Organic Evolution Exam 4

The Great Chain of Being

A linear ranking of species, from non-living objects to plants, animals, humans, and the diety.

Haeckel’s Pedigree of Man

A linear ranking of species. Has Monera at the bottom, moves up to inverts, vertebrates, mammals, and is topped with “MAN”.

Internal Nodes vs Tips

The tips of branches are not the same as the bases of branches. Other species are more like cousins.

All Living Lineages

All lineages have existed for the same time since they diverged from their common ancestor.

Carl Woese

A biologist from the University of Illinois Urbana Champaign that wrote a letter to Francis Crick because he intended to trace the ancestry of Earth’s organisms to the last universal common ancestor.

Hunting the Universal Tree

Woese intended to sequence the 16S small subunit rRNA of a plethora of bacteria species. SSU rRNA was a good candidate because it was essential and slow evolving.

A Third Domain of Life

These organisms look like bacteria because they are unicellular and prokaryotic, but they also seem to be extremophiles. A big question was where archaea fit into the tree of life.

Unique Feature of Archaea

The membrane lipids are unlike those of bacteria and eukaryotes. They have branching and an ether linkage instead of an ester linkage.

Similarities of Archaea to Eukaryotes

The RNA polymerase and ribosome genes are more like eukaryotes, and they possess histones.

The Web of Life

In 1999, Ford Doolittle offered a much more tangled model of evolutionary relationships.

The Sea Fan of Life

In 1999, Bill Martin offered this “tree” that looks more like a sea fan. “This is not an answer to a question, it is a picture of a problem.”

The Ring of Life

In 2004, Rivera and Lake offered another way to visualize the relationships of Earth’s organisms as a ring of life.

Endosymbiosis and HGT

Gene transfer from bacterial mitochondria and plastids to nuclear genome of eukaryotes.

Mitochondrial Genome

There are currently only 37 genes left: 2 rRNAs, 22 tRNAs, and 13 protein subunits (all involved in oxidative phosphorylation).

Stationary Genes

Ribosomal genes don’t seem to move via HGT.

The Tree of One Percent

In 2006, Dagan and Martin criticized ribosomal trees as being the “tree of one percent”.

Animal Trees May be Webs Too

160 genes were used in 24 fish species to build 160 different trees.

First Animal Tree (1866)

Ernst Haeckel drew the first phylogenetic tree of animals. It included vertebrates, mollusks, echinoderms, coelenterates, and articulates. It is unclear what traits he used to establish these relationships.

Ctenophores as the Outgroup (2008)

Dunn et al published a sweeping phylogenetic tree from sequences of 40 Mb of expressed DNA from 29 animals in 21 phyla. They found support for the idea that ctenophores were the animal outgroup.

What Sponges are Like

No tissues, nerves, muscles, or symmetry. Pass the blender test. They feed via filtering suspended particles from a current that runs through their spongy bodies.

What Ctenophores are Like

Nerves, muscles, have a mouth and gut, a third tissue layer, fail the blender test, and they look just like cnidarian jellies.

Weird Ctenophores

No miRNAs, polyspermy, non-homologous 3rd tissue layer, rotational symmetry, lacks many bilaterian neurotransmitters, and has a gelatinous illusion.

Complex Sponges

Epithelia, respond to stimuli, possess neurotransmitter genes, and have a chanoflagellate illusion.

Choano Homology

Morphological similarity between choanocytes and choanoflagellates. A parsimonious solution was identified as a single gain and then a single loss of collared cells.

What if the ctenophore sister is correct?

The earliest animals probably had mouths and guts and likely were predators. And had nervous systems and muscles? Or did the nervous system evolve twice?

Reproductive Isolation Leads to Genetic Divergence

The longer two species are apart, the more dissimilar become their genomes.

Genetic Saturation

The result of multiple substitutions at the same site in a sequence, or identical substitutions in different sequences, such that the apparent sequence divergence rate is lower than the actual divergence that has occurred.

Are ctenophores getting pulled by long branch attraction?

When some fungi are added to the tree, ctenophores can get pulled all the way out of the animal kingdom.

Highest Confidence in the Tree of Life

Morphology and genes agree.

Shaken Confidence in the Tree of Life

Morphology and genes disagree.

No Confidence in the Tree of Life

Not only does morphology disagree with genes, but genes also don’t even agree with genes.

Evolutionary Explanations for Disease

Defenses, conflicts, novel environments, trade-offs, and constraints.

Defenses

Some discomforting conditions are actually the body’s defenses against illness.

Conflicts

With other organisms cause disease

Novel Environments

A mismatch between current and ancestral environments can lead to disease.

Trade-offs

Some diseases represent tradeoffs that come with advantageous traits.

Constraints

Bad design can be a result of constraints on evolutionary paths.

Fever is a Defense

If fever is a response to an infection, should we avoid taking fever reducers? A 2015 randomized control study found no effect of fever reducing drugs.

Sickle-Cell Anemia

Genetic disease caused by a hemoglobin missense mutation. Both the mother and father have to pass on the mutation (ss).

Malaria

Communicable disease caused by RBC-attacking parasite

HbAHbA

Normal phenotype, but dies due to malarial infection.

HbAHbS

Sickle cell trait, but lives due to protection from both malaria and sickle cell.

HbSHbS

Sickle cell disease, but dies due to sickle cell disease.

The Upside of Disease

Many genetic diseases seem to offer benefits in other respects.

Osteoporosis

Vitamin D allele that is associated likely protects against tuberculosis.

Cystic Fibrosis Allele

Likely protects against typhoid.

Diabetes

May have even helped humans survive an ice age.

Not Enough Virulence

Won’t grow to high enough population size to become transmitted.

Too Much Virulence

Might stop the host from interacting with other possible hosts.

Directional Disease Disparity

In early 1991, there was an outbreak of cholera starting in Peru in South America and spreading to the rest of the continent. By the end of 1991, there were 2,840 deaths in Peru, 672 in Ecuador to the North, and only 2 in Chile to the south.

Chilean Cholera Chilled Out

This is because Chile maintains its water, so there is no vector to pass the disease around.

Vectors Change the Game

If there is a separate vector, such as a mosquito, good health in the host no longer impacts the spread of the disease. Results in a higher virulence in the host, but still low virulence in the vector.

Water Vector

Waterborne diseases do not require a healthy host to spread. Disinfecting water not only limits disease spread but also the disease virulence. The Yamuna River in India has been an infamous disseminator of disease, as people drink from the river where clothes are washed.

Hospital Vectors

Healthcare worker hygiene is extremely important, as doctors and nurses can act as vectors themselves.

Why age?

The most accepted answer was given in 1957 by George Williams. He was disturbed by the prevailing hypothesis that aging evolved to make room for younger organisms to maintain the species.

Evolution of Senescence

Because pre-reproductive life is what matters. Some beneficial alleles will pose detrimental effects in late life, but those will have less of an influence on fitness.

Antagonistic Pleiotropy

Many alleles affect many traits, many tissues, and or many life history stages. Some alleles likely have positive effects in one life history stage and negative effects in others.

Youth Effect Wins

The theory posits that the effect in youth will always influence fitness more than that in older ages.

Steve Austad (1993)

He found that opossums that had migrated to Sapelo Island, GA, about 10,000 years ago indeed lived 25% longer than the mainland population and produced smaller litters.

Slower Senescence (Opossums)

The collagen in the tendons of the opossum tails showed signs of slower aging.

Long Live the Birds

Birds of the same size and same metabolic rate have lower rates of senescence than mammals. Except for bats, they are slower to age than other mammals.

Evidence for Pleiotropic Genes

Chico: A mutation in a gene involved in the IGF pathway results in smaller body size, lower fecundity, and longer life span.

Contrary Evidence for Pleiotropic Genes

No trade-off is found. Contrary to prediction, Methuselah flies bred for longevity showed an increase in early fecundity.

Darwinian Logic

Things that can self-replicate will tend to persist. The better they can self-replicate, the more likely they will be to persist. The differences in ability to self-replicate are largely determined by random changes.

Plausibility of Intermediates

Living organisms are not intermediate forms; however, they do show that less complex forms can still perform useful functions. “No animal ever made a living by being an intermediate stage on some evolutionary pathway.” -Richard Dawkins

Random Mutation and Selection

However, Darwin suggested that complex adaptations would have to occur gradually.

Time with Evolution

In 1992, it was reported that in response to invasive trees with large fruit, a Florida soapberry bug evolved 25% longer beaks in a few decades. If this rate of evolution were sustained for 10,000 years, their beaks would become 18 miles long.

The 5% of a Wing Problem

George Jackson Mivart asked in On the Genesis of Species (1871), what good is 5% of a wing?

Vertebrate Blood Clotting

If one clotting factor is removed, blood won’t clot. Pufferfish lack three of these genes and have a functional system. Sea squirts do not clot blood, but have homologous genes for all but two of the clotting factors.

Long-Term Evolution Experiment

On February 24, 1988, Richard Lenski started a long-term experiment where 12 flasks of the same E.coli population independently were kept in a limited glucose environment.

LTEE Setup

Every day, a small aliquot of E.coli is transferred from each of the 12 flasks into flasks with fresh medium with a limited amount of glucose, where the bacteria grow until they run out of food. Repeat.

Cit+ in Ara-3

The Ara-3 population had developed a very rare ability in E.coli to consume citrate in the presence of oxygen.

Cit-

The citT gene is silent when O₂ is present.

Cit+

The citT has been duplicated, and this duplicate must be landed by the promoter for a nearby gene rnk, which is active when O₂ is present.

Cit+ Mutations

First, there needed to be a mutation to the gene gltA, which increases the expression of citrate synthase, improving growth on acetate. Without this first mutation, the duplication of the citT/rnk genes results in much lower fitness. Then, a third mutation occurred, duplicating the citT/rnk gene promoter set, increasing citT expression. This led to the super growth that clouded the flask.

Color Vision

Opsins in old-world primates were duplicated and led to trichromate vision. Old-world primates are the only mammals on Earth with a third opsin.