3330 Exam 2 Review Spring 2011 Chapter 8 Key Concepts Eduardo Sixto ~Based on microfossils there is a two billion year diversification period where cells created by abiogenesis, ~4.0-3.5 Bya, developed into the basis for the eukaryotic cells, 2.5-2.8 Bya. ~The first successful protocells would have been heterotrophs. It is assumed that after raw material become short on supply some of these cells become photosynthetic autotrophs, cyanobacteria. ~Methane concentrations in ancient rocks suggest that some of the cells produced methane as a byproduct from metabolic pathways. ~Stromatolites in the coast of Australia support the theory that life had diversified 3.4 Bya and existed in structured, biological ecosystems. ~All organisms are bound by four essential facts1) they share a common inheritance 2) their past has been long enough for inherited changes to accumulate 3) the discoverable relationships among organisms are the result of evolution 4) discoverable biological processes explain how organisms arose and how they were modified through time by the process of evolution. ~The first two kingdoms recognized were Plantea, plants, and Animalia, animals. This later changed to account the bacteria as another kingdom, the Protista. ~In 1938 a proposed kingdom for bacteria and the blue-green algae was called Kingdom Monera. ~In 1969 the fungi, classified as plants, were elevated into their own kingdom, Kingdom Fungi. ~ Carl Woese, having performed genetic comparisons on different cell species, was able to define three domains for the living world. The Eubacteria, which include the bacteria and cyanobacteria, Archaea, the cells that have cell walls made of different molecules from those found in bacteria and cells which often live under more rigorous conditions, and the Eukarya, which included slime molds, ciliates, and the multicellular kingdoms of the Plantea, Animalia, and Fungi. ~Archaebacterial traits distinguishable from Eubacteria are the different cell wall chemistry, membrane lipid chemistry, major nutrient metabolic pathways, ribosomes and RNA polymerase and DNA associated with histones, like Eukaryotes. ~The Last Universal Common Ancestor of all organisms today had DNA as the hereditary material, DNA replication with helicase and DNA synthetases, ribosome-based protein synthesis, several common metabolic pathways, ATP, phospholipid bilayer cell membrane, and active transport across membranes. ~Cyanobacteria fossils are the oldest fossils found in Western Australia from about 3.5 Bya making it surprising due to the fact that the earliest rocks are only dated back to 3.8 Bya. ~Cyanobacteria dominated the globe for 2 billion years, with some forms still existing today. They produced large quantities of oxygen by photosynthesis which would slowly eliminate the reducing atmosphere of early earth. ~Eukaryotic cells probably arose through endosymbiosis and incorporation (e.g. chloroplast, mitochondria). ~Horizontal Gene Transfer, HGT, is affective by a virus or a small, circular DNA particle known as a plasmid that contains a foreign gene and as much as one-third of some prokaryotic genome has been acquired through HGT. ~Less than ten-percent of eukaryotes acquired one or two protein families through HGT. ~The three main ways of prokaryote HGT are 1) Transformation, the up-take of naked DNA from the external environment 2) Conjugation is the process by which one bacterium transfers genetic material to another through direct contact. During conjugation, one bacterium serves as the donor of the genetic material, and the other serves as the recipient. They do not have to belong to the same species. The donor bacterium carries a DNA sequence called the fertility factor, or F-factor. The F-factor allows the donor to produce a thin, tubelike structure called a pilus or conjugation tube, which the donor uses to contact the recipient. The pilus or conjugation tube then draws the two bacteria together, at which time the donor bacterium transfers genetic material to the recipient bacterium. Typically, the genetic material is in the form of a plasmid, or a small, circular piece of DNA of plasmid DNA, though in some circumstances, it might be a part or all of the main bacterial "chromosome" or main circular DNA genome. 3) Transduction, or transfer via viral infection. ~ prokaryotic HGT may be a beneficial process since they reproduce asexually, but with HGT a cell can acquire a gene that confers survival or a novel characteristic which enables them to thrive in harmful conditions or to utilize a new metabolite. It is through this process that resistance to antibiotics can be transferred from one bacterial cell to another. ~Another classic example for HGT is the origins of Mitochondria and Chloroplast from endosymbiosis. ~Archaebacteria acquired organelles by endosymbiosis. ~Early Eukaryotes has cell walls, were aerobic heterotrophs, and eventually developed sexual reproduction, which would lead to the decline of HGT among Eukaryotic lineages likely to the alternative sexual recombination. Chapter 8 People Robert Ahlers & Nanci Macias Two Kingdoms Aristotle (384-322 BCE) Greek Philosopher, student of Plato, Great Chain of Being Classified life into two kingdoms Aristotle's Two Kingdoms: Plantae (L. planta, plant) Animalia (L. anima, breath, life) This classification lasted for more than 2000 years Two Kingdoms becomes Three Carolus (Carl) Linnaeus (1707-1778) Swedish biologist, founder of systematics Clarified the Two Kingdoms of Life and recognized a third Kingdom (1735) Linnaeus' Three Kingdoms: Plantae Animalia Lapideum (minerals) Charles Darwin (1809-1882) British naturalist, wrote On the Origin of Species (1859) All true classification is genealogical Grand analogy: Evolution is a branching tree Only after his theory was published did biological evolution become an acceptable alternative to earlier explanations Organisms change over time Three Kingdoms of Organisms: John Hogg (1800–1869) Sir Richard Owen (1804–1892) British comparative anatomist Ernst Haeckel (1834-1919) German naturalist, embryologist, artist (Art forms in Nature) Haeckel made the most extensive classification Haeckel Three Kingdoms: Plantae Animalia Protista Two Empires (Domains) of Organisms: Édouard Chatton (1883-1947) Defined the terms ProKaryota and Eukaryota (1925) The terms had little impact on classification for decades Chatton's Two Domains: Prokaryotes (single-celled organisms) Eukaryotes (multi-celled organisms) Three Kingdoms become Four Kingdoms Herbert F. Copeland (1902-1968) -wrote The Classification of LOWER ORGANISMS (1956) -Proposed a four-kingdom classification (1938) -Moved the two prokaryotic groups---bacteria and "blue-green algae"--- into a separate Kingdom---Monera Copeland's Four Kingdoms: Monera (prokaryotes) Protista (primitive eukaryotes) Metaphyta (plants) Metazoa (animals) Two Domains Became Five Kingdoms (still 2 Domains- - -Prokaryotes and Eukaryotes) Robert Harding Whittaker (1920–1980) American plant ecologist Elevated the fungi to their own Kingdom (1969) Whittaker’s Five Kingdoms: Monera (prokaryotes) Protista (primitive eukaryotes) Metaphyta (plants) Metazoa (animals) Mycota (fungi) Five Kingdoms Became Three Domains Carl Woese (1928 - ) American microbiologist, wrote The Genetic Code (1967) -Catalogued presence/frequencies of various sequences in the 165 rRNA components of ribosomes in representataives of the 3 Kingdoms. -Determined archaebacteria should be placed in separate domaindefined Archaea -3 Domains with 5-6 nested Kingdoms Woese's Three Domains: Eubacteria (Bacteria) - prokaryote (lacking a nucleus or other membrane-bound organelles) unicellular organisms with cell walls which include peptidoglycan and may be distinguished by the Gram stain (positive, negative, or variable); most are heterotrophic and some are photosynthetic, a minority are chemotrophic. Most are either coccal (spherical), rods, or spiral forms Archaea (Archaebacteria) - prokaryote (lacking a nucleus or other membrane-bound organelles) unicellular organisms with cell walls which lack peptidoglycan and are not easily distinguished by the Gram stain; they may be heterotrophic, photosynthetic, or chemotrophic. Some live in extreme environments. They are the sister group to Eukarya because they use histone proteins in their DNA supercoiling. Eukarya (Eukaryota) Five Kingdoms become Six Thomas Cavalier-Smith (1942- ) published extensively on the classification of protists, wrote Predation and Eukaryote Cell Origins: A Coevolutionary Perspective (2008). -Has been tinkering with the classification for more than a decade and his taxa remain controversial--he rejects the three-domain system entirely. -Divided the domain Eukaryota into nine kingdoms. (1981) -Reduced the total number of eukaryote kingdoms to six. (1993) -Classified the domains Eubacteria and Archaebacteria as kingdoms, adding up to a total of eight kingdoms of life (Plantae, Animalia, Protozoa, Fungi, Eubacteria, Archaebacteria, Chromista, and Archezoa) -His classification treats the archaebacteria as part of a subkingdom of the Kingdom Bacteria (2004) Cavalier-Smith's Six Kingdoms (2004): Bacteria Protozoa Chromista Plantae Fungi Animalia Chapter 9 People Study Guide Patrick Arevalo & Isabel Torres Lynn Margulis (1938- ) a. American Biologist who was born on March 5, 1938 b. University Professor in the Department of Geosciences at the University of Massachusetts Amherst c. She helped proposed endosymbiosis i. Used to explain the origin of mitochondria and chloroplasts Thomas Cavalier-Smith d. Born on October 21, 1942 e. Professor of Evolutionary Biology at the University of Oxford f. He proposed the taxa of Rhizaria in 2002. Shama Barnabas 1982 Along with fellow co-workers produced a tree of life that took into account the nucleotide sequences from 5s rRNA and amino sequences. This phylogeny provided strong support for the Symbiotic theory of organelle function Chapter 9 Review Kelly Anderson & Isabel Torres Concepts and Vocabulary Evolution of Eukaryotes As early as 1.5 Bya eukaryotic cells appear as fossils Early eukaryotes were single-celled organisms or simple filaments Today, most eukaryotic cells are multicellular and all contain a nuclear membrane and organelles Kingdom Protista: all unicellular eukaryotes. Probably not monophyletic Endosymbiotic events provided mitochondria, chloroplasts Microtubules drive the nuclear chromosomal division (mitosis) Five Eukaryotic Supergroups Plantae (Archaeplastida): Charophyta (stem group), red algae, green algae, and land plants Excavata: o Various Protistans o many with parasitic lifestyles Giardia, Trichomonas, Trypanosoma Chromalveolata: o first proposed by Thomas Cavalier-Smith o algae, heterotrophic ciliates, water molds, dinoflagellates, diatoms o protistan parasites Plasmodium falciparum Rhizaria: advocated for by Cavalier-Smith. o Heterotrophic protistans Foraminiferans, radiolarians Unikonta: o Parasitic Protistans, choanoflagellates, fungi, animals, and Amebozoans (slime molds), amoeba The two popular theories to explain the origin of the membrane bound organelles Endosymbiosis - a well supported hypothesis which explains the origin of chloroplasts and mitochondria and their double membranes; This concept postulates that chloroplasts and mitochondria are the result of many years of evolution initiated by the endocytosis of bacteria and blue-green algae. According to this concept, blue green algae and bacteria were phagocytized but not digested; they became symbiotic instead and subsequently co-evolved with considerable horizontal gene transfer between the nuclear and organelle genomes. Other data supports an endosymbiotic origin for the eukaryotic nucleus. Invagination – the plasma membrane was engulfed or invaginated to form the endomembrane system. Along with the theories above, were two models explaining the origin of the Eukaryotes, the Nucleus First-Mitochondria Later Model and the Mitochondria-Nucleus Co-origin model. Origin of Eukaryotes Endosymbiosis: When ancient anaerobic eukaryotic cells engulfed prokaryotic organisms and established a symbiotic relationship with the prokaryote. The prokaryotes were retained as cellular organelles – mitochondria and chloroplast – providing eukaryotes with additional sources of DNA. Free-living bacteria developed mutually beneficial relationships within a host prokaryotic cell Aerobic bacteria developed into mitochondria Cyanobacteria developed into chloroplasts Organelle DNA differs from Nuclear DNA Location: organelle vs. nucleus Organization: singular circular vs. multiple linear strands Function: Which proteins coded for and how regulated Mode: of replication and inheritance Mitochondrial DNA Single double-stranded DNA molecule Many mitochondria in each cell Similar to prokaryotic DNA because no histones or proteins, and no introns Chloroplast DNA single double-stranded circular DNA inherited uniparentally from the maternal (seed) parent 1/4th of DNA of cell Origin of Various Photosynthetic Eukaryotes The origin of early eukaryotic ancestors leading to the lineages of animals and fungi was probably and independent event from that of the origin of plants Transfer of Genes Between Organelles and Nucleus Many transferred back and forth o Ex: genes for amino acid synthesis Improve efficiency and reduce mutations Genes transferred to and from the eukaryotic nucleus are a form of Horizontal Gene Transfer o Complicated the establishment of phylogenies The Molecular Clock: uses mutation rates to estimate evolutionary time Mutations at a given locus add up at a constant rate in related species o This mutation rate is the ticking of the molecular clock o As more time passes there will be more mutations at a relatively constant rate o Each DNA sequence or polypeptide product will exhibit its own "clock" speed because mutation rates vary Mutation rates are estimated by linking molecular data and real time from the fossil record o Higher rates are better for closely related species o Lower rates are better for distantly related species Organelle DNA as a Molecular Clock The Molecular Clock is a powerful tool for estimating the dates of lineage-splitting events Mitochondrial DNA and Ribosomal RNA Different nucleic acid molecules or gene loci have different mutation rates Ribosomal RNA used to study distantly related species o Lower mutation rates that most DNA Mitochondrial DNA is used to study closely related species o 10 x faster mutation rates than nuclear DNA o Passed down from other to offspring, so it is not subject to recombination, making it easier to trace. Using DNA as a Molecular Clock Easy to use DNA from living species to draw conclusions about phylogeny and times of divergence Harder to use DNA from fossils and museums because probable contaminated by other DNA and only have small amounts of DNA Eukaryote Characteristics DNA organized as linear chromosomes Many cytoplasmic membrane-bound organelles Eukaryotic cytoskeleton and ribosomes Presence of external cell wall variable Sexual reproduction predominates, various means of gene recombination Unicellular or multicellular Eukaryotic Cell Plant Same basic components as the animal PLUS: o cellulose cell wall o central vacuole (sequesters various chemicals) o chloroplasts that carry out photosynthesis Eukaryotes package DNA differently Transcription and Translation in Prokaryotes and eukaryotes prokaryote genes lack: o introns, no pre-mRNA processing o No nucleus, no separation between DNA and cytoplasm o Methods of gene regulation differ Gene Expression DNA contains a sequence of nitrogenous bases which codes for the sequence of amino acids in a protein Triplet code: each code is composed of 3 nitrogenous bases (A, C, G, or U in mRNA) from genetic code During transcription o 1 strand of DNA serves as a template for formation of mRNA Messenger RNA is processed with intron removal, before leaving the nucleus (note*the bases of mRNA are complementary to the base sequence of DNA) mRNA carries the codon sequence to the ribosomes (ribosomal RNA and protein) in the cytoplasm Translation: mRNA codons determine the order of tRNA peptide bond formation produces primary structure of protein at the ribosome Oxidative Nutrient Metabolism Breakdown products of carbohydrates, fats, and proteins enter various metabolic pathways where energy is harvested Oxygen is used up, Carbon dioxide is given off Nutrient Catabolism Pathways are all Interconnected Photosynthesis Sunlight + 6H2O + 6CO2 C6H12O6 (nutrient sugars)+ 6O2 o autotrophic prokaryote, protistan and plant cells contain various membrane-bound photosynthetic pigments (phycobilins, caretenoids, and chlorophylls) which can trap light and convert light energy to chemical energy (ATPs and NADP+s). light energy drives one of three independent forms of atmospheric CO2 capture (C3 carbon fixation, C4 carbon fixation, and Crassulacean Acid Metabolism); photosynthetic eukaryotes contain chloroplasts as the organelles of photosynthesis. The derived chemical energy also powers the light independent Calvin cycle which generates the glucose which may be used in cellular respiration and starch synthesis. Landmarks in Time Around 2.0 Bya: eukaryotes develop from prokaryotes by complex means including endosymbiosis and develop sexual reproduction and colonial life forms Around 1.8 Bya: O2 levels rise sufficiently that the atmosphere becomes oxidizing Around 1.3-0.6 Bya: multicellular (metazoan) life evolves (several times?) Chapter Ten Plants Ashley Schmidt & Trent Gaasch Important Facts: Land plants evolved from organisms similar to some living green algae some ~460 Mya Leaves and multicellularity evolved many times Fungi are not simple plants but a sister group of animals Many of the adaptations of land plants reflect the transition from water to land. Horizontal gene transfer, endosymbiosis, differentiation of somatic and germinal tissues, and mechanisms of fertilization were important in plant evolution. Kingdom Viridiplantae: o Includes land plants and green algae ( red and brown algae excluded) o All green plants appear to be derived from a single species of freshwater algae. o All green algae can be split into two major clades: 1.) Chlorophytes: exclusively aquatic 2.) Charophytes: aquatic forms which gave rise to the land plants General Information about plants Multicellularity probably began when dividing cells stopped separating after mitosis and cytokinesis o Advantages include increased size and opportunity for cell differentiation and specialization Multicellular organisms then evolved into forms in which most cells were somatic while a few were reproductive, forming gametes by meiosis Using 18S rRNA, rbcL (ribulose-bisphosphate carboxylase gene), and nuclear and mitochondrial genomes sequences, investigators demonstrated that numerous lineages of aquatic algae invaded the land Transformation of one of these lineages gave rise to two major lineages: o chlorophyte green algae o charophyte algae and the land plants Alternation of generations - The occurrence in one species' life history of two or more different forms differently produced, usually an alternation of a sexual form using meiosis to generate recombinant gametes with an asexual form using mitosis to generate identical clonal offspring in the life cycle of a multicellular plant or animal. In land plants, the asexual form/tissue is composed of haploid cells and the sexual form/tissue is composed of diploid cells. In the earliest evolved land plants (bryophytes), the haploid sporophyte tissue was dominant, i.e., it was the tissue of the individual that persisted throughout life while the diploid reproductive tissue formed a temporary additional structure during periods of sexual reproduction which were often times of environmental stress. In the later derived land plants, primarily the ferns, gymnosperms, and angiosperms, the diploid sporophyte tissue is dominant, and the gametophyte tissue is reduced to small numbers of temporary cells that exist only during the time for fertilization, e.g., ovules and polar bodies in females, and pollen grains and pollen tubes in males. The four major plant groups are 1.) Seedless non-vascular plants- these are plants with no seeds or veins. These are the simplest plants; they have limited distribution and are restricted to wet areas, and collectively known as bryophytes (liverworts, club mosses, and hornworts). They the first fossil evidence is of them appeared to date back to 420Mya in the Devonian period, and then later in the Carboniferous 350Mya ago. They major importance of bryophytes is that they represent the beginning transition from water and the dominance of a diploid sporophyte life cycle. a. Bryophytes: i. The “simplest” land plants, limited to moist environments, are bryophytes ii. Liverworts at 420 Mya; iii. Mosses at 350 Mya iv. Bryophytes were important in two major transitions: 1. water to land; 2. haploid gametophyte-dominated life cycle to a diploid sporophyte-dominated life cycle. Vascular seedless plants- the evolution of the cambium permitted plants to increase in size. The cambium is the tissue from which new cells are produced to increase the diameter of plant stems. This allows plants to grow taller allowing them to receive more light and nutrients through xylem and phloem tubes. These plants reproduce by using spores which need to be spread by the environment. One of the most common plants in this group is ferns. Ferns are also the first vascular plants with true leaves. 1.) Gymnosperms- are plants which contain cones or alternatives to seeds contained in true fruits. These are plants such as ginkgo, cycads, and cypress trees. a. Gymnosperms are plants with “naked seeds” i. Ovule is exposed on a scale at pollination b. There are four living groups i. Coniferophytes ii. Cycadophytes iii. Gnetophytes iv. Ginkgophytes c. All lack the flowers and fruits of angiosperms d. Probably descended from progymnosperms i. Seeds had evolved by end of Devonian period ii. Adaptive radiation in Carboniferous and early Permian produced the gymnosperm divisions iii. Largely replaced seedless vascular plants iv. Better adapted to drier (Pangean) climate 2.) Angiosperms- these are flowering plants and also closely tied to dicots, which have two seed leaves. These plants have elaborate flowers which are used as reproductive organs which can be specific to certain animal pollinators or open to any pollination method. a. Their origin is a mystery b. Evolution and elaboration of flowers as reproductive organs c. Evolution of diverse flower structures that enable insects, birds, and less often other animals to pollinate them d. Evolution of diverse seed forms and mechanisms of dispersal e. Life Cycle i. The double fertilization in Angiosperms to produce the nutritive triploid (3N) endosperm is the pinnacle of advanced parental care in plants ii. It is comparable to the cleidoic egg of reptiles, birds, and montremes, and then the intrapouch and intrauterine development of embryos seen in the marsupial mammals iii. 1. Mitotic division produces embryo a. Rudimentary root b. One (monocots) or two (dicots) seed leaves iv. 1. Mitotic division produces energy-rich endosperm 2. Ovule matures into a seed v. Why double fertilization? 1. Synchronizes development of food storage with seed development 2. Without fertilization, neither will occur a. Resources are not wasted on infertile ovules Origin of leaves- the origin of leaves has two good hypotheses: 1.) The telome hypothesis which says leaves arose from webs between flattened branches. 2.) The enation hypothesis which says leaves arose from small flaps or extensions of tissue along the stem. *We know that leaves evolved multiple times therefore, either of the two modes for the origination of leaves can explain how the may have developed between different lineages. Transitions for plants: Origin of the land plants (embryophytes) o Land Plant Phylogeny o Origin of the vascular plants (tracheophytes) o Early Vascular Plants “Vascular” refers to the presence of conductive tissue: xylem that enables water to reach the erect parts of the plant; phloem that enables nutrients to be distributed from the leaves and stems. Cooksonia, the first vascular land plant, appeared about 420 Mya -Only a few centimeters tall -No roots or leaves -Homosporous Origin of the seed plants (spermatophytes) Origin of the flowering plants (angiosperms) Plant Life Cycles As more complex land plants evolved: 1.) The spores became unequal in size 2.) The diploid stage became the dominant portion of the life cycle 3.) The gametophyte became more limited in size 4.) The sporophyte became nutritionally independent These changes, along with improvements in morphology allowed radiations into drier habitats Moving onto Land Three evolutionary changes: o reduction in the size of the gametophyte o evolution of easily dispersible pollen o and encasement of spores in seeds Allowed plants to avoid desiccation and so move away from water Flower population mechanisms: In order for a flower to be pollinated, pollen must be moved from the anthers to the stigma of the same or different flowers Whatever moves or carries the pollen is called a vector. There are five different classes of vectors: o wind / water / insects / mammals / birds Flowers and the animals which pollinate them have often evolved very close relationships in which both are totally reliant on each other The plant for reproduction, the vector for some aspect of it biology, often nutrition Chapter 10 Plants: Part two Dani Joslin and Ashley Schmidt Angiosperms- evolution and elaboration of flowers as reproductive organs, evolution of diverse flower structures to allow insects, birds and other organisms to pollinate them, also evolution of diverse seed forms Sperm plus egg equals diploid zygote 1. Mitotic division produces embryo Sperm plus nuclei equals 3n nucleus 1. Mitotic division produces energy rich endosperm 2. Ovule matures into a seed Double Fertilization 1. Why? Synchronizes development of food storage with seed development 2. Without fertilization neither will occur Angiosperm radiation1. Radiation of angiosperms marks the transition from the Mesozoic era to the Cenozoic era 2. Adaptive radiation made angiosperms the dominant plants on earth by the end of the cretaceous Convergent Evolution Produces Ecological Equivalents 1. Cacti from all different places Coevolution1. Plant-pollinator coevolution is responsible for the diversity of flowers 2. The pollinator gains nectar, and pollen and the plant gains cross pollination Coevolution- Plants have influenced the evolution of animals and vice versa Darwin and coevolution1. Darwin hypothesized that a hawk moth with a long proboscis would exist to pollinate the Madagascar star orchid, a century later such a hawk moth was found Fungi1. First appeared along with the first vascular plants in the Silurian Fungi- are not simple plants, share an ancestor with animals, are more closely related to animals than plants Characteristics1. Eukaryotic, non-photosynthetic, some are parasitic, uni or multicellular, avascular 2. Have an alternation of generations life cycle, reproduction by spores or asexually, non-motile usually, decomposers and recyclers of nutrients in environment 3. Absorptive heterotrophs, release digestive enzymes to break down organic materials or their hosts, store food energy as glycogen, build complex carbohydrate cell walls 4. Some are internal or external parasites, a few of them act like predators and capture prey like roundworms 5. Some are edible and some are poisonous 6. Produce both sexual and asexual spores, classified by the sexual reproductive structures, some have no sexual phase 7. Penicillin is made by the penicillium mold Reproductive structures1. Basidia, sporangia, and asci 2. Spores consist of- haploid cell, dehydrated cytoplasm, protective coat 3. Spores germinate when they land on a moist surface Classification by nutrition1. Saprobes are decomposers and mold or mushrooms 2. Parasites- harm host, rusts and smuts 3. Mutualisms- both benefit, lichens and mycorrhizas Major groups of fungi 1. Basidimycota- club fungi 2. Zygomycota- bread molds 3. Chytridiomycota- chytrids 4. AM fungi- arbuscular mycorrhyizas 5. Ascomycota- sac fungi 6. Lichens- symbiosis Lichens- mutualism between fungus, algae and they form a thallus or body Chapter 11: People Meghan Garrett & Megan Snyder Richard Owen (1804-1892): An English biologist, comparative anatomist, paleontologist who coined the term Dinosauria. Owen wrote Archetype and Homologies of the Vertebrate Skeleton (1848) and On the Nature of Limbs (1849). He regarded the vertebrate frame as consisting of a series of fundamentally identical segments, each modified according to its position and functions. This was an early attempt to argue for constraints on organismal design from purely physical, mechanical, chemical principles. Owen remained anti-Darwinian until his death. Sir William D’Arcy Thompson (1860-1948): A scientist who advocated structuralism as an alternative to survival of the fittest in governing the form of species and also argued for constraints on organismal design. D'Arcy Thompson 's most famous work was On Growth and Form (1917). The central theme of On Growth and Form is that biologists of the early 20th century overemphasized evolution as the fundamental determinant of the form and structure of living organisms, and underemphasized the roles of physical laws and mechanics. On the concept of allometry, Thompson wrote: "An organism is so complex a thing, and growth so complex a phenomenon, that for growth to be so uniform and constant in all the parts as to keep the whole shape unchanged would indeed be an unlikely and an unusual circumstance. Rates vary, proportions change, and the whole configuration alters accordingly." William Bateson (1861-1926): A British geneticist and a Fellow of St. John's College, Cambridge. He was the first person to use the term genetics to describe the study of heredity and biological inheritance, and the chief populariser of the ideas of Gregor Mendel following their rediscovery in 1900 by Hugo de Vries and Carl Correns. He was the first to recognize homeotic mutations and coined the term in his book Materials for the Study of Variation (1894). David Raup (1966): An American paleontologist and paleobiologist who developed such an approach to plot the morphologies of organisms in the three dimensions in what he termed morphospace, which he represented as a cube with different features of organisms along each axis. Raup’s analysis showed that the known morphologies of shelled invertebrates cluster in one region of morphospace, a cluster that demarks the limits of the body plan in these organisms and that not all forms were found in nature. Raup concluded that unoccupied morphospace represented impossible morphologies, nonadaptive morphologies and/or constraints on morphology François Jacob: Wrote a paper, in 1977 that is credited with enticing many researchers into molecular biology, that proposed gene regulation as critically important in development, in evolution, and as a target for natural selection. Joseph L. Kirschvink: Originator of the snowball earth concept in 1989, a self-reversing climate instability driven by ice-albedo feedback. Adolf (Dolf) Seilacher: A German paleontologist who placed Ediacaran organisms into a distinctive group, the Vendozoa, which he and others regard as unrelated to any animals; a separate evolutionary experiment. Guy Narbonne: A Canadian paleontologist who invoked repeated structure based on fractal repeats of a frond structure in his analyses of early Ediacaran organisms to identify a major group which he named rangemorphs. Narbonne is cautious when it comes to saying whether rangemorphs were animals or an alternative (and earlier evolutionary experiment in multicellularity. Ch 11 Key Concepts and Vocabulary Kayleen Parker Key Concepts: The entire earth was encased in a sheet of ice 1 km thick two to four times between 725 and 635 Mya. (Snowball Earth) Communities of enigmatic organisms -- the Ediacaran / Vendozoan Biota -- existed in the Upper Precambrian more than 565 Bya, before animals appear in the fossil record. o Formed complex ecosystems. o Disappeared early in the Cambrian. Based on molecular evidence we can conclude that animals originated in the Precambrian 700-750 Mya. Animals of all major phyla first appear as fossils 545 Mya in the Early Cambrian Burgess Shale and equivalent faunas worldwide. Stem taxa of animal phyla therefore must be Precambrian in age. Reasons for the origination of animals include the elaboration of genes and embryonic development, environmental and climate changes in the level of atmospheric oxygen. Bauplan concept: placed more emphasis on the physical and chemical restraints on organisms and how that forced them to evolve a certain way Types of temporal bone openings: o Anapsid- ancestral form with holes only for the eyes and nostrils( turtles) o Synapsid- form that has one other hole besides the ones for the eyes and nostrils (mammals) o Diapsid- form that has 2 other holes besides the ones for the eyes and nostrils (crocodilians, birds and dinosaurs) Homeobox genes that pattern animal bodies originated before animals, plants, and fungi arose. They encode for transcription factors. About 5545 Mya in the Early Cambrian, an explosive radiation of multicellular organisms with soft and hard tissue appears in the fossil record. Multicellularity facilitated cellular specialization within organisms and structural differences between organisms, the evolution of different modes of food gathering, and enormous increase in body size. Some explanations to how animals radiated and diversified so quickly: o A rise in atmospheric oxygen o Changing geological features o Recovery from snowball earth o Origination or elaboration of embryonic development o Diversification of mechanisms of gene regulation o The evolution of predator-prey interactions associated with the opening up of new ecological zones Animal origins: o choanoflagellates are ~150 living species (no fossils) of singlecelled and colonial protistans (the collared flagellate cell morphology is similar to the choanocytes (collared cells) of sponges and ribbon worms); they are motile predators who were either animal ancestors or choanoflagellates and animals descended from a common protistan ancestor; their synapomorphies include certain cell adhesion molecules. o The absence of features usually associated with prey capture, and the absence of digestive tracts, led to proposals that many Ediacaran / Vendozoan organisms may have depended on photosynthetic or other types of symbiosis with microorganisms. o The organisms in the Ediacaran / Vendozoan Biota did not have larval forms, eyes, mouths, anuses, intestinal tracts, or locomotory appendages. Characteristics of animals: o Eukaryotic, never photosynthetic o Multicellular, usually with differentiation into tissues; avascular and vascular forms o Life cycle lacks alternation of generations o No cell walls o Sexual and asexual reproduction by often complex structures and life cycles o Enhanced responsiveness and motility due to nervous, endocrine, and musculoskeletal systems Animals arise: o By the beginning of the Cambrian 545 Mya, many different types of animals were present, recognizable, and can be classified on the basis of their different body forms. o Burgess Shale Fauna: A 545 My old limestone reef assemblage of superbly preserved fossils located in British Columbia, Canada at 160 m deeps and more than 20 km long and which records the Cambrian Explosion of animal body forms. Includes arthropods, sponges, brachiopods, polychaete worms, echinoderms, cnidarians, and mollusks. o 3 important conclusions to assign organisms from Burgess Shale to clades: These organisms are crown taxa that already had evolved the characters that define the phyla of living animals. Morphological gaps separated these crown taxa. Origination of phyla from stem taxa has to be sought in earlier form in older deposits. The only evidence we have to recognize and classify Early Cambrian organisms is morphological. o One class of morphological evidence comes from the preservation of cleavage-stage animal embryos in Late Precambrian and Early Cambrian rocks. While not numerous, these specimens have given us a glimpse of jellyfish development 530 Mya, and of the presence of segments in early embryos. The absence of any fossilized larval stage strongly suggests that early animals developed directly without a larval stage (direct development). A Cambrian “Explosion” o The diversity of Cambrian organisms could be interpreted as adaptive radiation in which many new ecological opportunities were made available for organisms with the capacity to evolve in diverse ways so as to occupy and exploit the changing environments. o Divergence among major Cambrian lineages began in the Precambrian about 700 Mya. o Modifications during the Cambrian added hard parts and mineralized skeletons that provided leverage for evolving muscles, support for body organs, enclosures for gills and filtering systems, and protective shells and spines. Causes of the Cambrian Radiation: o Geological, environmental and climatic conditions o Changing oxygen levels o Predator-prey relationships o Evolution of embryonic development and body plan specification o New sources of genetic variation and changes in gene number and regulation Geological conditions: o Animal fossils may be absent from Precambrian rocks because geological conditions prevented fossilization or destroyed and fossils present; the heat and pressure involved in Precambrian mountain building has been proposed as an important factor limiting fossilization. However, prokaryotic and eukaryotic organisms were preserved in the Precambrian so it is unlikely that the Cambrian discontinuity is unreal and merely the consequence of geological metamorphism or imperfect fossilization. o Plate tectonics and sea level changes would also have played a role in new environments. Rising Oxygen Levels o Oxygen forms a protective blanket of ozone that could have facilitated the expansion and radiation of multicellular animals in shallow waters, tide pools, and nearby rocky surfaces. o Aerobic metabolism, which is dependent on oxygen, facilitated the use of new sources of energy, permitting increase in body size. o Animals capable of exploiting Early Cambrian oxygen would have possessed a battery of common genes including those for hemoglobin, which is a conveyer of molecular oxygen. Predator-prey relationships o There was a change in the modes of feeding facilitated by rising oxygen levels. o Predators feed on the most abundant prey species, reduce the numbers of prey, and so allow other species to use resources formerly monopolized by the dominant prey. o Crucial Vertebrate Transitions: o origin of jaws o o o o o o origin of fins and later limbs for locomotion origin of the lungs origin of the cleidoic egg origin of the advanced water conserving vertebrate kidney two separate origins of endothermy and associated insulation origin of pouch or placenta for embryo support and protection Shared Embryonic Development and Body Plan Specification o Most distinctive morphological features of almost all adult animals: Axes of symmetry, usually anterior-posterior (A-P), dorso-ventral (D-V), and left and right (L-R). Paired appendages Similar tissues and organs Homeobox genes o Contain the homeobox o Each homeobox gene codes for a polypeptide sequence about 60 amino acids long called a homeodomain. Major conclusions from studies of comparative gene structure and function: o These important developmental (regulatory) genes all share a common, highly conserved, and evolutionary ancient role as transcription factors. o A common genetic evolutionary origin underlies the conservation of the basic developmental pathways that establish animal body plans. o What has changed with evolution is context; the specific function of these conserved regulators varies from cell lineage to cell lineage, tissue to tissue, organ to organ, as well as from time to time during development. Mammalian Shared Derived Characters o Endothermy with insulating hair and subcutaneous fat o Mammary glands; extended parental care o Uterus and colon (no cloaca) o Dentary-squamosal jaw joint o 3 ear ossicles o Expanded cerebral cortex o Heterodonty and buccal cavity (cheeks) Vocabulary: 1) Ediacaran Fauna / Ediacaran Biota- multicellular organisms that remain enigmatic. 2) Archaeopteryx- the 'missing link' that shows a transitional stage between birds and dinosaurs 3) Heterodonty- applies to animals that possess more than one type of tooth morphology 4) Ichthyosaur- giant marine reptile that lived during the Mesozoic era. Developed from land reptile that made the transition back into the water. 5) Biota- a more appropriate term for the organisms found in a region or a geographical period. 6) Fauna- refers to the animal life found in a region or a particular time. 7) Stem taxa-the earliest representation of a lineage. There can only be one stem taxon for a lineage. 8) Crown taxa- the terminal branches of a lineage arising from a stem taxon. A single lineage may have more than one crown taxon. 9) Vendozoa- a distinctive group of Ediacaran organisms that are regarded as unrelated to any animals. 10) Modularity-concept that units of life, such as gene networks, aggregations of cells and organ primordial, develop and evolve as units (modules) that interact with other modules. 11) Fractal-a shape that can be split into parts each of which has the same shape as the original (a fern leaf). 12) Rangemorphs-existed in complex ecological communities with more than one trophic level with frond-like organization 570-575 Mya. 13) Monoblastic animals - show the simplest metazoan organization, having a single germ layer such as sponges. Although they have differentiated cells, they lack true tissue organization. 14) Diploblastic animals - members of the phyla cnidaria and ctenophora show an increase in complexity, having two germ layers, the endoderm and the ectoderm organized into recognizable tissues. The embryonic ectoderm develops into the epidermis, nervous system, and, if present, nephridia; the embryonic endoderm develops into the gut and associated glands. 15) Triploblastic animals - possess a mesoderm as well as the endoderm and ectoderm. They are the remaining animal/metazoan phyla from flatworms to birds and mammals, most of which show bilateral symmetry. They develop recognizable organs. The embryonic ectoderm develops into the epidermis and its derivatives, nervous system; the embryonic endoderm develops into the gastrointestinal, respiratory and urinary tract and their associated glands, the secretory cells of the endocrine glands, and the auditory system; the embryonic mesoderm develops into body cavity linings, if present, mesenteries, parts of the reproductive system, musculo-skeletal systems, blood vessels and blood cells, the kidneys, the adrenal cortex, and the dermis and other connective tissues. 16) The plankton explosion-a marked increase in size, diversity, ornamentation and turnover rate among eukaryotic plankton (acanthomorphic acritarchs), which is tentatively attributed to predation by eumetazoa. 17) Morphospace-3-D representation of the morphological characters of an organisms or group of organisms used to show how much of the possible range of morphologies is expressed. 18) Protostomes - the majority of triploblastic coelomate invertebrate metazoans other than echinoderms, most of whom show bilateral symmetry, a clade of organisms whose embryonic blastopore becomes the mouth of the adult. 19) Deuterostomes - the majority of triploblastic coelomate metazoans, the echinoderms, chaetognaths, hemichordates, and chordates, most of whom show bilateral symmetry, a clade of organisms whose embryonic blastopore becomes the anus of the adult. 20) Acoelomates-no true body cavity (flatworms) 21) Pseudocoelomates - triploblastic metazoan animals which possess a "false" body cavity, in which a fluid-filled cavity is only partially bounded by mesodermal tissue; lacking any mesenteries to support internal organs; and no muscular layers around the gut tube to provide peristalsis; examples include round worms and some other protostome invertebrates. 22) Coelomates - triploblastic metazoan animals which possess a true body cavity lined with a mesodermal lining; having internal organs suspended in mesenteries; and muscular layers around the gut tube to provide peristalsis during digestion; examples include most bilaterally symmetrical animals, most invertebrates and the chordates 23) Cephalization-an evolutionary trend in which nervous tissue becomes concentrated toward one end of an organism, eventually producing a head region with sensory organs. 24) Co-evolving arms race-successive rounds of selection for predator responses to their prey’s protective devices, followed in turn by adaptations by the prey to their predator’s devices, promoting diversity. 25) Homeobox genes - any of the evolutionarily conserved genes which are translated into embryonic regulatory (homeo)proteins that act as DNA binding transcription factors that provide the primary signals and initiate the pathways in animals that help differentiate bands and clusters of cells that organize the pattern (anterior/posterior, dorsal/ventral, right/left) of body regions and the formation of particular structures such as internal organs, and body extensions, sense organs, antennae, wings and legs, etc. They exist and play similar roles in the development of higher plants and fungi. 26) Morphogens- activate pathways leading to the development of an organism’s form or part of an organism. 27) Antennapedia complex-cluster of six Antennapedia-linked genes first discovered in fruit flies whose activation converts anterior into posterior body structures. 28) Homeotic mutations (homeosis)-In modern genetic usage, homeotic mutations cause the development of tissue in an inappropriate position; for example, bithorax mutations in Drosophila produce an extra set of wings. 29) Bricolage-(tinkering) a term that rightly places the emphasis on modification of existing genes. 30) Homeodomain- part of a transcription factor that binds to DNA, there by regulating mRNA production. 31) Hox gene family-homeobox gene in vertebrates, taking the gene name from the first two letters of the orthologous gene in Drosophila and adding an x. Show colinerarity, control organogenesis, are homologous among Metazoans. Example of a hox gene mutation extra ribs. 32) Gene regulation- has emerged as a central mechanism explaining developmental and evolutionary change. 33) Paralogous genes (paralogues)-two or more different loci in the same organism that are sufficiently similar in their nucleotide sequences (or in the amino acid sequences of their protein products) to indicate they originated from one or more duplications of a common ancestral gene. 34) Orthologous genes (orthologues)- gene loci in different species that are sufficiently similar in their nucleotide sequences (or amino acid sequences of their protein products) to suggest they originated from a common ancestral gene. 35) Gene family- two or more gene loci in an organism whose similarities in nucleotide sequences indicate they have been derived by duplication from a common ancestral gene. 36) Ostracoderms- the earliest vertebrates (shell-skinned) are groups of extinct, primitive, jawless fishes that were covered in an armor of plates of true bone tissue. Small, slow swimming, bottom-dwellers. Likely the first animals to use their gills for respiration. 37) Orthogenesis- progressive pattern of improvement of a species without much branching (example: the teeth of horses) 38) cleidoic egg- the type of egg laid by reptiles and birds; it allows them to reproduce out of and away from water by providing a moist environment for the embryo Chapter 12 People By Nickolaus Willis & Zachary Meyer Ernst Mayr - One of the most influential evolutionary biologists of the twentieth century, was a staunch defender of The Modern Synthesis, a synthesis that he played a role in creating. His last book, “What Evolution Is”, published 2001, is a thorough and thoughtful exploration of Evolutionary Biology Francois Jacob and Jacques Monod (1910-1976) - In 1961 on the genes governing the production of enzymes involved in lactose sugar metabolism in the bacterium E. coli. This is the first study leading to the discovery of gene regulation. For this fundamental discovery, they received the 1965 Nobel Prize in Physiology and Medicine. Andre Lwoff (1902-1994) - The director of the Pasteur Institute where Jacob and Monod conducted their experiments, received the 1965 Nobel alongside of Jacob and Monod. Andrew Fire and Craig Mello - Winners of the 2006 Nobel Prize in Physiology and Medicine for their research on RNAi in animals. Barbara McClintock (1902-1992) - In the 1940’s and 1950’s she discovered both Transposons and Gene Regulation. Her work was ignored and misunderstood for decades until in 1983 she won the Nobel Prize in Physiology and Medicine for her discovery of Genetic Transposition. Edward B. Lewis - The American geneticist and founder of developmental genetics studied the bithorax and related mutants in Drosophila and their controlling homeotic genes in DNA in the 1970s through 1990’s. This led to the new subdiscipline ”Evo-Devo” [evolutionary development]. He laid the groundwork for our current understanding of the universal, evolutionarily conserved strategies controlling animal development. Chapter 12 Terms & Concepts Lyddia Wilson & Zachary Meyer Regulatory mutation: changes that generally affect genes controlling genetic pathways or networks Natural selection acts on existing phenotypic variation Mutations are necessary for evolution o Spontaneous mutations o Induced mutations o Somatic mutations o Germline mutations Point mutations occur through substitutions, insertions, deletions, transposition Point mutations can be silent (more likely when it occurs in the third position of the codon triplet), replacement, or stop codon o Sickle Cell is an example of a point mutation; it results from a mutated allele of the hemoglobin beta chain. A mutation will only be passed to offspring if the mutation occurs in the germ cells leading to gamete production Somatic mutation: mutation acquired in any other cell – will not be a heritable mutation Most chance mutations are likely to disrupt and not improve protein function if there is any effect at all Sense mutation: change in DNA base, no change in amino acids Missense mutation: change in DNA base and change in amino acid, but protein still functional Nonsense mutation: change in DNA base and change in amino acid, and the protein is non-functional, a fragment, or not produced at all Pleiotropic effects – multiple effects o A mutation can have a wide variety of effects if the individuals with the mutant allele are exposed to a wide variety of environmental conditions or selection pressures. Transposons or “jumping genes” direct the synthesis of additional copies of themselves in the host genome Transposons may cause frameshift or other mutations. Chromosome number variation o Entire sets of chromosomes o Single chromosomes within a set Polyploidy = repetitive doubling o More than 2 homologous sets of chromosomes o Commonly found in plants o May occur due to abnormal cell division with nondisjunction o Especially common among ferns and flowering plants Plants may become tetraploid due to self-fertilization as well as less commonly in animals by parthenogenesis (reproduction by females without fertilization by males Plants may be able to survive better being polyploidy than animals because they can tolerate extremely divergent structural relationships, unlike animals Changes in the appearance (phenotype) of a chromosome (usually observed in karyotype analysis): o Deletions & deficiencies: remove chromosomal material o Duplications: improperly repaired chromosome breakage moves genes (DNA fragments) from one homologous chromosome (which now has a deletion) to the other homologous chromosome (which now has a duplication). Gene duplications are the source of most new genes (loci) as well as the development of families of related genes, such as the globin chain families. o Inversions: reversals in chromosome gene order o Translocation: improperly repaired chromosome breakage moves genes from one homologous chromosome to another nonhomologous chromosome, the resulting hybrid segregating together at meiosis; balanced translocations (in which there is no net loss or gain of chromosome material) are usually not associated with phenotypic abnormalities, although gene disruptions at the breakpoints of the translocation can, in some cases, cause adverse effects, including some known genetic disorders; unbalanced translocations (in which there is loss or gain of chromosome material) nearly always yield an abnormal phenotype. In the simplest cases of translocation, a single locus would move; in the largest case, an entire chromosome might be added to a nonhomolog. Inversion loops protect linked alleles from being separated by crossing over o Alleles in the inverted region are protected and passed as unit to future generations microRNAs (miRNA) regulate translation of mRNA into protein in plants and animals When a diploid gamete fertilizes a normal haploid gamete a triploid individual is produced. These sets of 3 like chromosomes have difficulty in the close alignment of synapsis Equal crossing over provides new arrangements of alleles but has little potential for new variation Unequal crossing over causes duplications on one chromosome and deletions on the other. The duplications allow for new possibilities for gene function in eukaryotic evolution. Mutations are expressed in gene activity: o Changes within a gene product o Changes in the regulation of a gene or its product o May affect rate at which a gene is produced or whether or not the protein is produced Phenotypic variation: anatomy, biochemistry, physiology, behavior, etc. Genotypic variation: alleles, loci, chromosomes, genomes Mutation events increase genetic variation in populations and give natural selection material from which to generate adaptive evolutionary changes Most mutational processes are harmful and lead to decreased adaptation most of the time o But individuals being so numerous and given many millions and billions of years to work with, beneficial changes do occur 3 Major regulatory mechanisms control transcription of DNA o ciso transo RNAi-regulation Minor mechanisms: o Transposons o Posttranscriptional modification Cis-Regulation elements o Elements reside upstream from promoter region on same chromosome o Transcription factors – bind to cis-regulatory elements to encourage or discourage transcription Trans-regulation o DNA sequences that encode transcription factors o Reside on other DNA molecule than the regulated gene o TF’s can bind to cis-reg. elements or CAAT and TATA boxes adjacent to a structural gene. Posttranscriptional modifications of eukaryotic nuclear (not organelle) mRNA o Introns must be removed from the transcribed pre-mRNA base sequence and there can be options as to which introns are removed and which exons are spliced to form the functional mRNA o Addition of the 5' (7-methylguanylate nucleotide) cap reduces degradation of the capped mRNA by 5' exonucleases; facilitates exit to the cytoplasm through the nuclear pore and assists in orienting the capped end of the mRNA to the ribosome to initiate translation o Addition of poly-A tails of various lengths affects the lifespan of the mRNA in the cytoplasm before it is degraded and therefore, how many polypeptide chains can be translated from one mRNA o Other modifiers (proteins and regulatory RNAs) can bind to the mRNA to delay or prevent translation. Small interfering RNA (siRNA), sometimes known as short interfering RNA or silencing RNA, is a class of double-stranded RNA molecules, 20-25 base pairs in length. siRNA plays many roles, but it is most notable in the RNA interference (RNAi) pathway, where it interferes with the expression of specific genes with complementary nucleotide sequences. siRNA functions by causing mRNA to be broken down after transcription,[1] resulting in no translation. siRNA also acts in RNAi-related pathways, e.g., as an antiviral mechanism or in shaping the chromatin structure of a genome. microRNA (miRNA) - small non-coding RNA molecules (containing about 22 nucleotides) found in plants, animals, and some viruses, which functions in RNA silencing and post-transcriptional regulation of gene expression. Encoded by eukaryotic nuclear DNA in plants and animals and by viral DNA in certain DNA viruses, miRNAs function via base-pairing with complementary sequences within messenger mRNA molecules. As a result, these mRNA molecules are silenced by one or more of the following processes: 1) cleavage of the mRNA strand into two pieces, 2) destabilization of the mRNA through shortening of its poly(A) tail, and 3) less efficient translation of the mRNA into proteins by ribosomes. miRNAs resemble the small interfering RNAs (siRNAs) of the RNA interference (RNAi) pathway, except miRNAs derive from regions of RNA transcripts that fold back on themselves to form short hairpins, whereas siRNAs derive from longer regions of double-stranded RNA. The human genome may encode over 1000 miRNAs, which are abundant in many mammalian cell types and appear to target about 60% of the genes of humans and other mammals. miRNAs are well conserved in both plants and animals, and are thought to be a vital and evolutionarily ancient component of genetic regulation though they appear to have evolved independently from the ancestral state in the two kingdoms and to have different modes of action. miRNAs can be carried by vectors from one cell to another and so may participate in HGT. Transposable elements: o Think of them as molecular parasites which may accidentally create adaptive (or harmful) mutations and phenotypic variations o Transposons: produce special transposase enzymes that allow it to insert copies of itself into various target sites in an organism’s nuclear Chapter 13 People Maranda Stokes & Kathryn White Bernard Kettlewell- field studies in Britain in the 1950s tested the hypothesis that bird predators were altering the frequencies of the color morphs based on the moths’ contrast to their backgrounds (tree bark) when they were at rest. Experiments: studies demonstrated that native birds did eat peppered moths. Release and capture studies in two areas indicated that peppered forms survived in greater numbers in unpolluted forests while melanic forms survived in greater numbers in soot polluted forests. In his famous experiment, he placed moths on dark and pale tree trunks and showed that background strongly influenced moth survival against predation. His career’s work was summarized in The Evolution of Melanism: a study of recurring necessity; with special reference to industrial melanism in the Lepidoptera (1973). Pietrewicz and Kamil (1977) tested if choices by moths were selectively advantageous. Experiment: Trained blue jays to respond to slides of moths by pecking a button for a food reward whenever they spotted a moth. Results showed that blue jays spotted moths less often on birch trees and especially when moth was oriented with its head up Judith Hooper was a British journalist who wrote Of Moths and Men. The book attacked Kettlewell . It has been dismissed by scientists for lack of scientific understanding, prejudice and careless journalism. Godfrey H. Hardy (English mathematician 1877-1947), Wilhelm Weinberg (German physician 1863-1937), W.E. Castle (American geneticist) each independently concluded that the original proportions of the genotypes in a population remain constant from generation to generation as long as the five H-W assumptions are met: p2 + 2pq + q2 = 1 (the Hardy-Weinberg Equation) p2 = individuals homozygous for first allele 2pq = individuals heterozygous for the alleles q2 = individuals homozygous for second allele R. A. Fisher (one of the founders of population genetics) noted that the greater the genetic variation upon which selection for fitness may act, the greater the expected improvement in fitness. Sewall Wright (1889-1988) proposed that genetic drift can be quite important in changing allele frequencies among populations when the effective size of the population is small. His proposal is known as the shifting balance theory. Peter R. and B. Rosemary Grant concluded from their long-term study of selective changes in Darwin’s finches on the Galapagos Islands, “The population tracks a moving peak in an adaptive landscape under environmental fluctuations, and there is more than one individual fitness optimum within the range of phenotypes in the population. Sewall Wright, R.A. Fisher J.B.S. Haldane-acknowledged founders of the neo-darwinian theory of evolution based on population genetics. Chapter 13 Terms & Concepts CJ Parchman & Kathryn White Key Concepts Without variation there would be no evolutionary change Mutation provides one source of genetic variation Mutation is not entirely random: some parts of the genome are more susceptible to mutation than are others The large amount of polymorphism at gene loci provides a much greater source of genetic variation than do the relatively few new mutations that arise each generation. At the population level, allele frequency provides a measure of genetic variations Genetic drift within a population and gene flow between populations provide sources of genetic variation Genetic variation provides the row material enabling evolutionary change in response to natural selection Large-scale geographical patterns of species distribution can be determined using the genetic history of populations Mutation - any change in the cell’s DNA base sequences Mutation rate – the probability that a gene will mutate when the cell divides Contributions to enhanced variation at the population level: - Mutation - Random drift in gene frequencies within a population - Gene flow between populations Quantitative trait loci (QTL) - regions of that contain blocks of genes, often influencing characters that show continuous variation, such as height or weight Contributions to the maintenance of genetic diversity (genetic polymorphism) within populations: -randomness of mutation -variation in mutation rates among genes and among species -frequency of alleles in populations -ability of DNA to repair itself Mutations supply an important source of variation upon which selection acts and which selection incorporates into evolutionary change. Optimal mutation rates are advantageous. Hot Spots of Mutation - specific nucleotide sequences that are the sites where the nucleotide change is less readily repaired or compensated for than is a sequence change at another site Mutation rates are not only low, they are not constant. As with other essential traits, mutation rates seem mostly selected for optimum values, balancing on the delicate adaptive line between retaining prevailing adaptive features yet facilitating the origin of new features. A remarkable way in which some organisms accumulate mutations without experiencing immediate effects is to bind their gene products with heat shock proteins. Heat shock proteins (hsp) - molecular chaperones that help other proteins maintain their normal 3D conformation and prevent them from degrading. • Heat shock proteins may be disabled in new stressful environments – dramatic change in temperature – dramatic change in pH – dramatic change in salinity Evolutionary potential and genetic variation are two sides of the same evolutionary coin. Genetic polymorphism - The presence of two or more alleles, each at a frequency of 1% or more, at a gene locus in the gene pool of a deme or of an entire species over a succession of generations. Genetic polymorphism provides a much greater source of genetic variation with the potential for evolutionary change than do the relatively few new mutations that arise in each generation. Genetic polymorphism is called balanced polymorphism when the persistence of the different alleles cannot be accounted for by mutation alone. In such cases, selection and/or migration are often the cause. Researchers may focus on obvious phenotypic changes such as Mendel observed, called discontinuous variation, evidenced in characters that form a few distinct phenotypic classes, e.g., red, pink, or white flower color; or on small changes or continuous variation, evidenced in characters for which the plots of the distribution of the variation form a bell-shaped curve or normal distribution, e.g., height or body mass of most animals or plants. Enzyme polymorphism-Change in catalytic ability due to change in temperature, osmotic environment, pH, DNA sequence polymorphism-Changes in bases, codons, introns, exons, etc. Polygenic inheritance, also known as quantitative or multifactorial inheritance refers to inheritance of a phenotypic characteristic (trait) that is attributable to two or more genes, or the interaction with the environment, or both; do not follow patterns of Mendelian inheritance (separated traits). Instead, their phenotypes typically vary along a continuous gradient depicted by a bell curve Population- group of individuals of the same species that can interbreed with one another Polymorphism – many traits display variation within a population – Due to 2 or more alleles that influence phenotype Polymorphic gene- 2 or more alleles Monomorphic – predominantly single allele Single nucleotide polymorphism (SNPs) – Smallest type of genetic change in a gene – Most common – 90% of variation in human gene sequences Balanced polymorphism- the persistence of two or more different genetic forms through selection Quantitative trait loci (QTL) – all of the genes (alleles) in a particular region of a chromosome that affect a quantitative aspect of the phenotype QTL analysis enables us to isolate suites of genes acting on particular parts of the phenotype at particular stages in ontogeny and to determine their relative affects. In the 1930’s, it became accepted that: 1.) Evolution is a population phenomenon that 2.) can be represented as a change in gene (now allele) frequencies because of the action of various natural forces such as mutation, selection and genetic drift, and that 3.) these changes can lead to differences among populations, species, and higher clades. This population genetics view of evolution became known as the neo-Darwinian theory with its emphasis on the frequency of genes in populations as the basis of evolutionary change. Population genetics deals with genes as alleles and gene frequencies as allele frequencies. Allele frequencies (the frequencies of individual alleles) and the gene pool (all the alleles of all individuals in the population) are two major attributes of a population. Hardy-Weinberg principle –The conservation of gene (allelic) and genotype frequencies in large populations under conditions of random mating and in the absence of evolutionary forces, such as selection, migration, and genetic drift, which act to change gene frequencies. 1) diploid organisms 2) sexual reproduction 3) generations are non-overlapping 4) equally viable genotypes The Hardy-Weinberg principle is the founding theorem of population genetics. Population – a group of sexually interbreeding or potentially interbreeding individuals Nonrandom Mating- mating between specific genotypes shifts genotype frequencies – Assortative Mating: does not change frequency of individual alleles; increases the proportion of homozygous individuals – Disassortative Mating: phenotypically different individuals mate; produce excess of heterozygotes Deme – local population of organisms of one species that interbreed with one another more than they do with other demes and share a distinct gene pool. The considerable genetic variability in human groups shows that populations of modern humans are demes. Genetic load - the extent to which a population departs from an optimal genetic constitution; the loss in average fitness of individuals in a population because the population carries deleterious alleles or genotypes. Genetic death - can be classified as either sterility, inability to find a mate, or by any means that reduces reproductive ability A population may receive alleles from a nearby population in a process known as gene flow or sometimes as migration because individuals, gametes, or even individual genes, move from population to population, taking their alleles with them. At least three factors have an impact on the recipient population: 1. the difference in gene frequencies between the two populations 2. the proportion of migrating genes incorporated into each generation; and 3. the pattern of gene flow, whether occurring once or continually over time. 4. Gene flow-a movement of genes from one population to another Gene flow-a movement of genes from one population to another Genetic drift – a consequence of random fluctuations in gene frequencies that arise in small populations; in large populations, it is countered by selection Effective population size (Ne) – formula for calculating the number of parents who actually contribute offspring to the next generation. (Ne) = (4NfNm/(Nf+Nm) where Nf in the number of female parents and Nm is the number of male parents. Ne is the number of parents who actually contribute offspring to the next generation. We can conclude that genetic drift increases with variation between populations, but on the average, not in any particular direction. R.A. Fisher formulated a fundamental theorem that essentially states that the greater the genetic variation upon which selection for fitness may act, the greater the expected improvement in fitness. Variation itself is subject to selection, and so the propensity to vary (variability) is an important attribute of organisms. Phylogeography – The study of the evolutionary processes regulating the geographic distributions of lineages/groups by reconstructing genealogies of individual genes, groups of genes or populations. The neo-Darwinian theory 1. Evolution is a population phenomenon 2. Evolution when there is a change in gene (now allele) frequencies in a population because of various natural forces such as mutation, selection and genetic drift 3. These changes in allele frequencies lead to differences among populations, species, and higher clades 4. This population genetics view of evolution became known as neoDarwinian theory with its emphasis on the frequency of genes in populations Five agents of Evolutionary Change: 1. Gene Flow 2. Selection 3. Nonrandom mating 4. Genetic drift 5. Mutation Founder Effect - A situation encouraging genetic drift that occurs when a few individuals (founders) derived from a large population begin a new colony. Since these founders carry only a small fraction of the parental population’s genetic variability, different gene frequencies can become established in the new colony. Bottleneck Effect – A situation encouraging genetic drift that occurs when a population is reduced in size and later expands in numbers. Since the survivers carry only a small fraction of the parental population’s genetic variability, different gene frequencies can become established in the surviving population. Shifting Balance Theory- proposed by Sewall Wright in 1931 1. Genetic drift, acting on genetic variation at various loci, allows a number of demes to change their allele frequencies. As fitness changes such demes are modeled as moving across non-adaptive valleys to different parts of an adaptive landscape, a model discussed in Chapter 15. 2. Selection pushes some of these demes up the nearest available adaptive peak by changing allele frequencies even further. 3. Variation at other loci provides further opportunity for genetic drift to move a population to a higher adaptive peak. 4. A deme that has a high fitness coefficient tends to displace other demes of lower fitness by expanding in size or dispersing outward and changing the genetic structure of other demes through migration. 5. Environmental change such as a stream of seismic earthquakes, can act on populations by changing the environment to which populations must adjust or perish. Channeling selection in new directions encourages populations to continually shift their genetic structures. “The population tracks a moving peak in an adaptive landscape under environmental fluctuations and there is more than one individual fitness optimum within the range of phenotypes in the population.” –P.R. and V.R. Grant 6. Selection, time, and genetic accident are needed to achieve the most optimum genotypes, although genetic loads and changes in the environment can oppose achieving the optimal genotype. Red Queen Hypothesis - the hypothesis that adaptive evolution in one species of a community causes a deterioration of the environment of other species. As a consequence, each species must evolve as fast as it can in order to continue to survive. It comes from Lewis Carroll's Through the Looking Glass in which the Red Queen said to Alice, “Now, here, you see, it takes all the running you can do, to keep in the same place.” Chapter 14 People David Hansen & Trent Gaasch Thomas Austin in 1759 introduced 24 wild rabbits Oryctolagus cuniculus for sport hunting in Austrailia that spread out of control. Robert H. MacArthur (1930-1972): One of America’s major 20th century ecologists. A leader in moving ecology from a descriptive to an experimental discipline. He did research on niches and foraging behaviors. The Robert H. MacArthur Award is awarded for meritorious contributions to ecology. Edward O. Wilson (1929-Current ): One of America’s major 20th century evolutionary biologists. A specialist in social insects who became a major theorist and later a major advocate for understanding and protecting biodiversity. Founder of a subdiscipline: Sociobiology: The New Synthesis (1975). Richard Lewontin: • American evolutionary biologist. • Captured the essence of the niche and of the evolutionary relationships of an organism to its (self-made) environment in his 2000 book, “The Triple Helix: Gene, Organism, and Environment.” Chapter 14 Concepts and Vocabulary Emily Towery & Trent Gaasch Co-evolution is the set of mutual evolutionary influences shared between two or more species occupying a common habitat; possible when there is some overlap among the niches of two or more species; when two (or more) species: (1) exert selective pressures on each other, and (2) evolve in response to each other Because each species is evolving in response to the other, one important feature of co-evolution is that the: • Selective environment is constantly changing • Also, selective pressures will be strongest when there is a close ecological relationship • Species do not evolve in a vacuum • Darwin emphasized competition between members of the same species for limited resources • Ecologists emphasize the competition between different species for the same limited resources • Co-evolution includes competition for both abiotic and biotic resources Co-Evolution with Pathogens: Thomas Austin’s rabbits population boom; introduction of myxomavirus; mortality rates in rabbits about 90%; now rabbit population is smaller but virus only has about 40% mortality rate because of surviving resistant rabbits and evolution of less virulent pathogen Definitions of Niche Where an organism is found and what it does there • The role of an organism in an ecosystem • The role of a species within a community • All the functional roles of an organism in a biological community • A unique ecological role of an organism in a community • The environmental habitat of a population or species, the resources it uses and its interactions with other organisms • The status of an organism within its environment and community as it affects the survival of the species • The role or functional position of a species within the community of an ecosystem • The physical and functional role of an organism within an ecosystem Competition arises when two groups depend on the same limited environmental resources so that each group causes a reduction in the other’s numbers, often with important ecological or behavioral consequences. • Three consequences of competition are outlined below: o Resource partitioning The situation in which competing groups of organisms minimize the harmful effects of direct competition by using different aspects of their common environmental resources o Character displacement: Phenotypic differences accompany resource partitioning among coexisting groups o Competition Exclusion The principle that two species cannot continue to coexist in the same environment (niche) if they use it in the same way. Important ecological relationships that give rise to coevolution: 1. Predator and Prey – predators can reduce the possibility of a dominant species reaching its carrying capacity; prey species crash first, then predators starve Defenses against Predators: Camouflage Startle Responses - When a prey species can change its appearance suddenly and therefore frighten or distract a predator; example include wing or body displays that reveal eyespots, or other color changes from behavior that confuse the predator, such as flicker fusion when a striped snake starts moving and the stripes become a blur. Flash Coloration - a patch of bright contrasting color that is revealed, e.g., by unfolding wings, apparent only during motion on an otherwise neutrally tinted animal and that is believed to distract the attention of predators who lose sight of the prey when it comes to rest and the flash color patch is obscured Aposematic Behaviors Aposematic Colors Toxicity Mimicry Ingestion Defenses: Spikes & Horns & Thorns - a tough, sharp, protective defensive external surface projection to reduce the desire of biting organisms to bite into the target organism's tissues; it includes spikes, horns, thorns, spines, etc. (They may serve other adaptive purposes as well.) Ingestion Defenses: Fangs & Tusks - sharp teeth which may be used to discourage predators from biting a target organism. (They may serve other adaptive purposes as well.) Ingestion Defenses : Armor - a tough, protective defensive external covering to reduce the penetration of biting organisms into the target organism's tissues; it includes cell wall material, shells, exoskeletons, dermal thickenings, bones and bony plates, etc. Ingestion Defenses: Toxic Chemicals 2. Parasite and Host 3. Mutualists 4. Competitors(as described above) Resource Partitioning Character Displacement Competitive Exclusion Detritivores – eukaryotes (certain protistans and animals) which use for the mechanical breakdown (chewing) to feed on dead organic material (detritus) Decomposers – prokaryotes (certain bacteria) and eukaryotes (certain protistans and fungi) which use externally secreted enzymes for the chemical breakdown (chemical digestion) to feed on dead organic material (detritus) bone morphogenic protein 4 (Bmp-4) – a homeobox (hox) gene; its expression is a major contributor to jaw size and tooth development in fish as well as beaks in birds; controls dorsi-ventral differentiation of mesodermal tissues in other animals Change in expression of a single gene explains why significant morphological change can occur in just a few generations, as observed in the Darwin’s finches. phenotypic plasticity - facultative ability of a single genotype to produce more than one phenotype: • The variation in phenotype (for a given genotype) which occurs due to the influence of environmental factors. • Can represent the small and sometimes trivial differences which we observe in identical twins (perhaps a taller, more muscular twin works out more or has better diet than other twin). • Represents the sorts of regular changes observed when individuals of the same genotype develop or behave differently when they live in different environments • One phenotype may be a negative consequence of an inadequate environment. • Phenotypic plasticity can evolve like any other potentially adaptive trait Examples of Phenotypic Plasticity • Interactions between individuals of predator and prey species of rotifers (Phylum Rotifera); when the predator is present, the prey species detects predator chemicals and grows defensive spines • Daphnia species respond to predators; individual water fleas have the potential to grow a “helmet” and longer spine when exposed to chemicals from various of their natural predators (midge larvae and fish); the genetic potential was already present in the Daphnia genome, but it requires the action of the predator’s chemical cues to activate the genes for the altered morphology • In spadefoot toads: when crowded, large cannibalistic morphs develop which prey on the normal tadpoles • Moth Nemoria arizonaria: something in the oak plant tissue consumed by the caterpillar drives the change in morphology (spring caterpillar morph resembles blossom of tree, summer morph resembles twig on tree) Life history strategies occur along a continuum characterized as r- and K-selection • Where individual species fall on the r-K continuum is largely determined by the environment in which they live and the environment they live in is influenced by their presence and life styles • McArthur & Wilson developed an elegant system for describing the stability and age distribution of natural populations known as “r/K selection” The variables r and k in r-and k-selection come from the logistic equation for population growth I = rN (K-N / K) calculates the annual growth of a population I = the annual increase for the population, r = the annual growth rate: (birth rate + immigration rate) – (death rate + emigration rate) N = the population size K = the carrying capacity: (max density at which population can exist in given environment) Habitat Succession Stage Population Growth Potential vs. Extinction Potential Competition Among Individuals Life History Traits and Mortality r-Strategist unstable, variable, ephemeral, unpredictable early “weedy” colonists, good dispersal abilities maximized, exponential; less vulnerable to extinction K- Strategist long term stability variable, reduced; resources exceed demand; weak competitors precocial young, early maturity onset, shorter generation time; mortality high, variable and unpredictable continual and intense, resources in short supply; good competitors altricial young, late maturity onset, longer generation time; mortality low, more constant and predictable climax community, reduced dispersal abilities low, at equilibrium; vulnerable to extinction Body Size small Fecundity high and Dispersal Rates Resource high but individual Allocation to offspring are of low quality; Reproduction reduced parental care Life Strategy many offspring, few Trade Off survive to reproduce larger low low but individual offspring are of high quality; increased parental care few offspring, most survive to reproduce Climax community – stable community; likely to persist for long periods of time The Red Queen Hypothesis - the hypothesis that adaptive evolution in one species of a community causes a deterioration of the environment of other species. As a consequence, each species must evolve as fast as it can in order to continue to survive. It comes from Lewis Carroll's Through the Looking Glass in which the Red Queen said to Alice, “Now, here, you see, it takes all the running you can do, to keep in the same place.” The Red Queen Hypothesis is used to describe two similar ideas based on co-evolution relationships or evolutionary arms races; one relating to extinction probability, the other to the value of sexual reproduction. • The original idea, proposed by Leigh Van Valen in 1973, is that coevolution could lead to situations for which the probability of extinction is relatively constant over millions of years rather than being proportional to the population's lifetime. In tightly coevolved interactions, e.g., predator and prey, or host and parasite, the sudden evolutionary change by one species could lead to the extinction of other species and that the probability of such changes might be reasonably independent of species age. This is the long term paleontological macroevolutionary perspective. • The other idea, advocated by W.D. Hamilton, among others, relates to the benefit of sexual reproduction. This idea is that coevolution, particularly in evolutionary arms races between hosts and parasites, could lead to sustained oscillations in genotype frequencies. As one genotype of host is most susceptible, its most effective parasitic genotype will prosper. However, this forms a selection pressure to favor a resistant host. When that resistant host genotype appears or merely increases in numbers, a new selection pressure forms on the original parasite genotype, which is now less infectious or virulent in the new host genotype. Thus, one host genotype will replace a former one, only to be followed by parallel replacement of genotype in the parasite. Sexually reproducing species which allow recombination of alleles among different individuals in their populations will have the potential for more rapid evolutionary change, speeding up the oscillations in genotypes of hosts and parasites, even if no new alleles arise in either gene pool. This hypothesis can also explain the shift between sexual and asexual modes of reproduction in species capable of both forms of reproduction. This is the short term neontological (living species) microevolutionary perspective.