Download Variation

phenotype - morphological, physiological, biochemical or
behavioral characteristics, resulting from a variety of sources
genotype - genetic constitution (of an organism or a population)
e.g., A1A1 or A1A2 or A1B1 / A1B2, etc.
i.e., homozygote, heterozygote, multilocus
gene - classically phenotypic, but technically a DNA sequence
that is transcribed and translated into protein, as well as its
related promoters and modifiers
allele - a version of a gene
haplotype - a haploid genotype or allele (it the alleles are
distinguished by nucleic acid sequence), or a profile of alleles
(e.g., fingerprint)
mutation - verb: alteration of genetic material; noun: an altered
form of genetic material
locus - a position or site on a chromosome, as small as a base or
as large as a gene
polymorphism - more than one allele at a locus in a population
polygenic trait - more than one locus controlling a phenotype
additivity
phenotype of offspring is due to the combined or "added" effects
of 2 or more loci
A allele adds one unit of effect to phenotype
B allele adds two units
genotypes

effect

B 1 B1
2
B1B2
4
B2B2
6
A1A1
3
A1A2
4
A2A2
5
5
7
9
6
8
10
7
9
11
dominance - the property of one allele affecting phenotype to the
complete or incomplete exclusion of another allele
may be rare or common or neither, advantageous or deleterious
or neither
recessive - opposite of a dominant allele
epistasis - nonadditive interaction of two or more loci on a
phenotype or fitness; modification of phenotypic expression of
one locus by another; analogous to dominance of one locus over
another
pleiotropy - multiple effects of a single gene
e.g.1, Waardenberg syndrome in humans, defective allele for
pigmentation responsible for both (some cases of) blue eyes
and deafness; 40% of white cats with blue eyes are deaf, or
ipsilaterally blue-eyed and deaf
e.g.2, phenylketonuria  defective allele of phenylalanine
hydroxylase gene responsible for converting phenylalanine to
tyrosine  mental retardation, eczema, light skin
e.g.3, sickle cell anemia  "tower skull", impaired mental
function, heart failure, pneumonia, rheumatism, paralysis,
abdominal pain, kidney failure, fibrosis of spleen
incomplete dominance = semidominance = - intermediate
phenotype of heterozygote but not equal effects from both alleles
codominance - protein products of both alleles in heterozygote
detectable phenotypically
overdominance (heterosis, heterozygote advantage, or hybrid
vigor) - heterozygote has phenotype or fitness characteristics
outside the range of either homozygote (more fit)
underdominance - heterozygote disadvantage
linkage disequilibrium - nonindependent assortment of 2 or
more loci or of particular alleles at two or more loci
due to physical proximity or meiotic drive/segregation distortion
or selection
genotype frequency - the proportion of a population with a
certain genotype, e.g., 25% A1A1 50% A1A2 25% A2A2
allele frequency - the proportion of gene copies in a population
with a certain allele (remember that there are 2 gene copies per
diploid organism)
allele freq = sum (2 per homozygote + 1 per heterozygote)
total number of gene copies of all alleles
example
genotypes
A1A1
A1A2
A2A2
genotype frequencies
(0.25)
(0.50)
(0.25)
alleles
A1
A2
allele frequencies
(0.50)
(0.50)
i.e., 1(0.25) + ½(0.50) = 0.50
Sources of Phenotypic Variation
Genotype
Environment
Epigenesis – mitotically and meiotically heritable changes in
gene expression that do not involve a change in DNA sequence,
or differentiation and morphogenesis from “above” (other than)
nucleotide sequence
gene regulation by non-coding RNA (ncRNA), including small
(sRNA), micro (miRNA), and inhibitory (RNAi)
cytosine modifications, e.g., methylation
histone modifications, e.g., lysine acetylation
repressor proteins
endosymbionts
maternal effects, e.g., nutrition, toxins
indirect effects, e.g., enlargement of the vertebrate brain due
to hydrostatic pressure within the neural tube
Heritability
heritability is the proportion of phenotypic variance that is
attributable to genetic variance
Conceptually:
2
h =
VG
VG + VE
=
VG
VP
VG = genotypic variance
VP = phenotypic variance
VE = environmental variance
Heritability
Phenotype of offspring
h2 is actually the coefficient of determination (r2) in a regression
analysis, i.e., how much of the variation in y is explained by
variation in x (values range from 0.0-1.0)
r² = 0.8749
phenotype of parents