Diversity of life notes

Contents

Module 1: Major Events in the History of Complex Life

1. Biological diversity and disparity
2. Evolution
3. Phylogenies
4. Genes
5. Ediacaran period (635-541 MYA)
6. Cambrian explosion (541 MYA)
7. Did the Cambrian explosion really happen?
8. What was the cause of the Cambrian explosion?

Module 2: Generation of Biological Diversity

• Hawaii
• Biogeography
• The origin of humans
• Sexual selection

Module 3: Big Questions

• Evolution of beauty
• The scientific method
• Are there limits on what evolution can achieve?
• Are we alone in the universe?
• Morality, human personality, and emotion

Major Events in the History of Complex Life

Earth originated 4.5 BYA.
Life originated 4 BYA.
Complex life appeared 541 MYA.

Complex life is multicellular, mobile organisms that interact with each other and their environment.

Problem: Given the apparent productivity of complex life on Earth, why did it take 3 billion years after the earliest evidence of life for complex, diverse life forms to occur?

Biological diversity and disparity

Diversity is the number of different kinds of organisms. Disparity is the range of different kinds of organisms. Lower taxonomic levels like "genera" usually represents diversity and higher taxonomic levels like "classes" or phyla" usually represents disparity.

Disparity has only happened once, during the Cambrian Explosion. Diversification events have happened multiple times.

The long-term trend in biological diversity is net positive, but there have been many mass extinctions. This chart by Sepkoski (1981) shows the change in diversity over geological time in terms of number of marine families.

Evolution

Evolution is the change in gene frequencies in a population over time. There are 4 mechanisms of evolution: mutation, migration, drift, and selection. Mutation is the only mechanism that actually introduces novelty.

For natural selection to occur, we make a few assumptions:

1. Traits are heritable
2. Traits impact fitness
3. Traits that positively impact fitness are selected for, and traits that negatively impact fitness are selected against

Speciation happens when there is reduced gene flow between populations, and they become reproductively isolated. Species are usually defined as the largest group of organisms in which two individuals can produce fertile offspring.

Phylogenies

Diversity can be explained by lines of descent. Cladograms are based on shared traits, while phylogenies are cladograms that are specifically based on shared genes. Note that some organisms that are closely related are dissimilar, and vice versa. Relatedness is based on the most recent common ancestor (MRCA). Recency is measured in genealogical time, not calendar time.

A monophyletic group (single tree), or a clade, consists of a MRCA and all of its descendants. A paraphyletic group consists of a MRCA, but not all of its descendants.

The crown group is the MRCA of all living members of a clade, and all of its descendents. It is a type of monophyletic group that must have living descendants by definition. The pan group is the crown group and all organisms that share an ancestor with the crown more recently than any other living organism. The stem group is the pan group minus the crown group.

On the vertebrate phylogeny, agnatha, osteichthyes, and reptilia are paraphyletic groups. The rest are monophyletic groups.

On the bird and crocodile phylogeny, pterosauria and dinosauria are sister groups. Crown group Aves is the Neornithes. Pan group Aves is all animals more closely related to Neornithes than to Crocodylia, which includes archeopteryx, dinosauria, and pterosauria.

Phylogenies can tell us about when a trait evolved. For example, we can infer that the MRCA of all animals had a nervous system because all animals except sponges have a nervous system.

Genomic data is unclear about whether ctenophores or sponges are the sister group to all other animals.

Genes

There is a DNA binding protein which regulates gene expression. Thus, genes are turned on when they are needed.

There is a 180 base-pair sequence present in most homeotic genes which regulate development. This sequence was called the homeodomain, homeobox, or hox genes. It was once assumed that the degree of disparity should be proportional to the degree of genotypic similarity. However, hox genes are able to produce large changes in morphology with small changes in genotype.

Similarities in the homeobox sequence suggest that all hox genes arose from a single gene that was duplicated multiple times and allowed to perform new tasks.

Hox genes are part of a set of regulatory genes called the developmental genetic toolkit. The toolkit is highly conserved across animals, and it is responsible for the development of body plans. It turns out that complex traits like eyes didn't evolve multiple times independently, but rather evolved once and were lost in some lineages.

One example is the eyeless gene (Pax-6, smalleye) which seems to be a master gene for eye development. Inserting smalleye from mice into fruit flies causes them to develop normal fruit fly eyes, not mice eyes.

Ediacaran Period (635-541 MYA)

Before the Cambrian explosion, no fossils of large organisms were thought to have existed. This is why the period after the Cambrian explosion was called the Phanerozoic period ("visible animal"). The discovery of Charnia masoni (600 MYA) in 1957 changed this view.

More Ediacarian fossils were found, including dickinsonia, kimberella, spriggina, and Ikaria wariaootia.

Dickinsonia was important because it showed that Ediacaran organisms were animals. All animals today have cholesteroids, and cholesteroids were found in dickinsonia fossils but not in the surrounding sediment. Furthermore, the superficially bilateral symmetry of dickinsonia and other Ediacaran organisms suggested that they were bilaterians.

Cambrian Explosion (541 MYA)

The Cambrian Explosion was the first diversification event, and it also represented the onset of animal disparity. It led to to the appearance of most animal phyla (37).

It is defined by the first appearance of the trace fossil Treptichnus pedum.

Fossils that appeared in the Cambrian Explosion include trilobites and anomalocaris ("anomalous shrimp"). They had complex features like segmented bodies, compound eyes, exoskeletons, and appendages.

Did the Cambrian explosion really happen?

The existence of the Cambrian explosion is supported by:

1. The reading of the fossil record
2. Molecular clock analysis by Erwin et al. (2011)

First, the fossil record shows a rapid increase in disparity during the Cambrian explosion. However, the fossil record is imperfect. For fossilization to happen, the following needs to occur:

1. The fossil is buried in quick-moving sediment
2. The fossil is not destroyed by geological processes
3. The fossil is found after millions of years

This means that the animals that are fossilized could be biased towards those that lived in environments with quick-moving sediment, had hard parts, and were large enough to be seen.

The fossil record is supported by the molecular clock. Erwin et al. estimated divergence times of animal phyla and found that most phylum-level crown-group divergences occurred during the end of the Ediacaran and the Cambrian.

The molecular clock is a method that uses the mutation rate of genes to deduce the time when two organisms shared a common ancestor. We know that $g(t) = r \times t$, where $t$ is time since divergence, $g(t)$ is the number of genetic differences, and $r$ is the rate of genetic change. Finding the rate requires calibration with known divergence times from the fossil record.

What was the cause of the Cambrian Explosion?

There are three things that need to be explained:

1. Why it was the only increase in animal disparity
2. Why it happened 541 MYA
3. Why it was so rapid (10 MY)

We do know that for the Cambrian explosion to occur, it was necessary to have an environment that can support animal life and to have the genetics machinery that can produce wide disparity. However, these are not sufficient conditions, and none of the environmental explanations can create a causal link. It is possible that the onset of disparity only happened once because evolution was able to quickly find all ecologically viable morphologies.

Here are more detailed hypotheses from Marshall 2006:

1. Increase in O2

   Limited O2 could have limited animal evolution, since it is necessary for collagen synthesis. It is generally agreed that animals could not have evolved if O2 was <1% present (Towe limit). The problem with this theory is that substantial O2 had already exceeded the Towe limit long before the Cambrian explosion. While O2 is necessary for the increase in diversity, it is not a sufficient condition.

   

2. Snowball Earth

   The Earth experienced deep freezes during the Cryogenian period and Ediacaran period, and Ediacaran organisms appeared after the last of these events, the Gaskier Glaciers. The problem is that the last deep freeze was much earlier than the Cambrian explosion, so the causal link is unclear.

3. C isotope anomaly

   There was a large negative carbon isotope anomoly that has been assumed to cause the Ediacaran mass extinction and the Cambrian diversification event. It is true that isotope anomalies and mass extinctions could lead to diversification, such as mammal diversification after the KT boundary. However, this is not a fair comparison since the KT event involved the replacement of a few clades by a sister clade. The link between the C isotope anomaly and the Cambrian explosion is not clear.

4. Developmental genetic toolkit

   Hox genes regulate other genes that control growth, development, and patterning. Current bilaterians possess a set of 7 common, interchangeable Hox genes, so the MRCA of all bilaterians must have had these genes. Since molecular clocks place the earliest bilaterian long before the Cambrian, we know that Cambrian animals must have possessed Hox genes.

   A relatively small change in Hox genes can lead to a large change in morphology, so this this is both necessary and sufficient for the large increase in disparity during the Cambrian explosion. The problem is that Hox genes existed for over 100 million years before the Cambrian explosion, so it does not explain why the Cambrian explosion didn't happen sooner.

5. Adaptive radiation

   The first evidence of predation occurred near the end of the Ediacaran, perhaps leading to biomineralized shells and hard skeletons. This could have been facilitated by oxygenation of the atmosphere, leading to the establishment of bottom-up food webs. While this arms race is a necessary and sufficient condition for the increase in diversity, it does not explain the rest of the Cambrian explosion.

References:

• Marshall 2006: Explaining the Cambrian "Explosion" of Animals
• Erwin et al. 2011: The Cambrian Conundrum: Early Divergence and Later Ecological Success in the Early History of Animals