Bio 111 Exam 3 Notes PDF

Lecture 19 Gene flow ➔ Gene flow is the movement of alleles between populations (migration) ◆ When individuals leave one population, join another, and breed ◆ Equalizes allele frequencies between the source and recipient populations Will lead to change in allele...

Lecture 19 Gene flow ➔ Gene flow is the movement of alleles between populations (migration) ◆ When individuals leave one population, join another, and breed ◆ Equalizes allele frequencies between the source and recipient populations Will lead to change in allele frequency - evolution Will increase/maintain NOT DECREASE genetic variation (heterozygosity) ➔ Gene flow can be random with respect to fitness ◆ Evolutionary change due to gene flow is directly proportional to: m the fraction of population moving p2 - p1 the difference in allelic proportion among the populations ➔ The presence or absence of gene flow has important implications for conservation of threatened species ➔ Decline of gene flow between isolated wild populations is well documented (isolating events include habitat fragmentation), gene flow between wild and captive populations is also well documented (can be beneficial or detrimental) ➔ What are the effects of gene flow between captive bred and wild populations? Some trout are wild Some raised in hatchery and released to supplement diminishing population ◆ DNA tests were conducted to study the fitness of: Individuals with 2 wild parents Individuals with 1 wild and 1 captive bred parent 16% lower fitness Individuals with 2 captive bred parents 38% lower fitness ◆ What causes this? Selection for higher fitness in the hatchery does not translate to higher fitness in the wild  ➔ Same thing occurred in salmon. Efforts to augment wild population using captive bred fish has positive and negative effects ◆ More fish reduces impact of fishing ◆ Lower average fitness will have negative effect ➔ When it occurs naturally gene flow does not reduce fitness ◆ It can replenish alleles in a population that has lost alleles due to genetic drift This should increase genetic variation ➔ Gene flow can increase or decrease fitness spending on the situation ◆ However, movement of alleles between populations always tends to reduce their genetic variation Mutation ➔ Evolutionary mechanisms like natural selection and genetic drift reduce genetic diversity over time ➔ In contrast, mutation restores genetic diversity by creating new alleles, not only new combinations of alleles ➔ Mutation can occur in a number of ways ◆ Point mutations - change in single base pair of DNA May result in a different amino acid in a polypeptide May change the regulation of the expression of other genes Mostly neutral or deleterious ○ Missense change an amino acid ○ Silent do not change amino acid due to redundancy (do not change phenotype) ○ Frameshift shift reading frame altering meaning of subsequent codons ○ Nonsense change a codon that specifies an amino acid into a stop codon ◆ Chromosome level mutations ○ Inversion segment of a chromosome breaks off flips around and rejoins ○ Translocation section breaks off and becomes attaches to another ○ Deletion segment is lost ○ Duplication a segment of a chromosome is present in multiple genes  ◆ Lateral gene transfer (horizontal gene transfer) Transfer of genes from one species to another ➔ Mutation produces beneficial alleles on rare occasions ◆ Increases fitness of individuals ◆ Increase in frequency in a population due to natural selection ➔ Mutation can produce neutral allele with no effect on fitness ◆ When a point mutation causes ➔ Mutation mostly results in deleterious alleles ◆ Decrease fitness of individuals ➔ Mutations are random with respect to fitness of the individual ➔ Although mutation can change the frequencies of alleles over time, mutation does not occur enough to make it an important factor in changing allele frequencies ➔ Mutation can be a significant evolutionary process in bacteria and archaea they have short generation times and high mutation rates which is not the case in eukaryotes Mutation Rates Human germline mutation rate = 1.2 x 10^-8 ➔ Human genome size is 3 billion base pair = haploid ➔ Number of mutations per generation in a diploid human ◆ 37 in haploid (x2 in diploid) ➔ Mutation is slow compared with selection, genetic drift, and gene flow ◆ But mutation can have a large effect when combined with one of the other mechanisms E coli - how mutation affects evolution ➔ Richard Lenski set up 12 populations of E coli and allowed them to reproduce 10,000 generations ➔ E coli reproduces asexually so mutation is its only source of genetic variation (no gene flow) ➔ Relative fitness of descendant generations increased dramatically overtime in jumps ➔ Hypothesized that this pattern resulted from novel mutations arising and conferring a fitness benefit under selection ➔ After a major beneficial mutation occurred, fitness changed little for a time until another random mutation produced an increase in fitness ➔ Demonstrated combination of mutation and natural selection Pea Aphids  ➔ Feed on sap ➔ Two phenotypes - red and green ◆ Polymorphism maintained by balancing selection ➔ Ladybird beetles prey on red aphids, wasps lay eggs on green aphids ◆ Color comes from carotenoid pigments not from their food which is plant sap ➔ Aphids first animals discovered that generate their own carotenoids ◆ The genes that code for the metabolic pathway came from lateral gene transfer from a fungal symbiont Additional point mutations occurred after the lateral gene transfer to allow aphids to synthesize yellow, red, and green carotenoids Then a deletion produced green aphids Therefore, sometimes a loss of function allele can be adaptive ➔ Mutation is the ultimate source of genetic variation ◆ Crossing over and independent assortment shuffle existing alleles into new combinations ◆ Only mutation creates new alleles ◆ Mutation just happens not because organisms want or need it ➔ Without mutations, evolution would stop ➔ Mutation alone is usually inconsequential in changing allele frequencies alone over a short time period ➔ Each of the 4 evolutionary mechanisms has different consequences for allele frequencies ➔ All violate HW assumptions ➔ Ultimate result of these mechanisms is genetic diversity Lecture 20 What Are Species? ➔ If gene flow stops, allele frequencies in isolated populations can diverge and populations begin to evolve independently Divergence will occur as a result of: ○ Mutation ○ Natural selection ○ Genetic drift  ◆ This genetic divergence may eventually result in speciation ➔ Speciation: splitting event that creates two or more distinct species from an ancestral species, gradually or abruptly ➔ Species: evolutionarily independent population or group of populations Three Species Concepts ➔ Biologists commonly use 3 approaches for identifying species: ◆ Biological species concept: E Mayr Main criterion for identifying species is reproductive isolation ○ Results in lack of gene flow between populations ○ Members of populations do not interbreed or fail to produce viable or fertile offspring after mating ○ Not initially absolute gradual process Biologists categorize that stop of gene flow between populations as either: ○ Prezygotic: individuals of different species are prevented from mating successfully ○ Postzygotic: hybrid offspring do not survive or reproduce Disadvantages of biological species concept: ○ 1. Reproductive isolation cannot be evaluated in: ◆ Fossils Ex. Trilobites, Elk vs. Red Deer ◆ Species that reproduce asexually ○ 2. Not easily applied to things that don’t overlap geographically ➔ Morphospecies Concept ◆ Individual lineages differ in size shape or other morphological features ◆ Distinguishing features most likely arise if populations are independent and isolated from gene flow ○ Widely applicable: ◆ Useful when there is no data on the extent of gene flow ◆ Equally applicable to sexually, asexual, and fossil species  ◆ Disadvantages: One polymorphic species may be classified as more than one species Cannot identify cryptic species that differ in non-morphological traits Features used to distinguish species are under this concept are subjective ➔ Phylogenetic Species Concept ◆ Identifies species based on evolutionary history Based on rationale that all species are related by common ancestry On phylogenetic tree, a monophyletic group consists of ancestral population and all descendants ◆ Monophyletic groups are identified by synapomorphies (unique to monophyletic group) Homologous traits found in common ancestor and descendants but missing in more distant ancestor ○ Ex: fur or milk-producing glands in mammals Therefore, a species is defined as the smallest monophyletic group on the tree of life ◆ Advantages: It can be applied to any type of population (fossil, asexual, or sexual) Logical because different species have different synapomorphies due to lack of gene flow and independent evolution ◆ Disadvantages: Phylogenies are currently available for only a tiny (through growing) subset of populations on the tree of life Critics point out that it would probably lead to recognition of man more species than either of the other species concepts ➔ Researchers use all 3 species concepts to identify evolutionarily independent populations in nature ◆ Crosses to test compatibility ◆ Population genetics to characterize genetic exchange ◆ Phylogenetocs to identify evolutionary history Mechanisms of Reproductive Isolation ➔ Prezygotic Isolating Mechanisms: ◆ Temporal Isolation: populations are isolated because they breed at different times Spotted skunks ○ Eastern SS and Western SS mate at different times of the year ◆ Habitat Isolation: populations are isolated because they breed in different habitats (ecology is important) Garter snakes ○ Different species live in different habitats ◆ Behavioral Isolation: populations do not interbreed because their courtship displays differ Birds ○ To attract females, male songbirds sing species-specific songs ◆ Gametic Isolation: matings fail because eggs and aspen are incompatible Sea Urchin ○ Differences in binding proteins determine which species can mate ◆ Mechanical Isolation: matings fail because male and female reproductive structure are incompatible Drosophila ○ Subtle differences in morphology of genitalia (some of the most rapidly evolving characters) ➔ Postzygotic Isolating Mechanisms ◆ Hybrid (In)Viability: hybrid offspring do not develop normally and die as embryos ◆ Hybrid Sterility: hybrid offspring mature but are sterile as adults (can’t produce offspring themselves because of difefrent numbers of chromosomes) Ex. Mule = male donkey x female horse ○ Mules have high vigor, infertile Linking Microevolutionary Processes with Macroevolutionary Patterns. ➔ Haldane’s rule:  ◆ Males are sterile in XY taxa (flies, mammals) and females are sterile in ZW taxa (birds, butterflies) Lecture 21 3 Modes of Speciation ➔ Allopatric Speciation (most common way new species form) ◆ Genetic isolation happens when populations become geographically separated ◆ Populations that live in different areas are in allopatry Separation that begins with geographic isolation ◆ Geographic isolation occurs in 2 ways: Dispersal: a population moves to a new habitat, colonizes it, and founds a new population ○ Biogeography is the study of how species and populations are distributed geographically that can tell us how dispersal and vicariance events occur ◆ Colonization can lead to speciation ○ Ex. Grant’s compared parents and offspring from large ground finches (Geospiza magnirostris) that colonized the island of Daphne Major with those from a nearby island ○ Colonists represented a new allopatric population, but could this have led to speciation? ◆ Average beak size in colonist population was much larger than those of nearby population ◆ Partially due to genetic drift and partially due to natural selection favoring alleles associated with large beaks on the island ○ Grants concluded that both mechanisms contributed to the change in beak size in the large ground finches ○ New population is not a separate species yet, because there is still some gene flow ○ Over time, the populations could continue to diverge Vicariance: the physical splitting of a habitat  ○ When a physical barrier such as a mountain range uplifting or a river splitting the geographic range of a species, vicariance has occurred ○ Ex: Researchers compared the DNA sequences of trumpeters from different areas of the Amazon basin the geological events that occurred ◆ They found evidence of isolation of populations by vicariance ◆ Initially, the formation of the Amazon split the ancestral population ◆ The formation of the river systems then subdivided the populations ➔ Parapatric Speciation ◆ Genetic isolation happens when populations change gradually along a cline (spatial gradient of character change along an environmental variable) Geographic features like latitude or elevation impose a gradient of selection pressures and phenotypic and genetic changes happen Ex. House mice increase in body size and build bigger nests in the north ➔ Sympatric Speciation ◆ Populations or species that live in the same geographic area - close enough to interbreed - live in sympatry Researchers traditionally believed that speciation could not occur among sympatric populations because gene flow would overwhelm any differences among populations Sympatric speciation can be initiated by 2 types of events ○ External events ◆ Ex. disruptive selection based on different ecological niches or mate preferences ○ Internal events ◆ Ex. chromosomal mutations Niche: range of ecological resources that a species can use and the range of conditions it can tolerate Even though sympatric populations are not geographically isolated, they may be reproductively isolated by adapting to different habitats via disruptive selection ◆ Ex. Apple maggot flies mate on apple fruits and their larvae use the apple for food source  Hawthorn maggot flies feed and mate on hawthorn fruits Apple maggot flies originated from hawthorn flies after apples introduced in North America (1700s) Experiments show that each species respond strongly to its on fruit scent Hybrid individuals do not orient to fruit scent as well as their parents do, resulting in lower reproductive success (since they do not find fruit and mates as well as their parents do) ➔ Disruptive selection has the potential to cause rapid divergence among sympatric species ◆ Affects gene flow directly via prezygotic isolation ➔ Although sympatric speciation can occur, it is not common Lecture 22 Instantaneous Speciation in Plants ➔ Sympatric Speciation by Polyploidization ◆ If populations become isolated, it is unlikely that mutation alone could cause them to diverge appreciably since it occurs at a low rate ◆ However, one type of mutation, polyploidy, can cause speciations An error in meiosis or mitosis results in more than 2 sets of chromosomes ◆ Polyploids may be: Autopolyploid (auto=oneself) ○ Doubling of chromosome number ○ Chromosomes are all from same species ○ Reproductively isolated from original population ○ Can breed with other tetraploid but not with diploids (sterile offspring) ○ According to the biological species concept, this occurred in a single generation aka instantaneous speciation Allopolyploid (allo=different) ○ Parents of offspring of different species mate and an error in mitosis occurs resulting in viable non sterile offspring  ○ New tetraploid species may be created when two diploid species hybridize ○ Offspring will be sterile ○ Have 2 copies of 2 sets of chromosomes ◆ Advantages of being a polyploid: Higher levels of heterozygosity than diploids Can tolerate higher levels of self fertilization because they are not as affected by inbreeding depression are diploids Genes on duplicated chromosomes can diverge independently ➔ Speciation by polyploidization: ◆ Driven by chromosomal level mutations and occurs in sympatry ◆ Is instantaneous ◆ High genetic diversity of polyploids has enabled rapid diversification of plants Potential Outcomes of Secondary Contact ➔ If divergence has occurred and prezygotic isolation exists, then mating between the populations is rare, continue to diverge ➔ When prezygotic isolation does not exist populations may interbreed and may erase distinctions between the two populations ➔ Other possible outcomes are reinforcement or the development of stable hybrid zones Reinforcement: ➔ If two populations diverges extensively and are genetically distinct, the fitness of hybrid offspring will be lower than the parents fitness ➔ Natural selection for traits that prevent interbreeding among populations is called reinforcement - selection for prezygotic isolating mechanism Hybrid Zones: ➔ Sometimes the hybrid offspring of diverged population can mate and produce viable offspring ➔ A hybrid zone is a geographic area where interbreeding between 2 populations occurs ➔ Depending on the hybrid offspring fitness and extent of breeding between parental species, hybrid zones can be ◆ Narrow or wide ◆ Long or short lived ◆ Stable in one place or move over time  ➔ Example: Townsend’s Warblers and Hermit Warblers hybridize extensively where their ranges overlap ◆ Hybrid offspring have intermediate characteristics relative to the parents ◆ Data from mitochondrial DNA shows: Most hybrids form when Townsend's warbler males mate with Hermit warblers Principles of Phylogenetics ➔ Goal in evolutionary biology: ◆ Reconstruct evolutionary history of life on Earth over large periods of time ➔ Biologists use two major tools to do this: ◆ Phylogenetic trees: current taxa ◆ Fossil record: historical taxa Can be used separately or in combination ➔ Phylogeny: evolutionary history of a group of organisms ➔ A phylogenetic tree is a graphical summary of history of life that shows the evolutionary relationships among genes and species ◆ Revolutionized study of evolution: Can be used in taxonomy to define species Can be used in medicine to study the spread of disease Can aid in identifying species that are a conservation priority Can be used in agriculture to identify wild relatives for breeding with current crops ➔ Tree of life is the most universal phylogenetic tree because it depicts evolutionary relationships among all living organisms Terminology ➔ Branch: represents a population through time ➔ Node (fork): represents a point where a branch splits, hypothetical most recent common ancestor (represent speciation events) ◆ You can rotate around any node and the trees are the same ➔ Tip (terminal node): represents the endpoint of a branch, living or extinct taxon ➔ Root: most ancestral branch ➔ Outgroup: taxon that diverges before the taxa of interest did so, helps to “root” the tree  ➔ Polytomy: node that divides into 3 or more branches ◆ Taxa are always located on branch tips, never within the tree, because none of the taxa are presumptive ancestors of other ◆ Closely related taxa are depicted as sister groups that share a recent common ancestor Lecture 23 How to build phylogenies ➔ Relationship among taxa cannot be known with absolute certainty ➔ Relationship depicted in phylogenetic trees must be estimated from the best available data ➔ Phylogenetic trees are hypotheses that can be tested ➔ Two ways to construct phylogenies: ➔ Character-state data ◆ First step in inferring evolutionary relationships is to determine which taxa to compare and which characteristics to use ➔ Genetic distance data ◆ A character or trait is any genetic, morphological, physiological, or behavioral characteristic to be studied Each character has two possible states: present or absent ○ Some traits wind up being useful, others not An outgroup is a sister group that shares a recent common ancestor with taxa being studied but is not part of study group ○ Used to establish whether a trait is ancestral or derived ◆ An ancestral trait is a character that existed in an ancestor ◆ A derived trait is one that is modified from ancestral trait, found in a descendant. Originated via mutation, selection, genetic drift Ancestral and derived traits are relative (depend on taxa being compared) ◆ Outgroups also evolve (do not represent ancestors of other taxa in the tree), therefore  multiple outgroups are often used to estimate phylogenetic relationships ○ Homology: trait similar due to common ancestry Identify differences between paraphyletic and polyphyletic relationships ➔ Paraphyletic group: ancestor but not all descendants ➔ Polyphyletic group: not ancestor and not all descendants ➔ Homoplasy: similarity not due to common ancestry ➔ Differences between homologies and homoplasies ➔ Homologies are traits that are shared among related species ➔ Homoplasies are traits that unrelated species share ◆ Convergent evolution leads to homoplasies Lecture 24 Learn phylogenetics case study in mammals ➔ Traits may be similar due to independent evolution (convergent evolution) ➔ A reversal in a character change may occur, creating the appearance that no change occurred (ex. loss of limbs in snakes) ➔ ​Using the Data Matrix to Estimate a Tree ◆ Species may form monophyletic groups based on one trait but part of a different monophyletic group using another trait ◆ Example: Snakes and lizards group together based on presence of an amniotic egg but not based on presence of limbs ◆ We have to rely on further analyses to resolve these complications ➔ Parsimony: used to identify the most likely tree, principle of logic ◆ States that the most likely explanation or pattern is the one that implies the least number of changes ◆ Computer programs can compare theoretically possible branching patterns to determine the most parsimonious tree ➔ Trees created using character states focus on branching patterns ◆ Branch length is arbitrary Other methods create trees where branch length represents genetic difference or time since divergence  ○ Scale bars are present in these trees Are Streamlined Bodies in Dolphins and Ichthyosaurs Homologous or Convergent? ➔ Ichthoysyars (extinct aquatic reptiles) and dolphins are very similar ◆ Streamlined bodies ◆ Large dorsal fins and flippers ➔ Phylogenetic analysis, however, indicated that these similarities are not due to common ancestry ◆ Dolphins are in the mammal clade and ichthyosaurs are closely related to lizards The similarities result from convergent evolution Whale Evolution: A Case Study Data Set 1: Phylogeny Based on Morphological Traits ➔ Hippos, cows, deer, and pigs are artiodactyls ◆ They have hooves, even number of toes, and unusual pulley-shaped ankle bone (astragalus) ➔ Traditionally, phylogenetic trees based on morphological data place whales as the outgroup to artiodactyls (do not have astragalus) Data Set 2: Phylogeny Based on DNA Sequence Data ➔ DNA sequence data suggests a closer relationship between whales and hippos than between whales and other artiodactyls ➔ The tree with whales and hippos as sister taxa would require 2 changes to the astragalus trait ➔ Evolution of astragalus in artiodactyls: ◆ The loss of the astragalus in whales ◆ Is less parsimonious than a tree with just one change Conclusion: Whales Are Closely Related to Hippos ➔ Whales descended from land dwelling artiodactyls that feed in shallow water ➔ In 2001, fossil artiodactyls were found that also support this hypothesis. ◆ They have an unusual ear bone found only in whales ◆ A pulley-shaped astragalus ➔ The combination of DNA sequence data and fossil data clarified the relationship between whales and artiodactyls Principle of Parsimony ➔ Old idea that can be traced back to Aristotle ➔ Occam’s razor: the simplest explanation is the best explanation ➔ In the absence of other data, the best hypothesis minimizes the number of extra changes on tree due to homoplasy Method for finding most parsimonious tree: ➔ Must have a way to count changed on any given phylogeny ➔ Must be able to search among all possible phylogenies for the one that minimize changes Lecture 25 How to use DNA Sequences to create phylogenies ➔ Recently most biologists rely on RNA and DNA sequences from different organisms ◆ Compare homologous sequences of the nucleotides ◆ Fewer sequence differences between two species suggest a closer relationship ◆ Example: Land Plant: A-T-A-T-C-G-A-G Green Algae: A-T-A-T-G-G-A-G Brown Algae: A-A-A-T-G-G-A-C ○ Compare sequences and assess the differences Land - Green 1 (most closely related, share the most recent CA) Green - Brown 2 Land - Brown 3 plesiomorphy: when all are a certain nucleotide letter, doesn't tell us anything (not informative) autapomorphy: when all are a certain nucleotide letter except one is different, doesn't tell us anything (not informative) Difficulties of large phylogenetic reconstructions ➔ Usually more than one gene or region is used ➔ Often greater than 500bp of sequence per gene ➔ Aligning genes is challenging and requires algorithms  ➔ More complex models are needed for DNA evolution and certain types of DNA evolution occurs more often than others: ◆ Transitions more frequent than transversions ◆ Synonymous more frequent than nonsynonymous Molecular clock and how to apply it ➔ DNA and protein sequences evolve at a rate that is relatively constant over time ➔ Most changes are neutral ➔ We can use the molecular clock to date nodes on a tree ➔ Molecular clock is not perfect ◆ It relies on neutral theory ➔ Some DNA sequence is rapidly evolving and will not tick in a clock-like manner Calibrating the molecular clock ➔ Compare DNA Sequence data from species that diverged as a result of geological events ➔ Look at DNA sequences from flightless beetle species ◆ Compare one gene from mitochondria (cox1) ◆ Divergence rate of 3.5% My^-1 for the cox1 gene was estimated ➔ Can also use fossils of known age to date nodes and calibrate clock Lecture 28 What species are our closest relatives? ➔ Three approaches to finding this: ◆ What are similarity and differences of living relatives? ◆ What does the fossil record show? ◆ What can we learn from studying our DNA? ➔ There are 500 species of primates Relationships among Hominids ➔ Our closest relatives ◆ Orangutans ◆ Gorillas ◆ Chimpanzees What can we learn about ourselves by looking at extant relatives? Humans and Relatives ➔ 99% similar at the DNA sequence level with chimpanzees ➔ Different number of chromosomes (human 46, chimpanzees 48) ➔ 20% of proteins are identical Changes in matings system may have caused changes in: ➔ Testicle size (sperm quantity) ➔ Penis size ➔ Sexual dimorphism ➔ Presence of penis bone (baculum) ◆ Humans have no baculum Important differences between humans and chimpanzees ➔ Dramatic increase in brain size in humans (3 times larger in humans) ➔ Bipedalism leads to major differences in skeletal structure ◆ Pelvis is modified for bipedal stance ◆ Spine enters base of skull vs back of skull What does the fossil record tell us about our ancestors? ➔ Fossils have been found of more than 6,000 individuals ➔ Homo neanderthalensis are our closest relatives Two models of human evolution: ➔ Multiregional hypothesis ◆ Modern humans evolve in different regions ➔ Out of africa hypothesis ◆ Modern humans emerge from africa and migrate (most data supports this) What can we learn from studying our DNA? ➔ Genomics fundamentally changed our understanding of human evolution ➔ First human genome assembly cost 1 billion dollars (1990-2003) ➔ Today we can do the same thing for $1,000 Example: identify genes under selection in humans ➔ Genes involved in immunity and defense emerge as candidates  ➔ Find certain alleles increase in frequency in some populations (lactose tolerance in Europeans) Genetic variation in humans is low ➔ Population genetics analyses indicate that humans went through a bottleneck ➔ Occurred 80,000 years ago ➔ Dow to effective population size of 15,000 individuals Genetic data consistent with out of Africa hypothesis ➔ Homosapiens evolved in Africa 300,000 years ago ➔ Africans have the most genetic variation ➔ Non-africans have just a subset of that variation ➔ Early phylogenetic methods of mtDNA put the out of Africa transition at 50,000 years ago Genomics applied to human fossils give us a view into the past ➔ DNA gets preserved more easily in cold climates ➔ (European and Siberian Caves) ➔ Current sequencing technologies are perfect for degraded DNA ➔ Human contamination was an early issue Neanderthals genome gives us some important clues about our closest relatives ➔ Along with other data suggest small effective population of 10,000 individuals ➔ Evidence of hybridization between humans and Neandertals ➔ Detected in non-African individuals Denisovans New species from DNA extracted from a tooth found in a cave Lived in Asia Non-Africans have 1-4% Neanderthal DNA High altitude adaptation in Tibetans comes from Denisovan hybridization (EPAS1) Hybridization between different Homo Species appears to have occurred more than we previously thought ➔ Hybridization also called introgression ➔ Some is adaptive but some could be maladaptive QUESTIONS Does gene flow increase or decrease genetic variation within a population? Gene flow generally increases genetic variation within a population by introducing new alleles. Does gene flow increase or decrease genetic variation between two populations (one source and one recipient)? Gene flow tends to decrease genetic variation between two populations by making their allele frequencies more similar. Does gene flow always increase fitness? No, gene flow does not always increase fitness. It can have neutral, positive, or negative effects on fitness depending on the context. What is an example from lecture of gene flow in the wild? Did hybrids have higher, lower, or intermediate fitness in this example? An example is gene flow between wild and captive-bred trout. Hybrids with one captive-bred parent had lower fitness compared to fish with two wild parents. Can you obtain new genetic diversity (with new changes to the DNA sequence) without mutation? No, mutation is the ultimate source of new genetic diversity, as it creates new alleles. Are most point mutations good, bad, or neutral (in regards to fitness)? Most point mutations are neutral or deleterious, with beneficial mutations being rare. Do mammals have a high mutation rate or a low mutation rate relative to fruit flies? What about bacteria? Mammals have a lower mutation rate relative to fruit flies, while bacteria can have higher mutation rates due to their short generation times. Does mutation have a fast effect, or a slow effect, on the fitness of a population? Mutation usually has a slow effect on fitness in a population unless combined with other mechanisms like selection. Fill in the blank: Escherichia coli was used as a model system to study __________. Escherichia coli was used as a model system to study mutation and evolutionary processes. Why are ladybugs and pea aphids a good example of balancing selection? They demonstrate balancing selection because predators target different color morphs, maintaining color variation in the population. Why was horizontal gene transfer important for aphids? What trait did they gain via horizontal gene transfer, and why was it beneficial? Aphids acquired carotenoid synthesis genes from fungi via horizontal gene transfer, allowing them to produce pigments that help in camouflage and predator avoidance. What is the ultimate source of genetic variation? Mutation is the ultimate source of genetic variation. How is parapatric speciation different from allopatric speciation? Parapatric speciation occurs along a cline within the same region, while allopatric speciation involves geographic separation. How is parapatric speciation different from sympatric speciation? Parapatric speciation involves adjacent populations with gradual changes across a gradient, whereas sympatric speciation occurs within a single geographic area without physical separation. What is the difference between homoplasy and homology? Give an example of both. Homology refers to traits shared among species due to common ancestry. For example, the limb bones of humans and whales are homologous.  Homoplasy refers to traits that are similar due to convergent evolution, not common ancestry. An example is the streamlined body shapes of dolphins and ichthyosaurs. What is the difference between DNA transitions and transversions? Is one more common than the other? Transition is a substitution between two purines (A ↔ G) or two pyrimidines (C ↔ T). Transversion is a substitution between a purine and a pyrimidine (A or G ↔ C or T). Transitions are generally more common than transversions. How does fossilization occur? Fossilization occurs when an organism is buried rapidly, and its remains are preserved through processes like permineralization, compression, or casting, depending on the environmental conditions. How did chloroplasts originate? Chloroplasts originated from a symbiotic relationship between a eukaryotic cell and a photosynthetic cyanobacterium. The cyanobacterium was engulfed by the host cell, eventually evolving into chloroplasts. What is the main change that is thought to have driven the Cambrian explosion? The main change thought to drive the Cambrian explosion was an increase in atmospheric oxygen, allowing for more energy-intensive forms of life to evolve. What happened as a result of the Cambrian explosion? The Cambrian explosion led to a rapid diversification of animal life, with many major animal phyla appearing within a relatively short period. What is the heterogametic sex? What is the heterogametic sex in flies? Mammals? Birds? Butterflies?  The heterogametic sex is the sex with two different sex chromosomes (e.g., XY or ZW). ○ In flies and mammals, males are heterogametic (XY). ○ In birds and butterflies, females are heterogametic (ZW). Why is the heterogametic sex important for Haldane’s rule and reproductive isolation? Haldane’s rule states that in hybrids between species, if one sex is absent, rare, or sterile, it is usually the heterogametic sex. This is important for reproductive isolation because it highlights how genetic incompatibility affects the heterogametic sex more severely. How is a cryptic species different from a regular species? A cryptic species is morphologically similar to other species but genetically distinct. These species are often difficult to distinguish by appearance alone. How many monophyletic groups does this tree have? This tree has four monophyletic groups (A, B, C, and D), assuming each branch represents a separate group. What does it mean to be a generalist cichlid? What about a specialist? Which one is risky and why? A generalist cichlid can thrive in a variety of habitats and consume different types of food, while a specialist cichlid is adapted to a specific environment or food source. Being a specialist is riskier because environmental changes or the loss of their specific resource can threaten their survival. What is an example of speciation by ploidy?  An example of speciation by ploidy is the formation of a new plant species through polyploidy, where an error in cell division results in extra sets of chromosomes, creating a reproductively isolated group. Explain the main difference between autopolyploidy and allopolyploidy. Autopolyploidy occurs within a single species when chromosome duplication results in extra sets of chromosomes. Allopolyploidy occurs when two different species hybridize, and an error in mitosis or meiosis doubles the chromosome number, resulting in a fertile hybrid. In the apple maggot fly example from class, what is the type of prezygotic isolation mechanism? The prezygotic isolation mechanism in the apple maggot fly example is habitat isolation, as the flies lay eggs on different types of fruit (apples and hawthorns), reducing the chances of interbreeding. What is the most common form of speciation? Allopatric speciation is the most common form, occurring when populations are geographically separated. Does allopatric speciation happen via dispersal, vicariance, or both? Allopatric speciation can happen via both dispersal (when individuals colonize a new area) and vicariance (when a physical barrier divides a population). How can one species diverge into two, even if there is not an isolating barrier? (hint: two types of events) A species can diverge due to disruptive selection, where different ecological niches favor different traits, and sexual selection, where different mating preferences develop within the population. What kind of selection are the apple maggot flies and hawthorn maggot flies an example of? The apple and hawthorn maggot flies are an example of disruptive selection, where different environmental pressures favor different traits. What kind of mutation can cause speciation all by itself? Polyploidy, particularly in plants, can cause speciation by itself, as it results in an organism with a different number of chromosomes, leading to reproductive isolation. Are autapomorphies informative for phylogenetics? Why or why not? No, autapomorphies are not informative for phylogenetics because they are unique to a single taxon and do not provide information about relationships among taxa. Are allopolyploids formed due to an error in mitosis or meiosis? Allopolyploids are typically formed due to an error in mitosis, which doubles the chromosome number after hybridization, allowing the organism to be fertile. Why can it be beneficial to be a polyploid? Being polyploid can be beneficial as it increases genetic diversity, allowing polyploids to tolerate inbreeding and self-fertilization, and potentially adapt to a wider range of environments. Does speciation via polyploidy happen slowly or quickly? Speciation via polyploidy can happen quickly, often in a single generation, particularly in plants. Is reinforcement an example of prezygotic or postzygotic isolation? Reinforcement is an example of prezygotic isolation, as it strengthens barriers to prevent interbreeding between diverging populations. What is the difference between a phylogeny and a phylogenetic tree? A phylogeny is the evolutionary history of a group of organisms, while a phylogenetic tree is a graphical representation of that history, showing the relationships between species or groups. What are 3 real-world applications of phylogenies? Phylogenies are used in: ○ Medicine to track the spread of diseases.  ○ Conservation to identify species that are a priority for protection. ○ Agriculture to identify wild relatives of crops for breeding purposes. Are phylogenies always completely correct? Why or why not? No, phylogenies are not always completely correct because they are hypotheses based on available data. New data or better methods can refine or alter our understanding of evolutionary relationships. What are 2 kinds of data you can use to make a phylogeny, and what are the advantages or disadvantages of both? Morphological data: Advantage is that it can be used with fossils, but it may be less accurate if traits are influenced by environmental factors. Molecular (DNA) data: Provides more precise information but is limited to living organisms or well-preserved fossils with recoverable DNA. Do outgroups represent the ancestral state? Outgroups help to infer the ancestral state but do not necessarily represent the exact ancestral condition. Can traits be lost, gained, or either throughout evolutionary time? Traits can be both lost and gained over evolutionary time. Can you have more than one outgroup? Yes, it is possible to have more than one outgroup to provide additional context for rooting the phylogenetic tree. Are Streamlined Bodies in Dolphins and Ichthyosaurs Homologous or Convergent? The streamlined bodies in dolphins and ichthyosaurs are convergent, as they evolved independently in response to similar environmental pressures. Where do whales belong on the tree of life?  Based on the morphospecies concept: Whales are placed as an outgroup to artiodactyls (hoofed mammals). Based on DNA sequence data: Whales are closely related to hippos, sharing a common ancestor within the artiodactyls. What are synonymous changes to DNA sequences, and how are they different from nonsynonymous changes? Synonymous changes do not alter the amino acid sequence of a protein and are often neutral in terms of fitness. Nonsynonymous changes alter the amino acid sequence, which can affect the protein's function and potentially the organism's fitness. How many sites are informative in the samples below? Are there any autapomorphies? Analyzing the samples: ○ Informative sites would be those that vary in a way that can help infer relationships between samples. In this case, specific sites would need to be counted based on differences across species. ○ Autapomorphies would be unique changes in individual species. For example, if a single sequence has a unique nucleotide that is not shared with any others, it would be an autapomorphy. What is mtDNA and how is it different from nuclear DNA? Which one do we use in phylogenetics? mtDNA (mitochondrial DNA) is inherited maternally and is separate from nuclear DNA, which is inherited from both parents. mtDNA is commonly used in phylogenetics because it evolves relatively quickly, providing insights into recent evolutionary relationships. Did Neandertals live in small groups or large groups? Did they move around or stay in one specific area? Neandertals likely lived in small groups and had a more limited range, often staying within specific areas rather than moving around extensively. How do fossils form? What conditions are required? Is it the same for all kinds of fossils?  ○ Fossils form when an organism is buried quickly in sediment, preventing decomposition. Conditions include rapid burial and slow decomposition. Fossilization processes can vary, resulting in different types like permineralized, compression, and cast fossils. How do researchers estimate the age of a fossil? ○ Researchers estimate fossil age through radiometric dating of surrounding rock layers or by using index fossils from the same strata with known ages. What are the four main reasons scientists would consider the fossil record to be limited or biased? ○ The fossil record is limited by habitat bias, taxonomic bias (favoring organisms with hard parts), temporal bias (favoring more recent fossils), and abundance bias (favoring common or long-lived species). When did Earth form? Is this the same time that life on Earth began? ○ Earth formed approximately 4.6 billion years ago. Life began later, around 3.5–3.8 billion years ago. What causes adaptive radiation? ○ Adaptive radiation is often triggered by ecological opportunities (e.g., new habitats or resources) or evolutionary innovations (traits that allow species to exploit new niches). What triggered the Cambrian Explosion? ○ The Cambrian Explosion was likely triggered by a combination of increased oxygen levels, the evolution of predation, and changes in the environment. What are the main features of vascular plants? ○ Vascular plants have specialized tissues (xylem and phloem) for transporting water and nutrients, a waxy cuticle to prevent water loss, true roots, stems, and leaves. How are gymnosperms and angiosperms different? ○ Gymnosperms produce "naked seeds" without flowers or fruits, while angiosperms produce seeds enclosed within fruits and have flowers as reproductive structures. What are the defining characteristics of animals? ○ Animals are multicellular, lack cell walls, are heterotrophic (consume other organisms for food), and have specialized cells and tissues. Do all animals reproduce sexually? ○ No, while most animals reproduce sexually, some can reproduce asexually through methods like budding or fragmentation.  How were animals historically classified (hint: 3 main ways described in lecture)? ○ Animals were historically classified based on body symmetry, the number of germ layers (e.g., diploblastic or triploblastic), and body cavity structure (coelomate, acoelomate, pseudocoelomate). What are the 5 most important evolutionary transitions in vertebrates? ○ Key transitions include the evolution of jaws, lungs, limbs, amniotic eggs, and endothermy (warm-bloodedness). You are studying the mechanisms of reproductive isolation between two genetically divergent populations of kangaroos... Is this postzygotic isolation or prezygotic isolation? ○ This is prezygotic isolation because males from one population do not recognize females from the other population as potential mates, preventing fertilization. You find that females from one population mate with males of the other population, but they don’t produce offspring. Is this postzygotic isolation or prezygotic isolation? ○ This is postzygotic isolation because mating occurs, but there is no viable offspring production. TRUE OR FALSE: Mutation and polyploidy are both necessary for evolutionary change. False. Mutation is necessary for creating new genetic diversity, but polyploidy is not required for evolutionary change. Corrected: Mutation is necessary for evolutionary change, while polyploidy is one mechanism by which it can occur, particularly in plants. TRUE OR FALSE: Genetic isolation happens when populations change suddenly along a cline. False. Genetic isolation typically occurs when populations are separated by geographic barriers or other isolating mechanisms, not suddenly along a cline. Corrected: Genetic isolation happens when populations are separated by barriers to gene flow, which may or may not involve gradual change along a cline. TRUE OR FALSE: We observe gradual changes in animals as elevation increases, but not as latitude increases.  False. Gradual changes can be observed as both elevation and latitude increase, often due to environmental gradients. Corrected: We observe gradual changes in animals as both elevation and latitude increase. TRUE OR FALSE: Reproductive isolation includes any mechanism that stops gene flow between two populations. These can be prezygotic or postzygotic. True. TRUE OR FALSE: If we estimated the molecular clock to be 2% sequence evolution every million years for a specific bird species, and we see that the birds have 10% nucleotide sequence divergence with another species, we can estimate that the two species diverged 10 million years ago. True. TRUE OR FALSE: According to the phylogeny on the left, frogs are a common ancestor of humans and ducks. False. Frogs are not a common ancestor of humans and ducks; they share a common ancestor further back in evolutionary history. Corrected: Frogs are not a common ancestor of humans and ducks, but they share a common ancestor with them. TRUE OR FALSE: According to the phylogeny on the left, the MRCA (most recent common ancestor) of frogs and ducks is node B.  False. The MRCA of frogs and ducks would be found at a node further down the tree, not at node B. Corrected: The MRCA of frogs and ducks is located further back in the phylogeny, not at node B. TRUE OR FALSE: According to the phylogeny on the left, humans and cats are a monophyletic group. True. TRUE OR FALSE: According to the phylogeny on the left, ducks and frogs are a paraphyletic group. True. Ducks and frogs form a paraphyletic group if the group does not include all descendants of their common ancestor. TRUE OR FALSE: According to the phylogeny on the left, node E is a polytomy. True. Node E is a polytomy if it represents an unresolved branching pattern with multiple lineages diverging simultaneously. Species Concept Table Species Main Criterion Advantages Disadvantages Concept Biological Ability to Clear criterion for Not applicable to Species interbreed and identifying asexual or fossil Concept produce fertile species through species; difficult to offspring reproductive test in wild isolation populations Morphospeci Distinct Can be used with Subjective; may not es Concept physical fossils and reflect evolutionary characteristics asexual species relationships Phylogenetic Smallest Applicable to all Requires detailed Species monophyletic types of genetic data, may Concept group on a organisms, recognize many phylogenetic including fossils species tree and asexual species Prezygotic Isolation Table Type of Definition 3 Examples Prezygotic Isolation Temporal Species breed at Frogs breeding in different seasons, Isolation different times plants flowering in spring vs. summer, nocturnal vs. diurnal mating times Habitat Species live or Aquatic vs. terrestrial garter snakes, Isolation breed in different apple vs. hawthorn maggot flies, habitats mountain vs. lowland habitats Behavioral Species have Different bird mating songs, unique Isolation different mating frog calls, firefly light patterns behaviors or signals Mechanical Physical Different flower structures for Isolation differences pollination, incompatible genitalia in prevent successful insects, size differences in spiders mating Gametic Sperm and egg Sea urchin sperm that can’t fertilize Isolation are incompatible eggs of another species, pollen specificity in plants, chemical incompatibility in coral spawning Postzygotic Isolation Table Type of Definition 3 Examples Postzygotic Isolation Hybrid Hybrids fail to Sheep-goat hybrids, leopard-frog Inviability develop properly hybrids, salamander hybrids that die or die early as larvae Hybrid Hybrids are sterile Mule (horse-donkey hybrid), liger Sterility and cannot (lion-tiger hybrid), zebroids (zebra reproduce hybrids) Hybrid Hybrids are fertile, Rice hybrids with reduced fitness in Breakdown but their offspring future generations, cotton hybrids are inviable or with sterile progeny, hybrid fish with sterile reproductive issues in F2 generation Evolutionary Mechanisms and Genetic Variation --- Define Effect on Genetic Variation Natural Differential survival Can increase or decrease genetic Selection and reproduction variation depending on the selection based on heritable type (e.g., directional, stabilizing, traits disruptive) Genetic Random changes in Decreases genetic variation, Drift allele frequencies due especially in small populations to chance events Gene Movement of alleles Increases genetic variation within Flow between populations populations, decreases variation between populations Mutation Random changes in Increases genetic variation by DNA sequence that introducing new alleles create new alleles Types of Selection Type of Implication for Implication for Drawing Selection Diversity Mean Phenotype Directiona Reduces diversity by Shifts the mean Drawing of a l favoring one extreme phenotype in one shifted bell curve phenotype direction to one side Balancing Maintains or Mean phenotype Drawing showing increases diversity remains stable two peaks or stable variation Disruptive Increases diversity by Creates two Drawing with a favoring both distinct peaks in curve that has extremes phenotype two peaks Types of Chromosome-Level Mutation Type of Description Drawing Chromosome-Leve l Mutation Deletion A section of the Drawing of a chromosome is lost chromosome missing a segment Duplication A section of the Drawing of a chromosome is chromosome with a duplicated repeated segment Inversion A section of the Drawing showing a chromosome is reversed segment flipped in orientation Translocation A section of one Drawing showing a chromosome is attached segment moved to a to another chromosome different chromosome Point Mutations Type of Point Descripti Drawin Mutation on g Silent A change in a nucleotide that Drawing: A codon with one Mutation does not alter the amino acid nucleotide changed but sequence due to redundancy in still coding for the same the genetic code. amino acid. Missense A change in a nucleotide that results Drawing: A codon Mutation in a different amino acid being change resulting in a incorporated into the protein. This new amino acid in the can alter the protein's function. sequence. Nonsense A change in a nucleotide that converts a Drawing: A codon Mutation codon into a stop codon, causing changed to a premature termination of translation and stop codon (e.g., typically resulting in a nonfunctional UGA). protein. Frameshift The insertion or deletion of a Drawing: Sequence with Mutation nucleotide that shifts the reading an extra or missing frame of the codons, leading to nucleotide, causing a entirely different amino acids shift in subsequent downstream of the mutation. codons. Transition A substitution of a purine for a purine Drawing: A swap Mutation (A ↔ G) or a pyrimidine for a pyrimidine between similar (C ↔ T). This is more common than types (A to G or C transversions. to T). Transversion A substitution of a purine for a Drawing: A swap Mutation pyrimidine or vice versa (A or G ↔ C between different or T). This is less common than types (A to C or G to transitions. T). QUIZ QUESTIONS Which of these is not a species concept? Biological Postzygotic Morphological Phylogenetic If the RR genotype frequency is 0.5 and has a relative fitness of 1.3, what is the frequency of Rr genotype after selection? Can’t tell not enough information. Which of the following is false with regards to sexual selection in elephant seals? Female elephant seals mated to large males can have upwards of 40 offspring over their lifetime. There is low variance in reproductive success of females. Male male competition is driven by high variance in male reproductive success. Large aggressive males are more likely to contribute to the gene pool. Imagine that two populations of diverging organisms still mate with each other but some of the males from population one fail to fertilize the eggs of population two. This would be evidence of prezygogjc isolation in the form of. Gametic isolation Haldane's rule suggests that we would typically expect hybrid males to be sterile in crosses between different species of butterfly. False Experiments done by Richard Lenskin using E. coli demonstrated that: Certain mutations can lead to increased fitness. What is considered a limitation of the biological species concept? Doesn’t work well for species with overlapping geographic ranges. Doesn’t work well with sexually reproducing organisms. Doesn’t work well for fossils. Doesn’t work well for species that are easily crossed in a lab. All are TRUE about binomial nomenclature except: It requires that an organisms name be represented by a genus name and specific epithet. Naming rules are set by International Commission on Zoological Nomenclature. It was originally advocated by Charles Darwin. All names are in Latin. The most parsimonious tree is always the correct representation of how evolution actually occurred. True False What is not a term used to describe a phylogenetic tree? Polytomy Node Branch Root Bud Using the phylogeny below. Which species is most closely related to fish? They all are equally related Frog Mouse Lizard Human You are studying the apple/hawthorn maggot fly (discussed in class) and you observe that crosses between male apple flies and female hawthorn flies produce sterile male offspring. What else would be TRUE regarding this system. The reciprocal cross is a male apple fly crossed to a female hawthorn fly Disruptive selection has lead to apple and hawthorn flies. The apple/hawthorn maggot fly is an example of allopatric speciation. This result is not consistent with Haldane's rule. Allopolyploids are produced when a single species doubles its chromosome number. True False A repeated trait that is the result of independent evolution and not shared ancestry is referred to as a: ancestral trait homoplasy node polytomy Certain types of DNA evolution happen more often than other types, requiring more complex models to understand phylogenetic relationships. For example, transitions happen more frequently than transversions. True False All of these lead to issues in the fossil recorded EXCEPT: Soft bodied organisms are fossilized more easily than hard bodied organisms. More recent fossils are more common. Above ground organisms far from sediment are not fossilized as frequently. Highly abundant species are found more regularly than rare ones. Imagine you sequence 1,000 nucleotides of the coxi gene from two beetles in North America that you think are different species. After counting the number of nucleotide differences between the sequences, you find they differ at ~7% of bases. Based on these data and given the mDNA cox1 divergence rate estimate from class, approximately how many years ago did these beetle species split? approximately 3.5 million years ago approximately 1 million years ago approximately 2 million years ago approximately 14 million years ago approximately 4.7 million years ago What is FALSE about the Cambrian Explosion:  The Hox genes evolved and diversified allowing for more complex body plans. The explosion was driven by the diversification of other lineages and emergence of predation. Was an important period for angiosperm evolution. The first arthropods arose. Given this phylogeny below, if the ancestral trait is large abdomen, how many evolutionary events are needed to explain the tree? What if small abdomen is the ancestral trait? 1 and 2 2 and 3 2 and 2 3 and 2