Learning Goals and Objectives Evolution and Speciation Goal

Learning Goals and Objectives: Evolution and Speciation Goal: to understand Darwin’s theory of evolution by natural selection • Describe the observations that led Darwin to propose a theory explaining the origins of biological diversity • Distinguish between “descent with modification” and “survival of the fittest” • Outline the main tenets of Darwin’s theory • Interpret phylogenetic trees to determine relationships between species or individuals • Predict changes in a population that is under stabilizing, disruptive, or directional selection Goal: to relate our modern understanding of genetics to evolution of populations • Relate “population” and “gene pool” • Calculate allele and genotype frequencies for a population • Calculate expected genotype frequencies for populations that are in Hardy-Weinberg equilibrium • Evaluate genotype frequency data to determine if a population is in HWE, and propose an explanation for why a population may not be in HWE (i. e. , identify the H-W assumption that is being violated, and explain how) • Identify the characteristics of populations that are not evolving • Compare and contrast the factors that would cause a population to evolve Goal: to understand how species form • Explain how genetic changes in populations can lead to speciation • Compare and contrast the three main definitions of “species” • Distinguish between allopatric and sympatric speciation • Explain the mechanisms by which reproductive isolation is maintained • Evaluate information about one or more populations to determine if they are the same species, and explain why or why not

Darwin’s Foundation: Empirical Thought • Relies on observation to form an idea or hypothesis • Contrast with rationalism • Shift toward empirical thought encouraged scholars to look for the basic rationale behind a given process or phenomenon

Darwin’s Observations • Darwin spent more time on land than water; traveled overland met up with the Beagle at ports • Focus on geology • Collected many specimens

Observations on Natural History • “Local” similarities • Galapagos island fauna • Endemic • Distinctive traits • Galapagos Island finches

Darwin’s Foundation: Other Contemporary Ideas • Geology (Hutton and Lyell) “The present is the key to the past” Gradualism • Zoology Species change over time

Major Tenets of Darwin’s Theory • Species change over time • Species that share a common ancestor may have distinct current forms • Natural selection drives changes from the ancestral form

Descent with modification Evolution via accumulation of adaptations over time • Adaptations are phenotypic changes that increase an individual’s fitness • Variation within a given species Traits heritable – passed from parent to offspring o Genetic basis not yet known o • Natural selection More offspring produced than can survive o Competition for limited resources o Individuals with better traits flourish and reproduce o • If two populations diverge sufficiently, new species result

Species relationships can be depicted in phylogenetic trees

As in family trees, more closely related species share a more recent common ancestor

Modern Synthesis Take: Darwin’s theory of evolution by means of natural selection Add: Mendel’s explanation of heredity Resulting synthesis: Evolution results from heritable changes in one or more characteristics of a population or species from one generation to the next

Biological evolution occurs on multiple scales • Microevolution Small-scale changes that occur within a species • Macroevolution Large-scale changes that accumulate over time to generate new species

Peppered Moths A classic example of microevolution (and cryptic coloration)

Evolution results from changes in allele frequencies over time Allele frequency Light allele Dark allele Time The change in the population’s dominant phenotype is due to changes in the population’s dominant genotype

A population is a group of sexually reproducing individuals Each individual possesses two alleles at each locus; the sum total of all the alleles found in a population is known as the gene pool

Population genetics is the study of changes in allele and genotype frequencies We will focus on one allele at a time, but it is possible to study many alleles simultaneously. Let D = dark and d = light In a population of 100 moths, there are 14 moths with the DD genotype, 46 moths with the Dd genotype, and 40 moths with the dd genotype. What is the frequency of the D allele? What is the frequency of the d allele? Let p = F(D) and q = F(d) If only two alleles are possible, p + q = 1

Population genetic analyses compare observed frequencies to theoretical ones Results are compared to a hypothetical expectation in which no change occurs. This theoretical population must exhibit certain characteristics: 1. Mating must be random. 2. The population is infinitely large. 3. There is no migration into or out of the population (also known as gene flow). 4. There is no mutation. 5. Selection does not affect the survival of individuals with particular genotypes. When these conditions are met, genotype frequencies can be calculated if allele frequencies are known.

Population genetic analyses compare observed frequencies to theoretical ones If these conditions are met, the frequencies of the alleles in the population = the frequencies of gametes with particular genotypes. These gametes come together to make zygotes. Frequencies of zygote genotypes are determined by the multiplication rule. F(DD) = F(D) x F(D) = p 2 F(dd) = F(d) x F(d) = q 2 F(Dd) = F(D) x F(d) + F(d) x F(D) = pq + qp = 2 pq This is summarized in the equation for calculating genotype frequencies in populations in which these conditions are met: p 2 + 2 pq + q 2 = 1

Population genetics is the study of changes in allele and genotype frequencies We will focus on one allele at a time, but it is possible to study many alleles simultaneously. Let D = dark and d = light If F(D) = 0. 37 and F(d) = 0. 63, what are the expected frequencies of the DD, Dd, and dd genotypes if the population is in Hardy-Weinberg equilibrium?

Changes in allele frequencies show that a population is evolving You have been tracking the frequency of an allele that is responsible for feather length in a population of hummingbirds over time. Heterozygous individuals and those homozygous for the L allele have longer feathers, while homozygous ll individuals have shorter feathers. In the table below, the number of individuals with each genotype in five generations of the population is indicated. Violations of which three Hardy-Weinberg assumptions would be most likely to produce the observed results over the five generations?

The Hardy-Weinberg assumptions are often violated in real populations 1. Mating must be random. 2. The population is infinitely large. 3. There is no migration into or out of the population. 4. There is no mutation. 5. Selection does not affect the survival of individuals with particular genotypes.

Inbreeding increases homozygosity Average yeild of corn (bushels/acre) % Homozygotes in population The “random mating” assumption is violated when related individuals reproduce. Generations of inbreeding As homozygosity increases, deleterious alleles are more likely to be expressed in the phenotypes of individuals in the population.

Many populations are not “infinitely large” In small populations, genetic drift causes random fluctuations in allele frequencies that inevitably lead to fixation (F(A) = 1) of one allele. In a population bottleneck, a population becomes much smaller, and genetic drift can act very rapidly to change allele frequencies. X X X X X X X

A founder population is another example of a population bottleneck When a new founder population breaks off from a larger starting population, the allele frequencies in the new population will match the founders, not the original population Original Population The blue allele has been lost, and the green increased in frequency to 0. 66

At any particular locus, mutation is generally too rare to affect allele frequencies Mutation rates can be estimated by comparing the genome sequences of parents with their children. Kong et al. (2012) identified an average of 77 new mutations per generation. Given that the human genome is 3. 2 gigabases (3. 2 x 109) bases, this corresponds to 77/(3. 2 x 109) = 2. 4 x 10 -8 mutations per base , or 1 mutation per 42 million bases

When advantageous mutations arise, selection can increase the frequency of the beneficial allele Lactase persistence more common Lactose intolerance more common

Different types of selection produce changes in observed phenotypes Stabilizing selection keeps the mean phenotype the same over time. If this selection is relieved, variation will increase. If this selection becomes stronger, variation will decrease.

Different types of selection produce changes in observed phenotypes Directional selection causes the mean to shift in one direction or the other, and the phenotype becomes more extreme over time. Developmental or other constraints can limit how extreme the phenotype becomes.

Different types of selection produce changes in observed phenotypes Disruptive selection favors both “extremes” of a particular phenotype. If disruptive selection becomes stronger, the differences become even more extreme.

As changes in genes accumulate, populations diverge and can become different species

Darwin’s Finches A classic example of macroevolution Last common ancestor of all modern finch species The ancestral species underwent an adaptive radiation to generate many new species, each adapted to a specific diet

Speciation As two different populations evolve, eventually there comes a point when they can no longer be considered as belonging to the same species.

Genetic incompatibilities can arise when populations diverge Genotype of ancestral population Locus 1 Population diverges; new allele arises New allele becomes fixed in the population Locus 2 If the AA BB genotype is lethal, the populations are different species. Population diverges; new allele arises New allele becomes fixed in the population

Species Concepts • Morphological: species are identified by distinctive physical characteristics • Biological: species are reproductively isolated • Phylogenetic/lineage: each species is a branch on the tree of life

Speciation occurs when populations become isolated • Reproductive isolation • Geographic isolation (allopatric speciation) • Sympatric speciation

Reproductive Isolation • • Prezygotic isolation o Mechanical: “lock and key” mechanism o Temporal o Behavioral o Habitat o Gametic Postzygotic isolation: reduced hybrid reproductive fitness or viability

Sympatric speciation results when subgroups within a population stop mating If different sub-populations prefer different habitats or exhibit different behaviors that reduce mating between them, genetic changes can accumulate that absolutely inhibit gene flow.

Observations of evolutionary change • • • Biogeography Convergent evolution Fossil record Selective breeding Homologies o Anatomical o Molecular

Biogeography • • Study of the geographical distribution of extinct and modern species Isolated continents and island groups have evolved their own distinct plant and animal communities • • Endemic species are only found in a very restricted area (e. g. and island) Island fox (Urocyon littoralis) evolved from mainland gray fox (Urocyon cinereoargenteus) California Santa Barbara Channel Islands San Miguel Santa Cruz Santa Rosa Santa Barbara channel Anacapa (b) Gray fox (Urocyon cinereoargenteus)

Convergent Evolution 2 species from different lineages show similar features because they occupy similar environments The long snouts and tongues of giant anteaters and echidnas allow them to catch and feed on ants The sea raven and longhorn sculpin produce antifreze proteins that allow them to survive in very cold water These analogous structures (or proteins) are adaptations that evolved independently in different species.

Fossils • Even with an incomplete fossil record, evolutionary changes can be observed in the fossil record

Tiktaalik roseae “Fishapod” • Illuminates steps leading to evolution of tetrapods • Transitional form – provides link between earlier and later forms • Had broad skull, flexible neck, eyes on top of head, primitive wrist and 5 fingers • Peek above water and look for prey

Was Tiktaalik the first animal to undergo the aquatic to terrestrial transition? Amphibian tetrapod 360 Early amphibian Millions of years ago (mya) LATE DEVONIAN PERIOD Expanded ribs Flat head, eyes on top Neck 370 Scales Tiktaalik roseae Fins 377 380 Fish

Selective breeding / artificial selection • Programs and procedures designed to modify traits in domesticated species • Also called artificial selection • Nature chooses parents in natural selection while breeders choose in artificial selection • Made possible by genetic variation • Breeders choose desirable phenotypes • Selection can be stabilizing, disruptive, or directional

Homology • Fundamental similarity due to descent from a common ancestor • Anatomical • Developmental • Molecular

Anatomical homology • Homologous structures are derived from a common ancestor • Same set of bones in the limbs of modern vertebrates has undergone evolutionary change to be used for many different purposes • Vestigial structures are anatomical structures that have no apparent function but resemble structures of presumed ancestors

Whale pelvic bones are an example of a vestigial structure

Molecular homology • Similarities in cells at the molecular level • All living species use DNA to store information • Certain biochemical pathways are found in all or nearly all species • The same type of gene is often found in diverse organisms • Sequences of closely related species tend to be more similar to each other than to distantly related species