Biology Final Study Guide PDF

Define phylogeny and explain how phylogenies are being used Phylogeny is the evolutionary history and relationships among species or groups of organisms. Phylogenies are used to study evolutionary patterns, trace lineage divergences, and understand traits’ origins. It has applications in conservatio...

Define phylogeny and explain how phylogenies are being used Phylogeny is the evolutionary history and relationships among species or groups of organisms. Phylogenies are used to study evolutionary patterns, trace lineage divergences, and understand traits’ origins. It has applications in conservation biology, medicine, and agriculture to determine things like identifying evolutionary distinctiveness, evolution of pathogens, and crop origins. Define phylogeny and explain how phylogenies are being used Data sources include morphological data, which are physical traits that can be observed and measured like anatomical features, developmental patterns, fossil evidence, and coloration. It can be applied to both living organisms and fossils, but analogous traits may appear similar to convergent traits despite not having common ancestry. These methods assume that the fewest evolutionary changes are correct, determining the most probable tree based on data. The steps are to first identify characters and their states, organize characters into a matrix, and then use algorithms to construct the tree. Use examples to distinguish homology and analogy. What structures are useful to develop a tree? Homology are features that are inherited from a common ancestor, like vertebrate forelimbs in humans, whales, and birds. Analogous traits are features due to convergent evolution, not shared ancestry, like the wings on bats and insects. Only convergent traits are used in constructing phylogenetic trees. What is adaptive radiation? Be able to recognize its pattern on a phylogenetic tree Adaptive radiation is the rapid evolution of diverse species from a single ancestor, often due to new ecological opportunities. Examples include Darwin's finches and mammalian diversification. It is a single species rapidly evolving into a diverse set of species to occupy different ecological niches in an effort to occupy different ecological niches. It has the key features of rapid diversification, common ancestry, and adaptation to new niches. Adaptive radiation is represented by multiple branches radiating from a single node, indicating rapid speciation from a common ancestor. What is the taxonomy? What is the hierarchical classification system of living organisms? Taxonomy is the science of classifying organism, from broad to specific: The order is doman, kingdom, class, order, family, genus, species, or “Dear King, Please Come Over For Good Sex” What are the rules of binomial nomenclature? Examples? Binomial Nomenclature contains a two part Latin name. The Genus is capitalized, while the species is lowercase. It is italicized. It is a universal naming system to avoid confusion across languages. Homo sapiens is the binomial nomenclature name for humans. Use the examples to describe the monophyletic group, paraphyletic group and polyphyletic group Monophyletic groups include a common ancestor AND all of its descendants. Examples include mammals. Paraphyletic include a common ancestor but NOT all descendants. Examples include reptiles, which excludes birds. Polyphyletic include species from multiple ancestors, like grouping bats and birds together since they can both fly. Understand what the outgroup is; what is the function of using outgroup(s) for a phylogenetic tree? How to select outgroup(s)? An outgroup is a taxon outside the ingroup used to root the tree. Its purpose is to distinguish between ancestral and derived traits. It is closely related to the ingroup but not a part of it. If the ingroup is various species of birds, the outgroup could be a reptile species like crocodiles because birds and crocodiles have a common ancestor, but crocodiles diverged before the diversification of birds. Understand the differences between shared ancestral characters and shared derived characters. Shared ancestral characters are found in both the common ancestor and all of its descendants, like the backbone in vertebrates, while shared derived characters are unique to a specific clade, like feathers in birds. Use examples to explain convergent evolution Convergent evolution is the independent evolution of similar traits in unrelated lineages, like wings in bats and insects or flippers in penguins and dolphins. They reflect environmental pressure, not shared ancestry. Analogous structures are the result of convergent evolution. Know the recent common three-domain and six-kingdom systems. What are 3 domains? What are 6 kingdoms? Which kingdom has recently been abandoned The three domains are bacteria, archaea, and eukarya. Bacteria contain prokaryotes with peptidoglycan cell walls. Archaea contains prokaryotes without peptidoglycan, which are often extremophiles. Eukarya is the domain containing plants, animals, fungi, and protists. The six kingdoms are Eubacteria (Bacteria), Archaebacteria (Archaea), Protista, Fungi, Plantae, Animalia (Eukarya). Protista is being reorganized into multiple groups. Taxon any group of organisms (species, genus, etc.) Clade a monophyletic group, including a common ancestor and all of its descendants, representing a complete branch of the evolutionary tree, accurately reflecting relationships Sister Taxa these are groups sharing an immediate common ancestor Nodes are points representing divergence events Branch Point is the node that the lineage splits at Polytomy is the node with unresolved relationships, where more than two lineages descent from one single ancestral lineage Basal Taxon is the early diverging lineage from a common ancestor Cladistics is the method of classification based on shared derived characters Understand essential concepts of historical geology & evolution, including Phanerozoic eon, plate tectonics, continental drift; mass extinction, the first cell, the first genetic material (RNA world hypothesis), adaptive radiations etc The phanerozoic eon was divided into the paleozoic, mesozoic, and cenozoic eras, marked by significant evolutionary events like the cambrian explosion, dinosaur evolution, and mammalian dominance. Plate tectonics and continental drift happened and influenced biodiversity, habitat distribution, and evolutionary pressures. Events like the Permian extinction (largest) and the Cretaceous Paleogene extinction that paved the way for new life forms. Early earth conditions enabled the formation of RNA as the first genetic material because it can store genetic information, catalyze ribozyme reactions, self replicate, and evolve, leading to self replicating systems and primitive cells. Adaptive radiation led to rapid evolutionary diversification following events like mass extinctions. Describe how chemical and physical conditions on early Earth made the origin of life possible Early earth had intense volcanic activity, UV radiations, and a reducing atmosphere with methane, ammonia, and water vapor. It experienced a chemical evolution where the formation of organic molecules like amino acids and protocells in hydrothermal vents or shallow pools helped to start life. RNA, the first genetic material, capable of catalysis and self-replication, predated DNA. Identify major phylogenetic groups of prokaryotes The major groups of prokaryotes are bacteria, including cyanobacteria, gram positive bacteria, and proteobacteria, and also archaea, including methanogens, extreme halophiles, and thermophiles. Describe the structural and functional adaptations of prokaryotes They can be spherical, rod shaped, or spiral. Bacteria have peptidoglycan cell walls, while archaea have unique membrane lipids but no peptidoglycan. Gram stain is how bacteria is differentiated.Gram positive bacteria contains a thick peptidoglycan layer that stains purple. Gram negative bacteria has a thin peptidoglycan layer and an outer membrane that stains pink. Extremophiles thrive in extreme conditions. Halophiles love salt, Thermophiles love heat, methanogens produce methane in anaerobic conditions. Autotrophs produce their own food, while Heterotrophs consume organic material to eat. Briefly describe prokaryotic genetic recombination, including transduction, transformation, and conjugation. Transformation is the uptake of foreign DNA from the environment, but transduction is DNA via bacteriophages, and conjugation is the direct transfer of DNA through pili. Describe ecological roles played by prokaryotes. 1) What are cyanobacteria? Main features (including the structures and functions). Cyanobacteria are photosynthetic and contribute to oxygen production. They contain heterocysts for nitrogen fixation. 2) Heterocysts and N-fixation Heterocysts are specialized cells fixing nitrogen in anaerobic environments 3) Explain stromatolites These are fossilized cyanobacteria colonies providing evidence for early life. Give examples of the beneficial and harmful effects that prokaryotes have on humans (symbiosis) Prokaryotes provide the gut micro bacteria that help to digest food and synthesize vitamins. They help to break down pollutants in the environment. Rhizobium bacteria are also responsible for converting atmospheric nitrogen into usable forms for plants. Harmful bacteria can cause disease in humans, like pneumonia and food poisoning. They also lead to infections like tuberculosis and cholera. The overuse of antibiotics has led to resistant strains of bacteria, posing health risks. What is endosymbiosis? What is secondary endosymbiosis? Endosymbiosis is a symbiotic relationship where one organism lives inside the cell of another. According to the endosymbiont theory, certain organelles in eukaryotic cells, such as mitochondria and plastids, originated when ancestral eukaryotic cells engulfed free living prokaryotic cells. These cells evolved into permanent organelles. Secondary endosymbiosis occurs when a eukaryotic cell that already contains an endosymbiont (algae with chloroplasts) is itself engulfed by another eukaryotic cell, so that plastids are surrounded by more than two membranes. 1.​ Mitochondria and Plastids have double membranes, suggesting engulfment 2.​ They contain circular DNA similar to prokaryotic genomes 3.​ Their ribosomes resemble those of prokaryotes 4.​ They replicate independently via a process resembling binary fission. Use Volvox and Choanoflagellates as examples to explain how multicellularity has evolved in green algae and animals from different single-celled ancestors, respectively Green algae (volvox) evolved through the formation of colonies where cells specialize for distinct functions. Volvox represents a transition to multicellularity. Choanoflagellates are the closest relatives of animals. They were single celled, resembling sponges. These both highlight convergent evolution, where multicellularity arose independently in green algae and animals, driven by environmental pressures and genetic innovations. List four “Supergroups” of Eukaryotes with representative organisms, specifically, 1) Excavata: Eulenozoan (euglenid); Trypanosoma (causing sleeping sickness) Transmitted by flies 2) SAR: diatoms, dinoflagellates (causing "red tide"); Ciliates (Paramecium), forams (foraminiferans - symbiotic with photosynthetic algae), brown algae Diatoms are photosynthetic contributors to the carbon cycle Dinoflagellates cause harmful algal blooms and are bioluminescent Ciliates are known for cilia used in movement and feeding Brown algae includes kelp forests 3) Archaeplastida: red algae, green algae, plants, charophytes are green algae most closely related to plants (not Chlorophytes!) Red algae is the source of agar and nori. Green algae includes chlorophytes and charophytes (closest relatives of plants) Plants originated from charophytes. 4) Unikonta: amoebas (Amoebazoans); multicellular slime mold (check its interesting life cycle (Figure 25.23); what is the closest living relative of an animal? Includes amoebas with pseudopodia used for movement and phagocytosis. Slime molds are multicellular. Unikonta also includes choanoflagellates, the closest relative of animals. Identify "protists" on the eukaryotic phylogeny. Why is the kingdom "Protista" no longer considered a valid clade Protists are scattered across all major eukaryotic supergroups, including diverse organisms like amoebas and algaes. The kingdom protista is no longer considered a valid clade because it is paraphyletic, meaning it does not include all the descendants of the most common ancestor, do not form a cohesive evolutionary lineage and instead are a catch all group for eukaryotes who do not fit in other categories, and some protists are more closely related to other plants or animals than each other. What is horizontal gene transfer? What are the evolutionary implications? Horizontal gene transfer is the movement of genetic material between organisms, bypassing traditional parent-to-offspring inheritance. This can occur through mechanisms like transformation, transduction, or conjugation in prokaryotes, and endosymbiosis or gene capture in eukaryotes. The evolutionary implications of horizontal gene transfer is genetic innovation, introducing new genes and functions, accelerating evolution. It blurs lineages challenging the tree like view of evolution, creating a web of life. It facilitates rapid adaption. Describe common features of fungi and explain the fungal adaptations for their terrestrial life. Common features of a fungi include a cell wall made of chitin, heterotrophic nutrition, hyphae and mycelium. Hyphae are thread like structures that form a network (mycelium) that maximize surface area for absorption. They also use spores to facilitate reproduction. Their adaptions include spore production that produces spores that are resistant to harsh conditions. Hyphae can penetrate soil and organic matter to access nutrients. They form mycorrhizal associations with plants to enhance nutrient uptake. They help to store water through mycelium. Draw the life cycle of fungi, discuss the main features of fungal life cycle, including the stage plasmogamy, karyogamy, dikaryon (heterokaryon), meiospore, mitospore etc. Understand the ploidy of each stage. Plasmogamy is the fusion of cytoplasm from two parent mycelia without nuclear fusion, forming a dikaryotic stage (n+n). Karyogamy is the fusion of nuclei to form a diploid (2n) zygote. Meiosis produces haploid meiospores from the diploid stage. Mitospores are haploid spores produced asexually for rapid production. Haploid (n) dominates the fungal life cycle. The dikaryotic (n+n) is unique to fungi, where two nuclei can coexist without fusing. Use examples to describe mutualistic symbiotic relationships between fungi and other organisms (plants, animals or protists). Fungi and plants - mycorrhizae is a symbiosis where fungi enhance water and nutrient uptake for plants. In return, plants provide carbohydrates. Fungi and animals - ants cultivate fungi to digest plant material, which they use as food Fungi and Algae- lichens are symbiotic associations where fungi protect the photosynthetic partner, which provides sugars. What is the closest lineage of protists to fungi? The closest lineage of protests to fungi is the nucleariids in the opisthokonta clade. Fungal diversity and phylogeny: know the following representative fungi of each major group (Figure 26.16): mushrooms, sac fungi, mycorrhizae, yeast, chytrids, and bread mold fungi. Chytrids are aquatic fungi with flagellated spores. Zygomycetes are bread molds. Glomeromycetes form mycorrhizae with most plants. Ascomycetes are sac fungi including yeasts and penicillin fungi. Basidiomycetes are club fungi, including mushrooms. Understand the ecological roles of fungi Fungi are decomposers that break down organic material, recycling nutrients into ecosystems. They are mutualists that enhance nutrient uptake in plants, protecting hosts from pathogens, and forming lichens. They are pathogens, infecting plants, animals, and humans. They are involved in food production, like fermentation, and are also a source of antibiotic medications like penicillin. Chitin is the structural polysaccharide in fungal cell walls. Hyphae are the filamentous structures of fungi Mycelium is the network of hyphae Endophytes are fungi living within plant tissues, providing benefits. Lichens symbiosis between photosynthesizers and fungi Describe the general characteristics and derived traits of plants (embryophytes). General characteristics of plants are that they are multicellular, eukaryotic, and photosynthetic organisms with cell walls containing cellulose. They use chlorophylls a and b for photosynthesis and exhibit alternation of generations with sporophyte and gametophyte phases. They are adapted to terrestrial environments. The derived traits of plants are that embryos are protected within a maternal tissue. Sporopollenin is a durable polymer in spores and pollen walls, protecting them from desiccation. Apical Meristems are regions of cell division at roots and shoots for growth. The cuticle is a waxy layer that prevents water loss. The stomata are pores for gas exchange. What is the closest relative of plants? What features and data support this close relationship? The closest relative of plants are zygnematophyceae, a group of green algae. The supporting data includes similarities in chlorophyll structure, the presence of cellulose-synthesizing protein complexes, molecular phylogenetics showing shared DNA, as well as the shared production of sporopollenin. What are the adaptations for plants to be able to live on land? Plants have structural adaptations like the cuticle and stomata to minimize water loss. Their vascular tissues, xylem and phloem, are used for water and nutrient transport. They have roots or rhizoids for anchoring and absorption. They have reproductive adaptations like protected embryos, spores with sporopollenin for desiccation resistance, and seeds for dispersal and dormancy. Sporopollenin is a mechanically robust and chemically inert biopolymer that constitutes the outer protective exine layer of plant spores and pollen grains Describe the vascular tissues and the differences between xylem and phloem Xylem conducts water and minerals from roots to shoots, supported by lignified tracheids. Phloem transports sugars and other organic nutrients from sources to sinks. Describe the general features of vascular plants Vascular plants have a dominant sporophyte phase, the presence of xylem and phloem, and they have specialized leaves. Plant phylogeny and diversity - "embryophytes" - nonvascular plants, seedless vascular plants, and seed plants (gymnosperms & angiosperms), with representatives from each Embryophytes include nonvascular plants, seedless vascular plants, and seed plants. Nonvascular plants (bryophytes) include mosses, liverworts, and hornworts Seedless Vascular plants include ferns, club mosses Seed plants include gymnosperms (pines) and angiosperms (flowers) Zygnematophyceae are the closest green algae relatives of plants Sporangia/Gametangia are the structures for spore and gamete production Xylem/Phloem are the vascular tissues for transport Tracheid are lignified water-conducting cells Microphyll/Megaphyll are types of leaves Homosporous/Heterosporous are spore production types What are the common features of seed plants? Seeds contain an embryo, nutritive tissue, and a protective coat. They have pollen grains that are male gametophytes for fertilization without water. Heterospory is the production of microspores and megaspores. Describe the structure of a seed and the functions of each part. The embryo is the developing plant. The nutritive tissue provides sustenance, the endosperm or cotyledons. The seed coat protects against environmental damage. Diagram the structure of an ovule The ovule is made of the integument, megasporangium, and the megaspore. Its function is to develop into a seed after fertilization. The integument is the protective outer layer. The megasporangium is the tissue producing the female gametophyte. The megaspore develops into the female gametophyte. The function is to become a seed after fertilization. What are the evolutionary advantages of seeds, compared with spores? Seeds provide protection of the embryo from environmental stress. It provides nutritional support during early development. It enhances dispersal mechanisms. Dormancy allows survival during unfavorable conditions. Describe the structure of the flower and fruit and the function(s) of each part. Flowers have sepals that enclose and protect the flower bud. Petals attract pollinators, while stamens are the male reproductive organs (anther and filament). The farpels are the female reproductive organs (stigma, style, ovary). The fruit develops from the ovary after fertilization, protecting the seeds and aiding in dispersal. What are the key features of the angiosperm life cycle? Double fertilization is when one sperm fertilizes the egg to form a zygote, while a second sperm combines with two polar nuclei to form the endosperm. The endosperm (3n) provides nutrition, while the embryo (2n) becomes the new plant. The seed coat (2n) is the protective covering, What is pollination? What are the differences between pollination and fertilization? Pollination is the transfer of pollen from anther to stigma, involving wind, water, or animals. Fertilization is the fusion of sperm and egg to form a zygote. Megaspore/microspore are the haploid spores that develop into female and male gametophytes. Integument is the layer of tissue that forms the seed coat Pollen grain is the male gametophyte surrounded by a protective coat Epiphyte is a plant growing on another plant for support, NOT nutrition Cotyledon is a seed leaf providing nutrients during germination Angiosperms/gymnosperms are flowering and non flowering seed plants, respectively Which group of protists is phylogenetic sister to Metazoa? Why? The protist group choanoflagellates is phylogenetically sister to metazoa, supported by conserved genes, morphological similarities, and evolutionary insights. Describe 3 types of animal symmetry with examples. Asymmetry- no symmetry (sponge) Radial Symmetry- body parts arranged around a central axis Bilateral Symmetry- Divisible into mirror-image halves along one plane What features are shared by sponges and choanoflagellates? Interpret these observations Both have cells with a flagellum surrounded by a collar of microvilli Both feed through phagocytosis These similarities support the hypothesis that sponges and choanoflagellates share a common ancestor, representing an evolutionary step towards multicellularity What are the advantages of bilateral symmetry for bilaterians? Bilateral symmetry enables streamlined locomotion for directional movement. The concentration of sensory organs at the anterior end enhances environmental awareness. They have specialized internal organ systems supporting complex functions. These advantages make bilaterians highly adaptive and diverse. Key Terms: Endoderm- innermost germ layer, forming the digestive tract Ectoderm- outermost germ layer, forming the skin and the nervous system Mesoderm- the middle germ layer, forming the muscles and organs Body Plan- it is the structural framework of an organism Cephalization- development of a head with sensory organs Coelomates Animals with a true coelom, a body cavity lined with mesoderm Hemocoel - Body cavity is partially lined with mesoderm Acoelomate- Animals without a body cavity, flatworms Metazoa- Multicellular animals Eumetazoa- animals with true tissues Bilateria Animals with bilateral symmetry Protostome mouth forms before anus during development Deuterostomia anus forms before mouth Lophophore feeding structure with ciliated tentacles Trochophore larval stage in some lophotrochozoans Common Features of Phylum Porifera: Porifera have an asymmetrical body plan, lacking true symmetry. They have no true tissues or organs. They have pores for water flow, choanocytes for feeding, and spiracles for support. Hox Genes: Functions and Significance: Hox genes control body plan and segment development. The gene duplication allows for diversification of body structures, driving evolutionary innovation. Three Hypotheses for the Cambrian Explosion: With increased predator-prey dynamics, the arms race led to rapid morphological diversification. There was more oxygen in the atmosphere, allowing for larger and more complex organisms. The evolution of Hox genes enabled novel body plans. Diploblastic vs. Triploblastic Animals Diploblastic animals have two germ layers, with no mesoderm Triploblastic animals have three germ layers, allowing for muscles and organs Animal Phylogeny and Clades: Key Clades: Porifera, Cnidaria, Ctenophora, Eumetazoa, Bilateria, Lophotrochozoa, Ecdysozoa, Deuterostomia. Representatives of Bilaterian Clades: The Lophotrochozoa include bryozoans, rotifers, annelids, mollusks Ecdysozoa are roundworms (nematoda) and insects (arthropoda) Deuterostomia are hemichordates, echinoderms, and chordates Common Features of Chordata: Notochord. - flexible rod Dorsal hollow nerve cord. Pharyngeal slits.- openings for feeding/respiration Post-anal tail. Origins of Tetrapods They evolved from lobe finned fishes like Tiktaalik (transitional fossil), with limbs for walking, lungs for breathing air, robust skeleton Amniotes These are animals with amniotic eggs: reptiles, birds, mammals. They have adaptations like waterproof skin and efficient lungs. These are animals with specialized eggs for land Homo Sapiens Symmetrical, Bilateral, Deuterostomia, Craniata, Jawed (Gnathostomes), Tetrapod, amniote, mammal, eutherian, Endothermic.