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85 Cards in this Set

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What are some features of retroposed pseudogenes?
* No introns
* No regulatory sequences
* Already been processed through txn
* Impossible for duplication of blocks of genes
* Poly-A tail
* Duplicated unlinked to original
* Individual genes retrotransposed, unless entire operon
What does it mean to be processed?

What does it mean to be a pseudogene?
What are 2 ways that paralogous genes can maintain same function after duplication? How can these processes be distinguished?
1) Gene Conversion/Concerted Evolution - 2 paralogous genes have similar functions

2) Purifying Selection - Selective forces that prevent against mutations allowing paralogous genes from diverging

These 2 ways are distinguished by looking at *silent* gene mutations. Synonymous gene mutations cannot be affected by purifying selection thus we would see silent mutations. Gene conversion homogenizes duplicated genes, thus we would NOT see silent mutation differences.
Think about synonymous mutations
Discuss the RNase enzymes in colobine monkeys, in particular the roles of positive selection and relaxation of purifying selection.
RNase -> Originally used to break down RNA in body
Duplicated RNase1B -> Duplicated copy changed to break down rapidly-dividing benificial bacteria in stomach before food moved to intestine.

Positive Selection -> RNase1B under pressure by more acidic stomach environment
Relaxation of Purifying Selection -> Due to fact gene was *duplicated* thus, a functional copy still exists
How is positive selection detected in the RNase/Colobine monkey example?
See duplication of gene.

This duplicated gene goes through rapid cahnge/evolution.

Mutations are *non-synonymous* which is opposite of purifying selection.
Compare positive selection to purifying selection
What are 2 models for Functional Specialization & Neofunctionalization? Explain.
1) Dykhuizen-Hartl Effect
- No positive selection required
- Result of neutral evolution
- After gene duplication, random mutations fixed in 1 of 2 genes due to gene redundancy
- Example of RELAXED PURIFYING SELECTION
- Upon change in environment or genetic background, these cause new gene function

2) Alternative Model
- Requires positive selection
- Specialization occurs either before or after gene dup'n
- After, few nuetral substitutions create new/weak fnc. + selection accelerates fixation of advantageous mut's
- Before, ancestral gene already has 2 functions. Subfunctionalization
Although both models are not named after each respective effect, they discretely describe each.
What are 2 examples of Neofunctionalization? Explain.
Neofunctionalization -> duplicated gene acquires novel funciton

1) Totally unrelated new function such as duplication of RNase in humans created antibacterial agent

2) More likely, possibility for related functions such as duplication of Opsin gene lead to red & then green sensitive eyes
What is neofunctionalization? What are its 2 extremes?
What are all possible gene fates of duplicated genes? Explain.
1) Neofunctionalization

2) Redundancy
a) Pseudogenization/LOF
b) Neofunctionalization in
CODING sequence
c) Neofunctionalization in
REGULATORY sequence
d) Subfunctionalization
(partial redundancy)
- "C" and "D" can both lead to further neo and/or sub fnc'n
See Figure 1 of "The Evolutionary Dynamics of Plant Duplicated Genes"

There are 4 fates for a gene that is redundant
What is an example of subfunctionalization in plants?
MADS-box gene family which controls vegitative & reproductive development.

Duplication of gene (AG-like) expressed in stamens & carpels. One become expressed solely in stamens (ZMM2) and other solely in carpels (ZAG1)
Think of subfunctionalization through changes in regulatory sequences.
Describe 1 way plants can evolve recognition to novel pathogens.
* Duplication of defense genes
* Cause evolution of different pathogen recognition functions & defense mechs from SAME ancestral genes
* Purifying selection will be relaxed due to multiple gene redundancy, greater ability to evolve/adapt through positive selection pressure by pathogen
2 chefs are better than 1.
What is "Concerted Divergence"? Discuss.
A phenomenon that occurs when 2 interacting genes (with no homology) are both duplicated and their duplications both diverge "in concert" together through expression or function.
Lets get together and diverge!
What is reciprocal loss?
When opposite members of a gene pair are lost in 2 daughter species. See figure 1 in "Multiple Rounds of Speciation Associated w/ Reciprocal Gene Loss in Polyploid Yeasts"

- Also refers to silencing of reciprocal copies of genes in different organs (copy A expressed in liver, B expressed in heart)
Genes have 2 copies. What does reciprocal mean?
What is duplicated gene silencing?
Phenomenon where upon gene duplication, one copy is silenced (through expression regulation) to prevent over-dosage of gene product
C'mon... you know this.
How does reciprocal loss or gene silencing result in "Speciation"?
- "Divergent Resolution"
- When daughter species/populations mate (or have allopolyploidy event), hybrids lack both copies of gene
- Leads to hybrid inviability, reproductive isolation, and SPECIATION
Think about effects of reciprocal gene loss
What is an allopolyploid?
A polyploid event that leads to an organism w/ chromosomes from >1 species

EG: Triticale = 6 chromosomes; 4 from WHEAT, 2 from RYE
AKA Amphiploid. Diff species involved...
What kinds of changes in genome structure & expression can occur following polyploidy?
- Expression @ EQUAL, UNEQUAL, or COMPLETE GENE SILENCING
- Larger nucleus to hold more genetic information
- Gene Silencing COMMON in polyploidy events
- Differential expression/silencing in different organs
- Epigenetic regulation of silenced genes -> histone modification, gene methylation
Think visually about these aspects. What happens to expression as well?
What are some possible mechanisms for gene silencing?
- epigenetic regulation
- cytosine methylation
- histone modifications
- positional effects from higher-order changes in CHROMATIN structure
- Mutations in PROMOTER or OTHER cis-acting elements

- Post-transcriptional silencing as well? Sequence marked for degradation?? I dunno
Think of normal gene regulation mechanisms
What are some hypotheses for why some genes are silenced in polyploids?
- Result of something higher up in chromosomes (i.e. packing requirements)
- Dosage requirements prevent over-expression of gene
- In allopolyploids 1 gene copy may better interact w/ other proteins/enzymes
How can reciprocal gene loss have an effect on fitness & reproductive isolation in a hybrid?
- Changes location of functional copy of gene
- 50% chance that offspring of 2 reciprocal gene orgs will have nonfunctional gene @ reciprocal locus
- If this gene is responsible for reproductive traits, results in LESS VIABLE offspring.
- Bateson-Dobzhansky-Muller Model
Think of case where reciprocals mate!
How is passive gene loss (in duplicated genes) a mechanism for establishment of reproductively isolated lineages?
Passive Gene Loss - NO selection pressures to retain a duplicated gene.
- In case of 2 different special haploids fusing to become a diploid that cannot form viable spores, but still be able to divide mitotically
- If diploid continues to divide, it may lose alleles from every locus that is NOT haploinsufficient??
- Upon mating of diff lineages arising from this, we get inviable spores (reciprocal gene loss has double null mutants)
Hrm... not sure about this one
What is haploinsufficient?
A genetic loci w/ only 1 wild-type allele present.
What are speciation genes?
- Genes that diverge in function DURING or SOON AFTER speciation

- Generally contribute to differential adaptation between species

- Contribute to lineage isolations, which leads to speciation
:P
Discuss the Sequence Evolution of odsH and unc-4 (Figure 2; Gene Duplication and Speciation in Drosophila)
- The figure depicts how unc-4 and odsH diverge after gene duplication event.
- Certain subset contains unc-4, others contain odsH
- Rate of nonsynonymous mutations increasing further down evolutionarily recent timeline in Drosophila
unc-4 and odsH from single genetic duplication event.
What did researchers find with the rise of the duplicated gene, Odysseus in Drosophila?
- OdsH duplicated shortly before speciation event
- This duplication allowed it to gain new function (redundancy)
- Because of speciation, new copies are VERY free to diverge in order to further isolate new species from ancestor
- Helps out in speciation
- Thus it is a "speciation gene"
- Caused sterility in unc4/odsH hybrids -> drives speciation further
- Fast rate of evolution
What was unique about this gene duplicating around speciation? Speciation Gene.
What is a homeolog?
A pair of genes duplicated by polyploidy
What are paleopolyploid events?
Ancient polyploidy events older than 10 million years
Think of root words!!
How many molecular mechanisms are there for creating new genes?
1) Exon Shuffling - ectopic recomb of exons and domains from DISTINCT genes

2) Gene Duplication - classic model of duplication w/ divergence

3) Retroposition - New gene duplicates are created in new genomic positions by reverse transcription & reinsertion

4) Mobile Elements - IE a transposable element (TE) directly recruited by host genes

5) Lateral Gene Transfer: Gene laterally transmitted b/t organisms. I.E. transfers from org A to org B which then diverges to form org C

6) Gene Fusion/Fission: 2 adjacent genes fuse into 1, or vice versa

7) De novo - Coding region originates from a previously non-coding region
There are 7 different mechanisms
Discuss the *formation* of the jingwei gene in Drosophila.
- Ancestor contained 2 single-copy genes 1) yellow emperor and 2) Adh.
- Yellow emperor was duplicated at some point
- duplication from ymp became yande, and diverged
- Just before speciation, Adh mRNA retrotransposed into 3rd intron of YANDE
- Adh mRNA recombined w/ first 3 yande exons to create JINGWEI
3 main actors. Yellow emperor, Yande, and ADH. Figure it out from there!
What are some *characteristics* of the jingwei gene in Drosophila.
- The first YOUNG gene to be studied in depth
- 2 million years old
- chimeric protein b/t ADH and yellow-emperor
- Novel mashup of functioning
?
What is the "Waiting Model" for duplicate gene evolution?
Duplicated genes are still expressed, must wait through neutral mutations until a significant mutation takes place that causes FUNCTIONAL DISTINCTION
- For now, duplicate copy has redundant functioning
What is the "Immediate Model" for duplicate gene evolution
Adaptive Evolution plays a role in creation & evolution of new genes
- No waiting time for evolution of new function.
- Evolution of recently created genes is accelerated, see immediate functional changes.
Give an example of CONVERGENT gene evolution.
- Antifreeze Glycoproteins in ANTARCTIC NOTOTHENIOID vs NORTHERN COD
- Sequences nearly identical, but from different ancestors that did not bear this antifreeze gene
- Looking at sequences, we see differences in exon-intron structure & phylogenetic distribution
In paper "Origin of Sphinx, a young chimeric RNA gene in D. melanogaster", how was sphinx gene detected in the organism?
Made a probe out of ATP synthase chain F gene and ran FISH and Southern Blot on multiple drosophila including melanogaster.

FISH -> Visualization of probe in *2* places only in melanogaster
SOUTHERN -> Shows band for sphinx only in melanogaster
2 common methods used. FISH & Southern.
Discuss the origin of Sphinx.
- 2 to 3 MYA
- A chimeric gene
- Recruited 1 intron/exon sequence w/ regulatory elements from an unknown sequence
- Recruited a 2nd exon from a retroposed sequence of ATP synthase chain F
- Independent TE called "S" travelled w/ this fragment
What are the 3 hypotheses for this origin of Sphinx
1) Retropositioned element landed into the S sequence located in the current position of SPHINX

2) Retropositioned sequence landed into S sequence which then moved to current position

3) S was upstream of ATP and was cotranscribed together to new location
Diff combinations of 1 event
What is the evidence that SPHINX is an RNA gene?
1) No ORFs w/ significant coding potential
2) Computational evidence shows nonsynonymous polymorphisms in 1st and 3rd ORFs = no protein-encoding constraints imposed by normal protein coding region
What is the evidence that SPHINX is FUNCTIONAL? How strong is this evidence?
1) Experiments shows recruitment of exon/intron w/ experimentally regulated sequence

2) Development & Maintenance of well-defined splice sites -> uncharacteristic of pseudogenes

3) Sexual & Developmental specific splicing

4) In/Del mutations are found ONLY in NONCODING regions -> functional constraints

5) Higher substitution rate than nonfunctional sequences; due to positive selection

* Very strong evidence, especially b/c pseudogenes are rare in drosophila
pseudogenes...
What are some ways that DNA TEs can modify gene regulation?
1) TEs can contain a promoter that changes expression of gene it inserts itself into

2) Insertions in promoters or other regions alter tissue-specific patterns of expression

3) Insertions of transposon footprints (leftovers of TEs once gone) can be sustained by genes/regulatory seq's

4) Some non-autonomous elements function as introns -> modifies alternative splicing.
4 ways
How are corn kernel phenotypes used to study transposon behavior?
- Corn kernel phenotypes are unstable
- White kernel -> has TE
- Pigmented kernel -> has NO TE
- Large pigmented spots -> early excision of TE
- Small pigmented spots -> late excision of TE
Think about bio 335
What is the "C-Value Paradox"?
Paradox that states there is a lack of correlation between an organism's complexity and its genome size
correlation...
Explain how LTR TEs help account for the "C-value Paradox" in grass genomes.
- LTRs are LONG TERMINAL REPEATS
- Single largest elements in plant genomes
- We see a correlation w/ fraction of LTRs and genome size
Describe how the time of retrotransposon insertion (of LTRs) can be estimated... (See Figure 3 of "Plant Transposable Elements: Where Genetics Meets Genomics")
We look at sequence divergence of each LTR from the baseline LTR. The fewer changes an LTR copy has, the newer it is.

Factor this in w/ known nucleotide substitution rate for the organism of question, and you know how old the LTR is.

Think... NESTED LTRs

See Figure 3
Think "Phylogenies"...
What are 4 ways in which new insertions of retrotransposons can be regulated? Which one is most common for PLANT LTRs?
1) Transpose under biotic stress
2) Transpose under abiotic/environmental stress
3) Epigenetic Silencing -> Methylation of Cytosine, etc...
4) Post-Transcriptional Silencing -> RNA helicase, SNase degrades mRNA transcripts

* #3 is most common - transcriptional regulation. This is b/c the plant has a defensive mech that disables "inserted" DNA since it thinks the DNA is viral!
-----------

1) Transcription
2) Translation
3) reverse txn
4) cDNA
How are phylogenetic analyses done w/ TE sequences?
- Computational analysis
- Multiple alignment of ALL 191 Ty3/gypsy reverse transcriptase AA sequences in arabidopsis
- Phylogeny shows HETEROGENOUS families of LTRs
- Active Transposase can be reconstructed through phylogenetic analysis using subset of inactive TE copies
Could phylogenetic analyses be done w/ non-autonomous elements?
- Yes, but we'd need a transposase present to excise the LTRs to see where they're defined
?!?! FIX ?!?!
Explain how stress-induced mobilization of the Tnt1 retrotransposon from TOBACCO was detected
- Isolation of plant protoplasts activates stress response that start txn of Tnt1
- Some Tnt1-encoded mRNAs converted into ds cDNA
- These DNA frags insert into genome
- Now, the DNA is digested w/ EcoRI
- "ADAPTORS" are ligated to ALL frags, mix used as template for 1-2 rounds of PCR
- PCR uses primers good for Tnt1 TE sequences
- New integration events appear as ADDITIONAL BANDS on blot

SEE FIGURE 4?!

Dont understand how/why bands are lower...
?!?! FIX ?!?!
How are retrotransposons epigenetically regulated by transcription silencing?
Cytosine Methylation; Heterochromatin
- Thought to be a defensive mechanism to prohibit importation of "foreign" matter into a gene
- Prevents retroviruses from doing harm (use similar mech to TEs)
Think retroviruses?
Explain how genes flanking the retrotransposons are silenced or activated
- Epigenetic changes

SILENCING - High expression of antisense transcript can cause dsRNA & subsequent post-txn gene silencing as cell thinks its foreign RNA from virus

ACTIVATING - LTR as alternative promoter to gene's normal promoter whose readout activity is same orientation as adjacent genes txn.
What are the steps in a LINE's lifecycle? How many?
SHORT ANS: Transcription, Reverse Transcriptase, Random Insertion into Genome

LONG ANS:
1) Full-length replication competent L1 is transcribed
2) RNA is transported to cytoplasm where ORF1 or ORF2 are translated & form ribonucleoprotein particle
3) This particle associates w/ the RNA that encoded it
4) Activation of retrotransposon occurs, RNP imported into nucleus
5) L1 RNA rTranscribed at target site using "target-primed reverse transcription" (TPRT)

*** IT COPIES ITSELF, not EXCISES! ***
Pretty simple... similar to retrotransposons except for ONE key difference!
Explain the mechanisms by which LINE-1 retroelements can disrupt genes.
1) Gene disruption... it inserts a copy w/in an active gene

2) Non-allelic homologous recombination... Same LINEs on non-hom chromosomes cause recombination which leads to +/- genetic material, lead to translocation?

3) Deletions/Rearrangements... These are reported to sometimes occur at the target site of L1 insertion. Gene @ site disappears or is reversed/rearranged

4) Alternative splicing... Create exon splitting / alternative splicing due to insertion into intron
There are 4 main ways
Explain ways how LINE-1s can generate functional alleles.
1) Epigenetic Regulation... L1 sequence becomes methylated, initiate heterochromatin formation, repress txn of nearby genes

2) 5' or 3' transduction... upstream or downstream sequences (respect.) transcribed together with L1 & copied to multiple sites

3) Transcriptional Elongation Defects... The longer the piece of L1 that is copied into a gene's intron, the stronger its attenuation (weaker expression)

4) Premature Polyadenylation... insertions into a gene can truncate txn, creating novel protein isoform

5) Gene Breaking... Full-length antisense L1 insertions into introns & cause txn truncation as well as create downstream transcript init @ L1 antisense promoter. Createas 2 transcripts from 1 gene -> subfunctionalization?!
There at 5 main ways
How is it that maize AND barley both exhibit a gene colinearity that is present in some but not all strains?
- Helitrons
- HelA and HelB responsible (3 genes in 1, 1 gene in other)
What paper is this from?
Genes were missing in the bz region of B73 strain maize, yet they are found elsewhere in the genome. Are these missing genes adjacent to one another at the alternate locations?
- Took the McC strain that had the genes present at specified region and sequenced it
- Used sequence and "BLAST-N"'d the sequence agains the B73 strain
- RESULT: Found 99% ID with McC bz region in other ares of B73 line. As well, at least SOME genes are neighbors -> 2 and part of a 3rd gene are 1 contig, rest of 3rd and 4th another contig
Easy one... think about it
Why is the HelA helitron present in some maize lines but not in others?
- This is b/c helitron never visited these lines. If it did, and "left" again, we would still have evidence b/c HELITRONs thought to copy-paste, not cut-paste
Compare HELITRONS with MULE TEs
1) Most sequences captured by both are FRAGMENTS, not whole

2) 1 element can have >1 fragment

3) sequence acquisition at the DNA level -> conservation of introns, transcripts initiate w/in or outside element

4) Potential to create new genes through multiplication
4 different ways
What is the ROLLING CIRCLE MODEL of helitron replication & gene capture?
1) Nic sequence at 5' end
2) Polymerase works its way across fragment(s). Normal 3' palindrom termination signal bypassed -> cause capture of adjacent sequences until NEW pallindrome found.

3) This creates 1 strand that forms a ss circle.
4) This strand now becomes template for 2nd strand.

*** Capture of whole vs fragment of gene depends on where helitron inserted itself
2 part question. Remember, its not replicating circular bacterial DNA
What causes the C-value paradox/enigma?
Amplification & proliferation of "repetitive fractions of the genome"
- LINES
- SINES
- LTRs
Why is Gossypium (cotton) a good genus/group to study for genome size variation?
- Wide range of species that have wide range of genome sizes
- range from 88 Mb (raimondii) to 2460 Mb (exiguum)
- Allows authors to create a phylogeny of the species, and see why/where they differentiated
How did researchers estimate copy numbers of transposon types?
- Took a sample from the genome and made a good estimate from that sample as to the copy number
- Then, using formula, extrapolated that data based on the size of the genome from the species they looked at
extrapolation...
Compare amt of different types of TEs in Gossypium
Majority of TEs are LTRs, especially in larger genomes.

- LTRs comprised 9-40% of genomes

- LINEs were pretty strong, but were 2.8 to 5.1% of genomes
Compare amt of TEs compared w/ tandem repeats (TRs) in Gossypium
Class II TEs (cut and paste) and Terminal Repeats were less abundant/rare
- Obviously because they don't regularly copy themselves

TE I's DO copy themselves, so they are WAAAAAAY more abundant
In the Gossypium paper, how did the authors analyze the sequence relationships among the gypsy TEs? What did they find?
- Analyzed through BLAST analysis

Found 3 distinct types gypsy-like TEs
1) Gorge1 - sim to arabidopsis gypsy seq
2) Gorge2 - sim to maize seq
3) Gorge3 - sim to lillium henryi seq
Why is Gorge3 a recently active TE?
1) High level of seq ID to G45/G84 which are both currently txnly active TEs
2) Shows high seq ID to 165 present ESTs
3) Large # of Gorge-3 found in Whole Genome Shotgun sequencing (What does this mean? Lots of copies not divergent).

- All show it hasn't had time to mutate much since its active days
3 different reasons. Think of mutational divergence over time...
Where in the Gossypium genome do they think genome evolution occurs?
- Many high-copy #s of LTRs shown to accumulate in HETEROCHROMATIN

- Eurchromatic regions are HIGHLY CONSERVED

- Looked at 104 kb strand of contig seqs surrounding a gene. Found no evidence of genome size variation/evolution present
What would be an alternative approach to studying genome size evolution w.r.t. TEs? How would the info obtained be different from/complementary to what was found in study?
- FISH of TEs to examine if classes of TEs fall into characteristic places, or all found randomly in heterochromatin?

- FISH visually proves where most class I TEs have inserted

- Look at variation of intron lengths for common genes, even though this has been proven to not happen by literature

- Look at TR copy numbers; could be up to 20-fold increase sez one paper?
What characteristics of mitochondrial DNA make it useful for studying history of human populations?
1) High copy # due to...?

2) Lack of recombination; non nuclear genetic material

3) High substitution rate; quickly diverge

4) Maternal mode of inheritance
4 ways
A phylogeny tree was created for using each species' mDNA. How does excluding mDNA's D-loop help this analysis?
- Increased bootstrap values between species, thus increasing confidence in phylogeny trees.

- D-loop exhibits homoplasy

- Homoplasy = sequence similarities that arise due to convergent evolution, not common ancestor
What is homoplasy?
What is homoplasy?
- Sort of opposite of homologous
- Similar sequences across organisms that look homologous but are in fact similar due to convergent evolution
- Gives false confidence when creating phylogenies using this data
Convergent evolution
What differences exist between mitochondrial DNA and Y chromosome data?
- Looked at aboriginal populations in Australia & NG
- Mitochondrial diversity GREAT b/t populations
- Y-chromosome diversity not so much -> 1 haplotype found in 50% of males
- Homogenization of mDNA W/IN tribe which leads to genetic drift & observed divergence!!!
- Multiple Wives = less Y chromosome diversity?
What is DNA barcoding?
Process of rapidly identifying species based off of an agreed-upon sequence that shows:
- little intraspecific divergence
- large interspecific divergence
Why do we need DNA barcoding?
- increase in extinction rates
- large task ahead of us (1-2 million classified, 10 million total)
- difficult to ID species due to cryptic species/morphology
Give examples of how DNA barcodes helped
1) resolve ID difficulties
2) define cryptic species
3) reveal undescribed species
1) Cave-dwelling spiders w/ small adult population meant it was hard to use morphology of "kids"/larvae to determine species

2) Parasitoid Flies: Originally thought to have 3 species, found 15 out of them due to high morph simil.

3) Springtail bird in Canadian Arctic. Identified 2nd species
think about what would cause each type of problems
How is DNA barcoding done?
1) Select 648 bp seq. from CoI gene in mitochondria

2) Extract from specimen & amplify w/ PCR; sequence amplification

3) Use this as "barcode" and run through DB of previously-found species seqs. - If w/in 10% variation of 1 species, thats its species.
- If >10% variation, it is a new species not found in catalogue
What are some limitations of DNA barcoding?
1) DIMINISHED RESOLVING POWER - Some species have particularly slow mutation rates of mtDNA (Cnidarians).

2) INTRASPECIFIC VARIATION OVERLAPS WITH INTERSPECIFIC RANGES - species have such high variation w/in itself that this range overlaps w/ interspecific ranges and prevents you from determing species (Amphibians)

3) INDELs - complicate alignments & inferences about species (Gastropods)
Cnidarians, Amphibians, Gastropods
What are some criticisms of barcoding?
1) Unscientific b/t it generates INFORMATION, not KNOWLEDGE; no testing of a hypothesis

2) Skeptical of the utility of DNA barcoding

3) DB of species a way for 1st world countries to monopolize taxonomic info

4) Lack flexibility of committee style consensus of existing botanical & zoological codes
How are X & Z chromosomes similar?
- superficial similarities b/t X & Z
- both large chromosomes
- both bear many genes w/o much to do w/ sex determination
How are Y & W chromosomes similar?
- involved in male sex & spermatogenesis
- small
- highly heterochromatic
- retain FEW active genes
Discuss characteristics of sex chromosomes in fish.
Fish seen to be of 3 different types
1) Gonochorists - genetic/polygenic/temp/enviro dependent determination

2) Hermaphrodites - change sex based on needs

3) Unisex species - all female

** Some are male heterogametic, others are female heterogametic **
What evidence is there that some fish sex determination systems have evolved RECENTLY?
- Homomorphic sex chromosomes required before transition b/t sex-determining systems
- Highly diff/degraded sex chroms could be lethal (YY or WW)

- EVIDENCE: Morph differentiated sex chromosomes ID'd in only 10% of fish studied. Thus, highly homomorphic
- EVIDENCE: minimal sequence diff b/t sex chromosomes
- EVIDENCE: observed that seqs that are sex specific in 1 species are autosomal in another
What are features of sex determination mechanisms & chromosomes in different birds? Discuss some of these diff sex chrom morphologies...
- All species tested carried ZW system
- Z is uniform and large
- W varies from homomorphy to large variation to Z
- This variation of W depends on if bird can fly or not.
- No W-contained female determinants found.
- Perhaps Z-dosage dependent male determinants?
How are X and Y chromosomes thought to have evolved from AUTOSOMES?
- 1 member of chromosome pair acquires a sex-determining gene
- It obtains more male-advantage alleles over time
- Recombination becomes suppressed due to lack of homology
- Copy becomes fixed as a MALE sex chromosome
- Mutations/deletions rapidly degrade this chromosome
- Know X and Y were a pair b/c they share a "pseudoautosomal" region
- Explains why X doesn't have many "sex-determining" genes on it
Discuss how X and Y contain ancient & added regions. How does the chicken genome sequence compare to human X and Y?
- comparison of X crhom of marsupials, monotremes, humans
- Used FISH to show 1 ancient region common among all X chromosomes
- These are all very diff groups so common ancestor must be OLD
- Genes in recently-added X region lie in SAME ORDER on chicken chrom 1
- Genes in ancient region X region lie largely on chicken chrom 4p
- Y shows corresponding ancient & added regions, albeit very different in size to X. Also has few genes transposed from OTHER chroms
Why do some genes on X escape X chromosome inactivation? How is X chromosome inactivation thought to have evolved?
- Some genes require the double dose given to operate properly
- Other genes may be located on a relatively NEW region of "X" not yet recruited into X-inactiv
- The X chromosome becomes txnly silent @ embryonic stage

- As a gene on X has its Y counterpart "Deleted", if it has deleterious dosage effects, it will more likely be part of inactivated region. Otherwise, it isn't a big deal to get extra dosage in XX, and thus is left alone.
*** Clustering of regions NOT affected by silencing shows lag b/t Y-degredation & X-chrom inactivation ***

- Caused by evolution/addition of heterochromatic regions at embryonic stage?

- Occured as Y degraded -> histone mod, DNA meth, binding to RNA
What are some hypotheses to the origin of SEX, REPRODUCTION, and BRAIN genes on X? What accounts for some being involved in both reproduction & brain function?
1) Genes recruited to "X" from other locations in genome (unlikely due to little change from ancestor)

2) Genes on "X" w/ generic fnc in BOTH sexes acquires new roles due to SEX-SPECIFIC selection

3) An autosome well-endowed w/ these types of genes was chosen as a SEX-CHROM

- Genes involved in both R & B due to generic ancestor genes being under 2 selective forces at once, shaping it for dual-purpose
- If woman could see big brain, she knows he is reproductively fit?!
3 possibilities
How do some genes functioning for brain AND reproductive systems affect speciation?
- These genes on the X-chromosome have a propensity for attracting more of the same type of genes.
- Creates pre & post-mating reproductive barriers which drive subpopulations into isolation
- This causes speciation
Discuss the fate of genes on the Y chromosome...
- These genes mainly for sex determination
- Most genes on Y fall into one stage or another of evolutionary degradation/divergence from X
- Some active, others partially active, yet others completely inactive & soon to be deleted