many of the ecological niches still found in marine habitat today.
Did Gene Duplication Trigger the Cambrian Explosion?
Many researchers predicted a strong association between the order in which animals lineages appeared during the evolutionary
history, the number of Hox genes present in each lineage, and each lineage’s morphological complexity and body size.
The logic behind this “new genes, new bodies” hypothesis was that existing homeotic genes could have been duplicated before
and during the Cambrian explosion, producing new body plans and appendages,
A cladogram of Hox genes in animals in general supports this hypothesis at a gross level.
The following conclusions can be inferred from this cladogram:
o The number of genes in the Hox cluster appears to have expanded during the course of evolution.
o How genes appear to have been duplicated because the genes within the cluster are similar in the structure and base
o The entire Hox cluster was duplicated several times in the lineage leading to vertebrates.
Both duplication of Hox genes and changes in expression and function of existing genes have been important in making the
elaboration of animal body plans possible.
Adaptive Radiations
Dense groups of bushy branches called star phylogenies or polytomies (aka polychotomies) can be observed in the tree of life.
These star phylogenies represent speciation events that were so rapid that the order branching cannot be resolved. (card
carrying cladist perspective)
If rapid speciation in a single lineage is followed by divergence into many different adaptive forms, then a process known as
adaptive radiation has taken place.
Adaptive radiations can be triggered by ecological opportunity and morphological innovation.
(Figure 27.11)
Ecological Opportunity as a Trigger
One of the most consistent triggers of adaptive radiations is ecological opportunity, meaning that availability of new types of
For example, biologists have documented adaptive radiations of the Anolis lizards of the Caribbean islands.