Evolution Thru Final

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Natural selection (Darwin)

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– differences among individuals in survival and reproduction

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Sexual selection (Darwin)

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– differences among individuals in success at getting mates

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Sexual selection (modern synthesis)

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– a difference, among members of the same sex, between the average mating success of individuals with a particular phenotype versus individuals with other phenotypes (e.g., long tail feathers versus short tail feathers in barn swallows)

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Sexual dimorphism

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– a difference between phenotypes of males and females of a species (e.g., coloration in many bird species)

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“Eggs (or pregnancies) are more expensive than ejaculates.”
Females:

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-Females typically make a larger parental investment (energy and time) in each offspring than males
-A female’s potential reproductive success is relatively small
-A female’s realized reproductive success is likely to be limited more by the number of eggs she can make (or pregnancies she can carry) than by the number of males she can convince to mate with her
-Access to males will not be a limiting resource for females
-Therefore, females should be choosy

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“Eggs (or pregnancies) are more expensive than ejaculates.”
Males:

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-A male’s potential reproductive success is relatively large
-A male’s realized reproductive success is likely to be limited more by the number of females he can convince to mate with him than by the number of ejaculates he can make
-Access to females will be a limiting resource for males
-Therefore, males should be competitive

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Intrasexual Selection: Male-Male Competition

Types of intrasexual selection:

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Males interact with one another to monopolize access to females
-Combat
-Sperm competition
-Infanticide

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Intersexual Selection:
Reasons for females to be choosy:

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Female Choice
Males advertise for mates, therefore, females choose males
-Better genes for their offspring
-Direct acquisition of resources
-Sexy-son hypothesis

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Role Reversal
What happens when access to males is a limiting resource for females?

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- Sea horses and pipefish as examples
-males take over rearing young and females become competitive
-seahorses and pipefish with brood pouches
-(limiting resource is the brood pouch)

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Elements of sexual selection

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-variation
-heritability
-differential mating success

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Adaptation

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– a trait that increases one’s fitness

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Modes of Selection:

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Directional Selection
Stabilizing Selection
Disruptive Selection

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Methods used to test hypotheses about adaptations:

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Experiments
Observational studies
Comparative method

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Directional selection;

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-increases the proportion of the one most fit phenotype, might expect in unpredictable environments
-moves peak of bell curve one way or the other
-example; mice in lava areas against sandy areas-pushes phenotype toward more advantageous morph, mice will get darker on lava rock habitats and lighter alleles eliminated

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Purifying selection

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elimination of unfavorable alleles

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Disruptive selection;

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-2 or more phenotypes are fitter than the intermediates (similar to under dominance, but coat color usually influenced by multiple loci),
-might expect in area with mosaic of habitats
-example; mice in lava areas against sandy area, distribution splits into bimodal distribution with dark and light morphs but no prevention of mating so does not lead to speciation, could if there was a heritable preference that prevented morphs from breeding with each other

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Stabilizing selection;

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intermediate phenotype is the fittest
-outliers eliminated, bell curve becomes tighter with fewer variants,
-might expect in a stable environment

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Experiments to evaluate hypotheses about adaptations, what is the adaptive significance of wing markings and wing waving in the tephritid fly;

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5 treatments, untreated control, tephritid fly with wings cut and reglued to test for affect of cut and glue, tephritid fly with housefly wings to determine if waving causes difference, housefly with tephritid wings to test if pattern causes differnce, and untreated housefly control, all 5 groups tested with jumping spiders and other predators, 3 null hypothesis-no mimicry, other predators won’t attack, jumping spider wont attack, -mimicry deters other predators, -mimicry deters jumping spiders, data suggests both traits are needed and that it does seem to deter jumping spiders from attacking

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Observational studies, why do giraffes have long necks?;

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-hypothesis propose for reaching high leaves, seeing predators, & for dominance fighting,
-Observational study looked at foraging during drought by counting bites at certain heights and found the average number of bites highest at chest height,
-suggesting that neck height is not for feeding,
-potential problems-doesn’t account for abundance of forage, doesn’t consider how tree height may have changed over evolutionary time

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Comparative method, Why do some bats have relatively large testes, what other species have relatively large testes and why?;

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-looked at social group size compared to log testes mass-found loose correlation between large group size and testes size,
-may be due to polygamous mating and sperm competition where the male producing more sperm will fertilize more females
-other species include big horn sheep, chimps and other mammal species where multiple males are mating with females

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experiments

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-most powerful for testing hypothesis
-good experiments restrict the difference between study groups to a single variable

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observational studies

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-may be next best method for evaluating a hypothesis when experimentation is impractical
-seed to find circumstances in nature that resemble an experiment

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comparative method

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seeks to evaluate hypothesis by testing for patterns across species, such as correlations among traits, or correlations between traits and features of the environment
-proper application requires knowledge of the evolutionary relationships among the species under study

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New Frontiers in evolutionary study

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phylogenomics, environmental genomics, proteomics, functional genomics, evo-devo

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Proteomics

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Studying proteins to include gene expression at different times during development or in response to different environmental challenges

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Phylogenomics

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-Inspiring new questions about what genes are doing in certain species
-focuses on the evolutionary analysis of genome sequence data

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Environmental genomics

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Understanding the genes present in a habitat without necessarily knowing which species those genes belong to

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Functional genomics

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Characterizing the function of genes and documenting when they are expressed and in what quantities

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Evo-devo

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-Understanding the genetic changes responsible for evolutionary innovations
-looks at how development has affected body plan and adaptations over time

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Genomics

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-Genome projects, -Patterns in Parasitic Genomes, -Chimps and Humans

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Genome

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genetic material of an organism

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Human Genome Project

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-began in 1991 -working draft released in 2000 -”complete” genome released in 2003 (~92% of the human genome-other 8% junk DNA and hard to sequence) -only about 1.2% of the genome codes for proteins in humans, some of it could be eliminated without loss of function but other sections important just not understood

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Genome Projects

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-23 genome projects (driving force is money that can be made, pharmaceuticals, breeding-horses and dogs, rather than pure science) -Fungi (10) -Protists (6) -Animals (4) -Plants (3)

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pharming

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-modeling substances off other organisms genes
-use of genetic engineering to insert genes that code for useful pharmaceuticals into host animals or plants that would otherwise not express those genes. As a consequence, the host animals or plants then make the pharmaceutical product in large quantity, which can then be purified and used as a drug product. Some drug products and nutrients may be able to be delivered directly by eating the plant or drinking the milk. Such technology has the potential to produce large quantities of cheap vaccines, or other important pharmaceutical products such as insulin.

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Genome sequencing has allowed us to

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-estimate total gene number -document gene order -Characterize the function of at least some genes -Fully describe the size and composition of gene families -Make comparisons across species

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Patterns in parasitic genomes

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-extremely small genomes -loss of many genes for normal metabolism -contain virulence genes for adhesion (intestinal lining), toxin production, enzymes to break down host cell walls (get into host), ect -vertebrate parasites with many genes coding for variants of membrane proteins (for getting around immune system responses -red queen hypothesis -have to evolve as fast as you can just to stay in place)

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Chimps and Humans

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-homologous genes differ by only about 1% -29% of the homologous proteins are identical, the other 71% are very similar -why are chimps and humans so different if the genes and proteins are so similar? -expression-the amount and timing of gene expression likely causes phenotypic differences seen between the species

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Transposable elements

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-“jumping genes” often found near centromeres where few expressed genes exist -generally considered genomic parasites-can disrupt things by jumping around-say if they land in the middle of a coding region of a gene, jump randomly, and create extra dna that must be copied -have the ability to move from one location to another in the genome -most leave a copy of themselves behind-increase in number, tend to be junk, increase total DNA , the faster replicating transposable elements that leave copies behind are more likely to be selected upon (they leave more ‘offspring’) -can carry along a chunk of host DNA, can form new genes this way

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C-value paradox

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in eukaryotes, the total amount of DNA found in a cell (C-value), does not correlate with the organism’s degree of morphological complexity or its phylogenetic position -the genomes of many organisms contain a great deal of extra DNA (junk DNA) -genomes are not cohesive communities of sequences contributing to the fitness of the individual (we carry around a huge amount of extra dna-our genomes are not focused on our fitness) -therefore, transposition can mix and match fragments of genes and produce novel combinations

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Categories of Transposable Elements-class I

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-Retrotransposons (LINEs, LTRs) and retrosequences (SINEs) -product of reverse transcription - RNA intermediate -transposition is replicative - copy of original is left behind -used as markers in evolutionary studies, do not code, accumulate mutations quickly, seems like we can carry quite a bit of transposable elements without a noticeable effect, see class Is in literature frequently now

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LINEs (long interspersed elements )

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- contain coding sequence for reverse transcriptase and may catalyse their own transposition -typically 6-7 kb in length -Human chromosome #22 with >14,000 LINEs (>13%)

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LTRs (long terminal repeats)

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-hallmark of retroviral genomes -mark insertion points of retroviruses

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LINEs and LTRs may have evolved from retroviruses

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retrotransposons resemble retroviruses that have lost the coding sequence required to make capsule proteins

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SINEs (short interspersed elements)

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-do not contain the coding sequence for reverse transcriptase -typically <500bp in length -human chromosome #22 with >16.8% of DNA accounted for by SINEs

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Categories of Transposable Elements-class II

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-Transposons - contain 1+ coding sequences -replicate via DNA intermediate (instead of RNA) -transposition is replicative or conservative (no copy left behind) -commonly inserted into plasmids -plasmid-borne transposons - responsible for drug resistance in bacteria

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Microevolution

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-changes at species and below that are accumulated over long periods of time to result in macroevolution

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Macroevolution

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(changes in body form & other large changes) -development studies help us comprehend how microevolution can lead to macroevolutionary changes

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Hox genes (function to regulate other genes and timing has big effect on determining body plan-can stimulate second set of wings to develop from haltare wings when right hox gene is stimulated at the right time)

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provide locational information to every cell -produce transcription factors that turn other genes on and off (regulatory genes) -turned on and off by other genes such as segmentation genes (can be regulated by other genes-length of time gene turned on changes final form) -hox genes can be mutated to have different effects (ex. whether hox gene results in legs or not) -diversification of animal body plan

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how do mutation rates vary between genomes?

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nuclear (slower to accumulate mutations due to repair mechanisms)
mitochondrial
chloroplast

coding (mutations will be selected against) and non coding (microsatellites, regulatory regions, psuedogenes, sines and lines, introns-tend to accumulate mutations because selection doesn’t eliminate them)

transitions and transversions
find most mutations in coding genes in 3rd position (synonomous-functionally the same, method of checking sequence data)

pseudogene (most mutations anywhere because they aren’t coding for a protein and selected upon)

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Biological species concept (BSC)

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– species are groups of actually or potentially interbreeding natural populations that are reproductively isolated from other such groups (Mayr 1942)
-(key point is reproductive isolation, but not functionally measured,
-determined based on phenotypic characters, measure allele frequencies, compare DNA sequences)
-very common definition and most familiar

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Phylogenetic species concept (PSC)

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– a phylogenetic species is an irreducible (basal) cluster of organisms that is diagnostically distinct from other such clusters, and within which there is a parental pattern of ancestry and descent (Cracraft 1989);
-a species is the smallest monophyletic group of common ancestry (de Queiroz and Donoghue 1990)
-important concept is monophyletic groups

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Sympatric speciation

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- evolution of reproductive barriers between subsets of a single, initially randomly mating population
-(overlapping ranges)
-randomly mating population that suddenly develops reproductive isolation -primary example is polyploidy in plants

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Parapatric speciation

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- evolution of reproductive barriers between neighboring populations, which maintain modest levels of gene flow
-(close or abutting ranges)
-mainly theoretical-evolution of reproductive barriers between neighboring populations
-might occur like in sand vs volcanic rock rodents

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Allopatric speciation

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- evolution of reproductive barriers between populations that are geographically separated by a physical barrier

-separated ranges
-mechanism of most speciation
-geographic barrier to interbreeding that allows isolated groups to accumulate independent mutations that will prevent interbreeding when they do come back together

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Mechanisms of Divergence

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Genetic drift
Natural selection
Sexual selection
Mutation

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Mechanisms of Isolation
Barriers to gene flow

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prezygotic barriers
postzygotic barriers

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Prezygotic barriers (premating)

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Potential mates (although sympatric) do not meet
Temporal isolation (by season or time of day)
Habitat isolation
Potential mates meet but do not mate (ethological or sexual isolation)
Copulation occurs but no transfer of male gametes takes place (mechanical isolation)
Gamete transfer occurs, but egg is not fertilized (gametic incompatibility)

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Postzygotic barriers (postmating)

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Zygote dies (zygotic mortality soon after fertilization)
F1 hybrid has reduced viability (hybrid inviability)
F1 hybrid viable, but has reduced fertility (hybrid sterility)
Reduced viability or fertility in F2 or backcross generations

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Allopatric speciation-dispersal vs vicariance (a splitting event)

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-can often determine if speciation was due to dispersal or vicariance by looking at phylogenetic tree and compare it to regional distribution

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dispersal

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-species from mainland migrate to different islands, begin picking up unique changes but can tell who is most closely related to who, region and taxon overlap each other in phylogenetic tree

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vicariance

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-barrier separates population, subpops begin accumulating changes, region and taxon clearly separated and grouped together on phylogenetic tree

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coalescence theory

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(every allele can be mapped to a common ancestor allele if you go back far enough) can produce gene trees (or trait trees ect...) that might explain how species are interrelated, important to remember individual trees are based on small data set and confidence comes from congruence of multiple trees-African eve hypothesis states that mitochondrial dna can be tracked back to one female in Africa

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Lineage sorting

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imagine a wolf population from which a few individuals are removed to breed into dogs, providing a subset of alleles that will each mutate, over time most common alleles have chance of being fixed and new alleles arise, given enough time and isolation dog pop will look more similar to each other than original pop, given enough time lineage sorting will develop where alleles from each group will be completely different, but what if you catch it before enough time has elapsed-incomplete lineage sorting, where you may still find alleles more closely related to parent pop than descendent pop

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competitive exclusion principle

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-if 2 species are competing for the same resource one species may die out or is pushed out, can result in competitive exclusion of one species-comparing fundamental niche and realized niche can show you if competitive exclusion is occuring

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resource partitioning

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-if 2 species are competing for the same resource and species can subdivide resource and split it
-differentiation of niches that enables similar species to coexist in a community

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ecological niche

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sum total of a species’ use of the biotic and abiotic resources in its environment

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character displacement

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see example of Galapagos finches
-the tendency for characteristics to be more divergent in sympatric populations of two species than in allopatric populations of the same two species