evolution 3B

Out of Africa Hypothesis

The hypothesis that modern humans (Homo sapiens) evolved in Africa and spread to other continents, replacing other Homo species ( Neanderthals) without interbreeding with them.

neutral theory

The hypothesis that much evolutionary change in genes and proteins has no effect on fitness and therefore is not influenced by Darwinian natural selection. • Kimura (1968) looked at α and β globin variation in mammals • Observed diversity requires 1 substitution every two years • Kimura argued most variation therefore must be neutral

fixation

The time to fixation (from origin of the mutation that will eventually be fixed until its ultimate fixation under pure drift), will of course be long: "diffusion theory" shows that this fixation time averages simply to 4Ne generations. Whereas the rate of origin and fixation (= micro) of new mutations is independent of population size, the rate of progress through the population is therefore directly proportional to population size. In a large population, it takes a very long time. For example, in a population of size 1 million, it takes 4 million generations. Under the neutral theory, then, the polymorphisms in large populations are due to a lot of neutral changes originating, and ultimately being lost, but passing through at such a slow rate that there are usually several alleles at any particular protein drifting through the population at the same time

Sequence Databases

- EMBL/NCBI/DDBJ/SWISSPORT

Genetic recombination and its role

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parthenogenesis

Asexual reproduction in which females produce offspring from unfertilized eggs.in multicellular organisms, eggs remain diploid and develop into individuals without fertilisation

Ashkanazi Jews

Ashkenazi Jews is the term used today to describe these Jewish people - individuals who built religiously-based communities centuries later in Central and Eastern Europe Closely related, human population is much tighter around 1000 years ago before migaration occurred

protogyny

Born a female, change to a male

Species-specific Genome Databases

ENTREZ/BLAST

Selectionist arguments for Genetic variation (i.e. Allozymes)

Balance school suggests selection (heterozygous advantage) maintains diversity BUT problems with genetic load in sexual organisms (think of sickle cell anaemia) ALSO Haldane - estimated maximum rate of one allele substitution every 300 generations under selection (c.1000 years in mammals)

Classical School

Before the late 1960s, it was generally believed that polymorphism (the presence of more than one allele in a population of genes) was relatively rare, and that evolution consisted mainly of: 1) mutation (mostly deleterious) 2) if advantageous, increase to fixation (or loss due to deleteriousness). • little genetic variability (GV) within populations • Mutations mostly deleterious, • fixation* rapid going from low freq in a population, fixed allele , all of the population has the same allele • most individuals homozygous for common wild-type allele

draw Y chromosome

Bigger, lots of repetitive sequences , diff haplotypes ( african, european.. Etc) can follow this through .. Color coding to see where theyre originated

Why is it important?

Cancer - heritable changes in gene expression responsible for cancer (Holliday 1979); tumour cells have aberrant, cell-heritable patterns of DNA methylationassociated with silencing of tumour repressor genes Hereditary Disease - defects in imprinted genes (i.e. epigenetic state depends on whether inherited from mother or father Epigenetic Epidemiology - maternal starvation and stress can have persistent effects in children, some lasting effects across generations,thalidimide-induced,retrotransposon related, prion related disease Epigenetic Defense Mechanisms - methylating foreign DNA or RNA-directed degradation of RNA transcripts are mechanisms used by cells to avoid or destroy parasites Cloning - somatic cells used for cloning need to be epigenetically reprogrammed Agriculture - epigenetics causes problems for genetic engineering for crop improvement- newly inserted genes can be silenced by methylation

MacDonald -Kreitmen Test

Compares proportion of synonymous / non-synonymous changes under neutrality with that observed between and within species

Tests for Neutrality

Comparing dN/dS ratios ( Ka and Ks) Compares: nonsynonymous (amino acid changing) substitutions per nonsynonymous site, synonymous (neutral) substitutions per synonymous site. assumes : if synonymous substitutions neutral, rate of substitution (fixation) equal to u nonsynonymous substitutions change the protein function dN/dS = 1 neutral dN/dS < 1 purifying selection dN/dS > 1 positive selection highly conservative test (difficult to detect ratio if selection only acts on a few sites) ... there is an alternative...

How is Genetic Diversity Assessed

Current and historical population sizes are (Ne) Population genetic structure Deviations from Hardy-Weinberg equilibrium (nonrandom mating, selection, population structure) Phylogenetic relationships Linkage to genes under selection

molecular clock hypothesis

DNA and protein sequences evolve at a rate that is relatively constant over time and among different organisms. A direct consequence of this constancy is that the genetic difference between any two species is proportional to the time since these species last shared a common ancestor. Rates of molecular change are constant enough to predict timing of evolutionary divergence Rates of molecular change are constant enough to predict timing of evolutionary divergence

the DNA evidence that supports the 'Out of Africa' hypothesis for human evolution

DNA evidence that almost certainly confirms the theory that all modern humans have a common ancestry.. fossil evidence/ mitochondrial eve/ Y chromosome

DNA sequencing

Determining the exact order of the base pairs in a segment of DNA.// Sanger sequencing // NGS sequence alignment - SNP calling

molecular evolutionary genetics

Discovery of structure of DNA opened way for "molecular evolutionary genetics" 1928 = Griffith: transfer of traits between bacteria 1943= Avery-McCleod-McCarty experiment: DNA as transforming agent 1952= Hershey-Chase experiment: role of DNA in heredity 1952 = Franklin & Gosling-photographed DNA 1953 = Watson & Crick: resolved double helical structure

divergent selection

Divergent evolution or divergent selection is the accumulation of differences between closely related populations within a species, leading to speciation. Divergent evolution is typically exhibited when two populations become separated by a geographic barrier (such as in allopatric or peripatric speciation) and experience different selective pressuresthat drive adaptations to their new environment. After many generations and continual evolution, the populations become unable to interbreed with one another.

Migration-evolutionary sense

Early humans first migrated out of Africa into Asia probably between 2 million and 1.8 million years ago. They entered Europe somewhat later, between 1.5 million and 1 million years. Species of modern humans populated many parts of the world much later. For instance, people first came to Australia probably within the past 60,000 years and to the Americas within the past 30,000 years or so. The beginnings of agriculture and the rise of the first civilizations occurred within the past 12,000 years.

redundancy and non coding DNA

Empirical data on protein sequences showed that amino acid evolution (i.e. substitution) was linear with time. Neutral theory could explain this, of course: if was approximately constant across species, and if most protein evolution were neutral, then the rate of evolution should be roughly the same in all lineages. Today.... These simple arguments are now known to be too simple. The molecular clock doesn't tick at a perfectly constant rate, in part because there are variations between genes, between different parts of lineages, and in part because with different generation times, mutation rates, and possibly even a bit of natural selection, it is all messier then was thought at first. As we shall see, there seems to be a lot more selection on molecular polymorphisms than we once thought. However, the neutral theory and the molecular clock arguments are still enormously useful because they are so simple. Somewhat like the Hardy-Weinberg, these ideas still form the "null hypothesis", or fundamental basis of all further molecular evolution studies: the neutralists have had an important and very useful effect on modern evolutionary biology. The molecular clock isn't perfect, but it still gives rough estimates of time since divergence, given some sort of calibration of phylogenies with geological time.

Components of Epigenetic phenotype 'reprogramming'

Epigenator - environmental signal that triggers intracellular pathway; can be transient Epigenetic Initiator - signal that responds to the epigenator and defines location of the epigenetic chromatin environment (e.g. DNA-binding protein, noncoding RNA) Epigenetic Maintainer - signal that sustains the chromatin / RNA / protein environment in the first and subsequent generations (e.g. DNA methylation, histone modifications, histone variants etc);

Agouti Locus in Mice

Epigenetic modifications have effects on phenotype, but they are generally considered to be cleared on passage through the germ line in mammals, so that only genetic traits are inherited Dogma at the time was that epigenetic marks have effects on phenotype but that they are cleared on passage through germ line (i.e. not inherited) -this paper was one of first to demonstrate inheritance of epigenetic modification -transposable element inserted upstream of the agouti gene causes ectopic expression of agouti protein, resulting in yellow fur, obesity, diabetes and increased susceptibility to tumours -variable expressivity of traits due to methylation of inserted element -screened for methylation using methylation-sensitive (HpaII) and and insensitive (MspI) enzymes (all first digested with BamHI)

evolution

Evolution occurs when there is change in the genetic material -- the chemical molecule, DNA -- which is inherited from the parents, and especially in the proportions of different genes in a population. Genes represent the segments of DNA that provide the chemical code for producing proteins. Information contained in the DNA can change by a process known as mutation. The way particular genes are expressed - that is, how they influence the body or behavior of an organism -- can also change. Genes affect how the body and behavior of an organism develop during its life, and this is why genetically inherited characteristics can influence the likelihood of an organism's survival and reproduction

McDonald-Kreitman test (and variations)

Exploits neutral prediction that dN and dS should be constant through time (most dN are neutral*) Compares fixed differences between species (divergence) to variation within species (polymorphism) at nonsynonymous and synonymous sites

genetic bottleneck

Extreme reduction in genetic variation in pop due to breeding of closely related individuals subsets of the population remain alive for genetic and non genetic reasons infection kills vast population population, has some kind of selective pressure bottlenecks can reduce the variation in a population

Pre-mating isolating mechanisms

Factors which cause species to mate with their own kind (assortative mating). a) Temporal isolation. Individuals of different species do not mate because they are active at different times of day or in different seasons. b) Ecological isolation. Individuals mate in their preferred habitat, and therefore do not meet individuals of other species with different ecological preferences. c) Behavioral isolation. Potential mates meet, but choose members of their own species. d) Mechanical isolation. Copulation is attempted, but transfer of sperm does not take place.

isolating mechanisms

Features of behaviors, morphology, or genetics which serve to prevent mating or breeding between two different species (e.g., temporal isolation, in which individuals are active at different times of the day, seasons, or mating periods; ecological isolation, in which individuals only mate in their specific habitat; behavioral isolation, when there are no sexual cues between representatives of the species; mechanical isolation, when there is no sperm transfer during an attempted mating; and gametic incompatibility, when there is sperm transfer without fertilization occurring). If mating can take place, there are four factors that prevent hybrid viability: zygotic mortality (fertilization but no zygote),hybrid inviability (embryo is not viable), hybrid sterility (resulting adult is sterile), and hybrid breakdown (first generation is viable but future generations are not).

Allozymes

First molecular tool used to assess variation within and between populations Quick and relatively cheap Still used to identify and characterize diversity in a number of pathogens and their vectors But, looking at phenotypes rather than genotypes (enzymes are gene products that can be subject to selection)

Inbreeding Coefficient, Fis

Fis = 0 for non-inbred population Fis = 1 for completely inbred population (under inbreeding, heterozygosity is lost at rate of 1/2Ne)

How are they inherited?

For a child to develop one of the genetic diseases prevalent among Ashkenazi Jews, they must inherit two mutations for the same disease. In every living person, genes are paired - in each pair, one gene comes from the mother and the other comes from the father. For recessive inheritance of a genetic disease to occur, both genes in a pair must be abnormal

directional selection

Form of natural selection in which the entire curve moves; occurs when individuals at one end of a distribution curve have higher fitness than individuals in the middle or at the other end of the curve

Why drink cow milk ?

Four Main Theories: 1, Reliable nutritious food resource 2, Important source of water (especially in arid environments) 3, Improves calcium uptake in Vitamin D (sunlight)-deficient populations 4, Protects against malaria (riboflavin may be protective)

Population Structure

Gene Flow (Fst) Genetic Distance Genetic Diversity Heterozygosity

The founder effect

Genetic drift that occurs when a few individuals become isolated from a larger population and form a new population whose gene pool composition is not reflective of that of the original population. he founder effect was defined by Ernst Mayr (1904-2005) as: "The establishment of a new population by a few original founders (in an extreme case, by a single fertilized female) which carry only a small fraction of the total genetic variation of the parental population.

Humans vs Neanderthals

German Neanderthal from 1856 mtDNA taken from right humerous sequenced 379bp non-coding region found 28 (7%) differences This implies: Human/Neanderthal split 600,000 years ago We know modern humans evolved in Africa 130,000 years ago Implies Neanderthals are not ancestral to humans

OCA2 Gene Expression

Haplotype analyses suggests the mutation arose near the Black Sea about 6,000 to 10,000 years ago

Hardy-Weinberg equilibrium

Hardy-Weinberg equilibrium predicts that: • allele and genotype frequencies in a population will remain constant from one generation to the next • allele frequencies can be used to predict genotype frequencies

Neanderthals

Homo sapiens neanderthalensis, a European variant of Homo sapiens that died out about 25,000 years ago.

co-evolution between Daphnia and a bacterial parasite

Host parasite interactio, parasite under selective pressure to infect host and vice versa , this is a competition and results in a cost ( parasite trying to infect , host trying to increase and not decrease fitness) Daphina magna vs bacterial endoparasite , their co-evolution Reproduce, produce spores, grow and go into next generatiom, some drop to bottom of pond and don't hatch Pond fills up with debris layers and spores , you endup with a time record of the genotypes of the daphnia spores as well as the bacterias witin the layers of the de

British Isles and Scandinavia

How british isles became 2 big islands and got seperated from europe

Time fixation at a locus

How long (many generations) will it take a neutral mutation to become fixed? In diploids, coalescence theory predicts that this value is 4Ne (Kimura and Ohta. 1969)

Genetic load and problems for the "Balance School"

However, Lewontin and others argued that to maintain such a high amount of genetic diversity would be too costly If heterozygotes at thousands of genes in the genome were advantageous, this would result in the production of a lot of homozygotes in every generation Inbreeding decreases the homozygosity Balance school suggests selection (heterozygous advantage) maintains diversity BUT problems with genetic load* in sexual organisms selection and neutralist arguments are born By the late 1960s, amino-acid sequences for proteins from a number of taxa were known, and the full implications for evolution of the degenerate DNA code for amino acids became apparent

human evolution

Human evolution is the lengthy process of change by which people originated from apelike ancestors. Scientific evidence shows that the physical and behavioral traits shared by all people originated from apelike ancestors and evolved over a period of approximately six million years.

homosapiens and apes

Humans are primates. Physical and genetic similarities show that the modern human species, Homo sapiens, has a very close relationship to another group of primate species, the apes. Humans and the great apes (large apes) of Africa -- chimpanzees (including bonobos, or so-called "pygmy chimpanzees") and gorillas -- share a common ancestor that lived between 8 and 6 million years ago. Humans first evolved in Africa, and much of human evolution occurred on that continent. The fossils of early humans who lived between 6 and 2 million years ago come entirely from Africa

Immunity Related GTPases

IRG genes make proteins that plays an important role in the immune system. Specifically, the IRGM protein helps trigger autophagy in cells infected with certain kinds of bacteria (Mycobacteria), including the type of bacteria that causes tuberculosis. Those genes link to crohns disease Crohn's disease is associated with inflammation within the digestive tract. Sequence variants on the autophagy gene IRGM contribute to Crohn's disease susceptibility. Stop codons and frwmeshift make genes don't work ( red ) Over evolutionary history, genes aquire lots of muations that they don't work however the function reappaeras to work ater millions of years . Polymorphism version that works and version that dosent unlikely events do occurr

Speciation Genomics and hybrid breakdown in Lake Whitefish (outbreeding depression)

Identifying the molecular basis of reproductive isolation among diverging lineages represents an essential step toward understanding speciation in natural populations. Postzygotic barriers can lead to hybrid breakdown, a syndrome that has been documented in several systems, potentially involving the reactivation of transposable elements. In northeastern North America, two lake whitefish lineages have repeatedly colonized postglacial lakes ~12,000 years ago, and a dwarf limnetic species has evolved multiple times from the normal benthic species. Reproductive isolation is incomplete between them; viable hybrids can be generated in the laboratory but significant mortality occurs and is associated with a malformed phenotype in backcross embryos, thus revealing a hybrid breakdown syndrome. By means of RNA-seq analyses, the objective of this study was to determine which genes were misregulated in hybrids and rigorously test the hypothesis of transposable element reactivation. We compared the transcriptomic landscape in pure embryos, F1-hybrids, and healthy and malformed backcrosses at the late embryonic stage. Extensive expression differences con- sistent with previously documented adaptive divergence between pure normal and dwarf embryos were identified for the first time. Pronounced transcriptome-wide deregulation in malformed backcrosses was observed, with over 15% of transcripts differentially expressed in all comparisons, compared with 1.5% between pure parental forms. Convincing evidence of transposable elements and noncoding transcripts reactivation in malformed backcrosses is presented. We propose that hybrid breakdown likely results from extensive genomic incompatibilities, plausibly encompassing transposable elements. Combined with previous studies, these results reveal synergy among many reproductive barriers, thus maintaining divergence between these two young whitefish species. •Parallel evolution in multiple lakes in dwarf pelagic / planktonivorous form and large, limnetic •Multiple QTLs identified for morphological and physiological traits

tajimas test

If neutral, same value of , based on S and π, D = 0 (normal dist of pairwise differences) D > 0 excess of sites with alleles at high / intermediate frequency (e.g. balancing selection, rapid shrinkage) (Bimodal dist of pairwise differences) D < 0 excess of sites with alleles at low frequency (e.g. purifying selection, rapid expansion) (Poisson dist of pairwise differences)

Mating systems

In reality, few populations completely randomly breeding because: Population subdivision Inbreeding = higher than random breeding with relatives Positive assortative mating - will increase homozygosity Negative assortative mating - will do the opposite

The cost of passing only half of the genes over to an offspring:

In sexual reproduction half of the genes in an offspring came from the father and half from the mother. The genetic relatedness between parent and offspring is therefore much lower than when the offspring is a direct genetic copy of the parent.

genetic history of the British Isles

It has developed in parallel with DNA testing technologies capable of identifying genetic similarities and differences between populations. The conclusions of population genetics regarding the British Isles in turn draw upon and contribute to the larger field of understanding the history of humanity in the British Isles Fine-scale genetic variation between human populations is interesting as a signature of historical demographic events and because of its potential for confounding disease studies. We use haplotype-based statistical methods to analyse genome-wide single nucleotide polymorphism (SNP) data from a carefully chosen geographically diverse sample of 2,039 individuals from the United Kingdom. This reveals a rich and detailed pattern of genetic differentiation with remarkable concordance between genetic clusters and geography. The regional genetic differentiation and differing patterns of shared ancestry with 6,209 individuals from across Europe carry clear signals of historical demographic events. We estimate the genetic contribution to southeastern England from Anglo-Saxon migrations to be under half, and identify the regions not carrying genetic material from these migrations. We suggest significant pre-Roman but post-Mesolithic movement into southeastern England from continental Europe, and show that in non-Saxon parts of the United Kingdom, there exist genetically differentiated subgroups rather than a general 'Celtic' population.

protein variation in natural populations

John Hubby and Richard Lewontin were a landmark in the study of genome-wide levels of variability. They used the technique of gel electrophoresis of enzymes and proteins to study variation in natural populations of Drosophila pseudoobscura, at a set of loci that had been chosen purely for technical convenience, without prior knowledge of their levels of variability. Together with the independent study of human populations by Harry Harris, this seminal study provided the first relatively unbiased picture of the extent of genetic variability in protein sequences within populations, revealing that many genes had surprisingly high levels of diversity.

Ozzy Osbourne Genome

Key findings 100,000 unique variants Neanderthal genes on ch10 Unusual ADH4 variant Rare dopamine variants

Selection vs Neutrality Debate

Kimura (1968) made calculations based on knowledge of amino acid sequences in - and -haemoglobin in man and other mammals. To explain the observed rates of amino acid substitutions (about 1 a.a. substitution for each 100 amino acid polypeptide per 107 years), we require in mammals over the whole genome an overall nucleotide substitution rate of about one nucleotide substitution per 2 years. Kimura argued that DNA evolution at this rate couldn't possibly be explained by selection. Haldane had made an earlier genetic load argument to show that new alleles could not be substituted via selection much faster than one every 300 generations (about 1 every 1200 years in humans!) without driving the population extinct due to genetic load. Kimura therefore argued that most of this variation and evolution must be neutral, and that slow, random genetic drift at very large numbers of simultaneous DNA polymorphisms was responsible. King and Jukes (1969) in a paper entitled "Non-Darwinian Evolution", amplified Kimura's hypothesis

lactose metabolism

Lactose is synthesized by lactose synthase. Lactose is cleaved by lactase

inbreeding

Long-standing idea that inbreeding is bad and mating with genetically different individuals is good •Deleterious recessive mutations normally "hidden" with outcrossing but are exposed after inbreeding due to increased homozygosity •Heterozygotes thought to have more adaptive potential (heterosis) •Inbreeding depression = reduction in fitness (reproduction or survival) of inbred vs outcrossed individuals

Genetic Drift and Tasmanian Devil Facial tumour disease

Mhc is very important for disease resistance e.g. Tasmanian devils. Tasmanian devils - endemic marsupial to Tasmania, effected by devil facial tumour disease which causes growths in the mouth which prevent feeding which causes death. It is a non-viral, highly aggressive, transmissable cancer first emerged during first emerged in 1996. It is only one of two known transmissable cancers - bizare because the cancer itself is the infectious agent. Studies have found that a lack of MHC variations because of population bottlenecks and declines, means that the tumours are not recognised as foreign - one of best examples of link between loss of genetic variation and disease. People often don't recognise tumours as non-self, the fact that it can be passed bewteen individuals and not be recognised, it's a bit like a skin graft, means individuals are very similar. Essentially so similar cancer can transmit between

summary

Molecular biology has transformed the way we understand evolution Neutral markers are the preferred currency in some studies Comparative analysis of sequences can reveal evolutionary processes in near and far time Genetic diversity estimates can provide similar insights

Molecular Evolution

Molecular evolution involves the application of evolutionary models (like neutral theory) to genetic variation to infer evolutionary processes (e.g. selection, adaptation, dispersal etc) Most genetic markers targeted to understand population processes are selectively neutral (WHY?) But how do we measure genetic variation ?

molecular evolution

Molecular evolution is the area of evolutionary biology that studies evolutionary change at the level of the DNA sequence. It includes the study of rates of sequence change, relative importance of adaptive and neutral changes, and changes in genome structure

summary

Molecular techniques, starting with protein electrophoresis, more recently DNA methods, came online beginning in the 1960s. Researchers made a major discovery. There was far more polymorphism than expected at the level of genes. �Classical school� evolutionists believed that most evolution by natural selection should have led to fixation of mutations that were advantageous; low levels of polymorphism should have resulted. Attempts to explain this superabundant polymorphism led to the neutral theory and ideas that neutral evolution might provide a molecular clock. Natural selection: the demise of the neutral theory Balancing selection �Positive selection� But neutral theory still provides an important baseline against which to judge models of selection. We now know there are many types of molecular evolution. Theory and data relevant to molecular evolution has many uses.

cystic fibrosis

Most common 'lethal' inherited disease Affects over 7,500 people in the UK 50% are under 15 and 70% are under 20 2.3 million people (1 in 25) are carriers One specific mutation , ttt deletion, heavily selected for in this particular population Protein is made but cant get into the membrane

Neutrality

Most loci are neutral / nearly neutral Truly neutral loci behave in predictable way - a molecular clock If you know the mutation rate and the effective population size, you know how long ago two alleles diverged Even if you just assume the mutation rate is constant, you can detect relative (if not absolute) divergence times. Knowing predicted time to fixation, and a constant mutation rate - you can detect historical expansions and contractions in Ne Departures from neutrality can tell us things about evolution and selection Neutral theory does not preclude selection - more of a null hypothesis Neutral loci can be physically linked to non-neutral loci

A scan for positively selected genes in the genomes of human and chimpanzees.

Mutations in 13,731 Genes synonymous mutations that don't change the amino acids were less frequent than non synonymous that affected aa sequence and this is completely random.. the genes that have more changes are actually from one type of gene they found that the Positively Selected Genes mainly were sex specific genes or immune system genes ( most significantly different, frequent)

Adaptive divergence between populations on a genome scale: a stick insect Timema cristinae

Natural selection can drive the repeated evolution of reproductive isolation, but the genomic basis of parallel speciation remains poorly understood. We analyzed whole-genome divergence between replicate pairs of stick insect populations that are adapted to different host plants and undergoing parallel speciation. We found thousands of modest-sized genomic regions of accentuated divergence between populations, most of which are unique to individual population pairs. We also detected parallel genomic divergence across population pairs involving an excess of coding genes with specific molecular functions. Regions of parallel genomic divergence in nature exhibited exceptional allele frequency changes between hosts in a field transplant experiment.

balancing selection

Natural selection that maintains stable frequencies of two or more phenotypic forms in a population. Selection maintains multiple variants e.g. Frequency dependent selection, Hz advantage, hitchhiking

Evolutionary Genetics under Neutrality

Neutral mutation rate per site = μ Effective populations size (breeding individuals) = Ne Number of gene copies at a locus in a diploid population = 2Ne Probability of fixation of any new allele 1/2Ne Probability of a mutation arising at a site 2Neμ 2Neμ x 1/2Ne = k New mutation rate = Fixation rate

Tristan da cuhna

Nine Y-chromosome haplotypes were found. Seven can be unambiguously associated with the seven surnames. These fall into two haplogroups: I: from south-western Europe (Italy) R: from north-western Europe (Dutch, English, Irish & Scottish). What of the other two haplogroups? Al done on STR Genealogy - haplotypes 15-12-25.. Those are repeats numbers Difference in haplotypes between 2 groups - STR mutation rates are much higher than point mutations

Choose your genetic marker

Non-conserved - hypervariable e.g. Microsatellite, antigenic loci. Recent events, variability between Individuals of same species

What is Epigenetics and what might it explain?

Norm of reaction": pattern of phenotypic expression of a single genotype across a range of environments (plasticity) "Genetic Assimilation" - the phenotype produced under a stressful condition becomes the phenotype for every condition -"Canalization" (robustness): ability of a population to produce the same phenotype regardless of variability of its environment or genotype

allele frequency

Number of times that an allele occurs in a gene pool compared with the number of alleles in that pool for the same gene

HERC2 Intron 86 Silencer

OCA2 eye colour silencer sequence conservation in the HERC2 intron 86. Some rare blue-eyed individuals are homozygous for EYCL2 mutations rather than for OCA2. ( other gene that has 2 alleles where brown is dominant to blue)

Uses of DNA Technology and molecular evolution

Phylogeny reconstruction - understanding the family tree of life. Conservation biology - saving species may require knowing who they are related to, how they evolved, and whether they are inbred Forensic science - identification of suspects requires population genetics knowledge; for instance, particular markers may have different frequencies in different ethnic groups. Positive identification of suspects must depend on knowledge of the frequencies in each group. Behaviour studies - understanding relatedness in natural populations is now much more firmly based on genetic markers than hitherto. Genetic analysis of offspring show that females of many birds that breed in pairs shows that they often have multiple partners; they indulge in "extra-pair copulation". This is also true for human families: I believe that a typical "non-paternity rate" in humans is around 20%.

examples

Population bottleneck Chagas Disease Genetic Drift and Tasmanian Devil Facial tumour disease

neutral-mutation hypothesis

Proposes that much of the molecular variation seen in natural populations is adaptively neutral and unaffected by natural selection. Under this hypothesis, individuals with different molecular variants have equal fitnesses. Supposing the neutral mutation rate for a given protein was micro , and the number of alleles in a diploid population is 2Ne micro (Ne is the effective size of the population), then the number of new mutations in every generation is 2Ne micro . These neutral alleles will either drift into the population, or (mostly) will simply be lost almost immediately. Given the 2Ne neutral alleles in the population, what is the probability that each one will eventually be fixed as a substitution? One of the alleles will eventually be fixed, but since each has identical fitness, each has the same probability, 1/2Ne. Thus the rate of origin of neutral alleles that will eventually be fixed (which must also be the approximate rate of fixation) in the population is 2Ne /2Ne = micro. The rate of origin and the rate of eventual fixation must be approximately the same, so the rate of fixation of neutral mutants will also be micro This startlingly simple new theory suggested that the rate of neutral molecular evolution was independent of the population size, and was simply equal to the neutral mutation rate

genetic drift

Random sampling Distorts allele frequencies Larger effects in small populations Can be caused by a population bottleneck Increased risk of extinction: fixation of deleterious alleles by chance loss of heterozygosity due to limited gene pool increased inbreeding, leading to exposure of deleterious recessive alleles (inbreeding depression Evolution and chance of speciation: sub-populations with significantly different allele frequencies new niches become available to exploit reproductive barriers between niches favour speciation

Fragment Analyses

Restriction Fragment Length Polymorphisms (RFLPs) - Cutting PCR products with restriction enzymes that recognize particular sequences micro satellites- repeat sequences, mutated by spillage during dna replication process they slip back and forth on each other / mutation rate is incredibly fast

Adaptation within a population: Drug resistance and in Salmon lice (Lepoephtheirus salmonis)

SNPs that dramatically improved population assignment, increased global genetic structure and resulted in significant genetic population differentiation. A large proportion of SNPs found to be under directional selection were also identified to be highly discriminatory. Our data suggest that it is possible to discriminate between nearby L. salmonis populations given suitable marker selection approaches, and that such differences might have an adaptive basis. We discuss these data in light of sea lice adaption to anthropogenic and environmental pressures as well as novel approaches to track and predict sea louse dispersal.

purifying selection

Selection that lowers the frequency of or even eliminates deleterious alleles. Selection against new variation e.g. conserved 'house-keeping' loci

genetic diversity and risk of extinction

Sexual reproduction as one big advantage over asexual reproduction: it increases genetic diversity. When a mutation arises in one individual it can spread to individuals with a different genetic background through sexual reproduction. In asexual reproduction a mutation is always 'locked' inside the genetic background it first occurred in. With sexual reproduction mutations can be combined with other mutations, they can be removed or they can survive in the population until they have a big enough impact on the fitness of the individual to be selected for or against. Sexual reproduction thus allows for a bigger genetic diversity and this allows species to adapt to changes in environment or to changes in other species it interacts with.

THE BENEFITS OUTWEIGH THE COSTS

Sexual reproduction evolved and has stayed for billions of years. This proves that the benefits of sexual reproduction outweigh the costs for most species. Not for all species, as micro-organisms can testify. There are examples of species that have been asexual for millions of years, the most famous being Bdelloid rotifers. In general species with a short generation time are much more likely to reproduce asexually than species with a long generation time.

human evolution 3 - variations

Some human genetic variation is adaptive and some is due to chance

Cytosine methylation dynamics in Arabidopsis - epigenetic neutrality and an 'epimolecularclock' ?

Stochastic changes in cytosine methylation are a source of heritable epigenetic and phenotypic diversity in plants. Using the model plant Arabidopsis thaliana, we derive robust estimates of the rate at which methylation is spontaneously gained (forward epimutation) or lost (backward epimutation) at individual cytosines and construct a comprehensive picture of the epimutation landscape in this species. We demonstrate that the dynamic interplay between forward and backward epimutations is modulated by genomic context and show that subtle contextual differences have profoundly shaped patterns of methylation diversity in A. thaliana natural populations over evolutionary timescales. Theoretical arguments indicate that the epimutation rates reported here are high enough to rapidly uncouple genetic from epigenetic variation, but low enough for new epialleles to sustain long-term selection responses. Our results provide new insights into methylome evolution and its population-level consequences

agouti locus in mice

The agouti locus helps determine coat color in mice, and this phenotype can vary from light to dark between genetically identical individuals. You have discovered a drug that reduces the variation in the agouti phenotype. What is a likely explanation for this drug's mechanism of action.

mammals digesting milk

The first humans to drink cow milk probably lived in Central Europe about 8,000 BC (400 generations). They would probably have been lactose intolerant from about five. Ingestion of small quantities of milk (with lactose at 4-8%) causes: abdominal pain, flatus and diarrhea Drink milk/ lots of sugar/e.coli eats off all the sugar

Mitochondrial Eve

The name given to the woman who is the most recent martilineal common ancestor to all humans. The mitochondrial DNA is all humans can be traced back to her.

..

The reproductive characteristics which prevent species from fusing. Isolating mechanisms are particularly important in the biological species concept, in which species of sexual organisms are defined by reproductive isolation, i.e. a lack of gene mixture. Two broad kinds of isolating mechanisms between species are typically distinguished, together with a number of sub-types

Linkage equilibrium and reduced genetic diversity around resistance loci

The salmon louse, Lepeophtheirus salmonis, is an ectoparasite of salmonids that causes huge economic losses in salmon farming, and has also been causatively linked with declines of wild salmonid populations. Lice control on farms is reliant upon a few groups of pesticides that have all shown time-limited efficiency due to resistance development. However, to date, this example of human-induced evolution is poorly documented at the population level due to the lack of molecular tools. As such, important evolutionary and management questions, linked to the development and dispersal of pesticide resistance in this parasite, remain unanswered. Here, we introduce the first Single Nucleotide Polymorphism (SNP) array Our results support the hypothesis of a single panmictic population of lice in the Atlantic, and importantly, revealed very strong selective sweeps on linkage groups 1 and 5. These sweeps included candidate genes potentially connected to pesticide resistance. After genotyping a further 576 lice from 12 full sibling families, a genome-wide association analysis established a highly significant association between the major sweep on linkage group 5 and resistance to emamectin benzoate, the most widely used pesticide in salmonid aquaculture for more than a decade.

SUMMARY OF EVIDENCE FOR SELECTION ON PROTEIN SEQUENCES

The situation at present is that selection seems to be important and detectable in many more proteins than were perhaps expected by the neutralists. What about genetic load? We still do not have a good idea exactly how many proteins are under this kind of selection, or what the strength of selection must have been: many of the molecules that have been examined were looked at carefully because it seemed likely that they would be under strong selection, an unfair sample, perhaps!

..

The two primary ways that species respond to heterogeneous environments is through local adaptation and phenotypic plasticity. The American eel (Anguilla rostrata) presents a paradox; despite inhabiting drastically different environ- ments [1], the species is panmictic [2, 3]. Spawning takes place only in the southern Sargasso Sea in the Atlantic Ocean [1]. Then, the planktonic larvae (leptocephali) disperse to rearing locations from Cuba to Greenland, and juveniles colonize either freshwater or brackish/saltwater habitats, where they spend 3-25 years before returning to the Sargasso Sea to spawn as a panmictic species. Depending on rearing habitat, individuals exhibit drastically different ecotypes [4-6]. In particular, individuals rearing in freshwater tend to grow slowly and mature older and are more likely to be female in comparison to individuals that rear in brackish/saltwater [4, 6]. The hypothe- sis that phenotypic plasticity alone can account for all of the differences was not supported by three independent controlled experiments [7-10]. Here, we present a genome-wide association study that demonstrates a polygenic basis that discriminates these habitat-specific ecotypes belonging to the same panmictic population. We found that 331 co-varying loci out of 42,424 initially considered were associated with the divergent ecotypes, allowing a reclassification of 89.6%. These 331 SNPs are associated with 101 genes that represent vascular and morphological development, calcium ion regulation, growth and transcription factors, and olfactory receptors. Our results are consistent with divergent natural selection of phenotypes and/or genotype-depen- dent habitat choice by individuals that results in these genetic differences between habitats, occurring every generation anew in this panmictic species

Models of Evolution:

Transitions vs transversions Base frequencies Different rates for each type of change Different rates across gene

turtles entwined - slow business

Turtles entwined, foundin a field of fossisl where there will lots of turtles, when they engage, they sink this takesminimal amount of times, they usually detangle and go back to normal but they sinked to the bottom and as they gotot the bottom low levels of oxygen , 47 million years

variation

Variation allows some individuals within a population to adapt to the changing environment. Because natural selection acts directly only on phenotypes, more genetic variation within a population usually enables more phenotypic variation. Some new alleles increase an organism's ability to survive and reproduce, which then ensures the survival of the allele in the population. Other new alleles may be immediately detrimental (such as a malformed oxygen-carrying protein) and organisms carrying these new mutations will die out. Neutral alleles are neither selected for nor against and usually remain in the population. Genetic variation is advantageous because it enables some individuals and, therefore, a population, to survive despite a changing environment.

Linkage Disequilibrium

When a pair of alleles from two loci are inherited together in the same gamete more/less often than random chance would expect its a measure of recombination Given two loci, each with pair of alleles at equal frequency (AaBb), if recombination occurs freely, expect equal proportions of each genotype = linkage equilibrium Linkage disequilibrium occurs when alleles are not randomly assorted (due to physical linkage or population structure) Multi-locus indices of association can also be calculated e.g the Index of Association : A prediction about genes under selection is that variation around the site that is under selection will be carried along due to LD ... hichthiking....

the zombie gene

When genes duplicate they have the possibility to acquire new functions ... more often they will mutate and have no residual function Duplicated genes acquire mutations so end up being pseudogenes. Once they are non-functional they can acquire new extra mutations

yeast example

Whole-genome duplication followed by massive gene loss and specialization has long been postulated as a powerful mechanism of evolutionary innovation. Recently, it has become possible to test this notion by searching complete genome sequence for signs of ancient duplication. Here, we show that the yeast Saccharomyces cerevisiae arose from ancient whole-genome duplication, by sequencing and analysing Kluyveromyces waltii, a related yeast species that diverged before the duplication. The two genomes are related by a 1:2 mapping, with each region of K. waltii corresponding to two regions of S. cerevisiae, as expected for whole-genome duplication. This resolves the long-standing controversy on the ancestry of the yeast genome, and makes it possible to study the fate of duplicated genes directly. Strikingly, 95% of cases of accelerated evolution involve only one member of a gene pair, providing strong support for a specific model of evolution, and allowing us to distinguish ancestral and derived functions Based on these observations, they determined that Saccharomyces cerevisiae underwent a whole genome duplication soon after its evolutionary split from Kluyveromyces, a genus of ascomycetous yeasts. Over time, many of the duplicate genes were deleted and rendered non-functional. A number of chromosomal rearrangements broke the original duplicate chromosomes into the current manifestation of homologous chromosomal regions

Y chromosome consortium

a collection of scientists who worked toward the understanding of human Y chromosomal phylogenetics and evolution. The consortium had the following objectives: web resources that communicate information relating to the non-recombinant region of the Y-chromosome including new variants and changes in the nomenclature. The consortium sponsored literature regarding updates in the phylogenetics and nomenclature

random drift in a large population

all populations are finite and will slowly drift toward fixation

deleterious alleles

alleles that lower fitness from a population Natural selection - deleterious alleles could be removed from their genes Females - choosing the fittest male to mate with , this removes deletrious mutations Mate choices are able to maintain fitness within a population

molecular genetics evolution

approach is much more robust and less subjective than looking at the anatomy

sex can be good for you

asexual reproduction is advantageous when organism is well suited to niche (local environment, including competitors) • when niche changes, the sexual species breed and recombine: producing many new genotypes, and some compete well in the new environment • meanwhile, the asexual species can't recombine, so can't create a wide range of genotypes, and thus can't evolve rapidly • so being a specialist asexual reproducer can be a problem... but mixed strategies are possible

asexual reproduction in aspen trees

aspen trees can reproduce sexually and asexually, Different colors of the trees are individual clones in one tree, one of the clones could be the ;largest organism in the planet coming from one parental strain.They produce quite quickly, they will be susceptible to whats changing around them , variation will start to arise in the clone,asexual reproduction intoduces spontaneous mutations that generates diveristy this generates a new phenotype.

why is immune system gene most prevalent ?

because selection is not constant, in a population an individual is by chance genetically tolerant to different infections but different generations don't always get the same infection so selection changes and diverges hence the genes are always selected in different ways moving in different directions

Y chromosome in evolutionary history

can be used for tracing evolutionary history because it stays essentially intact from father to son, barring mutations

recombination

can produce double mutants in one generation ( way of generating more diversity)

hydra

can reproduce sexually and asexually by the budding process

Ashkenazi jews unusual population

certain alleles are in high frequencies that are either absent or rare in other populations

founder effect

change in allele frequencies as a result of the migration of a small subgroup of a population The establishment of a new population by a few original founders (in an extreme case, by a single fertilized female) which carry only a small fraction of the total genetic variation of the parental population

Lactase Polymorphisms

changes have occurred to the lactase gene over time that led to lactase persistence= lactose intolerant mutation in the control region, single bp change leads to lactose intolerance leading to non transcription lactose tolerant are thus advantageous when drinking milk European lactose tolerance linked to SNP at C-13910 because: at a high frequency in Europeans at significant linkage disequalbirium Diff alleles in diff popul

chimps and humans

chimps share 99% of genetic material with humans, intelligent, social lives/nurturing are similar, both omnivores/bipedal/see color/use tools// they are more variable than humans at a genome level

outbreeding depression

decreased fitness breeding individuals too genetically different. epistasis and pleiotropy cause poor gene interactions

vacations

different variants are more frequent in some populations than others might be - adaptive - or by chance ( Founder effect)

intrasex competition

direct competition between two or more males or two or more females for access to members of the opposite sex

rapid random drift in small populations

drift can rapidly change allele frequencies in small populations • drift eventually leads to one allele becoming fixed

identity mistakes

end up mating with the wrong species

FST - The fixation index

equation

meso ( inter-population)

exchange of virulence factors - escape from mullers ratchet nuclear genome - adaptation to new alternative hosts/vector/transmission routes

Davenport

experiment eye color via mendels ideas and came to a conclusion that the brown color was dominant to blue color when they had kids with brown eyes and they themselves had blue eyes, The gene was found, gene that is involved in pigmentation , HERC2 gene- single bp gene control, intron on the gene next door blue eye colour in humans may be caused by a perfectly associated founder mutation in a regulatory element located within the HERC2 gene inhibiting OCA2 expression. How old mutations are.. Suggests that first blue eyes person lived around the black sea

August Weismann, 1897

f we bear in mind that in sexual propagation twice as many individuals are required to produce any number of descendants, and if we further remember the important morphological differentiations which must take place in order to render sexual propagation possible, we are led to the conviction that sexual propagation must confer immense benefits upon organic life. I believe that...sexual propagation may be regarded as a source of individual variability, furnishing material for the operation of natural selection

female pandas - slow business

female pandas ovulate just once a year and there is only a 36 hour window during which they can get pregnant

disruptive selection

form of natural selection in which a single curve splits into two; occurs when individuals at the upper and lower ends of a distribution curve have higher fitness than individuals near the middle Intermediate traits selected against e.g. Sympatric speciation

sexual reproduction advantages

genetic variation means less susceptibility to disease, better adaption, increased survival it is a slower rate than asexual as two partners are needed that need to be genetically different and only half the offsprings are reproducers this generates diversity as mates compete with each other ..

Jean Baptiste Lamarck

he proposed that by selective use or disuse of organs, organisms could acquire or lose certain traits which are then passed on to their children and future generations, eventually changing the species

excess males for females

high level of diversity, females able to make a choice about mating, this provides a mechanism for removing deletrious mutations from a population

Ashkanazi Jews: BRCA1

host of mutations within a gene Researchers think Ashkenazi genetic diseases arise because of the common ancestry many Jews share. While people from any ethnic group can develop genetic diseases, Ashkenazi Jews are at higher risk for certain diseases because of specific gene mutations.( THE FOUNDER EFFECT) it is a similar mutation to the ones in jews however the AG deletion is much higher than in other populations. The carriers of these newly mutated genes were unaffected by them, but their descendants were at greater risk for developing genetic diseases as a result of inheriting mutated genes. Over the course of Jewish history, many mutated genes, including the gene responsible for Gaucher disease, GBA1, were passed on from generation to generation

Mapping the epigenetic basis of complex traits

identified epigenetic QTLs associated with differences in methylation marks (epiQTLs) controlling flowering time and root length in the model plant Arabidopsis. These epiQTLs were mapped in genetically identical lines that differ only in their methylation marks. A small number of QTLs were able to explain up to 90% of the heritable variation in these traits. Thus, in plants, the heritability of some complex traits can be determined by epigenetic variation Quantifying the impact of heritable epigenetic variation on complex traits is an emerging challenge in population genetics. Here, we analyze a population of isogenic Arabidopsislines that segregate experimentally induced DNA methylation changes at hundreds of regions across the genome. We demonstrate that several of these differentially methylated regions (DMRs) act as bona fide epigenetic quantitative trait loci (QTLepi), accounting for 60 to 90% of the heritability for two complex traits, flowering time and primary root length. These QTLepi are reproducible and can be subjected to artificial selection. Many of the experimentally induced DMRs are also variable in natural populations of this species and may thus provide an epigenetic basis for Darwinian evolution independently of DNA sequence changes.

Neutralists

ike Kimura and King and Jukes, therefore, didn't deny that Darwinian evolution via natural selection occurred. They simply thought that these advantageous mutations, or "balanced polymorphisms" were extremely rare. Most polymorphisms, they argued, must be "effectively neutral". The probability of fixation of a neutral allele by drift is 1/2Ne, and if this is bigger than typical selection pressures, drift will outweigh selection. Thus the neutral theory doesn't even argue that most molecular polymorphisms are completely neutral, just that any selection pressures may usually be outweighed by drift. If the neutral theory is correct, we might expect to see more rapid evolution in regions of the genome not constrained by selection than in regions strongly constrained by selection. This is in general true: synonymous changes occur much more rapidly than non-synonymous changes overall. Thus most of the evolution seems to be due to base pairs that are not connected strongly with the phenotype, and most likely to have little effect on fitness

allele frequency equation

in a two allele system: frequency of allele A = f(A) = p frequency of allele a = f(a) = q f(A)+f(a)=p+q=1 in a two allele system frequency of genotype AA = f(AA) = f(A) * f(A) = f(A)2 = p2 frequency of genotype aa=f(aa)=f(a)*f(a)=f(a)2 =q2 frequency of genotype Aa = f(Aa) = 2 * f(A) * f(a) = 2pq •overall, p2 +2pq+q2 =1

Muller's Ratchet Hypothesis

in an asexual population all individuals are identical clones mutations will be passed onto all offspring • most mutations will be lost through drift • some neutral mutations will be fixed through drift • strongly deleterious alleles will be lost through selection advantageous mutations will be fixed by selection • some mildly deleterious mutations may increase in frequency by chance before selection can remove them • some deleterious mutations will be fixed through linkage to an advantageous mutation// once fixed, the only way to remove a deleterious mutation is by a new mutation at the exact same site some mildly deleterious mutations will be fixed through drift • mildly deleterious mutations will accumulate over time • leading to an irreversible loss of fitness

inbreeding

increases level of homozygosity this provides an advantage to deleterious mutations as they start to accumulate as make them less fit for the environment

mullers ratchet

is a process in which absence of recombination, especially in an asexual population, results in accumulation of deleterious mutations (harmful mutations) in an irreversible manner.[1][2] This happens due to the fact that in the absence of recombination, offspring at least bear the same mutational load as their parents (assuming reverse mutations are rare)[2]. Muller proposed this mechanism as one reason why sexual reproduction may be favored over asexual reproduction, as sexual organisms benefit from recombination. The negative effect of accumulating irreversible deleterious mutations may not be prevalent in organisms, which, while they reproduce asexually, also undergo other forms of recombination. This effect has also been observed in those regions of the genomes of sexual organisms that do not undergo recombination.

lactose metabolism

lactose in environment causes E coli to express the genes involved in the absorption and metabolism of lactose// lactase enables mammals to digest milk

low population density

makes sexual reproduction a slower process

Male anglerfish - slow business

male anglerfish so infrequently encounter a female that when they find one they attach to her body and fuse, atrophy and end up becoming just a pair of gonads ( takes many years to bump into a female down the sea

Endogamy

marriage between people of the same social category

sexual reproduction generates diversity

mates compete with each other and are chosen by the opposite sex.high proportion of males end up not mating and leads to death

pre-zygotic isolation

mating and fertilization are prevented

post-zygotic isolation

mating occurs, but offspring are sterile or inviable Post-zygotic isolation between sister species = outbreeding depression

Tristan da cuhna

most isolate permanelty inhabited places on earth , small population, derived from 15 people that were originally there.. Most people derived from one scottish family name

gene flow

movement of genes between populations Homogenizes alleles between populations but increases heterozygosity within (cf with genetic drift) Analyses of gene-flow via Analyses of Molecular Variance (AMOVAs) & FST

positive selection

natural selection that increases the frequency of a favorable allele closely related species- compare genomes and sequences and see how different they are, some sequences change more than others and diverge more quickly than others Humans and Chimps diverged about 5 million years ago.Are their genes equally diverged or do some genes evolve more quickly?

Outbreeding

negative assortative mating will increase heterozygosity Wedekin et al 1995 Sweaty T-shirt study MHC diversity defines mate preference BUT extreme heterozygosity is observed in clonal organsims e.g. Bdelloid rotifers... or.... T. gambiense The Meselson effect - allele sequence divergence - in the absence of sex or gene conversion, alleles accumulate mutations independently of each other in same clonal lineage

asexual reproduction

no mate competition and no mate choice generates a low barrier to reproduction

founder effect

no variations are lost its just a subset of it drive somewhere else. Species that arrive in an island they never use to be in and when they arrive on the island the amount of variation is way less as populations in islands are way less

bdelloid rotifers

over 300 species - all cloned females, asexual reproduction for 85 million years no sex for 40 million years? • "an evolutionary scandal" - John Maynard Smith • no observed males or meiosis • "independent evolution of homologous chromosomes" • ancient degenerate tetraploid • desiccation and radiation resistant and capable of acquiring DNA by horizontal gene transfer • can undergo a cryptic form of meiosis in which homologues do not pair?

Tempreture since 1860

plataeu rise.. global warming/ human activities Tempretures get warmer by 2000, so temp may have had an effect on the population , and therefore dna variation

Hardy-Weinberg Principle

principle that allele frequencies in a population will remain constant unless one or more factors cause the frequencies to change a population is in Hardy-Weinberg equilibrium if: observed genotype frequencies = expected genotype frequencies • as HWE is based on random reassortment of alleles in the population, it is the null hypothesis but only if certain assumptions are met • the population is large • the population mates randomly • there is no selection • the mutation rate is low

positive selection

process in which advantageous genetic variants quickly increase in frequency in a population

Genetic Drift

random change in allele frequencies that occurs in small populations Genetic drift is a term used to describe the random (stochastic) sampling effects that result in allele frequency differences from one generation to the next (individuals who have no offspring, alleles not transferred in gametes) This random probabilistic process underpins the evolution of all neutral markers Alleles with a selective advantage / disadvantage can also be affected by this random process especially in small populations that are more susceptible to random sampling affects

founder effect (genetic drift)

rare allele occur in a higher frequency in a new population than they do in the general population 1- Asthma Does such an isolated population derived from a small number of individuals show evidence of Ernst Mayr's Founder Effect? According to Noe Zamel 23% of Islanders have asthma, with 57% showing some asthmatic symptoms. He suggests three ancestors were asthmatic. Genetic bases of complex diseases can be studied in countries or islands with low populations In big populations you have got lots of alleles so any genertic reason is possible 2- Glaucoma Peripheral vision .. Limited variation so more chances to try and find the genetic reason Gives rise to evolutionary medicne Islanders are likely to share the same pre-disposition genes. Islanders are essentially a single giant family

Lake Maracibo

rate is 70x higher in that population than any where else .. Why ? ... All due to one woman, Maria Concepcion Soto living 200 years ago who had 10 children and now has 18,000 direct descendants, 14,000 of whom are alive today. One woman who arrived there, when europenas were colonizing she came from spain and she had huntingson , mutant allele , bigger than normal , she had 10 children , she now has 18,000 decendants ( 8 generations) Classic founder effect, allele has been passed to generations due to chance in a founder population

By studying fossilized bones

scientists learn about the physical appearance of earlier humans and how it changed. Bone size, shape, and markings left by muscles tell us how those predecessors moved around, held tools, and how the size of their brains changed over a long time. Archeological evidence refers to the things earlier people made and the places where scientists find them. By studying this type of evidence, archeologists can understand how early humans made and used tools and lived in their environments.

sex specific gene

selections in male and females are different and are under selective pressure an allele might be advantageous in males but not in females

Red Queen Hypothesis

sexual selection allows hosts to evolve at a rate that counters the rapid evolution of parasites "for an evolutionary system, continuing development is needed just in order to maintain its fitness relative to the systems it is co-evolving with" Organism has to continue to evolve to maintain its ecological niche to prevent competetion

why are chimps more variable

smaller populations that's why chimps are more variable Populations were pretty stable until 1600 AD when the plague has striked, and populations started rising

Modern Evolutionary Synthesis

suggests that genetic mutations create heritable variation and that this variation is the raw material upon which natural selection acts describes the fusion (merger) of Mendelian genetics with Darwinian evolution that resulted in a unified theory of evolution. It is sometimes referred to as the Neo-Darwinian theory. The Modern Synthesis was developed by a number of now-legendary evolutionary biologists in the 1930s and 1940s

frequency dependent selection

the fitness of a phenotype depends on how common it is in the population an evolutionary process by which the fitness of a phenotype or genotype depends on the phenotype or genotype composition of a given population. • In positive frequency-dependent selection, the fitness of a phenotype or genotype increases as it becomes more common. • In negative frequency-dependent selection, the fitness of a phenotype or genotype decreases as it becomes more common. This is an example of balancing selection. • More generally, frequency-dependent selection includes when biological interactions make an individual's fitness depend on the frequencies of other phenotypes or genotypes in the population.[1] Frequency-dependent selection is usually the result of interactions between species (predation, parasitism, or competition), or between genotypes within species (usually competitive or symbiotic), and has been especially frequently discussed with relation to anti-predator adaptations. Frequency-dependent selection can lead to polymorphic equilibria, which result from interactions among genotypes within species, in the same way that multi-species equilibria require interactions between species in competition (e.g. where αij parameters in Lotka-Volterra competition equations are non-zero). Frequency-dependent selection can also lead to dynamical chaos when some individuals' fitnesses become very low at intermediate allele frequencies.

lactose intolerant

the inability to digest lactose, the sugar found in milk; most adult mammals (including humans) are lactose intolerant as adults

Outbreeding

the process of mating less closely related individuals when compared to the average of the population

Epigenetics

the study of changes in organisms caused by modification of gene expression rather than alteration of the genetic code itself. the study of environmental influences on gene expression that occur without a DNA change

sexual reproduction has drawbacks

time and energy spent looking for a mate • involves complex behaviour that is expensive • involves complex behaviour that is dangerous • risk of being attacked by mate • sexually transmitted diseases • risk of infertility

sex provides an opportunity for

transmission of diseases

Rates of change at neutral loci

θ = describes amount of genetic change expected at each nucleotide site if evolution is entirely neutral based on a coalescent approach Obtained from the mutation rate μ (which is also the fixation rate) and the time to fixation 4Ne θ = 4Ne x μ

Why compare sequence data ?

• Genetic distance analyses (pairwise relatedness among individuals) • Phylogenetic analyses (historical relatedness among species, populations or genes = geneology) • Population genetic analyses (compares variation within vs between populations to estimate gene flow, population size, historical demographics; selection; recombination) • Phylogeography (relating genetic to geographic distance)

Redundancy and non-coding DNA

• Neutral theory fits with out understanding of the genetic code • Multiple codons code for the same amino acid (e.g. GAA and GAG both specify glutamic acid) • Synonymous (no affect on AA) and non-synonymous (affect AA) mutations. • In eukaryotes, introns and 'junk' DNA comprise most of genome

Next Generation Sequencing (NGS)

• Produces millions of short reads • Assembled to reference genome Identify Single Nucleotide Polymorphisms (SNPs) across whole genomes

Whole genomic approaches

• allow more than just the analysis of genomic sequence diversity •Structural variation can be defined via inter- or intra- species comparison between assembled genomes •Duplications, inversions, deletions, insertions, translocations etc •Can also occur at the scale of whole chromosomes (aneuploidies, polyploidies) •Can have profound fitness consequences - not necessarily just negative (e.g. disease)

sex is good because

• allows rapid recombination to generate new genotypes • helps to maintain diversity in populations • protects against the accumulation of deleterious mutations

How can we measure genetic variation?

• analyses based on genotypes/allele frequencies • analyses based on sequence data • summary statistics (measures of diversity and polymorphism, heterozygosity, recombination) phylogenetic trees/genealogies

adaptive significance of sex

• asexual reproduction produces more offspring • asexual reproduction is easier • sexual reproduction has drawbacks • time and energy spent looking for a mate • involves complex behaviour that is expensive • involves complex behaviour that is dangerous • risk of being attacked by mate • sexually transmitted diseases • risk of infertility

social status

• dominants convert to females • subordinates convert to males

sexual reproduction generates diversity

• genetic recombination creates new genotypes in the population, so the fittest can be selected when environmental conditions change

the adaptive significance of sex

• given two conditions, asexual reproduction would yield twice the offspring of sexual reproduction • the conditions are that a female's reproductive mode (sexual or asexual) does not affect: • the number of offspring she can produce ( not true ) • the probability that her offspring will survive to breed • given these two conditions, an asexual mutant would out- breed sexual members of the same species, and finally take over entirely • as this does not occur: how do these conditions fail?

Adaptation and panmixa in American eels - a dead end street

•Animals found 'inland' are generally much larger and older when they return to the sea •Animals found in estuarine environments are smaller and mature earlier. •Animals in the great lakes region have suffered dramatic declines •Reintroduction estuarine areas have failed - larger phenotype animals are not recovered. •Genetic basis ? •18 microsatellite loci, FST = 0 means - no detectable differences.... ....need to scale up

speciation continuum

•At any given point in time, any population is somewhere on the speciation continuum •Pre- and post- zygotic isolation •Extrinsic pre-zygotic isolation - habitat isolation, assortative mating •Extrinsic post-zygotic - result from ecological or sexual selection (reduced fertility of hybrids / migrants) •Intrinsic post-zygotic isolation are genetic incompatibilities independent of environment •Back-flow - re-hybridisation - can occur before intrinsic barriers form

Transgenerational Epigenetics

•Epigenetic modification of genetic material and gene expression takes may forms •More common in plants, fungal and microbes than in mammals which have a sequestered germline RNA feedback loops- mRNA that promotes its own transcription non coding and coding RNA- maternal RNA chromatin marks- binding of methyl or ethyl groups to DNA and histones, or directly to DNA structural templating- prion proteins in yeasts/fungi

What kind of genomic signature typifies selection between populations

•Genomic data can be used to study the architecture of adaptation to novel environments (what genomic regions involved) •Easiest to observe under so called 'adaptation with gene-flow' •Markers with no fitness consequence in either environment behave 'normally' high geneflow (FST=approx. 0) •Markers with fitness consequences appear as 'outliers' (FST>0)

Recent sweep frustrates attempts to identify resistance genes

•Long distance identical haplotype sharing •Large linkage blocks (LG1 - 1.7Mb, LG5 - 6.2Mb) •Multiple coding ORFs, but not clear what genes responsible •Recent sweeps means minimal recombination •Genes will become easier to identify with time & recombination •Best to complement with a bottom-up approach e.g. QTL mapping

Evolutionary scaling of epigenetic effects

•Most cellular epigenetic modifications are reset during meiosis in primordial germ line cells •Further epigenetic modifications are also reset at fertilization •Relative contribution of different sexes to retained epigenetic variation in offspring can be different (?) •Importantly, the frequency and longevity of epigenetic mutations is highly variable •How much epigenetic information is transferred and how do epigenetics interface with molecular evolution ? Is it associated with heritable phenotypic traits ?

Where does adaptive variation come from

•New environment or selective pressure, how does organism adapt ? •Adaptation from SGR likely faster •Standing variation already 'road tested' by selection •Assists species to escape rapid environmental change 'evolutionary escape' •Standing genetic diversity as resource (conservation) •Standing variation as a challenge (drug resistance) •Distinct signature of 'selective sweeps'

Gene family expansion and adaptation

•Numerous examples of adaptive expansion of gene families by gene duplication •Gene duplication a solution to Susumu Ohno's dilemma - How do new genes evolve under continuous selection ? •So long as duplicates are not lost to drift or null mutations, neofunctionalisation is possible •Can have immediate 'dosage effects' - a brute way of modulating gene expression. •Underlies copy number variation in Leishmania and T. cruzi for example

Take homes

•Population genomics makes use of the same theory, just scaled up •Genome-wide signatures of selection can tell you about the architecture of adaptation •Bottom up and top down approaches best used together to identify target genes •Adaptation and speciation on a continuum •Natural replicates - parallel processes - favored be evolutionary geneticists studying speciation

Available drugs and resistance in sea lice

•Several classes of antiparasitic used Organophosphates Pyrethroids Avermectins Chitinase biosynthesis inhibitors. •Reduced louse sensitivity has been reported to all drugs •Many older classes are bring re- introduced in the face of avermectin resistance •Relatively few drugs licensed for use •Multiple resistance mechanisms (KDR, ABC transporters etc)

Take homes

•Structural mutations, genome duplications HGT, mobile genetic elements are a powerful force in molecular evolution •If genetics is a solar system, epigentics is a galaxy, them the potential combinations between the two systems are infinite (almost) •For evolutionary biologists, trans-generational effects are of most interest (imprinting, maternal effects) •Multiple transgenerational epigenetic mechanisms exixt •Epigenet control of phenotypes, links with Lamarckian Inheritance and Genetic Assimilation (adapt first mutate later, so long as the environment stays fixed)

"

•Whole genome outlier analysis based on FST indicates multiple genomic regions under diversifying selection •83% of SNPs divergent between one population pair •17% divergent between >2 population pairs •Thus most adaptive variation idiosyncratic, less is repeatable •Why ? •Gene ontology of parallel divergent SNPs around genes known to play role in balancing nutritional vs toxic effects of metal ions in feed plants.

many organisms persist with high levels of inbreeding Why?

•reduced population size makes drift potentially stronger than mutation and selection •more inbred have higher chance that changes become fixed faster •Purging •Outbreeding depression and local adaptation •Reproductive assurance •Trade-off between being sure you have a mating partner (inbreeding favoured) and fitness costs of inbreeding (outcrossing favoured

cost of sex - can be dangerous

Usually refers to a reduced rate of population growth of a sexual compared to an asexual population, owing to production of males. Bean weevil - sex can be dangeous, they have a penis that damages the females reproductive tract and prevents further mating Male bedbug, inseminates females ( body cavity) female small Amazonian frogs are frequently drowned by overzealous competing males • the male can promote the ejection of oocytes from the abdominal cavities of dead females and fertilise them bats eavesdrop on the sound of copulating flies , as flies sing the ocurtship song as they less aware of env this ca be dangeous as preys come along

male analog of mitochondrial eve

Y chromosome

Evoultion

a change in allele frequency in a gene pool

selective sweep

hitchhiking The situation in which strong selection can "sweep" a favorable allele to fixation within a population so fast that there is little opportunity for recombination. In the absence of recombination, alleles in large stretches of DNA flanking the favorable allele will also reach high frequency. •Closely linked markers to the selected gene 'hitchhike' with the marker • Reduced genetic diversity around the locus experiencing selection •In recent sweeps - increased linkage diseqeuilibrium

Phylogeography

the use of evolutionary trees in answering questions about the geographic distribution of organisms

asexual reproduction yields clones

• advantageous when conditions are favourable e.g. colonising a new environment when competition is low

Lamarck's second law

"All the acquisitions or losses wrought by nature on individuals, through the influence of the environment in which their race has long been placed, and hence through the influence of the predominant use or permanent disuse of any organ; all these are preserved by reproduction to the new individuals which arise, provided that the acquired modifications are common to both sexes, or at least to the individuals which produce the young" soft inheritance

Ashkenazi genetic diseases

- Tay sachs - BRCA1 - Huntigtons disease - Cystic fibrosis

Eye Colour

Blue eyes - european decendant and lots in mammals 80% light

Protandry

Born a male, change to a female

Ka/Ks test

Compares proportion of synonymous / non-synonymous changes under neutrality with that observed within species

Tajima's Test

Compares sequence diversity expected under neutrality with that observed

Neanderthals

Fossil and other evidence suggests Neanderthals and modern Humans co- existed in Europe as recently as 30,000 years ago. They are older so mustve left africa earlier Are they the same species? Dna sequences found in caves where you don't get degradation where bodies are frozen or desacdated .. Frozen ifin alpes mtDNA - most robust Genetic analysis of lice supports direct contact between modern and archaic humans. PLOS Biology 2: e340. Immune system gene surviving in archaic dna .. Helped them survive ( variant) Several waves: All populations have multiple origin so are similarly variant Multiple genome sequences / comparative sequences

Neanderthals

In Europe, another human species lived and adapted to life in the cold climates of the last Ice Age.

CF heterozygote advantage

Recently a heterozygote advantage was suggested to explain the high incidence (1:25 carrier individuals in Europeans) of the cystic fibrosis gene. This selective advantage was speculated to be due to a high resistance to chloride-secreting diarrhea, including cholera more likely to survive cholera/thphoid/tuberculosis it might be true but it dosen't run in all populations

Molecular evolution and/or mutational modes

Single base pair changes, substitution Non-coding regions: introns, 5' & 3' flanking regions Synonymous Non-synonymous, amino acid replacements Pseudogenes Insertions and deletions (Indels) "Slippage" (microsatellites) Gene conversion Concerted Evolution Transposition Retrotransposition Genomic evolution Codon usage bias Exon shuffling Gene duplication, multi-gene families Whole genome duplication

statistics to measure selection

Tajima's Test Ka:Ks Test MacDonald -Kreitmen Test

Ashkanazi Jews: Tay Sachs

Tay-Sachs disease is caused by a mutation in the Hexosaminidase A gene, which affects the ability of lysosomes to break down neurotoxic gangliosides.

Ashkenazi jews unusual population

Their population is unusual in that: relatively few founders significant population expansion and contraction endogamy unequal reproduction rate

transgenerational epigenetics

a subfield of epigenetics that examines the transmission of experiences via epigenetic mechanisms across generations

Muller's Ratchet Hypothesis

genetic drift and mutation lead to accumulation of harmful mutations that sex can solve

hermaphrodites

organisms that contain both female and male sex organs.( ovaries and testes)

if population is small

random sampling error in small populations can lead to large divergences from expected

FIS - The inbreeding coefficent, estimator = f

varies between -1 and + 1 FIS = -1 = All samples in pop heterozygous for the same alleles FIS = 0 = Hardy-Weinberg Allele frequencies FIS = +1 = All samples in pop homozygous for different alleles

gene duplications

whole genome duplication is the process by which an organism's entire genetic information is copied, once or multiple times which is known as polyploidy.[18] This may provide an evolutionary benefit to the organism by supplying it with multiple copies of a gene thus creating a greater possibility of functional and selectively favored genes. However, tests for enhanced rate and innovation in teleost fishes with duplicated genomes compared with their close relative holostean fishes (without duplicated genomes) found that there was little difference between them for the first 150 million years of their evolution

Whole Genome duplications (Ploidy / Aneuploidy)

•Coordinate duplication of the genome can allow for large scale adaptation to novel environments •Must of the genome underwent massive mutation and gene loss •One from each set maintained in the majority of cases •Where duplicates are retained - abundant neofunctionalisation •Conserved synteny of duplicated genes is clue to ancient event •95% of cases of accelerated evolution involve only one member of a gene pair

Lamarck's First law

"In every animal which has not passed the limit of its development, a more frequent and continuous use of any organ gradually strengthens, develops and enlarges that organ, and gives it a power proportional to the length of time it has been so used; while the permanent disuse of any organ imperceptibly weakens and deteriorates it, and progressively diminishes its functional capacity, until it finally disappears" adaptation

Muller's ratchet

"a kind of irreversible ratchet mechanism exists in the non- recombining species (unlike the recombining ones) that prevents selection, even if intensified, from reducing the mutational loads below the lightest that were in existence when the intensified selection started, whereas, contrariwise, 'drift' and what might be called 'selective noise' must allow occasional slips of the lightest loads in the direction of increased weight

evolutionary medicine

- Islanders are likely to share the same Asthma pre-disposition gene(s). Islanders are essentially a single giant family

summary

- Measures of selection look for departures from neutrality and can test important biological hypotheses - Genetic recombination is important in terms of sex and associated benefits, but also in terms of understanding inbreeding and hitchhiking - Genetic drift can fix deleterious alleles by chance, or drive speciation, and can arise through population bottlenecks - Population genetic parameters can provide important insights into mating systems

What does LD mean in sexual organisms

- Non-random association of alleles from inbreeding - Epispastic effects (functional linkage between alleles) -Hitchhiking (allele changes frequency because of selection at another locus) -Looking for patterns of hitchhiking can help identify genes under selection in sexual organisms

macro ( interspecies)

- escape from mullers ratchet nuclear genome - adaptation to new alternative hosts/vector/transmission routes

why is sex important in micro ( intra-population)

- escape mullers ratchet mt genome - exchange of virulence factors - exchange drug resistance markers

examples

- genome duplications in yeast - gene family expansion and adaptation - HGT and genome rearrangements in bacteria

Population structure, past and current demography

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Random effects (genetic drift due to bottlenecks, founder effects)

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Outbreeding depression, selection against intermediates and hybrid breakdown

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Post-mating isolating mechanisms.

.Genomic incompatibility, hybrid inviability or sterility. a) Gametic incompatibility. Sperm transfer takes place, but egg is not fertilized. b) Zygotic mortality. Egg is fertilized, but zygote does not develop. c) Hybrid inviability. Hybrid embryo forms, but of reduced viability. d) Hybrid sterility. Hybrid is viable, but resulting adult is sterile. e) Hybrid breakdown. First generation (F1) hybrids are viable and fertile, but further hybrid generations (F2 and backcrosses) may be inviable or sterile.

How is Selection Measured?

1) Establish genetic variation at sequences known or suspected to be subject to selection Whole genes or specific gene regions (e.g. antigen binding sites) 2) Establish direction and size of deviation from neutral predictions 3) Establish ratios of NS/S mutation (coding / non-coding) 4) Compare allele frequencies to Hardy-Weinberg expectations

How do we use genomics to study adaptation

1) Make abundant use of prior information to identify candidate regions of interest (QTL, transcriptomics, related organisms) with a clear phenotypic basis. 2) Generate genomic data from many individuals with populations of interest, scan for signatures of selection around you genes of interest to discover - are they actually important ?// •Generate genomic data •Scan genomic data between populations signatures of selection •Devise phenotypic impact of genomic variation

Fossil Evidence for Evolution

1) compared older and newer fossils 2) all animals derived from one ancestor 3) different selection pressures made animals of all certain striking features in common 4) gaps pointing out uncertaintes in our understanding of exactly how some species evolved.

How is Diversity Assessed

1- Allele Frequency and Genotyping Data (e.g. microsatellites, allozymes) -Ho = observed heterozygosity; calculated directly from diploid data He = expected heterozygosity; estimated based on allele frequencies predicted under Hardy-Weinberg equilibrium Na = Number of alleles per locus 2- Sequence Data - nucleotide diversity π (Tajima 1983) -theta θS (Watterson 1975) - population-wide change derived from number of polymorphic sites

QTL theory

1.Likelihood of co-segregation of two markers inversely proportional to their physical linkage - allows you to build physical map 2.Statistical test* to evaluate phenotypic differenced in F2 progeny separated by different markers alleles - significant difference = QTL. 3.Marker is NOT QTL - QTL must be identified by targeted sequencing

Asexual advantages and disadvantages

1.many offspring in short period of time 2.requires no energy to make gametes and find mate 3.all genetically identical- no variation every offspring is a reproducer

describe evidence that human populations have increased in size in recent history

2, Define the term 'Genetic Bottleneck' and review the evidence of the Toba catastrophe 3, Define the term 'Founder Effect' and show how it applies to Tristan da Cuhna 4, Explain why recent evolution in the human IRGM gene has caused it to be renamed the 'Zombie' Gene

different genotypes

3 different genotypes= the only way to generate combined phenotypes which might be selectively advantageous is if we produce asexually we have to wait for for the mutation to take place in clones, muation rates are very low, it would take ages to get the same or both mutations in the same clone

IGRM Alu-induced mutation

50 Million Years Ago: Alu integration into exon 2 disrupts ORF. Multiple stop codons and frame shift mutations accrue over time. Alu in genes make them unfunctionable , insertion Why is it functiona;? IGRM reactivation Viral element jumps inthat provides an element with a promoter 22 Million years ago: integration of ERV9 element serves as new promoter. 18 Million years ago: new SNP introduces new ATG start codon 12 Million years ago: new SNP removes problematic stop codon

Toba Catastrophe Theory

69,000 and 77,000 years ago, a super volcanic eruption occurred causing a global volcanic winter of 6 to 10 years, reducing human population to 1,000 and 10,000 breeding pairs directly related to us This has a global effect change // human populations were relatively low until recently

balance school of variation

A few people, such as "Dobzhansky, who began his career collecting beetles in Central Asia, and the British School ... who carried on the genteel upper-middle-class tradition of fascination with snails and butterflies" (Lewontin 1974: 30), believed that polymorphisms were fairly common, and indeed important. They believed and indeed showed that morphological and chromosomal polymorphisms, for instance, were retained because of heterozygous advantage or other forms of "balancing" selection • levels of genetic variation in populations high • most loci polymorphic • Individuals heterozygous for large number of loci • Suggested GV maintained by different forms of balancing selection, such as overdominant selection (heterozygous advantage)

achondroplasia

A form of human dwarfism caused by a single dominant allele; the homozygous condition is lethal achondroplasia is caused by a single mutation in the FGFR3 gene ecurrent frequent mutations in the male germline

Huntington's disease

A human genetic disease caused by a dominant allele; characterized by uncontrollable body movements and degeneration of the nervous system; usually fatal 10 to 20 years after the onset of symptoms.

Tay-Sachs disease

A human genetic disease caused by a recessive allele that leads to the accumulation of certain lipids in the brain. Seizures, blindness, and degeneration of motor and mental performance usually become manifest a few months after birth. 1 in 30 Ashkanazi Jews is a carrier for Tay-Sachs (1 in 250 outside) Most have 1278insTATC mutation One of earliest examples of population screening Ten times more freq in that population and the majority is an insertion this is to do with one particular allele its not something unusual about the behaviour of the population this suggests that at some point in history some important person must have had the allele that then passed it on to the next generations

Fixation and neutrality

A mutation whose fixation is independent of natural selection is termed a neutral mutation. Therefore selective neutrality of a mutation can be defined by independence of its fixation from natural selection • How do alleles become fixed (100% of individuals) within a population without selection ? • In the absence of selection, a random, probabilistic process Explains the 'rate of evolutionary change'

asexual reproduction

A reproductive process that involves only one parent and produces offspring that are identical to the parent.

sexual reproduction

A reproductive process that involves two parents that combine their genetic material to produce a new organism, which differs from both parents

Inbreeding

A selective breeding method in which two individuals with identical or similar sets of alleles are crossed.

quantitative trait loci

A set of genes that determines a complex character that exhibits quantitative variation. Quantitative trait loci (QTLs) are genetic regions associated with phenotypic traits that help to determine the underlying genetics controlling the magnitude of a specific trait

DNA evidence for evolution

All living organisms share genetic material made from the same building blocks and all use that material to code for proteins Does DNA (specifically Y-chromosome) evidence support the very well— documented genealogical evidence that the entire population of Tristan da Cuhna is derived from seven male lineages that correspond to the seven extant surnames? DNA analysis by mini-satellites (STRs). pcr/sequencing

Allozymes

Allozymes are allelic variants of enzymes encoded by structural genes. Enzymes are proteins consisting of amino acids, some of which are electrically charged. As a result, enzymes have a net electric charge, depending on the stretch of amino acids comprising the protein

Development of Evolutionary Theory

Allozymes--first widely used genetic markers (1960s & 70s) DNA cloning and sequencing (1980s) PCR--polymerase chain reaction (1990s) Fragment analyses (RFLPs, microsatellites, minisatellites, DNA fingerprinting, RAPDS) Comparative/functional genomics (2000s) Personalised/nonmodel genomics (2010s)

Gene family expansion - Monkey business

Although the complete genome sequences of over 50 representative species have revealed the many duplicated genes in all three domains of life, the roles of gene duplication in organismal adaptation and biodiversity are poorly understood. In addition, the evolutionary forces behind the functional divergence of duplicated genes are often unknown, leading to disagreement on the relative importance of positive Darwinian selection versus relaxation of functional constraints in this process. The methodology of earlier studies relied largely on DNA sequence analysis but lacked functional assays of duplicated genes, frequently generating contentious results. Here we use both computational and experimental approaches to address these questions in a study of the pancreatic ribonuclease gene (RNASE1) and its duplicate gene (RNASE1B) in a leaf-eating colobine monkey, douc langur. We show that RNASE1B has evolved rapidly under positive selection for enhanced ribonucleolytic activity in an altered microenvironment, a response to increased demands for the enzyme for digesting bacterial RNA. At the same time, the ability to degrade double-stranded RNA, a non-digestive activity characteristic of primate RNASE1, has been lost in RNASE1B, indicating functional specialization and relaxation of purifying selection. Our findings demonstrate the contribution of gene duplication to organismal adaptation and show the power of combining sequence analysis and functional assays in delineating the molecular basis of adaptive evolution

Doggerland

An area which is now beneath the southern north sea. It connected Britain to continental Europe. This was during the last glacial period. The land was flooded by rising sea levels around 6,500 to 6,200 B.C. This are helped people travel from one place to another. Doggerland was an area of land, now submerged beneath the southern North Sea, that connected Britain to continental Europe. It was flooded by rising sea levels around 6500-6200 BC As ice melted at the end of the last glacial period of the current ice age, sea levels rose and the land began to tilt in an isostatic adjustment as the huge weight of ice lessened. Doggerland eventually became submerged, cutting off what was previously the British peninsula from the European mainland by around 6500 BC.[6][9] The Dogger Bank, an upland area of Doggerland, remained an island until at least 5000 BC.[6][9] Key stages are now believed to have included the gradual evolution of a large tidal bay between eastern England and Dogger Bank by 9000 BC and a rapid sea-level rise thereafter, leading to Dogger Bank becoming an island and Britain becoming physically disconnected from the continent

Cystric Fibrosis

An autosomal recessive disorder caused by defective chloride transport that leads to high levels of mucus in the lungs and pancreas, high sweat chloride levels, and other digestive and respiratory problems, respiratory failure.

Sequential hermaphodtes

An organism that, during the course of its life, is capable of having both a male phase and a female phase of existence.

Phylogenetic Analyses

Approaches to Tree-Building Parsimony Genetic Distance Maximum Likelihood Bayesian Methods

aspen trees

Aspen trees- research into fertility, with the age of the clone, fetility of female decreses unlike new clones this decreases their fitness , refresh germline by undergoing sexual reproduction

OCA2: His615Arg variant

Association of the OCA2 polymorphism His615Arg with melanin content in East Asian populations: further evidence if convergent evolution of skin pigmentation Not control region, within the coding region so it changes the protein that reflects aspects of pigments

theta S

Average pair-wise sequence differences between sequences expected under neutrality for a given number of segregating sites

theta pie

Average pairwise differences observed between sequences for a given number of segregating sites