SexBias

males and females differ in physical traits and behavior

• occurs in most higher eukaryotes

male

-> often deleterious

troguh sexual selection

• male male competetion

• female choice

-> traits involved in male repoduction tend to evolve fast

• differential gene expression of genes that exist in both

• those that are expressed at a higher level in one sex than in the other

• determined thrpugh mircoarray or RNA-Seq

M/F = Male/female expression ratio

M/F > 2 = male-biased gene (MBG), log2(M/F) > 1 = MBG

M/F < 0.5 = female-biased gene (FBG), log2(M/F) < –1 = FBG

0.5 < M/F < 2 = unbiased gene (UBG), –1 < log2(M/F) < 1 = UBG

2000 MBG

2000 FBG

9000 UBG

30%

2800 MBG

4000 FBG

85% classified with very high replication

MBG

• MBG underrepresented on X chrom & FBG enriched

• 11% MBG on X

• 21% FBG on X

• 16% UBG on X

The Baseline: Females have two copies of the X chromosome (XX), while males only have one (XY).

The Mechanism: To balance this, Drosophila doubles the expression of the male X in somatic tissues, but this dosage compensation does not occur in the male germline (testes).

The Consequence: Because X-linked genes cannot achieve the high expression levels required for male reproduction in the testes, MBGs are suppressed on the X, driving a selective pressure for them to "escape" to autosomes.

The Problem: Expression of a male-biased gene can have a deleterious (harmful) effect if it gets turned on in females.

The Chromosomal Math: Because the X chromosome is inherited via XX females and XY males, it spends twice as much time in females (2/3 of its history) as it does in males (1/3 of its history).

The Outcome: Due to this asymmetry, evolutionary selection favors female interests over male interests on the X chromosome. This actively reduces or suppresses the expression of male-advantageous (but female-harmful) MBGs on the X.

The Mechanism: In Drosophila and mammals, the X chromosome becomes transcriptionally inactive (suppressed) during the process of spermatogenesis (sperm production) in the male germline.

The Consequence: Because many MBGs are highly active during sperm development, an X-linked location would completely block their expression when needed. This creates strong selective pressure for these testis-expressed MBGs to "escape" the X chromosome and move to autosomes via retrotransposition.

• compining expression date & comperateive genomic

• measure by Ka or Ka/Ks

MBG at nonsynomous sites

-> indicating faster rate of protein evolution in MBG

-> most strongest in reprodctive sites

-> FBG > UBG

1. MBG are under less selective constraint

   • accumulate many neutral aa changes that have no effect on fitness

2. MBG are subject to more positive selection

   • accumulate more adaptice aa replacements

The Logic: Natural selection is highly efficient in high-recombination zones because it reduces genetic interference (Hill-Robertson effect). Genetic drift (neutral evolution) is independent of recombination.

The Test: A positive correlation (faster evolution in high-recombination zones) directly supports Positive Selection because adaptive mutations are fixed more efficiently. A flat or negative curve would support Relaxed Constraints.

Drosophila Result: MBGs show a strong positive correlation, proving Positive Selection drives their rapid evolution and refuting relaxed constraints.

Relaxed Constraints: Predicts a parallel increase in both polymorphism and divergence (proportional/positive correlation), as neutral mutations accumulate and drift to fixation at equal rates.

Positive Selection: Breaks the correlation. It predicts low polymorphism (because selective sweeps rapidly wipe out variation) combined with high divergence (rapid fixation of adaptive traits between species).

Drosophila Result: MBGs show high divergence but low polymorphism, supporting Positive Selection and rejecting pure relaxed constraints.

in genetics refer to specific nucleotide locations within a protein-coding gene where a mutation can occur without altering the final amino acid sequence

1. The Core Concept: The MK test compares the ratio of non-synonymous (N) to synonymous (S) changes across two categories: Polymorphism (P, within species) and Divergence (D, between species).

2. The Neutral Baseline: Under strictly neutral evolution (or relaxed constraints), the ratios must be equal because mutations drift to fixation at the same rate they appear:

   Ds​/Dn​​=Ps​/Pn​​

3. The Signal for Positive Selection: If positive directional selection is actively driving rapid amino acid changes, it accelerates fixation between species while sweeping away variation within the population. This skews the ratio:

   Ds​/Dn​​>Ps/​Pn​​

4. The MBG Result: Hoden-specific MBGs consistently show an excess of non-synonymous divergence (Ds​Dn​​>Ps​Pn​​), statistically proving that positive selection (and not relaxed constraints) drives their rapid evolution.

X linked show stronger signal

• (Dn/Ds)/(Pn/Ps) = 3,4

• highest divergence

• rate of adaptive evolution is expected to be faster on X chrom if beneficial muation are on average recessive

• immediately seen by selection in males on X -> because hemizygous for X chromosom

• for autosoms needs longer until mutations freq high enough

1. 
   

   • The Mismatch: Because the X chromosome evolves so rapidly (Fast-X Effect), its genes drift away from the rest of the genome. In a hybrid male (XY), this unique X chromosome can no longer interact or "cooperate" with:

     1. The Y chromosome of the other species.

     2. The Autosomes (normal chromosomes) of the other species.

        
        

   • The Fatal Trap: Proteins from the X and these other chromosomes must work together to build sperm. Because the hybrid male is hemizygous (XY), there is no second, healthy X chromosome to mask these broken interactions.

   • The Outcome: The genetic network collapses, leading directly to complete hybrid sterility.