Biology 2970 Test #3

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Biological Species Concept
(Mayr)

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A reproductive community of populations (reproductively isolated from others) that occupies a specific niche in nature

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Prezygotic Barrier

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i.e. temporal (seasonal), ecological, behavioral, mechanical, gametic

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Postzygotic Barrier

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i.e. hybrid inviability, hybrid sterility, hybrid breakdown

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Reinforcement

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Does selection on hybrids with post zygotic barriers lead to prezygotic isolation? (conserves gametes)

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Problems with Biological Species Concept (BSC)

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1. *Applies to sexual forms only
2. *No temporal dimension
3. Not a single unit of evolution
4. Not practically testable

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BSC Criticism: Applies to Sexual Forms Only

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cannot apply to organisms that reproduce asexually

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BSC Criticism: No Temporal Dimension

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Assumption is that one is looking at species alive today but not looking at species through time. BSC only looks at a slice of time.

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BSC Criticism: Not a single unit of evolution

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Some use subspecies and some do not.
We want to identify species that have their own unique histories of evolutionary change and whether it has led to reproductive isolation or not, we need to be able to recognize that there may be a long line of separate species even if they may merge in the future

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Phylogenic Species Concept (Cracraft)

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A lineage of ancestral-descendent populations DIAGNOSABLY DISTINCT from other such lineages
(recognizes sexual and asexual, must have been some divergence of character that was genetic or molecular or characteristic etc., cumbersome)

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Sources of Allopatry

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1. Vicariance
2. Founder event

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Vicariance

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- source of allopatry
- subdividing a formerly continuous habitat (i.e. sea urchins in central America)

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Founder Event

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- Rare dispersal across a pre-existing barrier (i.e. galapagos Islands --> colonization)
- Prevention of Gene Flow

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Non-allopatric Speciation

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Geographic isolation does not precede evolution of species differences (controversial)

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Sympatric Speciation

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Multiple species lineages generated from an ancestor in an undivided geographic area (controversial)

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Darwinian Theories of Evolution

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1. Evolution as such
2. Common Descent
3. Multiplication of Species
4. Gradualism (Controversial)
5. Natural Selection (Controversial)

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Gradualism

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- Evolutionary change occurs in small increments
- Accumulation of small, quantitative changes leads to qualitative change (Lyell's definition)

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Intraspecific variation

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...is the raw material for evolving novel forms

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Controversy of Gradualism

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- Did all species arise through strictly gradualistic means?
- Contrasted with large phenotypic change in one generation (dwarfism)

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Developmental modularity (Goldschmidt)

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- Can lead to abrupt phenotypic change (Gecco-toe pad on tail)
- Hopeful Monster
- Homeotic mutations in flies (legs in eyes)
- These can be a part of evolution, many consider evolution as large and small changes
- This module did not inform Darwin (it was late 20th century)

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Case of the Ancon Sheep

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- one sheep had very short legs (dwarfism) and it was normal otherwise which mean it could not run away
- this was a favorable trait bred for in a new line of sheep
- Darwin: This is not evolution in nature, it would not be an advantageous trait in the wild

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For a condition to evolve...

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- increase in frequency
- prevail in a species

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Natural Selection

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A population-based mechanism of evolutionary change invoked to explain "adaptation"
- Darwin saw natural selection and gradualism and going hand in hand.
- Not a random process

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Random component of natural selection

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variation is produced at random with respect to another organisms needs

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nonrandom component

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organisms with favorable traits have higher rates of survival and reproduction, causing populations to accumulate the most favorable traits and to discard less favorable ones

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1st Observation of Natural Selection

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Organisms have great potential fertility, which promotes exponential growth of populations
- Thomas Malthus - political essay against wlefare

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2nd Observation of Natural Selection

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Natural populations normally do not increase exponentially but remain fairly constant in size (Darwin)
- There are a few exceptions but it does not last forever

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3rd Observation of Natural Selection

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Natural resources are limited (Malthus)

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Inference #1 of Natural Selection

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A STRUGGLE FOR EXISTENCE occurs among organisms in a population

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4th Observation of Natural Selection

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Variation occurs among organisms within populations
- animal breeding and systematics

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5th Observation of Natural Selection

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Heredity - characteristics of offspring are correlated with those of their parents in a population

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Inference #2 of Natural Selection

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Varying organisms show differential survival and reproduction, favoring advantageous traits (= natural selection)

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Inference #3 of Natural Selection

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Natural selection, acting over many generations, gradually produces new adaption and new species

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Teleology

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having a predetermined goal. In terms of evolution, a predetermined goal to produce a certain kind of organism

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Progressive adaptation

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later forms are superior to older forms in a general sense. Most people disagree...not necessarily a consequence of evolution by natural selection

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Adaptation

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trait that evolved by natural selection for a particular biological role

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exaptation

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a trait coopted by natural selection for a role incidental to that traits origin

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Components of an algorithmic formulation (Dennett)

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*substrate neutrality - a reproducing population with heredity and variation
* underlying mindlessness - no teleology
* guaranteed results - feeds on randomness to produce order

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Abstraction and simplification

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identify essential aspects of reality and remove distracting elements

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Sufficient parameters

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Look for minimum number of summary variables that would suffice to explain phenomenon being investigated

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"fitness"

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used as a mathematical measure of organisms ability to survive to a reproductive age, ability to find mates etc...

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What a good mathematical model has...

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1. reality - applies to real situations
2. generality - able to apply to different kinds of populations
3. precision - repeatability of measurements

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Molecular Basis of Evolution:3 properties of DNA

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1. DNA can replicate
2. DNA can mutate and recombine
3. DNA encodes RNAs + proteins that interact with environmental conditions to influence phenotype

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DNA Can Replicate: Identity by Descent

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replication without mutation (refers to alleles and associated phenotypes)

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DNA Can Replicate: Coalescence

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All copies of homologous DNA trace back to a common ancestral
- spatial and temporal distributions of homologous DNA
- mitochondrial and Y chromosome DNA is very good for studying coalescence

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Mutation

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- destroys identity by descent
- can produce favorable traits but does not disproportionally favor them

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Haplotype

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Set of identical haploid genomes for a specified unit of measurement. (=allele for measurements taken at the DNA/Chromosomal Level)

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Common Uses of Haplotype

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- bases present at polymorphic sites genetically linked on a DNA molecule
- may refer to nuclear or organellar genomes
- DNA sequences or restriction maps

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Gene Tree

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branches shoe lineal descent of copies of homologous DNA

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Haplotype Tree

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Branches denote mutational events in the evolutionary history of homologous DNA

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Unrooted Haplotype Tree

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Each Branch refers to a single base substitution at one of sites on aligned sequence

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Deme

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local population of breeding individuals that has physical continuity over time and space. The lowest biological level that can evolve

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Gene pool

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the population of gene copies that are collectively shared by individuals of a deme.
- The population of potential gametes that can be produced by individuals of a deme.
- Meiosis connects the deme to the gene pool
- Allele frequency characterizes gene pool when only looking at one locus

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What is Apoprotein E?

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- binds high density cholesterol and allows it to be transported through the blood
- Most people are heterozygous for Apoprotein E

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Hardy Weinberg Equilibrium

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p^2 - freq of AA
2pq - freq of Aa
q^2 - freq of aa
- medellian ratios only occur when p=q=.5

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Mutation Selection Equilibrium

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- mutation produces alleles and selection removes them
- if mutation rates are high enough in population that homozygosity occurs, mutations are removed (in lethal alleles)
- q^2 = u ~ sqrt(u) at equilibrium

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Mutation rate

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u = [# newly mutated copies]/[total # copies of homologous DNA]
- dimensionless number ~10^-5

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Hardy-Weinberg assumptions

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- infinitely large population
- random mating
- no mutation
- no migration
- no natural selection

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Phenotype

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any measurable trait, discrete or continuous

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Coronary Artery Disease (CAD)

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- obstruction and narrowing of vessels
- NO SINGLE factor, genetic or envrionmental, is either necessary or sufficient for CAD

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Two Major Features of most Genetic Traits

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1. Complexity of the genotype/phenotype relationship represents interactions among multiple genetic and environmental factors
2. Confoundment of frequency and apparent causation in complex systems

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Sickle Cell Anemia

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- HbA (glu) - normal
- HbS (val) - abnormal
1. phenotype of anemia - recessive
2. phenotype of electrophoretic mobility - co-dominant
3. phenotype of malarial resistance - dominant
4. phenotype of viability in natural environment - over dominant
- spleen will destroy sickle shaped cells which leads to anemic conditions
- HbS is necessary but not sufficient for anemia

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Heterozygotes of HbS

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- normal respiration under conditions in which they live

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Malaria parasite

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enters red blood cell and depletes oxygen from red blood cell through its activities causing cell to sickle in an oxygen depleted condition
- if HbS present this cell it will be destroyed along with parasite

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Genetic backgrounds of HbS Allele

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- ΨB - nonfunctional allele
- Gy, Ay - fetal genes that are only expressed at birth. Rare occasions it is expressed into adulthood and has an epistatic interactionwith HbS at B locus

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Gy and Ay Effects in Adulthood

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HbS homozygotes
- no longer has anemia to prevent sickling
- sickling does occur due to severe depletion of oxygen by malaria parasite and causes destruction of infected cells

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Major Features of Genetic Traits: Complexity of genotype/phenotype relationship

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- interactions among factors can cause phenotype
- no one factor is both necessary and sufficient for condition
- many factors neither necessary nor sufficient
- causes variation of a phenotype at population level not to match the causes of phenotype variation at organismal level

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PKU

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- considered a genetic disease
-homozygous recessive - excess of phenylalanine builds up due to inactive enzyme to convert to tyrosine
- born with normal brain but must have low phenylalanine diet to get normal intelligence while nervous system develops

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Mothers with PKU

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- p/p mothers have to go back on low phenylalanine diet while carrying child

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Scurvy

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- dietary disease
- human beings are almost all homozygous recessive for allele that allows body to make vit. C from precursors

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Confoundment Frequency

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A way of looking at how different alleles contribute to a phenotype
- i.e. if you have the B allele you have a 0.1 chance of having the allele...

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Quantitative Genetics

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analysis of genetic variance for continuously varying phenotypes

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Two ways for discrete genotypes to yield continuously varying phenotypes

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1. polygenic inheritance
i.e. height is proportional to number of capital letter alleles

2. environmental variation
i.e. number of facets within each genotypes varies with temperature at which fly was raised

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Norm of Reaction

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set of phenotypes associated with a particular genotype interacting with a variety of environmental conditions and genetic backgrounds

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Measured genotype approaches

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data are available for norms of reaction for each diploid genotype at a locus

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parametric mean

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measures where the distribution is centered

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variance

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average squared deviation of xi from the mean (how wide the distribution is)

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Adoption Study

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- Strong heritability seen in IQ in adopted children
- Heritability only measures the correlation between where the individuals lie in relation to the mean. Does not have to do with their actual IQ
-

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African American IQ Study

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- The high heritability found of IQ within populations is irrelevant to the conclusion that there are biological differences in IQs between two groups

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How Heritability can be Applied

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- only can use within a population
- completely irrelevant to genetic basis between population differences

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Genetic Variance vs. Environmental Variance

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How much phenotypic variance is associated with genotypic variance in a given generation?

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Additive vs. Non-additive genetic variance

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How much of genetic variance can be transmitted through gametes to influence phenotype variation in the next generation?

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Average Excess

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The average genotypic deviation caused by a gamete bearing allele i after fertilization with a second gamete drawn at random from the gene pool (=breeding value)

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Broad Sense Heritability

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How much of variation in one generation is associated with variation in genotype

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Narrow Sense Heritability

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Genotypic Variance that influences the phenotypic variance in offspring generation from the one we're studying

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Quantitative Trait Locus (QTL)

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locus whose variation contributes to populational variation of a continuously varying genotype
- helps us se how variation in genotype affects variation in phenotype

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Genome Scan

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saturated, genome-wide linkage mapping, SNP markers every 10 cM throughout genome.
- tells us where to investigate further

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What makes a good population for QTL analysis?

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1. High incidence of disease phenotype
2. high levels of linkage disequilibrium

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Tree Scan

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use haplotype tree to test SNP sites for influence on disease phenotype.
- find base subs affecting the disease within a candidate locus in the relevant gene region

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Production of linkage disequilibrium in a population

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1. hybridization b/w populations with contrasting haplotypes
2. founder event
- genetic recombination destroys linkage disequilibrium

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Retention of linkage disequilibrium

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- requires genetic linkage of sites that are in linkage disequilibrium

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Linkage Disequilibrium

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nonrandom association between allelic states of two SNP markers in haplotypes

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Analysis of Variance

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The primary methodological operation of quantitative genetics

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Heritable Phenotypes

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often have
1. no discrete categories
2. no single gene necessary or sufficient for a particular condition

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Correlation Coefficient

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Negative values have no biological interpretation in quantitative genetic estimates of heritability

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Identity by Descent

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Population genetic term for copies of homologous DNA that are identical (=same allele) because they were replicated from a common ancestral molecule in a previous generation without intervening mutation

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Identity by Descent

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Population genetic term for copies of homologous DNA that are identical (=same allele) because they were replicated from a common ancestral molecule in a previous generation without intervening mutation

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Mitochondrial DNA

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groups phylogenetically with bacterial genomes
*has to do with endosymbiotic theory

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example of prezygotic reproductive barrier

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illustrated by a contrast in seasonal flowering time between population

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teleology (alternative defn)

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rejected by Darwin's theory of natural selection

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Mitochondrial DNA

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groups phylogenetically with bacterial genomes

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Bayesian phylogenetics

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incorporates complex models of base substitution for a DNA sequence

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example of prezygotic reproductive barrier

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illustrated by a contrast in seasonal flowering time between population

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Genetic Evolution

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The fate of alternative forms of genes or gene combinations over space and time in a reproducing community

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teleology (alternative defn)

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rejected by Darwin's theory of natural selection

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Bayesian phylogenetics

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incorporates complex models of base substitution for a DNA sequence

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Genetic Evolution

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The fate of alternative forms of genes or gene combinations over space and time in a reproducing community

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Coalescence

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analytic tracing of copies of homologous DNA backward through past generations to their most common ancestor

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genetic drift

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random changes in allelic frequency in a population caused by finite population size and consequent sampling error across generations

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genome scan

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Pedigree analysis of genome-wide SNP markers every ~10cM together and a phenotype of interest to find regions that contain QTL for a phenotype of interest. The population used for can must have high levels of linkage disequilibrium among closely linked markers for the scan to work.

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system of mating

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guides calculation of genotype frequencies given allele frequencies

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A pair of evolutionary forces that explain evolutionary change measured for the homoglobin B pseudogene

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mutation and genetic drift

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Fitness

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sufficient parameter for a quantitative phenotype whose additive variance measures evolution by natural selection

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Assumptions

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unreal conditions used to facilitate study

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If the Dominant allele is rare...

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1. all copies of dominant alleles will be in heterozygotes
2. all copies of dominant alleles contribute equally to phenotypic variation
3. genetic variance is therefore ADDITIVE

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If a dominant allele is common....

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1. copies of dominant allele will occur in homozygotes and heterozygote genotypes
2. copies in heterozygotes contribute twice as much to populational variation as do copies in homozygotes
3. produces non-additive variance

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Epistatic variance

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non-additive genetic variance at the population level arising from interactions among genotypes at different loci.
*necessary but not sufficient for epistatic variance at population level

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Evolutionary forces in populations

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1. mutation - causes many small changes
2. genetic drift - random changes in allelic frequencies in a finite population due to sampling error

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allele

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one of two or more contrasting states of homologous genetic factors that segregate from each other in gamete formation, traditionally identified by contrasting phenotypes associated with them

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Copies of Homologous DNA

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any replicate copies of the same genetic locus regardless of whether they differ from other such copies (same of different haplotypes)