UNIT III A.  Descent with Modification(Ch19) B.  Phylogeny (Ch20) C.  Evolution of Populations (Ch21) D.  Origin of Species or Speciation (Ch22)

What have we covered? Where are we going?•  Population genetics, microevolution, evolution of

populationsEvolution is about POPULATIONS! Alleles at a single locus in an entire population •  Hardy Weinberg-Swallows handout!•  Genetic Drift•  Gene Flow•  Genetic Variation and its Preservation

Questions for-Zimmer Mosaicism

1.  List and describe the specific medical cases and research examples they step through in the article (I found roughly 9 see how many you can find).

2.  What is the difference between chimaeras and mosaicism?

3.  Is cancer a form of mosaicism?

4.  Can having genomes other than your own in your body be potentially beneficial?

1. Our emphasis will be on Using Hardy-Weinberg…

a. After a population has been selected upon you can use it to predict what the next generation genotype frequencies will be. (Cliff Swallows Example)

b. You can also use it as a clue to whether selection (or drift) is taking (has taken) place in a population. (Blood Type Example)

• Most human populations have two alleles for the MN blood group at a particular locus • Genotype can be determined from blood samples. • We go visit populations (Inuit, Native American etc..)

MM MN NN 835 156 9 We ask IS THIS POP IN HARDY-WEINBERG Equilibrium? 1.  Figure out the “underlying” allele frequency at this locus

in this population. 2.  Calculate how many of each genotype you would expect to

see…how?

MM MN NN 835 156 9 “Underlying” gene or allele frequencies are…(put all alleles in bucket) 835+835+156 156+9+9 2000 2000

Freq M=p=.913 Freq N=q=.087

What would we expect the genotype frequencies to be??Freq of MM (.913)2=.83Freq of MN 2(.913)(.087)=.16Freq of NN (.087)2=.008

Actual Observed Genotype FrequenciesMM=.835, MN=.156, NN=.009

•  The Hardy-Weinberg principle serves as a null hypothesis for determining whether evolution is acting on a particular gene in a population.

•  When genotype frequencies do not conform to Hardy-Weinberg proportions, evolution or nonrandom mating is occurring in that population.

2. Genetic Drift

What is it?

A sampling error problem

Imagine you are flipping a coin…

Genetic drift is important only when populations are SMALL

Imagine you have all the genes from a single locus of a single population in a bottle…

Is this a representative sample?

If only those in white box survive, what will new freq of R and r be?

Is genetic drift an example of evolution?

When do populations end up small?

bottlenecking…..

founder events……

Ex. Humans

• Pingelap Atoll 20,000 pop dropped to 20 in 1775-Typhoon

At least 1 of the 20 carried an allele that

when homozygous=loss of visionhttp://www.pbs.org/wgbh/evolution/library/06/3/l_063_03.html

Conservation examples…

This condition was in the news recently…Retinitis pigmentosa is a rare genetic condition associated with progressive loss of retinal photoreceptors (rods, then cones), resulting in night blindness, tunnel vision and, ultimately, severe visual disability and blindness. There is no current treatment for RP, which is considered an "orphan" disease by the Food & Drug Administration, thereby conferring advantages in terms of the regulatory pathway necessary for drug approval.

Participants are being enrolled in the first clinical trial that tests the use of retinal progenitor cells to treat retinitis pigmentosa, reported project director Dr. Henry Klassen of UCI's Gavin Herbert Eye Institute and Sue & Bill Gross Stem Cell Research Center. The product of stem cell research at UCI, these retinal progenitors are similar to stem cells in terms of potential regenerative properties, but they're specific to the retina.http://medicalxpress.com/news/2015-08-team-clinical-trial-stem-cell-based.html

Ex. Elephant seals

Northern’s reduced to 20(?) in the 1890s (less than 100)

Now about 127,000

24 loci

Southern pop has abundant variation

Ex. Cheetahs

52 loci and found no diversity

Skin transplants not rejected (MHC)

Low sperm counts

High infant mortality

Disease susceptibility

Ex. Florida Panther=Puma=Cougar=Mountain lion

Roelke et al. (1993).Nearly as low as Cheetahs

With Fresh Blood, Inbred Florida Panthers ReboundBy Robert Roy Brittposted: 18 August 2005

A controversial breeding program has improved the genetic diversity of inbred Florida panthers and the endangered animals are on the rebound, scientists announced today.

As few as 30 wild panthers roamed the Florida Everglades in the early 1990s. Abnormalities such as low sperm counts and heart defects were becoming common, studies found, and the kittens had low survival rates.

In 1995, researchers outfitted some female Texas panthers with radio collars and introduced them into four sections of the Florida Everglades. Some Florida panthers were also tagged.

Researchers monitored the cats and kittens and found that the hybrids had better survival rates, presumably because they were more genetically diverse. By 2003, three of the Texas panthers were still alive, and they were removed -- scientists figured enough fresh blood had been injected into the Florida population and they wanted to keep outside genetic exposure to a minimum.

Today, there are at least 87 wild panthers in Florida.

"More than three times as many hybrid kittens appear to reach adulthood as do purebred ones," Pimm and his colleagues write in a paper that will be published early next year in the British journal Animal Conservation.

And the hybrids are on the move. The purebred panthers rarely ventured beyond protected areas north of interstate 75 and west of State Highway 29. Hybrid offspring have moved south and east into new sections of the Everglades National Park and Big Cypress National Preserve. They're pushing into places that are less hospitable, but they're doing so with success, the scientists said.

The federal government has decided that the hybrids will be called Florida panthers for purposes of determining their endangered species status.

!Estimates today are 160???

Exciting Florida panther encounter…http://news.nationalgeographic.com/2016/04/160401-florida-panther-video-corkscrew-sanctuary/

http://www.cougarnet.org/confirmations

Mongolian Wild Horse

Foals captured in Mongolia in 1800s and shipped to Europe (After 1945 only two captive populations in zoos remained, in Munich and Prague. The most valuable group, in the Ukraine, was shot by German soldiers during WWII. ….By the end of the 1950s, only 12 individual Przewalski's horses were left in the world). Wikipedia…

Went extinct in wild in 1960s

9 used to start a new pop.

Reintroduced to Mongolia

Currently reproducing in wild!

Review

In very small populations (bottlenecks, founder events) variation is lost (alleles are lost)

AND

rare alleles can become common

common alleles might become less common

DUE TO

random changes in gene frequencies-not a result of selection

3. Gene flow

Movement of …..individuals or gametes…. between populations

Tends to reduce differences between populations that have accumulated because of natural selection or genetic drift…..

Gene flow is a big issue in the 21st century!

How are we genetically modifying crops?•  Herbicide tolerance-roundup ready corn•  Insect resistance…

HT=herbicide tolerance

Bt =toxin makes insect resistant

Most of the world‘s major crops naturally hybridize (share pollen) with wild relatives somewhere in the world……(corn, mustards, sunflowers, squash, carrots and strawberries)

Why is this a problem?“While corn and soy don’t have close wild relatives in the United States, canola, another widely planted GM crop, does. Herbicide-resistance genes from GM canola have turned up in wild, weedy mustard plants on roadsides in the United States, Canada and elsewhere.” https://www.sciencenews.org/article/gmos-haven%E2%80%99t-delivered-their-promises-%E2%80%94-or-risks

Mexico to start experimental planting of GMO cornhttp://www.reuters.com/article/idUSN0424072320090604Thu Jun 4, 2009 6:24pm EDT

MEXICO CITY, June 4 (Reuters) - Mexico, considered the birthplace of corn, is reviewing more than two dozen requests to begin experimental planting of genetically modified crops, the agriculture ministry said on Thursday.He said U.S. biotech food producer Monsanto Co (MON.N) is one of the companies who have applied for a permit to begin planting.

Supporters of GMO food, whose DNA is altered to be resistant to pests, say they boost yields. More than 70 percent of U.S. corn is genetically modified.

But farmers in Mexico's rural south, where corn has been grown for thousands of years, worry GMO corn will cross-pollinate with native species and alter their genetic content.

Corn was first planted in Mexico some 9,000 years ago and the country is now home to more than 10,000 varieties. The grain was adopted by Spanish conquistadors in the early 1500s and eventually spread to the rest of the world.

Under the current rules, GMO corn seeds are not allowed into certain parts of the country that are determined to be "centers of origin" for genetically unique corn strains found only in Mexico.

The other issue is…Organic farmersUniversity of Maine Researchers Warn of Seed ContaminationStudy Confirms Genetically Modified Corn Can Cross-Pollinate with Organically Grown Crops by Sharon Kiley Mack ORONO, Maine — Two University of Maine researchers are recommending that farmers who raise organic corn take special precautions to ensure their crops are free from cross-pollination if genetically modified corn is grown in nearby fields.

The scientists recently completed a two-year study that confirmed that organic crops can be contaminated by wind drift of pollen from transgenic crops.……..“Farmers who plant within 100 feet of transgenic crops can expect some pollen transfer,” said Michael Vayda of the UMaine Department of Biochemistry, Microbiology and Molecular Biology.

Vayda, in partnership with John Jemison of Cooperative Extension, conducted a two-year study which confirmed Monday that genetically modified corn can cross-pollinate with conventional hybrid corn.

Vayda said the issue is important because the presence of genetically modified components means that crops cannot be certified as organic under the standards of the U.S. Department of Agriculture or the Maine Organic Farmers and Gardeners Association (University of Maine-Bangor Daily News)

2. Genetic Drift

3. Gene Flow

4. Genetic Variation

4. Genetic Variation

What is it? How would you measure it in a population?

Why is variation important?

Where does new variation come from?

Mutation

Sexual reproduction

Recombination-Shuffling of existing alleles

How is variation preserved? (back of Chapter)

a. Diploidy…why does this preserve variation?

b. Selection itself may preserve variation-how?

Ex.

Ex. Niels Dingemanse University of Groningen, Netherlands

Genetic variation underlying exploration behavior in small birds!

Some highly exploratory others more cautious

When food scarce-who does well? (females)

When food common –who does well?

Gene flow study with this

Species…(Gene Flow p410)

Ex. Evolutionary Psychology…

“Why do we all have different personalities?

Why hasn't natural selection homed in on optimum character traits instead of allowing so much variability?

As the study of personality moves to a more scientific footing, we are starting to understand the underlying neurobiology, and to see that each personality trait is beneficial in certain circumstances and costly in others.

We may tend to think that some personality types are more desirable than others, but these new insights make it clear that there is no "best" personality. It really does take all sorts to make a world.”Nettle, New Scientist Feb 2008

c. What is this called?

Aa “do best” or have highest fitness

(AA get Malaria, aa get sickle cell disease)

d. Frequency dependent selection

Rare individuals have higher fitness..

“it is good to be unusual”

EX. Scale eating fish in text p415

Another example of frequency dependent selection-Snails infected by a parasitic worm

Red

Queen!

Large and Small scale “mutations”

Abnormal chromosome NUMBER or STRUCTURE (CH12 p241)

•  Abnormal NUMBER of chromosomes is called aneuploidy

Ex. Down’s syndrome and various fascinating disorders where are extra X’s or no Y

•  Abnormal STRUCTURAL issues such as a chunk is deleted, inverted, translocated, duplicated

Figure 12.14a

(a) Deletion

A deletion removes a chromosomal segment.

(b) Duplication

A duplication repeats a segment.

What is this called?

Figure 12.14b

(c) Inversion

(d) Translocation

An inversion reverses a segment within a chromosome.

A translocation moves a segment from one chromosome to a nonhomologous chromosome.

In addition to abnormal chromosome structure or number we also have POINT MUTATIONS (CH14 p288) a change in a single nucleotide

1.  Substitutions

2. Insertions/Deletions

1.  Substitutions 3 kinds…missense, nonsense, silent –WHICH ONE IS WHICH?A. does not involve a changed a.a.…because there is redundancy or wobble

B. does involve a change in a.a. (this may or may not be a problem-protein may have basically the same shape it may also be in a region of the protein where the exact sequence of amino acids is not essential to the protein’s function)

C. occurs when a codon for an amino acid is turned into a stop codon (translation is terminated prematurely so will be short, unfinished protein product so nonfunctional).

1.  Substitutions WHICH ONE IS WHICH?A. does not involve a changed a.a.…because there is redundancy (Ex CCG to CCA) Silent!

B. does involve a change in a.a. (this may or may not be an issue protein may have basically the same shape it may also be in a region of the protein where the exact sequence of amino acids is not essential to the protein’s function) Missense!

C. occurs when a codon for an amino acid is turned into a stop codon (translation is terminated prematurely so will be short, unfinished protein product so nonfunctional). Nonsense!

Point mutations (a change in a single nucleotide)

1.  Substitutions 2.  Insertions and deletions-why are these often

worse!!!