Evolution (16-17%)

Evolution of Genes with Related Functions

(Gene duplication + divergence) After duplication events, difference between genes undoubtedly rose from mutations that accumulated in gene copies over many generations. Necessary function was facilitated by one gene, while other copies of the gene accumulated random mutations. Natural selection acted on altered genes, maintaining them in the population.

Effects of Genetic Drift

1.) Genetic drift is significant in small populations. Chance events can cause allele to be disproportionately over or under represented in next generation. Chance events alter allele frequencies much more significantly on small populations. 2.) Genetic drift can cause allele frequencies to change at random- because of genetic drift, allele frequency may increase one year, and decrease the next. Genetic drift causes allele frequency change over time, (unlike natural selection that favors alleles over one another) 3.) Genetic drift can lead to a loss of genetic variation within populations- by causing allele frequencies to fluctuate over time, genetic drift can eliminate alleles from populations. Evolution depends on genetic variation, such losses can influence how well a population can adapt to change in environment. 4.) Genetic drift can cause harmful alleles to become fixed.

Endosymbiotic Origins

1.) Mitochondrion/Chloroplast inner membranes have enzymes and transport systems homologous to those found in plasma membranes of living bacteria 2.) Mitochondria and plastids replicate by splitting process that is similar to certain bacteria. Each organelle contains circular DNA, like chromosomes of bacteria, and are not associated with histones or large amounts other proteins. 3.) Mitochondria and plastids have cellular machinery (including ribosomes) needed to transcribe and translate DNA into protein 4.) In terms of size, RNA sequences, and sensitivity to certain antibiotics, the ribosomes of mitochondria and plastids are more similar to bacterial ribosomes than they are to cytoplasmic ribosomes of eukaryotic cells.

Formation of Hybrid Zone and Possible Outcomes for Hybrids Over Time

1.) Reinforcement (strengthening of reproductive barriers, hybrids gradually cease to be formed) 2.) Fusion (weakening of barriers, the two species fuse) 3.) Stability (continued production of individual hybrids)

Why Natural Selection Cannot Fashion Perfect Organisms

1.) Selection can only act on existing variations: favors only the fittest phenotypes among those currently in the population which may not be the ideal traits. New advantageous alleles do not arise on demand. 2.) Evolution is limited by historical constraints: Each species has legacy of descent with modification from ancestral forms. Evolution cannot scrap anatomy and build new complex from scratch. Operates on traits an organism already has. 3.) Adaptations are often compromises: Human athleticism owed to prehensile hands and flexible limbs, but they also lead to sprains, torn ligaments, and dislocations. Structural reinforcement compromised for agility. 4.) Chance, natural selection, and the environment interact Natural selection operates on a "better than" basis.

Allopolyploidy

2.) Allopolyploid- Fertile when mating with each other but cannot interbreed with other parent species (represent new biological species). *infertile hybrid that reproduces asexually can be changed from sterile to fertile in a subsequent generation. New fertile polyploid= Allopolyploid

Polyphyletic

A polyphyletic (Greek for "of many races") group is a set of organisms, or other evolving elements, that have been grouped together but do not share an immediate common ancestor. The term is often applied to groups that share characteristics that appear to be similar but have not been inherited from common ancestors; these characteristics are known as homoplasies, and the development and phenomenon of homoplasies is known as convergent evolution. The arrangement of the members of a polyphyletic group is called a polyphyly. Alternatively, polyphyletic is simply used to describe a group whose members come from multiple ancestral sources, regardless of similarity of characteristics. For example, the biological characteristic of warm-bloodedness evolved separately in the ancestors of mammals and the ancestors of birds.[citation needed] Other polyphyletic groups are protozoans and algae, as well as invertebrates. Many biologists aim to avoid homoplasies in grouping taxa together and therefore it is frequently a goal to eliminate groups that are found to be polyphyletic. This is often the stimulus for major revisions of the classification schemes. Researchers concerned more with ecology than with systematics may take polyphyletic groups as legitimate subject matter; the similarities in activity within the fungus group Alternaria, for example, can lead researchers to regard the group as a valid genus while acknowledging its polyphyly.

Genetic Drift: The Bottleneck Effect

A sudden change in an environment (fire or flood) may drastically reduce the size of a population. A severe drop in population size can cause a bottleneck effect. By chance alone, certain alleles may be overrepresented among the survivors, others underrepresented, and some may be absent altogether. Ongoing genetic drift is likely to have substantial effects on the gene pool until the population becomes large enough that chance events have less impact. Even if a population passes through a bottleneck it ultimately recovers in size, it may have low levels of genetic variation for a long period of time.

Abiotic Synthesis of Macromolecules

Abiotic synthesis of RNA monomers can occur spontaneously from precursor molecules (without help of enzymes or ribosomes). Protocells- all organisms must be able to carry out reproduction and energy processing (metabolism). *abiotic vesicles can exhibit certain properties of life (reproduction/metabolism/regulation of internal environment).

Evolution of Development

Adaptive evolution by natural selection. By sorting among differences in sequences of protein-encoding genes, selection can improve adaptations rapidly. New genes (created by gene duplication events) can take on new metabolic and structural functions, as can existing genes regulated in new ways.

Extensive Genetic Variation at Molecular Level

Adh gene in fruit flies- 18 variable sites within four exons of gene, only one of these variations results in an amino acid change. Some phenotypic variation does not result from genetic differences among individuals. Phenotype is the product of inherited genotype and many environmental influences (body builders alter phenotype but can't pass it on). Nonheritable variation- caterpillars have different appearances due to chemicals in their diet. A.) Raise on oak flowers (resemble the flowers), B.) raised on oak leaves (resemble twigs)

Key Role of Natural Selection in Adaptive Evolution

Allele favored by natural selection isn't fixed or guaranteed to be advantageous. Changing environments, populations..etc. Adaptations arise gradually over time as natural selection increases the frequencies of alleles that enhance survival or reproduction. As the proportion of individuals that have favorable traits increases, degree to which a species is well suited for life in its environment improves (that is adaptive evolution occurs). Adaptive evolution is a continuous, dynamic process.

Gene Flow

Allele frequencies can also change by gene flow, the transfer of alleles into or out of a population due to the movement of fertile individuals or their gametes. Gene flow tends to reduce genetic differences between populations. Gene flow can result in two populations becoming 1 if gene pool is similar enough. Alleles transferred by gene flow can also affect how well populations are adapted to local environment conditions.

Radiometric Dating

Based on decay of radioactive isotopes. Parent isotope decays into daughter isotope at a characteristic rate. The rate of decay is the half-life, the time required for 50% of the parent isotope to decay. *not affected by temperature, pressure or other environmental variables* Fossils contain isotopes of elements that accumulated in organisms when they were alive. Living organisms contain carbon-12 as well as radioactive isotope carbon-14. When organism dies it stops accumulating carbon. Carbon 14 decays to Nitrogen 14. Measuring ratio of carbon 14 to carbon 12 determines a fossil's age. Works for fossils up to 75,000 years old. Longer half life isotopes used for older fossils.

Systematics and Phylogeny

Biological systematics is the study of the diversification of living forms, both past and present, and the relationships among living things through time. Relationships are visualized as evolutionary trees (synonyms: cladograms, phylogenetic trees, phylogenies).

Genetic Drift

Chance events cause allele frequencies to fluctuate unpredictably from one generation to the next, especially in small populations= GENETIC DRIFT Allele frequencies also affected by chance events that occur during fertilization. Certain circumstances result in genetic drift having significant impact on population, 1.) Founder Effect 2.) Genetic Bottleneck

Habitat Differentiation

Change in habitat (like introduction of a new species of plant via humans) can cause sympatric speciation, species uses/exploits new species of plant.

Genetic Variation: Altering Gene Number or Position

Chromosomal changes that delete, disrupt or rearrange many loci are usually harmful. May not affect phenotype if genes left intact, can even be beneficial (translocation of part of one chromosome to a different can link genes in a way that produces a positive effect). Key potential source of variation Is duplication of genes due to errors in meiosis (unequal crossing over) slippage during DNA replication, or activities of transposable elements. Increase in gene number played a role in evolution. Remote ancestors of mammals had a single gene for detecting odors (duplicated many times) now humans have 380 functional olfactory receptor genes, mice have 1200.

Phylogenetic Tree Terminology

Clade- a group of organisms believed to have evolved from a common ancestor, according to the principles of cladistics.

Clines and Ecotypes

Clines and ecotypes are variants of a particular species adapted to a specific locale or set of environmental conditions. An ecotype is a population of individuals that all display the same local adaptation; it may also be called race, variety, or geographic variant of a species. A cline is a series of individuals or populations displaying gradual variation in appearance or function on a continuous gradient over a geographic area. A cline can contain many ecotypes. Although clines and ecotypes are not themselves species, they are a step on the way to speciation; when two populations diverge so much that they can no longer successfully interbreed, they can be said to have evolved into separate species. Some scientists consider ecotypes the equivalent of subspecies.

Gene Families

Collection of two or more very identical genes. TEM at top shows three of the hundreds of copies of rRNA transcription units in the rRNA gene family of a salamander genome. Growing RNA transcripts extend from the DNA, giving the feather appearance.

Hardy-Weinberg Equilibrium

Compare data to assess whether natural selection or other factors are causing evolution at a particular locus. No differences when compared with observed data= not evolving. In a population that is not evolving, allele and genotype frequencies will remain constant from generation to generation (only mendelian segregation and recombination of alleles at work). Such a population is in Hardy-Weinberg Equilibrium. Consider combination of alleles in all of the crosses in a population.

Conditions for Hardy-Weinberg Equilibrium

Condition Vs. Consequence if Condition does not hold 1.) No mutations - gene pool is modified if mutations occur or if entire genes are deleted or duplicated. 2.) Random mating- if individuals mate within a subset of the population, such as near neighbors or close relatives (inbreeding), random mixing of gametes does not occur and genotype frequencies change 3.) No natural selection- allele frequencies change when individuals with different genotypes show consistent differences in their survival or reproductive success. 4.) Extremely large population size- in small populations, allele frequencies fluctuate by chance over time (a process called genetic drift) 5.) No gene flow- by moving alleles into or out of populations, gene flow can alter allele frequencies

Origin of Life

Conditions on early earth made the origin of life possible: 1.) Abiotic (nonliving) synthesis of small organic molecules, such as amino acids and nitrogenous bases 2.) Joining of these small molecules into macromolecules, such as proteins and nucleic acids 3.) The packaging of these molecules into protocols, droplets with membranes that maintained an internal chemistry different than that of their surroundings 4.) The origin of self-replicating molecules that eventually made inheritance possible

Colonization of Land

Cyanobacteria and other photosynthetic prokaryotes coated damp terrestrial surfaces well over a billion years ago. Fungi, plants, and animals not until 500 million years ago. Plants and fungi worked together to colonize land (mycorrhizal relationships). Arthropods first animals to colonize land, 450 million years ago. Earliest tetrapods found 365 million years ago, and evolved from lobed fin fishes.

Ecological Species Concept

Defines a species in terms of its ecological niche, the sum of how members of species interact with nonliving and living parts of their environment. Same species in different ecological niches "not considered the same"

Morphological Species Concept

Distinguishes a species by body shape and other structural features. Applied to sexual and asexual organisms, can be useful without information on extent of gene flow. Relies on subjective criteria.

Divergent Evolution

Divergent evolution is the accumulation of differences between groups which can lead to the formation of new species, usually a result of diffusion of the same species to different and isolated environments which blocks the gene flow among the distinct populations allowing differentiated fixation of characteristics through genetic drift and natural selection. Primarily diffusion is the basis of molecular division can be seen in some higher-level characters of structure and function that are readily observable in organisms. For example, the vertebrate limb is one example of divergent evolution. The limb in many different species has a common origin, but has diverged somewhat in overall structure and function.

Eukaryotes: Origin of Mitochondria

Endosymbiosis. Prokaryotic cell engulfed a small cell that would evolve into an organelle found in all eukaryotes, the mitochondrion. Serial endosymbiosis- mitochondria evolved before plastids through a sequence of endosymbiotic events.

Evolution is NOT Goal Oriented

Evolution is like tinkering- a process by which new forms arise by modification of existing structures or existing developmental genes. Over time, such tinkering has led to the three key features of the natural world: 1.) The striking ways in which organisms are suited for life in their environments 2.) Many shared characteristics of life 3.) Rich diversity of life

Evolution of Genes with Novel Functions

Exon encodes for protein domain, a distinct structural and functional region of a protein molecule. Unequal crossing over during Meiosis can lead to duplication of a gene on one chromosome and its loss from the homologous chromosome. By a similar process, a particular exon within a gene could be duplicated on one chromosome and deleted on another. The gene with the duplicated exon would code for a protein containing a second copy of the encoded domain. Change in protein structure might augment its function by increasing its stability, enhancing ability to bind to a particular ligand, or altering some other property.

Sympatric Speciation: Polyploidy

Extra set of chromosomes (far more common in plants than animals). Two distinct forms: 1.) Autopolyploid- individual that has more than two chromosome sets all derived from a single species. In plants, failure of cell division could double chromosome number from 2n to 4n (tetraploid). A.) Tetraploid can produce fertile tetraploid offspring by self-pollinating or mating with other tetraploids. Tetraploids isolated from 2n plants because they produce 3n offspring that have REDUCED fertility. B.) Hybrid offspring.

Duplication of Entire Chromosome Sets (Polyploidy)

Failure to separate homologs in Meiosis I can result in one or more extra sets of chromosomes. In rare cases facilitate the evolution of genes (one set of genes can provide essential functions for organism, the extra stem can diverge by accumulating mutations). Genes with novel functions can evolve, as long as one copy of an essential gene is expressed, divergence of another copy can lead to its encoded protein acting in a novel way, changing the organisms phenotype.

Self Replicating RNA

First genetic material was most likely RNA not DNA. RNA plays a central role in protein synthesis, but it can also function as an enzyme-like catalyst. Such RNA catalysts are called ribozymes. Some ribozymes can make complementary short pieces of RNA, provided that they are supplied with nucleotide building blocks. Shapes of RNA molecules allow them to replicate faster than DNA.

Fossil Record

Fossil record biased towards species that existed for a long time. Incomplete chronicle of evolution. Sedimentary rocks are the richest source of fossils.

Allopatric Speciation

Gene flow is interrupted when a population is divided into geographically isolated subpopulations. Or when individuals move to remote area, away from population (Flightless cormorant).

Horizontal Gene Transfer: Antibiotic Resistance

Genes responsible for antibiotic resistance in one species of bacteria can be transferred to another species of bacteria through various mechanisms such as F-pilus, subsequently arming the antibiotic resistant genes' recipient against antibiotics, which is becoming medically challenging to deal with. Most thinking in genetics has focused upon vertical transfer, but horizontal gene transfer is important, and among single-celled organisms is perhaps the dominant form of genetic transfer. Artificial horizontal gene transfer is a form of genetic engineering.

Polytypic

Having several variant forms, especially containing more than one taxonomic category of the next lower rank. A polytypic genus contains two or more different species, while a polytypic species consists of two or more subspecies. Compare monotypic.

Heterochrony: Paedomorphosis

Heterochrony can also alter timing of reproductive development relative to development of nonreproductive organs. Sexually mature stage of a species may retain body features that were juvenile structures in an ancestral species. Paedomorphosis (ie. axolotls).

Horizontal Gene Transfer

Horizontal gene transfer (HGT) or lateral gene transfer (LGT) is the movement of genetic material between unicellular and/or multicellular organisms other than by the ("vertical") transmission of DNA from parent to offspring. HGT is an important factor in the evolution of many organisms. Horizontal gene transfer is the primary mechanism for the spread of antibiotic resistance in bacteria, plays an important role in the evolution of bacteria that can degrade novel compounds such as human-created pesticides and in the evolution, maintenance, and transmission of virulence. It often involves temperate bacteriophages and plasmids.

Hybrid Zones

Hybrids often less fit members of their parent species. In such cases, natural selection should strengthen pre zygotic barriers to reproduction, reducing the formation of unfit hybrids. (this is called reinforcement). If reinforcement is occurring, logical prediction is that barriers to reproduction between species should be stronger for sympatric populations than for allopatric populations.

Did life originate in Hydrothermal/Alkaline Vents?

Hydrothermal vents- areas on seafloor where heated water and minerals gush from earth's interior into the ocean. (TOO HOT) Alkaline vents- release water with high pH and warm rather than hot, may have been an environment more suitable to life than hydrothermal vents. The vents contain hydrocarbons and are full of tiny pores lined with iron and other catalytic minerals. Early oceans were acidic, so a pH gradient would have formed between the interior of the vents and the surrounding ocean water. Energy for synthesis of organic compounds could have been harnessed from this pH gradient.

Balancing Selection: Heterozygote Advantage

If individuals who are heterozygous at a particular locus have greater fitness than do both kinds of homozygotes, they exhibit heterozygote advantage. Natural selection maintains two or more alleles at that locus. *defined in term of genotype not phenotype* Exhibits stabilizing or directional selection depending on genotype/phenotype relationship. If phenotype of heterozygote is intermediate to both homozygotes, heterozygote advantage is a form of stabilizing selection.

Deme

In biology, a deme is a term for a local population of polytypic species that actively interbreed with one another and share a distinct gene pool. When demes are isolated for a very long time, they can become distinct subspecies or species. The term deme is mainly used in evolutionary biology and is often used as a synonym for population. In evolutionary computation, a "deme" often refers to any isolated subpopulation subjected to selection as a unit rather than as individuals. A deme in biological evolution is conceptually related to a meme in cultural evolution.

Convergent Evolution

In evolutionary biology, convergent evolution is the process whereby organisms not closely related (not monophyletic), independently evolve similar traits as a result of having to adapt to similar environments or ecological niches. It is the opposite of divergent evolution, where related species evolve different traits. On a molecular level, this can happen due to random mutation unrelated to adaptive changes; see long branch attraction.

Paraphyletic

In taxonomy, a group is paraphyletic if it consists of the group's last common ancestor and all descendants of that ancestor excluding a few—typically only one or two—monophyletic subgroups. The group is said to be paraphyletic with respect to the excluded subgroups. The arrangement of the members of a paraphyletic group is called a paraphyly. The term is commonly used in phylogenetics (a subfield of biology) and in linguistics. The term was coined to apply to well-known taxa like reptiles (Reptilia) which, as commonly named and traditionally defined, is paraphyletic with respect to mammals and birds. Reptilia contains the last common ancestor of reptiles and all descendants of that ancestor—including all extant reptiles as well as the extinct synapsids—except for mammals and birds. Other commonly recognized paraphyletic groups include fish, monkeys and lizards. If many subgroups are missing from the named group, it is said to be polyparaphyletic. A paraphyletic group cannot be a clade, which is a monophyletic group.

Natural Selection

Individuals in a population exhibit variations in their heritable traits, and those with traits that are better suited for the environment tend to produce more offspring than those who are not as well suited. Alleles passed to next generation in proportions different from current generation. In favoring some alleles over others, natural selection causes adaptive evolution, a process in which traits that enhance survival or reproduction tend to increase in frequency over time.

Sexual Selection

Individuals with certain inherited traits are more likely than other individuals of the same sex to obtain mates. Can result in sexual dimorphism, a difference in secondary sexual characteristics between males and females of the same species (size, color, ornamentation, behavior). Works several ways: 1.) Intrasexual selection- selection within the same sex. Individuals of one sex compete directly for mates of the opposite sex. (usually occurs among males, like a male with a herem of females who prevents other males from mating. Ritualized display discourage other competitors but don't risk injury/fitness reduction). 2.) Intersexual selection- also called mate choice, individuals of one sex (usually females) are choosy in selecting their mates from the other sex. In many cases female's choice depends on male showiness or behavior. Male traits correlated with good genes and/or health.

Stromatolites

Layered rocks that form when certain prokaryotes bind thin films of sediment together. Stromatolites and prokaryotes Earth's sole inhabitants for 1.5 billion years.

Linkage Disequilibrium

Linkage disequilibrium (LD) is one of those unfortunate terms that does not reveal its meaning. As every instructor of population genetics knows, the term is a barrier not an aid to understanding. LD means simply a nonrandom association of alleles at two or more loci, and detecting LD does not ensure either linkage or a lack of equilibrium.

Origins of New Groups of Animals

Mammals originated gradually from a group of tetrapods (amphibians, reptiles, mammals) called synapsids.

Mechanisms of Evolution

Microevolution- evolution on its smallest scale, (ie. evolutionary change in populations). A change in allele frequencies in a population over generations. Natural Selection Genetic Drift (chance events that alter allele frequency) Gene flow (transfer of alleles between populations)

Monophyletic

Monophyletic- is a group of organisms that forms a clade, which consists of all the descendants of a common ancestor. Monophyletic groups are typically characterised by shared derived characteristics (synapomorphies), which distinguish organisms in the clade from other organisms. The arrangement of the members of a monophyletic group is called a monophyly

Photosynthesis and Oxygen Revolution

Most atmospheric O2 is of biological origin (produced during water-splitting step of photosynthesis). When oxygenic photosynthesis first evolved, in photosynthetic prokaryotes, the free O2 it produced probably dissolved in surrounding water until it reached a high enough concentration to react with elements dissolved in water, including iron. Rising concentration of O2 in atmosphere likely doomed many prokaryotes. Oxygen revolution (2.3 billion years ago). Few hundred years later =rise of eukaryotic cell.

Genetic Variation: Rapid Reproduction

Mutation rates low in plants and animals, one in every 100,000 genes. Even lower in prokaryotes. Prokaryotes have many more generations per unit of time, so mutations can quickly generate genetic variation in their populations (same of viruses). RNA genome (of a virus) has a much higher mutation rate due to lack of RNA repair mechanisms in host cells.

Directional, Disruptive, and Stabilizing Selection

Natural selection alter frequency of distribution of heritable traits in three ways: Directional selection- occurs when conditions favor individuals exhibiting one extreme of a phenotypic range. Common when environment changes, or when members of a population migrate to a new (and different) habitat. (ie. beak depth in Galapagos finches) Disruptive selection- occurs when conditions favor individuals at both extremes of a phenotypic range over individuals with intermediate phenotypes. (ie. birds with large beaks crack large seeds, small beaks eat soft seeds, and intermediate struggle to do either). Stabilizing selection- acts against both extreme phenotypes and favors intermediate variants. Reduces variation and tends to maintain the status quo for a particular phenotype character.

Relative Fitness

Natural selection is the only mechanism that consistently causes adaptive evolution. Blend of chance and sorting, chance in creation of new genetic variations, and sorting as natural selection favors some alleles over others. Natural selection not random: consistently favors alleles that provide reproductive advantage, thus leading to adaptive evolution. Relative fitness: Contribution an individual makes to the gene pool of the next generation relative to the contributions of other individuals. Selection acts more directly on the phenotype, acts on genotype indirectly (via how the genotype affects the phenotype).

Change in Gene Sequence

New developmental genes arising after gene duplication events probably facilitated origin of novel morphological forms. Hox gene Ubx (ancestral to modern). Did not suppress leg formation in ancient arthropods (crustacean ancestor) but now suppresses leg formation in fruit flies. Change in nucleotide sequence of a gene may affect its function wherever the gene is expressed, while changes in the regulation of gene expression can be limited to one cell type. Thus change in regulation of a developmental gene may have fewer harmful side effects than a change to the sequence of the gene.

Genetic Variation: Formation of New Alleles

Originates when mutation, gene duplication, or other processes produce new alleles and new genes (happen rapidly in animals with short generation times). Sexual reproduction also results in genetic variation (old genes rearranged in new ways). Formation of new alleles- arise by mutation, (point mutation= change in one base of a gene) can have significant effect (sickle cell). Most new mutations that alter phenotype are at least slightly harmful. In some cases natural selection removes such harmful alleles (unless harmful alleles in diploid organisms are recessive/hidden from natural selection). Neutral variation- differences in DNA sequence that do not confer selective advantage or disadvantage. *only mutation in cell lines that produce gametes can be passed to offspring. Plants/fungi this isn't limiting, many cell lines produce gametes. *In animals most mutations occur in somatic cells and are not passed to offspring.

Paleoecology

Paleoecology (also spelled palaeoecology) is the study of interactions between organisms and/or interactions between organisms and their environments across geologic timescales. As a discipline, paleoecology interacts with, depends on and informs a variety of fields including paleontology, ecology, climatology and biology. Paleoecology emerged out of the field of paleontology in the 1950's, though paleontologists have conducted paleoecological studies since the creation of paleontology in the 1700s and 1800s. Combining the investigative approach of searching for fossils with the theoretical approach of Charles Darwin and Alexander von Humboldt, paleoecology began as paleontologists began examining both the ancient organisms they discovered and the reconstructed environments in which they lived. Visual depictions of past marine and terrestrial communities has been considered an early form of paleoecology.

Consequences of Continental Drift

Pangea (250mya)- plate movements brought together previously separated land masses into one super continent. 135mya- Pangea split into Northern (Laurasia) and Southern (Gondwana) landmasses 66mya (end of mesozoic)- Laurasia and Gondwana separated into present day continents. 45mya- Eurasia collides with India, forming Himalayas.

Adaptive Radiations

Periods of evolutionary change in which groups of organisms form many new species whose adaptations allow them to fill different ecological roles, or niches, in their communities. Occurs after each of the 5 big mass extinctions. Monotremes, Marsupials, Eutherians (placental mammals) all came from separate Adaptive Radiations

Genetic Variation

Phenotypic variation often reflects genetic variation, differences among individuals in the composition of their genes or other DNA sequences. "either or" genes- like Mendel's pea plants, flowers "either" purple "or" white. Characters that vary in this way are typically determined by a single gene locus, with different alleles producing distinct phenotypes. Genetic variation at the whole gene level quantified as average percent of loci that are heterozygous. Considerable genetic variation can be measured at the molecular level of DNA. Little of this variation results in phenotypic variation because many nucleotide variations occur within introns, noncoding segments of DNA lying between exons (regions retained in mRNA after RNA processing).

Polymorphism

Polymorphism is the occurrence of two or more clearly different morphs or forms, also referred to as alternative phenotypes, in the population of a species. To be classified as such, morphs must occupy the same habitat at the same time and belong to a panmictic population (one with random mating). Genetic polymorphism - where the phenotype of each individual is genetically determined A conditional development strategy, where the phenotype of each individual is set by environmental cues A mixed development strategy, where the phenotype is randomly assigned during development Polymorphism as used in zoology and biology involves morphs of the phenotype, and the term polyphenism can be used to clarify that the different forms arise from the same genotype. The term genetic polymorphism is also used somewhat differently by geneticists and molecular biologists to describe certain mutations in the genotype, such as single nucleotide polymorphisms (with detection methods RFLPs and amplified fragment length polymorphism), that may not always correspond to a phenotype, but always corresponds to a branch in the genetic tree.

Gene Pools and Allele Frequencies

Population is a group of individuals of the same species that live in the same area and interbreed, producing fertile offspring. Different populations (of same species) can be isolated geographically and rarely exchange DNA (Ie. Galapagos islands). Members of populations closely related to one another than to other populations of same species. Gene pool- consists of all copies of every type of allele at every locus in all members of the population. If only one allele exists for a particular locus in a population it is FIXED in the gene pool, and all individuals homozygous for that allele. Two or more alleles at a particular locus, individuals heterozygous. Presence of genetic variation does not guarantee that a population will evolve. When studying a locus with two alleles, the convention is to use p to represent frequency of one allele and q to represent the frequency of the other allele. *for loci with more than two alleles frequency must still equal 100%*

Selecting of Alleles at Random

Population of 500 flowers, frequency of allele for red flower (C^R) is p=0.7, and frequency of allele for white flower is (C^r) q=0.3. Bin with all 1000 copies of flower-color gene in population would contain 700 CR, and 300 Cr alleles. Each egg and sperm have 70/30% chances of containing allele for R/r. Probability of CR X CR is 0.49= 49% Cr x Cr is 0.09= 9% Cr x CR = .21 = 21% Freq of heterozygotes: pq + qp = 2pq = 58%

Cambrian Explosion

Present-day animal phyla appear suddenly in fossils formed 535-525 million years ago, early in the Cambrian period. Fossils of sponges, cnidarians, and mollusks appear in even older rocks dating from the late Proterozoic.

Speciation

Process by which one species splits into two or more species. Produced tremendous diversity of life. Microevolution: changes over time in allele frequencies in a population Macroevolution: broad pattern of evolution above the species level

Repetitive DNA

Pseudogenes- former genes that have accumulated mutations over time and no longer produce functional proteins. Repetitive DNA- sequences present in multiple copies in the genome.

Tempo of Speciation

Punctuated equilibria- periods of apparent stasis punctuated by sudden change. Gradual- species diverge from one another more slowly and steadily over time.

Gene Duplication Due to Unequal Crossing Over

Recombination during meiosis between copies of a transposable element flaking the gene. Such recombination between misaligned non sister chromatids of homologous chromosomes produces one chromatid with two copies of the gene and one chromatid with no copy.

Retrotransposon Movement

Retrotransposons- move by means of RNA intermediate that is a transcript of the retrotransposon DNA (leave a copy at original site of transposition). To insert at another site, the RNA intermediate is first converted back into DNA by reverse transcriptase, an enzyme encoded in the retrotransposon (also encoded by viruses). Another cellular enzyme catalyses insertion for reverse transcribed DNA at new site.

Speciation & Extinction Rates

Rise and fall of any particular group related to speciation and extinction rates of its member species. Rise of a group of organisms occurs when more. new species are produced than are lost to extinction. (reverse occurs for decline).

Genetic Variation: Sexual Reproduction

Shuffle existing alleles and deals them at random to produce individual phenotypes. Three mechanisms: 1.) Crossing over during meiosis (homologous chromosomes trade alleles) 2.) Independent assortment of chromosomes (distributed at random into gametes) 3.) Fertilization (bring together gametes with different genetic backgrounds).

Mass Extinctions

Significant long term effects, can destroy a thriving and complex ecological community. Course of evolution changed for forever. Takes 5-10 million years for diversity of life to recover to previous levels after a mass extinction. 6th Mass extinction- NOW!

Heterochrony

Slight genetic differences can produce major morphological differences between species. Large morphological differences can result from genes that alter the rate, timing, and spacial pattern of change in an organism's form as it develops from zygote to adult. "Evo-Devo." Heterochrony- an evolutionary change in the rate or timing of developmental events. Organism's shape dependent on growth rates of different body parts during development, changes to these rates can alter the adult form substantially (contrasting shape of human and chimp skulls). Other examples of heterochrony include increased growth rates of finger bones yielded the skeletal structure of wings in bats, slowed growth of leg and pelvic bones led to reduction/loss of hind limbs in whales.

Sympatric Speciation

Speciation occurs in populations that live in same geographic area. Less common than allopatric speciation. Occurs if gene flow is reduced by factors such as polyploidy, sexual selection, and habitat differentiation (these factors can also promote allopatry).

Biological Species Concept

Species is a group of populations whose members have the potential to interbreed in nature and produce viable, fertile offspring (but can't do so with other groups).

Evidence of Allopatric Speciation

Species of snapping shrimp separated by isthmus of Panama (15 species on Atlantic side, and 15 on Pacific side). Importance of allopatric speciation is also s suggested by the fact that regions that are isolated or highly subdivided by barriers typically have more species than do otherwise similar regions that lack such features. Reproductive isolation between a species increases as the geographic distance between them increases. Geographic isolation prevents interbreeding between members of allopatric populations, physical separation is not a biological barrier to reproduction (biological barriers intrinsic to organisms themselves).

Transposable Elements (Transposon/Retrotransposon)

Stretch of DNA (in prokaryotes/and eukaryotes) that can move from one location to another within the genome. Transposition- transposable element moves from one position to another by a type of recombination process. 75% of human repetitive DNA (44% of entire genome) is made up of transposable elements. Transposons- move within a genome by means of a DNA intermediate.

Synonymous & Nonsynonymous Mutation

Synonymous mutation rate (Ks) Mutations/substitutions of DNA base pairs that do not result in a change of amino acid sequence. Also known as a silent mutation. Non-synonymous mutation rate (Ka) or (Kn) Mutations/substitutions of DNA base pairs that result in a single amino acid change on a given polypeptide. Also known as a substitution mutation. Non-synonymous (missense mutation)/Synonymous (silent mutation) mutation ratio (Ka/Ks) Ratio of mutations that change a specific protein structure (non-synonymous, Ka) to mutations that do not change a specific protein. This ratio is used to estimate the selection pressure a given protein or section of DNA experiences. This ratio has been used in several ways: 1) to enhance gene predictions as areas of coding sequence will have a lower Ka/Ks ratio than non-coding areas; 2) determine differences in natural selection pressure on proteins. Neutral selection (Ka/Ks = 1) occurs when coding sequences Positive selection (Ka/Ks > 1) Purifying selection (Ka/Ks < 1)

Reproductive Isolation

The existence of biological factors (barriers) that impede members of two species from interbreeding and producing viable offspring. Barriers block gene flow between species and limit the formation of hybrids. Prezygotic barriers: Habitat isolation, temporal isolation (species breeding times day/season don't line up), behavioral isolation (mate recognition/blue footed boobies dance), mechanical isolation (morphological differences if mating is attempted), gametic isolation (sperm of one species may not be able to fertilize egg of another) Postzygotic barriers: reduced hybrids viability (survival impaired), reduced hybrid fertility (donkeys are sterile), hybrid breakdown (some hybrids are fertile but their offspring are not).

Balancing Selection: Frequency Dependent

The fitness of a phenotype depends on how common it is in the population. Scale-eating fish: left mouthed/right mouthed, trait determined by two alleles and simple mendelian inheritance. Left mouthed attack prey on the right flank (and right mouthed on the left). Prey species guard against attack from whatever phenotype of scale-eating fish is most common in the lake. From year to year, selection favors whichever mouth phenotype is least common. As a result the frequency of left/right mouthed fish oscillates over time and balancing selection (due to frequency dependence) keeps the frequency of each phenotype close to 50%.

Coevolution

The term coevolution is used to describe cases where two (or more) species reciprocally affect each other's evolution. So for example, an evolutionary change in the morphology of a plant, might affect the morphology of an herbivore that eats the plant, which in turn might affect the evolution of the plant, which might affect the evolution of the herbivore...and so on. Coevolution is likely to happen when different species have close ecological interactions with one another. These ecological relationships include: 1. Predator/prey and parasite/host 2. Competitive species 3 .Mutualistic species

Applying Hardy-Weinberg

Used as initial test as to whether or not evolution is occurring in a population. Equation has medical applications (such as estimating the percentage of a population carrying the allele for an inherited disease). Assumption of Hardy-Weinberg yields an approximation, real number of carriers may differ. Harmful recessive alleles hidden in a population because they are carried by healthy heterozygotes.

Genetic Drift: Founder Effect

When a few individuals become isolated from a large population, this smaller group may establish a new population whose gene pool differs from source population. Genetic drift, in which chance events alter allele frequencies, can occur in such a case (storm transporting individuals to a new island) because the Storm indiscriminately transports some individuals (and their alleles) but not others, from source population. Accounts for relatively high frequency of certain inherited disorders among isolated human populations.

Natural Selection & The Genome Evolution

Whole-genome shotgun approach (to map entire human genome) Earliest forms of life had minimal number of genes-those necessary for survival and reproduction. One aspect of evolution must have been an increase in size of the genome, with extra genetic material providing the raw material for gene diversification.

Paleontology

is the scientific study of life that existed prior to, and sometimes including, the start of the Holocene Epoch (roughly 11,700 years before present). It includes the study of fossils to determine organisms' evolution and interactions with each other and their environments (their paleoecology). Paleontological observations have been documented as far back as the 5th century BC.

Genome Size, Number of Genes, Gene Density, Introns

mb= Million Base Pairs

Hardy-Weinberg Equilibrium Equation

p^2 + 2pq + q^2= 1 p^2= expected frequency of dominant homozygous genotype 2pq= frequency of heterozygotes q^2= frequency of recessive homozygous genotype