Umich EEB 390 Exam 1

First started natural phenomenon ideas

The early greeks (change over time/not static, fossils and extinction, hypothesis testing

Carolus Linneas

father of taxonomy, defined species w/ hierarchy of groups

Jean-Bapiste Lamarck

inheritance of characteristics acquired in lifetime (opposed Darwin's idea of natural selection) and gradual change towards ideal form

Charles Lyell

 idea that landscapes had been created by a series of many small changes

Charles Darwin @ South America

Galapagos finches (beak size) and created natural selection. Learned that everything is related, the earth is very old, extinction is common, and there is extreme morphology

Requirements for natural selection

variation, heritability, selection

Alfred Wallace

came to Darwin about similar ideas of evolution; their work was published together by a friend

Origin of Species

made by Darwin; variation in phenotypes come from a common ancestor, variation is continuous and heritable, survival of the fittest, natural selection = how things change, laws of variation (later solved with genetics)

Problems with Origin of

Species

absence of transitional forms and sterile animals (haplodiploidy)

What Darwin was right about

natural selection and idea of a common ancestor

What Darwin was wrong about

inheritance, origin of variation, mass extinctions, structural constraint

what does natural selection act on

a phenotype

how is mutation affected by selection

mutation works independent of selection - they occur randomly

fitness

differential effect of a trait on reproductive success (variation always has fitness consequences)

Trade-Off

larger offspring survives with higher probability but need more resources so only a few large offspring can be produced

genetics of domestication

Siberian fox experiment of selective breeding for non-aggression but this lead to certain characteristics that followed along (floppy ears, curly tail, barking)

Darwin's framework for change over time

species diversity and descent with modification (all is still controversial b/c selection is too slow and there is an incongruence with the fossil record)

Neo-Lamarckism

inheritance of characteristics acquired in response to environmental conditions during a lifetime (alternative to Darwin)

orthogenesis

variation moves toward a specific goal (alternative to Darwin)

Mutationism

mutations lead to new species (alternative to Darwin)

theistic evolution

change is directed by god - proved false by end of 1800 (alternative to Darwin)

Genetics

the study of heredity - started by Mendel and Thomas Morgan

Modern synthesis

theory of evolution that incorporates genetics, systematics, selection, and other things - started by Haldane, Fisher, and Wright

population genetics

Study of allele frequency distribution and change under the influence of evolutionary processes -- consistent with natural selection

Ronald Fisher

provided statistical basis of inheritance (heterozygote advantage, large populations have more variance)

John Haldane

math to trace gene frequencies (rule of hybrid sterility, factors for evolutionary resistance)

Sewall Wright

inbreeding, drift, adaptation, adaptive landscapes

T. Dobzhansky

fruit flies and chromosomal changes (natural selection maintains diversity in wild populations)

Ernst Mayr

biological species concept, naturalist, evolution from geographic separation

Simpson

fossils and population genetics - disagreed with Mayr on speciation

post-synthesis controversy

later arguments different from what modern synthesis said. Also a public disconnect (debate of evolution ended for scientists but never fully for the public - creationism too high)

Synthesis controversy over units of selection and speed of change

Synthesis said selection acts on individuals or populations and change is slow. Later people said selection acts on higher species and speed is punctuated equilibrium

Punctuated equilibrium

evolutionary theory proposing that species experience long periods of stability (stasis) interrupted by shortbursts of significant evolutionary change (alternative to gradualism; fossil record shows both)

molecular biology data proves modern synthesis and evolution

nucleic Acids=variation, chromosome=inheritance, theory of gene=unit of selection, central dogma=DNA sequencing

Phylogeny

visual representation of relationships between entities with some metric of time included; need data and models (key = variation)

node

hypothetical ancestor (MRCA)

branch

evolution lineage

tip/taxa

species or individual entity

OTU

technical term for tip of the tree

topology

arrangement of branches

phylogeny as a hypothesis

there is always some uncertainty; it is a reconstruction of a phenomenon that you can't directly observe and never a "true" or "correct" tree

clade

group that includes an ancestor (most recent common ancestor) and its descendants - can only be monophyletic

monophyletic group

ALL descendants came from one common ancestor

paraphyletic group

Pertaining to a group of taxa that consists of a common ancestor and some, but not all, descendants

polyphyletic group

an unnatural group that does not include the most recent common ancestor and is disjointed taxa

polytomy

when a node is split into more than two descendants

soft polytomy

uncertainty in a phylogeny that can be resolved with more data

hard polytomy

very rapid divergence that creates uncertainty that cannot be resolved by adding more data

rooting

node that connects all the tips (can put this anywhere)

ingroup

A species or group of species whose evolutionary relationships we seek to determine

outgroup

one or more species included to provide direction or a comparison in a phylogeny

character vs. state trait

character=idea, state=thing you see (phenotype)

ancestral traits vs. derived traits

ancestral=from ancestral population, derived=trait in a changed state from when it was an ancestral form

homologous vs analogous traits

homologous=inherited and in all species, analogous=not because of ancestry

parsimony

to minimize the number of changes/steps to get to an observed tip (helps infer ancestral traits)

how can traits reverse back?

when a deeply nested clade does not have a derived trait (clade in another clade)

homoplasy

the evolution of similar traits or structures in different species that aren't due to a recent common ancestor (ex. eye)

Synapomorphy

a shared, derived character trait inherited from a common ancestor, used to define a group

Plesiomorphy

an ancestral trait shared by members of a clade that was inherited from a distant common ancestor

Symplesiomorphy

a shared ancestral trait shared between two or more taxa, such as the backbone in all mammals

cautions of phylogenys

always some uncertainty!!

Coelacanths

ancient group of fish related to the lobe-finned fish ancestors of the amphibians. Most recent fossil is 70-80 mill y/a but in 1938 they found another

Sister taxa

Groups of organisms that share an immediate common ancestor and hence are each other's closest relatives

Vestigial traits

those that have no current function but were important in the past

critics of Darwin and variation

critics said variation should run out eventually, but this is false and it is continuous

Mendel breeding experiments

used peas and artificially pollinated flowers - created hybrid species and concluded: heredity is not blending but a combination of discrete factors from parents

Law of Segregation

Mendel's law that states that the pairs of homologous chromosomes separate in meiosis so that only one chromosome from each pair is present in each gamete

locus

Location of a gene on a chromosome

homozygote

organism that inherits two alleles of the same type for a given gene (AA or aa)

heterozygote

organism that inherits two different alleles for a given gene (Aa)

dominant

heterozygote has phenotype of the allele

recessive

phenotype is not expressed in heterozygote

law of independent assortment

mendel's law that states that genes separate independently of one another in meiosis because they are not physically linked

recombination

(crossing over) a combining of genes or characters different from what they were in the parents

molecular genetics

the subfield of biology that studies the molecular structure and function of genes

central dogma

DNA (genotype) -> RNA -> Protein (phenotype); many ways to alter this process and get variation

transcription

RNA polymerase reads coding sequence of DNA and produces complementary RNA called messenger RNA (mRNA)

translation

process where strand of mRNA is decoded by a ribosome to produce an amino acid sequence

codon

genetic code of a three nucleotide sequence that codes for an amino acid; lots of redundancy for codes

promotor

signals to begin transcription where RNA polymerase binds

introns

Noncoding segments of nucleic acid that lie between coding sequences.

exons

expressed sequence of DNA; codes for a protein

expression of genes

how much gene product is made/the process of a gene being transformed into a product -- controls phenotype!!

epigenetic inheritance

Inheritance of traits transmitted by mechanisms not directly involving the nucleotide sequence (heritable changes in gene expression without changing DNA sequence) - basically irreversible

examples of epigenetics

x-inactivation, genomic imprinting, maternal effects

X inactivation in cat coats

one of two X chromosomes is randomly inactivated so only 1 active x-chromosome in female controls color

human height

overtime people are taller (changes over time) and height is highly heritable, can see based on slope of parent v offspring graph.

Polygenic trait

trait controlled by two or more genes at the same time

what mutations can affect

changes in protein structure, regulation/expression of the gene, silencing a gene, splicing of a gene → all lead to more variation

polymerase errors

DNA polymerase assembles the DNA nucleotides (building blocks)

hemoglobin mutation

mutated version of this allele leads to sickle cell anemia (problems for homozygotes); Β-globin allele is co-dominant and creates heterozygote advantage because it has malaria protection (common for Africans)

macromutations

Mutations with extensive and important phenotypic results ("hopeful monsters") - ex. colorful crest on a birds head

DFE of Mutation

requencies of mutations with various fitness consequences (distributions should be similar for species)

population level thinking

integrates selection with mendelian genetics

Hardy-Weinberg Principle

principle that allele frequencies in a population will remain constant unless one or more factors cause the frequencies to change

Hardy-Weinberg null hypothesis

no relationship between variables, all variation is random (NO selection, NO migration, NO non-random mutating, NO mutation, and NO drift (population size = ∞)

Hardy-Weinberg equilibrium

frequency of alleles in a particular gene pool remain constant over time (slope=0)

Hardy-Weinberg calculations

1) genotype frequencies (F[A,A], F[A,a], F[a,a])

2) allele frequencies (F[A] = p, F[a] = q

3) expected genotype frequencies (F[A,A] = p^2, F[A,a] = 2pq, F[a,a] = q^2)

4) do observed and expected genotype frequencies match? If yes, accept null and it is in equilibrium

H-W - relaxing selection

one allele favored over another