First lecture---MNF
Important urls
Basically our text for the next few lectures
https://evolution.berkeley.edu/evolibrary/article/evo_01
Good reviews and animations on current topics.
Introduction
Darwin’s theory had two major tenets, one was that all living things (organisms) are related through common descent and the other was that natural selection was the main mechanism by which diversity in form and function among organisms although related, occurred.
In Darwin’s own words from the Origin of the species, published in 1859
“No one ought to feel surprise at much remaining as yet unexplained in regard to the origin of species and varieties, if he makes due allowance for our profound ignorance in regard to the mutual relations of all the beings which live around us. Who can explain why one species ranges widely and is very numerous, and why another allied species has a narrow range and is rare? Yet these relations are of the highest importance, for they determine the present welfare, and, as I believe, the future success and modification of every inhabitant of this world. Still less do we know of the mutual relations of the innumerable inhabitants of the world during the many past geological epochs in its history. Although much remains obscure, and will long remain obscure, I can entertain no doubt, after the most deliberate study and dispassionate judgment of which I am capable, that the view which most naturalists entertain, and which I formerly entertained -- namely, that each species has been independently created -- is erroneous. I am fully convinced that species are not immutable; but that those belonging to what are called the same genera are lineal descendants of some other and generally extinct species, in the same manner as the acknowledged varieties of any one species are the descendants of that species. Furthermore, I am convinced that Natural Selection has been the main but not exclusive means of modification.”
Darwin did not like the term evolution because of its association in the vernacular with progress.
He preferred the phrase "descent with modification". Remember that he was working at the species level. But that the descent incorporated inherited modifications was always implied. https://evolution.berkeley.edu/evolution-101/an-introduction-to-evolution/
We will start with this working definition, somewhat modifying it and other terms as we go through the material for the next few weeks.
---- Evolution is descent with inherited modification through time. (Do not use this definition on midterm one----use the definitions provide by Dr. Thorne)
This definition will prove useful for us initially for the same reason it did for Darwin.
1. As Darwin, we often do not know the genetic basis of a trait or the interactions involved in that trait's expression.
Example: Blue eyes
Simple Mendelian inheritance of blue versus brown eyes.
B_ brown------- bb blue
In reality there are at least 6 genes involved in determining eye color. Also any other locus that affects melanin production can influence the expression of eye color.
A gene, OCA2, is considered one of the major genes responsible for the simple Mendelian model taught to you in high school.
Interaction among genes often leads to a good probability that two blue eyed parents can give rise to a brown eyed child. As investigators search for selection by genotyping, the possibility of such interactions often lead to terms as "predicted eye color".
For example there are papers that map geographic distribution of "alleles" that acknowledge that many of the "blue-eyed" individuals that they tally in their distribution may not have blue eyes, because of the interactions between all the loci involved in determining eye color.
Eye color is interesting because it is a good example of how we approach studying the evolution of human traits. Often investigators if they are interested in the gene expression, start with animal models to identify "genes" that may be involved.Th goal of the Human Genome project from 1990 to 2003, was to determine the sequence and location of the then estimated 100,000 genes in humans. That estimate began to be revised quickly to about 50,000 and then after the project to about 31,000. It is still being revised and current estimates are in low twenty thousands of genes.
That we share many of our genes with other animals was already known . That we share almost all of our functional genes with other organisms was more surprising.
Part of this is due to the way we define functional gene. Traditionally a functional gene is one that results in protein that does something.
What definitions did you learn for a gene?
Let's use this one for now, although most of the papers you will read will not use it.
Gene: A locus or interval along the chromosomal DNA that is transcribed into a functional RNA molecule or that is transcribed into RNA and then translated into a functional protein.
The amount of only transcribing loci that influence all functional genes studied was also surprising. Many such influences first begin to be expressed during development. Gave rise to new focus in evolutionary biology nicknamed EVO-DEVO.
https://www.youtube.com/watch?v=14yxfot5sq8
Switches that affect the timing and gradient of developmental events can be as important as those that act to turn on or off an event.
Example. Model: Zebra striped balloons.
2. Often expression of a phenotype is dependent on events that take place during development that can be highly influenced by past and present environmental factors.
Example: Imprinting--------More important in mammals than other animals.
All epigenetic effects fall under this consideration.
https://learn.genetics.utah.edu/content/epigenetics/nutrition
For some genes involved the rate of spontaneous gains and losses of individually
methylated sites (i.e. the epimutation rate) is estimated to be substantially higher than the genetic mutation rate(Graaf et al. 2015), creating new heritable variation that can ultimately enable adaptationFor those interested
https://royalsocietypublishing.org/doi/10.1098/rstb.2020.0111
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4973776/
Aside: One of the major questions in evolution is how natural selection creates "novelty", epigenetics' real contribution to evolutionary theory may be through providing a mechanism for this.
Take home message: Our definition of the inherited unit or gene is changing. In many cases we do know what type of unit or factor is inherited. This can make determing what "trait" is under selection difficult.
My favorit story: swordtails
Study guide:
Know definitions of terms introduced in this lecture. Examples: functional gene, transcribed only genes, imprinting.
Homework: Be prepared to answer this question.
Remnants of Neanderthal DNA in modern humans are associated with genes that influence skin and hair characteristics in a "fair" direction. Many illustrations portray them as having lighter skin, red hair, freckles and even blue eyes. Some recent researchers have suggested that even though their genomes may have contained "fair pigmenation genes" that most were probably olive to dark skinned with brown hair and eyes. How is this possible given the Mendelian model for blue eye inheritance you learned in high school genetics?
https://www.science.org/content/article/were-some-neandertals-brown-eyed-girls