Understanding Macroevolution: Biogeography and Biodiversity

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Goochland High**We aren't endorsed by this school

Course

BIO 289

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Biology

Date

Dec 11, 2024

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Uploaded by sjwright044

BIOL 280 Evolution Spring 2024Exam 4 Study GuidePart 1 – Module 4Ch. 14 – Macroevolution- Microevolution (below species level) vs Macroevolution (above species level)Microevolution = population processesMacroevolution = patterns of evolution of species - Biogeographical patternsForces that shape these distributions – climate, resources, temperature, pressures o Species diversity across latitudinal gradient (tropics vs temperate)o Biogeographic Regions (unique flora/fauna groups)Biogeographic region - delineate the larger areas of Earth’s surface within which organisms have been evolving in relative isolation over long periods of time, separated from one another by geographic features, such as oceans, broad deserts, ro high mountain ranges, that constitute barriers to migration. - Mechanisms underlying biogeographic patternsDispersal and vicariance underly the pattern of species distribution = drivers of the distribution of species and Biogeographyo Plate tectonicso Dispersal - movement of populations from one geographic region to another with very limited, or no, return exchange o Vicariance - formation of geographic barriers to dispersal and gene flow, resulting in the separation of once continuously distributed populations \Dispersal and vicariance can explain distribution patterns of taxa. Dispersal occurs when a taxon crosses a preexisting barrier (ex. ocean). Vicariance occurs when a barrier interrupts the preexisting range of the taxon, preventing gene flow between the now separated populations - dispersal may be facilitated by traits

- Using phylogenies & fossils to reconstruct biogeographyParaphyletic – include some, but not all descendants of the common ancestor – defined by sharedancestral characteristics. Monophyletic groups – shared derived characteristics that are unique to the group and include allthe descendants of a common ancestoro E.g., Marsupials, Cynoglossoideae70% of marsupials are in Oceania and 30% are in the Americas Australian marsupials evolved from an American ancestor Synthetic reconstruction of the colonization of different regions by marsupials based on both fossil evidence and phylogenetic evidence – inferred through speciation, dispersal, and extinction oThere was origin in asia then dispersant into north American and then dispersal back to asia and to south America to antarctica to Australia. Then there was extinction in asia, north America, and antartica – then re dispersal into north AmericanoThe final inference was based on multiple data sets and is much more complex than initially assumed- Biodiversity patternso Variation across time, space, unique events- Processes underlying biodiversity patternso Turnoverturnover is the total number of events; rate of change

Estimating turnover for groups of species can tell us something about their biology and/orenvironment§ Originations (speciation) & ExtinctionStanding biodiversity changes when either originations or extinction changesExtinction of a lineage happens when extinction > origination§ Estimates of standing diversityStanding biodiversity = speciation – extinctionD1 = diversity in time 1, D2= diversity at time 2 D1 + speciation – extinctions = D2Standing biodiversity is the total biodiversity in any given time period The rate of speciation and extinction are unlikely to be constant (variation across time and space, unusual catastrophic events We can estimate diversity change at different times in history from the fossil record§ How does variation in speciation & extinction rates influence standingdiversity?Diversification can happen gradually or suddenly Speciation and extinction can change standing diversity at the same time or separately Diversification rate (speciation minus extinction) relative to the presence/absence§ E.g., Diversity in tropicsFaster speciation and reduced extinction in the tropics contribute to the mammalian latitudinal diversity gradientThere are more species in the tropics because of warmer temperatures and higher precipitation - Rate of change: gradualism vs punctuated equilibriumGradual evolution is the traditional view of the fossil record, punctuated equilibrium is analternative that proposed – bursts of rapid change are separated by long periods of stasis and evolution is concentrated around speciation events = there is evidence of both patterns in the fossil record

- Large scale changes in biodiversityo Rapid speciation (e.g., Cambrian Explosion 540 MYA) – diversity arises -Rising ocean levels created new niches and resources and ocean chemistry-Rising global oxygen levels created a new energy availabilityo Mass extinction (e.g., Permian Extinction 65 MYA) – diversity disappears -Mass extinction is a statistically significant departure from background extinction rates that results in a substantial loss of taxonomic diversity -Background extinction is the normal rate of extinction for a taxon or biota o Environmental drivers of changeslarge scale environmental variation = important driver of turnoverCh. 15 – Species Interactions & Co-evolution- A species’ environment includes the community interactions with other species- Interactions have different effects on species’ fitnessVariation is important because it determines how populations change through natural selectiono Competition (-/-) - occurs when individuals use the same limited resource - lowers fitness of botho Consumption (+/-) - occurs when one organism eats or absorbs nutrients from another. - increases the consumers fitness but decreases the victims fitnesso Mutualism (+/+) - occurs when two species interact in a way that is mutually beneficial - increases fitness of botho Commensalism (+/0) - occurs when one species benefits but the other species is unaffected Interactions influence how natural selection shapes the variation that exists within populations ofeach species in the interaction- In order for co-evolution to occur:Coevolution = reciprocal evolutionary change between interacting species that is driven by natural selection, and reciprocal natural selection on traits For co-evolution to occur: heritable variation within species, interaction between specieo Heritable variation within specieso Species interactionso Reciprocal natural selection

- Table 15.1: really good summary of kinds of interactions and their evolutionaryOutcomesMutualisms are not altruistic - each sepceis si being shaped by natural selection to maximize its own fitness → so mutualisms can evolve into consumption (+/-) types of relationships- Specific vs. Diffuse Co-evolutionSpecific coevolution - reciprocal evolutionary change between two interacting species, driven by natural selection acting directly on those two speciesDiffuse coevolution - evolutionary change occurring in a collection of species, driven by natural selection which may not act independently on different specie so Examples of specific coevolution - Orchid/Moth, Bird/Butterflies-The orchid had a long nectar spur and it was hypothesized that the pollinator must also have a very long proboscis – then they found the mouth that had an extremely long proboscis as predicted by Darwin§ Coevolutionary alternation – due to species-specific evolutionary armsRaceThe bird and butterfly: predator-prey (antagonistic) co evolution – the selection on the predator to become a better hunter and there is selection on the prey to became better at avoiding being hunted so there is camouflage, mimicry, increased speed, increased armorThe benefit of the long nectar spur for the orchid – visitation by moth, less nectar production requiredBenefit for longer proboscis for moth – capturing more nectar per visitation

Co evolution (mutualistic) driven by specific interaction between the orchid and motho Examples of diffuse coevolution - Crossbill/Red Squirrel/Lodgepole Pine- the crossbill and red squirrels both eat lodgepole pine seeds – in some locations the squirrels are absent, but where they occur in the same place there is interaction between the speciesThere is variation in the pine cones so there is variation in the crossbill beak size and shapes – stabilizing selection on the birds beaksDirectional selection on the cone scale thickness- Theoretical concept of the Geographic Mosaic Theory of CoevolutionInteractions among species are shaped by - geographic variation in selection on species, geographic variation in reciprocal selection on both species, and geographic variation in the distribution of traits as a results of selection.- Specific example of Bee-Orchid mutualistic relationship & the effect of climate changeOrchid has deceptive display and odor that attracts male bees – the male beens attempt copulation with flower and gather pollen mass, male bees transfer pollinia to new flower pollinationMight not work as well now because of climate change male bees flight and coming out of hibernation is occurring earlier, orchid flowering occurring earlier, and female bee flight occurring earlier – but the change in timing of these events are not occurring at the same rate Ch. 17 – Human EvolutionHominid - member of the group of genera that make up the Great ApesHominin- members of the human lineage after the split from the most recent common ancestor with chimpanzees and bonobos- Review topics from McClung Museum Human Origins exercise- Primate lineage; time of origin; split between Chimp-Human lineagesThe closest extant primate relatives: chimpanzees and bonobos

Based on molecular clock – Pan-Homo is estimated to be the most recent common ancestor – 5-7 mya - Tools used to study human evolution: fossils, genetics, climate modelsFossils are incomplete, but growing (fossilization process rare), new finds often dramatically re shape hypothesesGenetics can reconstruct genealogical relationships among extant humans. Increasingly able to add genetic information from extinct human populationsClimate models - how did climate shape the evolution and migration of humans- Fundamentals of fossil homininsFossil hominins are Strictly African for 1st 5 million yearsFossils are not missing links but are representatives of branches from the evolutionary treeo Time frameGenus Homo - 2.5 mya - larger brain, smaller teeth/jaws, longer legs/shorter arms, shorterfingers and toes - only known from east Africa - stone tools, group hunting, evidence for social organization they evolved from the Australopithecine lineageAustralopithecus were all african and dated 1.5-4 mya = the key feautes: bipedalism, small brains, small canine teeth (omnivorous diet) – they had a mix of characteristics for climing and walking an intermediate between the chimpanzee and modern humano Geographic distributiono Evolutionary innovations

Important evolutionary changes - locomotion, jaw/teeth, and brain/skull changes (tool making, face size and architecture, representation, and language)- Various models of hominin phylogeny – which lineages gave rise to which- Why is understanding hominin phylogeny ONLY FROM FOSSILS difficult- Evolutionary trends in hominin evolution- the evolution of homo sapiens in Africa, followed by migration out of Africa = the replacement of other hominin species (H erectus, H neandertalensis)As there were independent waves of Homo sapiens out of Africa, there was a lot of replacement and or interbreeding with other hominin species – this is why some Europeans have trace amounts of neanderthal DNA- Mosaic nature of early hominin lineages- Origin of the genus Homoo When, where, characteristics- Various models of Homo phylogeny – which lineages gave rise to which- Migrations out of Africa: which lineages, when, where- Impacts of interbreeding between hominin lineages: Neanderthals, Denisovans- Environmental changes / variation as driver of human evolution & migrationo Savanna hypothesis vs. Variability Selection hypothesistwo hypothesis of climatic effect on human evolutionsavanna hypothesis warming and drying of climate influenced vegetation in Africa, tropical wet forest recedes; tropical dry forest and grasslands dominate, human ecolution is a specific response to those conditions: bipedalism (fewer trees and more grassland), jaw/teeth (fewer fruits and more grains) Variability selection hypothesis climatic variability changed climates across the planet,climatic variability increased temporally (more seasonal/annual variation), human evolution is a general response to changing conditions. Ch. 18 – Evolutionary Medicine- “Biological realities that make humans vulnerable to disease”Pathogens evolve faster than their hosts, natural selection often lags behind environmental change, trade offs make it nearly impossible for natural selection to solve certain biological problems, a species evolutionary history puts constraints on the potential changes

natural selection can bring about, some traits increase reproductive fitness at the cost of increasing vulnerability to disease, what may appear to be disease may actually be an adaptation- Traits / genes inherited from hybridization w/ Neanderthals & DenisovansWe inherited bigger noses, and we inherited HPV which is a sexually transmitted disease,some people have genes that hamper a drugs HIV protection - Examples / case studies- drugs are often designed without taking genetic variation into account. In particular, drug trials often have little genetic diversity among volunteers. But genetic variation among individuals may have important implications for drug efficiency o HIV drug & genetic variationo HIV genetic variation within a host (in vivo evolution)o HIV & Covid virus evolution traced by phylogeny- Why do pathogens evolve faster than their hosts and how does this impact naturalselection on both the pathogen & hostRed queen hypothesis - they have short generation times and many offspring, high mutation rate, and horizontal gene transfer in environment The red queen hypothesis is an evolutionary arms race with the immune system \With pathogens there is an opportunity for rapid evolutionary response via natural selectionNatural selection on pathogens may work in two ways: increase offspring ( more host resources used, more harm done to the host) or increase transmission rate (keep current host alive longer toincrease the rate of transmission to new hosts)Humans are always trying to keep up with the evolutionary … of the pathogensPrimary human pathogens viruses and bacteriaVery short generation time/ many offspringHigh mutation rateOpportunity for rapid evolutionary response via natural selection- Trade-offs in resource allocation of pathogensTrade offs between survival vs reproduction - can not always do everything the bestBiological challenges that evolution is not going to be able to solve

- Antibiotic resistance: how & whyDiscovered in late 1950sAntibiotic impose very strong natural selection on pathogensWith the high mutation rate and strong natural selection there becomes resistancePhylogeny showed that the new resistant bacteria were descended… → in vivo evolutionOver prescription of antibiotic when not necessaryNot completing course of antibiotics when prescribedMassive preventative use in agricultural systems → environmental exposure of bacteria to high levels of antibiotics- Proximate vs. Ultimate cause of disease perspective- proximate - disease results from biochemical, physiological, immunological response tothe environment and pathogens - physician's perspective- ultimate - ancestry and common descent; variation in the environment over time; ongoing genomic and evolutionary forces - ecological biologist perspective - Diseases associated with specific geographyo Sickle cell disease - o Lactase persistence - all mammals consume milk as infants - most mammals stop producing lactase at weaning including humans and milk is not part of the adult diet - lactase persistence is the continued production of lactose after weaning because milk has become readily available andthere's strong natural selection to favor individuals that could use it - Diseases of civilizationNatural selection shaped human sin different sets of environmental conditions than we encounter todayResults in a mismatch between optimal strategy associated with origin of traits vs modernenvironmentIncreasing rates of diet associated diseases/ disorders = obesity and type 2 diabetes o Causes due to change in human cultureChangesFamily sizeLess rural

More processed - less fresh foodGreater emphasis on sanitationoDramatically reduced infection and mortality rates As a result of the changes we had a big spike in autoimmune disorders – the changes eladto significant reduction in exposure to parasites and pathogens relative to pre history The lack of parasites and pathogens in modern cleaner environment results in overactive and or mis regulated immune responseso Hygiene / Old Friends hypothesisHuman immune system developed in an environment of constant exposure to a large population of parasite and pathogens and symbionts (bacteria and viruses) Genetic variation among individuals exists. Drugs are often designed without taking this variation into accountThe lack of parasites and pathogens in modern cleaner environment results in overactive and or mis regulated immune response Part 2 – Cumulative Exam – this will be heavily scenario-based. I will give you examples ofbiological systems and ask you to interpret them.- How does natural selection happen? (e.g., Fig 2.19 or Darwin’s Four Postulates)Descent with modification – all species share common ancestry and changes occur through natural selection Since more individuals are produced that can be supported by the available resource but population size remains stable, it means that there must be fierce struggle for existence among the individuals of a population, resulting in the survival of only a part, often a very small part, of the progeny of each generation.Survival in the struggle for existence is not random but depends in part on the hereditary constitution of the surviving individuals. This unequal survival constitutes the process of natural selection. A lot of the variation that is prevalent is heritable

Over generations this process of natural selection will lead to a continuing gradual change of populations, that is, to evolution and to the production of new species Adaptations = traits that have evolved by natural selection o Given a scenario, explain how natural selection is shaping a population (e.g.,similar to Darwin’s finches, beach & forest mice, etc.)- Age of the earth – why does it matter?4.5 billion years old based on oldest rocks this is much other than earlier estimates andit is plenty old for geological and evolutionary processes to shape modern earth Radioactive decay – Radioactive elements formed initially in stars and are present in planets because planets are formed from stellar debris the radioactive elements in rocks are assumed to be present there from formation of the rock. Half-life – amount of time it takes for half of the parent radioactive material to decay into its daughter element Radioactive elements with known decay rates allow us to estimate age of rocks - Phylogenetics – reading & interpreting a phylogenetic tree; using phylogenies tounderstand other processes/patterns (e.g., speciation, biogeography)a phylogeny is a visual representation of the evolutionary history of populations, genes, or species paraphyletic – the common ancestor and some but not all of the ancestors descendants polyphyletic – does not include the common ancestor of the groupmonophyletic – includes the common ancestor and all descendants of that ancestor

synapomorphy – an evolutionary derived character stat that is shared by a group of species (evidence of relationship)parsimony which is the best tree – the hypothesis that minimizes the number required evolutionary changes is preferred the shortest tree = the best estimate of the phylogeny- Central dogma – what are the links between genotype & phenotype?DNA RNA Protein Genotype is the genetic makeup of the individualPhenotype is the observable, measurable characteristic of an individual the morphology, physiology, behavior, and development The genotype leads to the phenotypeGenetic variation leads to phenotypic variation A mutation is the change in genotype which usually causes a change in the phenotype Types of mutations – deleterious alleles that lower fitness, neutral alleles that do not affect fitness, and beneficial alleles that raise fitnessAdvantageous mutations will often increase frequency in population, deleterious mutations will often decrease frequency in population - Hardy-Weinberg EquilibriumDarwin proposed evolution by natural selection: traits are variable within populations, traits are heritable, more offspring are born than can survive, non random reproductive success

Assumptions of the Hardy Weinberg -No natural selection-No genetic drift (=large population)-No gene flow-No mutation-Random mating -If the assumptions are met then there is no evolution and the allele and genotype frequencies stay the same

Fitness = the success of an organism at surviving and reproducing and thus contributing offspring to future generationsAbsolute fitness = is the number of offspring produced by an individual over their lifetime

Absolute fitness = survival * reproductive rate can range from 0 to infinity Relative fitness= the success of an individual at producing new individuals, standardized by the success of other individuals in the population Relative fitness = the absolute fitness of genotype/ absolute fitness of most fit genotype can range 0-1 fitness indicated by w Fitness depends on both survival and reproductionsurvival rate is the percentage of individuals born that survive to reproductive age. Reproductive rate is the average number of offspring for individuals of a given genotype o What are the assumptions? Why do they matter? What happens if noassumption is violated? What happens if specific assumptions are violated?- How do genetic drift, natural selection, gene flow shape allele frequencies inpopulations?The fate of alleles in population (genetic drift vs natural selection) depends on the magnitude of selection, initial frequency in pop, population size- What is heritability, why is it important, how do we use it?Heritability is the proportion of phenotypic variance due to genetic variation among individuals Broad sense heritability (H^2) is the proportion of total phenotypic variance that is attributable to genetic variance Narrow sense heritability (h^2) is the proportion of total phenotypic variance that is attributable to affects of additive alleles on genetic variance typically used to understand inheritance for quantitative traits Narrow sense can be calculated as the slope of a regression line comparing parents to offspring - What is sexual selection and how / why does it shape variation in populations?Sexual selection is a subset of natural selection with the same requirements there is differential reproductive success resulting from competition for fertilization ( there is competition among individuals of the same sex to access mates or competition to attract the opposite sex) Advantages of sex = combining beneficial mutations, faster evolution, generation of novel genotypes through recombination

Disadvantages of sex = search cost, risk of sexually transmitted infection, reduced relatedness (only pass half their alleles to their offspring because meiosis produces haploid gametes) sex has costs to the individuals but advantages to the population - How does natural selection influence life history?Natural selection favors individuals with traits that maximize the balance between survival and reproduction We see different life history strategies because fitness trade offs occur when resources arelimited this is called resource allocation= resources devoted to either growth and survival or reproduction Natural selection can shape how species allocate resources, tradeoffs between survival and reproduction influence strategies, males and females may have conflicting strategies becauseof different parental investment- What are the morphological, biological, and phylogenetic species concept and what arethe criteria that are used to determine whether groups of populations are one or twodifferent species? (e.g., given a scenario, how would apply the concepts?)morphological species concept – consistent differences in anatomy, morphology, behavior, diet, and distribution biological species concept – historical and ongoing examples of successful mating and the offspring are fertilephylogenetic species concept – phylogenetically distinct with exception of a population of known hybrid origin – introgression of brown bear genes into polar bears microevolution is evolution occurring within populations macroevolution is evolution occurring above the species level - What are the processes (pre-zygotic, post-zygotic) that can keep gene pools separate?Premating – isolating barriers that impede gene flow before sperm or pollen can be transferred to other speciesPostmating prezygotic – isolating barriers that impede gene flow after sperm or pollen has been transferred but before fertilization has occurredPostzygotic – isolating barriers that act after a zygote begins to develop - How does speciation happen – allopatric, parapatric, sympatric?

Allopatric happens when there is a geographical barrier created – barrier in gene flowParapatric – a new nich enters – interbreeding is still possible but genetic differences accumulate between population sthrough selection for adaptation in the new habitatSympatric – polymorphism occurs – assortative mating occurs such that subsets of the original metapopulation begin to form their own distinct gene pools. Genetic differences accumulate between subsets of the populations through selection and drift – genetic differences ultimately result in reproductive isolation