Gen3040 week 5 -evolutionary genomics PDF

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Active learning question on Evolutionary genomics...

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GEN3040 in-class concept questions for Lecture 13-15 (Evolutionary genomics) 1. Where do genes come from? New gene / Gene duplication in a genome can be derived from the following mechanisms: (1) Unequal crossing over at meiosis: during metaphase I, two pairs homologous chromosome possessing repetitive sequence regions may not line up exactly with its corresponding region. The resultant daughter cells (haploid cells) will possess different number of repeats.

(2) Unequal sister chromatid exchange: during meiosis II, two sister chromatids possessing repetitive sequence regions may not line up exactly with its corresponding region. Strand breaks on these chromatids will produce different repeats.

(3) Gene duplication at genome level - chromosome reduction at meiosis (e.g. autoploidy): (i) Autotetraploidy: direct fusion of 2 unreduced gametes = AA + AA = AAAA (ii) allopolyploidy: interspecific hybrid having a complete diploid chromosome set from each parent form = AA + BB = AABB 2. Examples of polyploidy in plant kingdom:

Name of the vege:

Mustard

Name of the vege:

Name of the vege:

Wild cabbage

Rapeseed, Canola

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3. Where do genes come from? HGT (Horizontal Gene Transfer) between species can be detected via 2 methods: a) Detection of sequences with unusual nucleotide composition b) Detection of genes for functions that is totally absent in all closely related species Example: Scientists detected DNA sequence of marine microorganisms in intestinal microbiomes of Japanese individuals. These bacteria live on red algae Porphyra sp. that Japanese use to wrap sushi, and are not found in the microbiomes of Americans. They concluded that the microbiota in Japanese gut acquire genetic materials from the marine microorganism through HGT.

4. Where do genes come from? Reverse transcription copies RNA copy back into DNA gene and incorporate back to genome.

All 19 breeds (chondrodystrophies are known in 19 distinct breeds) shared a unique transposed growth factor retrogene, named fgf4, or, fibroblast growth factor 4, are expressed in the long bones of 4-week-old puppies, but with several incorrect/abnormal conditions: (a) wrong spatial expression of the gene (b) wrong RNA level of the gene (c) miss timing expression

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These abnormalities caused premature closure of the growth plates in the long bones.

5. Where do genes come from? De novo requires non-genic sequence to be first transcribed, slowly accumulated mutation, acquired ORF (open reading frame), and translated into polypeptides which may not be functional. These ORF would be maintained by natural selection, if they were not deleterious or harmful to the organism. These adaptively advantageous sequences will evolve into new genes.

6. Describe 3 possible fates of duplicated genes: (i) Pseudogene: One of them accumulates a series of random deleterious mutations to become a ‘pseudogene’ and eventually ‘degenerates’ to become unrecognized as a homologue (ii) Subfunctionalization: duplicate genes with multiple functions A and B diverge by reciprocal loss (iii) Neofunctionalization: one of the genes mutate to produce a protein with new and useful protein

7. Amphioxus /lancelet is a form of primitive invertebrate species, that is closest living invertebrate to vertebrate which occupies an extremely important phylogenetic position in evolution vertebrates.

Using amphioxus (which consist of about 32 species of fish-like marine chordates in the order Amphioxiformes) as example, describe different conditions of sub-functionalization: 1.) Sub-functionalization (Complementary functions): one gene (with 2 different functions: A & B) – duplication – lost function A in gene 1; and lost function B in gene 2 – both genes are essential and will be preserved 2.) Different expression location: one gene – duplication – diverged into 2 subtypes (same function, one gene expressed uniquely in only one of the tissues) [e.g. GLUD1 & GLUD2: GLUD2 only express in nervous system]

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3.) Different stage/timing of expression: one gene – duplication – both gene 1 & 2 retain the original same function – but express at different developmental stages [e.g. duplication of β1-gene to δ- & β-globin only expressed in human adults]

8. 1a. What are the common consequences after whole-genome duplication or partial-genome duplication events in animals? 1b. Using Hox gene clusters as example, explain what are the advantages of genome duplications? Read also text in pages 688-690, Sanders & Bowman 2012 Answer 8: 1a. ● polyploidy ● pseudogenization, where pseudogenes could be expressed but in protein is inactive, or not expressed at all ● subfunctionalization may also occur

1b. . increase the complexity of the organism . increase number of DNA could give rise to more gene

Question 9:

1a. If you were to compare your genome sequence with another student in the class, how would it differ? 1b. What are the two main types of intraspecific variation? Describe their main characteristics. 1c. What methods can you use for discovery and genotyping of these variants? 1d. What additional difference might you see if your genome was compared to that of a subSaharan African? Answer 9:

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******************************************************************************** Question 10: What is the most likely model of human evolution, multiregional model (MRE) or recent African origin model (RAO)? Why Answer 10: Recent African origin model (RAO) are more reliable compared to multiregional model (MRE). It is because MRE will result in high genetic variation among human population after 2 millions years ago when homo eractus migrate out of Africa and evolve in homo sapien however in modern human, the nuclear gene can be traced back from Africa Question 11: https://www.youtube.com/watch?v=MJP-UPhELFY BBC Homo Neanderthalensis en Homo Sapiens https://www.youtube.com/watch?v=zOQ1mMocUMk Science Matters: Evolutionary History of the Human Species ** evolutionary biologist Christopher Wills Picture adapted from: http://www.theguardian.com/science/2013/jun/02/why-did-neanderthals-die-out

Why did the Neanderthals die out? Homo neanderthalensis dominated Europe and co-existed with Homo sapiens on this planet, but were replaced by the latter around 60 thousand years ago. Why? Answer 11:

******************************************************************************** Question 12: https://www.youtube.com/watch?v=_IXTUns1Q68 Science Bulletins: Tibetans Show Recent Evolution https://www.youtube.com/watch?v=vr6Y0vQWyNM Special Gene Possessed by the Sherpas - The Effect Of Restricting The Production Of Red Blood Cells https://www.youtube.com/watch?v=NnlwnXe2Vh4 5 Copyright © Monash University 2019. All rights reserved. Except as provided in the Copyright Act 1968, this work may not be reproduced in any form without the written permission of the host Faculty and School/Department.

Are Humans Still Evolving? Has evolution in human stopped? Watch the YouTube videos, discuss and provide evidence to support your argument.

Answer 12:

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GEN3040 in-class concept questions for Lectures 13-15 (Evolutionary genomics) Questions: 1) What are the new mutants emerged after (and before) the split of modern human and archaic human? ● Blue color triangle alleles/gene emerged in modern day human ● Red star (from archaic human) but modern day human shares the same alleles because of genetic introgression from interbreeding 2) What do Neanderthal and Denisovan DNA do? What survival advantage did they confer on our ancestors?

pink are african population blue are non-african population only non-african population interbred with neanderthal and denisovan (15k years ago) (Figure 1 will be shown in class) ** Pink and light-blue chromosomes = DNA fragments from two modern human populations ** Yellow chromosomes = DNA sequence from an extinct archaic population ** Archaic human population split from the modern human population more anciently than the two modern populations split from each other. ** Red stars = mutations occur in the archaic population --- are passed on to the ancestors of the light-blue modern population via genetic introgression ** Dashed line = admixture (genetic introgression) ** Red star mutations are swept to high frequency by selection 7 Copyright © Monash University 2019. All rights reserved. Except as provided in the Copyright Act 1968, this work may not be reproduced in any form without the written permission of the host Faculty and School/Department.

** Green star mutations = Mutations in the genealogy that are not uniquely shared ** Blue triangle = Mutations linked to evolution in modern human (Figure 1 will be shown in class) (1) Examples of mutations linked to evolution in modern human (Blue triangle ): ** Language gene = FOXP2 ~ Comparative analyses between chimp, Neanderthal and modern huam revealed a “language gene” named FOXP2, which had emerged in 500 kya (thousand years ago) (before split of Homo sapien and other Homo species) ~ New mutant of this FOXP2 gene was found in common ancestor of modern human and Neanderthal population, to permit them to enunciate as we do. ~ However, vocal communication is unique to modern human because of: (a) high speed facial movement on Homosapien that allow enunciation (b) homosapien evolve into larger brain size ** Brain size gene = ______ASEM________ ~ control brain size --- human brain volume has more than tripled since chimp-human ancestor (2) Examples of mutations occur in the archaic population --- are passed on to the ancestors of the light-blue modern population via genetic introgression (Red stars ) -EPAS1 ~ Adaptive introgression = closely related species can benefit from interbreeding ~ A species expands into a new territory --- new challenges (e.g. different climate, food, predators and pathogens) --- 2 strategies to adapt to new environments: (a) inherited gene from Denisovan due to genetic introgression from interbreeding of Denisovan and modern day human -> hence adaptation to highland (eg: EPAS1) (b) spontaneous mutation giving the new version of the gene (eg: mutated EPO gene) that increase the uptake of oxygen by 50% (eg: the cross country skier Eero Mantyranta) ~ useless Nea/Den DNA likely to be lost ~ beneficial DNA likely to be retained. Examples: Introgressed Gene / chromosome

STAT2 (chrom. 12)

Putative archaic source population

Function (usually skin color or immune system)

Population where selection occurred

Human immune system -

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HYAL2 (chrom. 3)

EPAS1 (chrom. 2)

BNC2 (chrom. 9)

POU2F3 (chrom. 11)

denisovan

increase the oxygen capability

Tibetan (90% of the population)

Related to skin pigmentation

70% of European

affecting the skin cell

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