Exam 3 Review Fall 2024 PDF

EXAM 3 STUDY FALL 2024 WHAT IS A MOLECULA R CLOCK? Two descendent lineages Two descendent lineages The two descendent lineages have diverged (after 25 have diverged (after 25 have diverged further by another million years) each lineage million years) each lineage...

EXAM 3 STUDY FALL 2024 WHAT IS A MOLECULA R CLOCK? Two descendent lineages Two descendent lineages The two descendent lineages have diverged (after 25 have diverged (after 25 have diverged further by another million years) each lineage million years) each lineage base mutation (after 50 million has a single bas mutation so has a single bas mutation so years) The lineages now differ by now they differ by two bases now they differ by two bases 4 bases A FIGURATIVE CLOCK USED TO MEASURE EVOUTIONARY TIME! Measures random neutral mutation in the DNA that occur at a constant, predictable rate in a species Neutral mutations are the most commonly expressed mutations- not selected for or against in natural selection Organisms that diverged fairly recently only have a few nucleotide differences, while those that diverged a long time ago, have many nucleotide differences WHAT IS NATURAL SELECTION? WHAT IS NATURAL SELECTION? the process by which organisms better adapted to their environment are more likely to survive and reproduce, passing on advantageous traits to future generations THINGS NATURAL SELECTION IS NOT… Perfection Progress- it does not inherently aim for "progress" or complexity, but instead favors traits that improve reproductive success in a given environment Harmony in Nature- Organisms are in constant competition for resources, and natural selection can lead to conflict as well as cooperation, depending on the ecological context- there is no harmony A justification for our own actions  Stabilizing selection is a natural selection process where individuals with average or moderate traits are more likely to survive and reproduce Human babies of intermediate birth weight Nesting birds are under stabilizing have higher survival rates compared to selection for the number of eggs laid very small or very large babies because having too few or too many eggs reduces reproductive success Diversifying selection is another type of selection that favors multiple extreme phenotypes within a population, leading to increased genetic diversity  YOU WERE NOT ALLOWED TO USE PEPPERED MOTHS IN YOUR PAPERS, BUT DO YOU KNOW WHAT TYPE OF SELECTION THEY ARE AN EXAMPLE OF? Directional selection: When natural selection favors one extreme phenotype within a population, causing the population to shift in that direction Also known as ”Industrial Kin selection is a natural selection process that favors traits that help an organism's relatives (shared genes) reproduce, even if it means the organism sacrifices its own survival and reproduction The (shared) genes still get passed on to the next generation Social insects, such as ants, bees, wasps, and termites, exhibit kin selection Generally, one reproductive queen and a colony of related workers who do not reproduce Kin selection can lead to the evolution of ALTRUISM… Altruism= behaviors of an individual that benefits another at a cost to itself Often involves actions that increase the reproductive success or survival of others, potentially at the expense of the altruistic individual’s own fitness  survival of the species Examples include animals sharing food, defending others, or engaging in cooperative care This sounds great, everyone helping for the good of the species! What could go wrong? …. Selfish mutants Even if altruism is advantageous at the group level, within any group altruists are liable to be exploited by selfish ‘free-riders’ who don’t behave altruistically These free-riders have an obvious fitness advantage- they benefit from the altruism of others, but do not incur any of the costs! So even if a group is composed exclusively of altruists, all behaving nicely towards each other, it only takes one single selfish mutant to bring an end to this paradise The selfish mutant will out-reproduce the altruists, and selfishness will eventually swamp altruism. ‘Subversion from within’ (Richard Dawkins) is generally thought of as a flaw to group selection and altruism  Learn more about the idea of evolution at the level of the gene and altruism by reading… ** You don’t need to read this for the exam, just a book recommendation if this is something that interest you! Venomous Eastern Coral Snake Non-Venomous Scarlett King Snake Batesian or Müllerian mimicry? Venomous Eastern Coral Snake Non-Venomous Scarlett King Snake Batesian mimicry! A harmless species evolves to imitate the appearance of a harmful species  Batesian or Poisonous to predators Contain different toxins, but still poisonous Müllerian mimicry?  Poisonous to predators Contain different toxins, but still unpalatable Müllerian mimicry! Both the mimic and the model are toxic or unpalatable to predators EXAMPLE OF THE FOUNDER EFFECT Eastern Pennsylvania is home to the Old Order Amish- a population of Amish people that originated as ~ 200 German immigrants in the 1700’s They have had a “closed” community since arriving- meaning they marry among themselves, with very few outsiders coming into their community= no new genetic variation They carry unusual concentrations of gene mutations that cause a number of otherwise rare inherited disorders, including a form of dwarfism- Ellis-van Creveld syndrome Involves short stature, polydactyly (extra fingers or toes), abnormalities of the nails and teeth, and, in about half of individuals, a hole between the two upper chambers of the heart  CAN YOU EXPLAIN WHY THIS IS A FOUNDER EFFECT? A population of Sephardic Jews from Spain fled the Spanish Inquisition and went to Ecuador in the late 15th century Some of them carried a genetic mutation that causes Laron syndrome (a form of dwarfism) There are now large portions of several Jewish communities in Ecuador with Laron syndrome *Fun Fact: these communities also have extremely low rates of cancer and diabetes because the mutation affects growth hormone receptors! In what situations would asexual reproduction be more adventageous over sexual reproduction? In a stable environment- no competitors or predators! Allows for quick population growth Don’t need to waste time or energy finding a mate Beneficial traits are passed on- all offspring have the same genetic makeup as the parent  Positive vs. Negative Assortative Positive Mating assortative mating= when individuals choose to mate with similar individuals based on their physical characteristics or genotype Negative assortative mating (disassortative)= when individuals choose to mate with dissimilar individuals Positive assortative mating can increase homozygosity, while negative assortative mating can increase heterozygosity in a population What is inbreeding and why is it bad?  Inbreeding occurs when two individuals that are closely related mated and have offspring It significantly increases the likelihood of offspring inheriting harmful recessive genes from both parents Higher risk of genetic disorders and reduced fertility Reduced genetic diversity It can lead to an overall decreased fitness in the population- this is known as inbreeding depression WHAT IS THIS?  SPIROCHETES Bacteria! ****Pathogenic species cause human diseases such as syphilis, Lyme disease, and periodontal disease  Polyandry in the Spotted Sandpiper Sandpipers can normally be found in the Arctic and subarctic. It is a pioneering species can quickly colonize a new habitat- quick response to reproductive failure, breeds at an early age, lays many eggs per female. The spotted sandpiper has invaded temperate climates, giving it a longer breeding season. Females arrive to breeding grounds first and compete for males as they arrive. Females lay up to four clutches and each male incubates the eggs and cares for the young.  What hypothesis says that species must constantly evolve and adapt to maintain their fitness in an environment where other species are also evolving?  The Red Queen Hypothesis! The core idea is that species are locked in a coevolutionary arms race, where adaptations in one species drive the evolution of counter- adaptations in another, leading to a continuous cycle of adaptation Think about it! An organism’s competitor or predator is adapting every generation, so the organism must also adapt every generation to stay alive It is often used to explain why sexual reproduction is advantageous- allows for greater genetic diversity, making it harder for parasites or predators to adapt to a single host genotype  Example of the Red Queen Hypothesis Biologist Robert Vrijenhoek has been studying the Mexican Poeciliid fish for more than 30 years Some species of Poeciliopsis reproduce sexually while others reproduce asexually Vrijenhoek found that the genetic diversity produced by sexual reproduction allowed the sexual fish to survive a parasite more successfully than the asexual fish Vrijenhoek suggests the sexual populations are able to keep up or adapt to new selective challenges, while the asexual populations are not Remember our friend LUCA from the first exam? (see the next slide for a refresher)  LUCA What does LUCA stand for? Last Universal Common Ancestor- but what does that mean? From LUCA, life is thought to have diversified into the different domains we have today—Bacteria, Archaea, and later Eukarya Was LUCA the first life on Earth? No! Probably many forms of life before/ at the same time as LUCA Is all life currently on Earth descended from LUCA? Yes! Even humans?- Duh! We are not special How do we know? Conserved genes and genetic code Basic biochemical pathways and molecular structures found in ALL life Now, let's add some more information that we know from studying molecular data…. Molecular evidence suggests that LUCA may have been a thermophile many ancient lineages thrive in high-temperature environments Molecular evidence shows that methanogenesis is one of the most ancient metabolisms and LUCA may have been a methanogen Anaerobic environments Metabolizes simple substrates and produces methane as a by-product LUCA is inferred to have had DNA because all modern life forms use DNA as their primary genetic material LUCA was not the first living organism but the most recent common ancestor of all currently living organisms  Who, or what, are the Archaea?! To start, they are a very ancient group of prokaryotes They “look” similar to bacteria, but are a different domain They have some things in common with bacteria and other things in common with eukaryotes They have histones and introns- same as eukaryotes Like bacteria, they lack a nucleus and membrane  Some human diseases are caused by eukaryotes, not just viruses and bacteria! Malaria Caused by Plasmodium falciparum It is a protist and belongs to the phylum Apicomplexa African sleeping sickness Caused by Trypanosoma brucei It is a protist and belongs to the phylum Kinetoplastida Candidiasis Oral thrush Caused by the over-growth of Candidia albicans It is a unicellular ascomycot yeast.  The life cycle of Plasmodium falciparum (Malaria) is complex! A mosquito ingests blood containing malarial gametocytes  the gametocytes unite in the mosquito midgut to form a zygote within the mosquito  the zygote transforms into a mobile stage, moves, and releases sporozoites that migrate into the salivary glands  these sporozoites are transferred during feeding, and enter the vertebrate bloodstream, where they move to the liver and invade, where they multiply, bud off from liver cells, and lodge in the lungs, where they have an opportunity to invade red blood cells  once encysted in a red blood cell, the parasites transform several times, multiply, and explode the cell, releasing asexual progeny to invade other cells, or gametocytes to be picked up by mosquitoes Sexual reproduction occurs in the insect host. Many rounds of asexual reproduction occur in the vertebrate host.  Asexual reproduction Sexual reproduction  Who are the fungi? Fungi are a major branch of Eukarya They have cell walls containing chitin They are heterotrophs- typically digest food extracellularly, and absorb it, as opposed to animals, which typically ingest food Most are multicellular but some have reverted to unicellular forms called “yeasts” Many ecological associations, including decomposers, parasites, mutualists, and commensals Phylogenetic studies based on molecular evidence (ribosomal RNA sequencing) have placed fungi in a clade closer to animals than plants  Meet the land plants! Remember- all land plants use chlorophyll a and b! There are several major groups- first up is: Bryophytes liverworts, mosses, and hornworts considered non-vascular plants, meaning they lack specialized tissue for water transport typically found in damp environments Around 25,000 species  Seedless vascular plants: ferns and horsetails Have developed vascular tissue for water transport, allowing them to grow taller than bryophytes, and reproduce via spores Around 12,000 species  Gymnosperms: Conifers Vascular Produce naked seeds (not enclosed in fruits) Around 1,000 species  Angiosperms: Flowering plants Vascular The most diverse group of land plants Produces flowers and seeds enclosed within fruits Around 260,000 species  Protostome vs Deuterostome Protostome and deuterostome are terms for members of major taxonomic groups of animals categorized by how they develop as embryos. In protostomes, the first opening in the embryo becomes the mouth. In deuterostomes, the first opening in the embryo becomes the anus, and the mouth develops later. Humans are here! We are in the group of deuterostomes, in the phylum Chordata, in the class Mammalia, all under the kingdom of Animalia in the domain of Eukarya!  Some example species of deuterostomes and Protostomes Sea stars and sea urchins Fish and horses Earthworm and leeches Clams and slugs Bees and shrimp  Monarch Butterfly Biosphere Reserve The Mexican government established the Monarch Butterfly Biosphere Reserve in 1986 Maintained by the Mexican government Protects key overwintering sites for the monarch butterfly The presidential degree protecting the site did not take into consideration the local communities of Otomi and Mazahua people, who had been using the land Illegal logging remains a significant threat to the Monarch Butterfly Biosphere Reserve, reducing the forest cover necessary for the butterflies' survival during winter  What is the largest animal group on Earth? The Ecdysozoa! Contains more than half of all animal species! Includes extremely diverse groups like arthropods and nematodes Ecdysozoans are defined by their ability to shed an exoskeleton (molting) to grow Notable members include insects, crustaceans, spiders, and TRUE or FALSE A whale is worth more dead than alive  TRUE or FALSE Whale watching is a huge source of revenue and brings in more money than whaling! Besides the economic reason to keep whales alive, they act as "ecosystem engineers," playing a key role in nutrient cycling by transporting nutrients from deep ocean depths to the surface through their feeding behavior, essentially fertilizing the water and stimulating the growth of phytoplankton, which forms the base of the marine food chain Ecosystem services are the direct and indirect benefits that ecosystems provide humans  Higher Level Taxonomic Diversity Some major branches on the tree of life are represented by just a handful, or just one, species. This is higher level taxonomic diversity loss of these species would mean the disappearance of a whole family, order, or class of organisms. For example, the Tuatara, two species of reptile endemic to islands off the coast of New Zealand, are the last remaining members of the class Rhyncocephala, a taxonomic group that flourished before the age of dinosaurs Ginkgo biloba is the only surviving species of the division Ginkgophyta, which dates back hundreds of millions of years. Its extinction would result in the loss of an entire division of plants TRUE or FALSE Mammals and lizards share a common ancestor  TRUE or FALSE Mammals evolved from a group of ancient amniotes called synapsids, which are distinct from the diapsids, the lineage that includes lizards, snakes, and other reptiles (as well as birds). They share a common ancestor.