Biodiversity, Speciation, and the Origin of Life General Biology 2 Week of 1/9/2012 and 1/16/2012

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2 Biodiversity, Speciation, and the Origin of Life General Biology 2 Week of 1/9/2012 and 1/16/2012

3 1 The Quick Reference Guide Biodiversity Characteristics of Living Organisms Process of Evolution Genes in the Natural Population Hardy- Weinberg Principle Causes of Microevolution Types of Selection What is a Species Modes of Speciation Adaptive Radiation Primitive Earth Alternative Mechanisms Origins of the 1 st Cell Fossil Dating Geological Time Scale Paleozoic Era Mesozoic Era Cenozoic Era Factors Effecting Evolution

4 January 9 th, Biology: The scientific study of living organisms and how they have evolved Two ways to examine evolution: evolution of all species and how those organisms change over time (both unity and biodiversity)\ 2 million named species million waiting to be described Biodiversity: 1. Level of Ecosystem (coral reefs, savannah, rain forest) 2. Species within ecosystems (similarities and differences) 3. Genetic variation at level of genes Characteristics of Living Organisms: - All living organisms are comprised of cells - Organisms maintain internal order - Chemical uniqueness - Hierarchy of organization (cells, tissues, organs, organ systems, organisms) - Energy use and metabolism - Energy is required to maintain order - Energy utilized via metabolism - Photosynthesis (source of all energy, converting sunlight into usable form): cellular respiration - Response to environmental change - Organisms react to stimuli - Adaptation/behaviors promote survival - Regulation and Homeostasis (disease: homeostatic imbalance) - Organisms regulate cells and bodies - Maintain relative stable internal conditions - Growth, Development and Reproduction: - Growth produces more and larger cells (mitosis) - Development produces organisms with defined set of characteristics (genome) - Reproduction sustains species of generations (sexual and asexual) - Genetic material cause offspring to have traits like parents

5 - Biological Evolution: - Population of organisms change over time - Evolution results in trait that promote survival and reproductive success (adaptations) 3 Process of Evolution 1. Variations are produced by chance mutations and sexual reproduction (crossing over, independent assortment, mutations) 2. Natural selection selects the fittest organisms 3. Natural selection leads to adaptation to a particular environment (environments may change) 4. Process occurs constantly in all species of life on earth (slow and mostly unobservable) Natural Selection acts on individuals in a species (they have features that make them different), Evolution is a property of populations Evolution: - Occurs generation to generation - Descendants are different from ancestors - Change in allele (gene) frequencies: changes in the genetic make up of population over time (generations). Natural selection acts on genotype through the phenotype Anagenesis: species changes over time Speciation: new species is created January 11 th, 2012 Genes in Natural Population - Genes can be monomorphic (99% = 1 allele, rare but has a few traits, ex. Pretty much all humans have thumbs) or polymorphic (2 or more alleles in population, ex. hair color, eye color, etc) Polymorphism comes about through various changes 1. Duplicated of gene region 2. Deletion of significant region of gene 3. Changes in single nucleotide (SNP, smallest and most common change in one gene to another)

6 Allele Frequency = 4 # of copies of a specific allele in a population total number of all alleles for that gene in population Genotype Frequency = # of individuals with a particular genotype total # of individuals in a population (occurs because of homologous chromosomes, sexual reproduction) Hardy Weinberg Principle: 1908: G.H. Hardy and W. Weinberg independently recognized - Genes remain in equilibrium (constant frequency) over time (in each succeeding generation of a sexually reproducing population) - Relates allele and genotype frequencies in a population P+Q=1 (allele frequency) (p + q) 2 =1 Expanded = p pq + q 2 =1 (genotype frequency) P= frequency of dominant alleles Q= frequency of recessive allele P 2 =Frequency of homozygous dominant Q 2 = Frequency of homozygous recessive genotypes 2pq= frequency heterozygous Example: Eye color: Brown: BB, Bb Blue: bb #/total bb = 25/100 = 0.25 Q 2 = > q= = p P = 0.5 P 2 =.25 Homozygous Dominant (BB) = 0.25 Heterozygous (Bb) = 0.5 Homozygous recessive: (bb) = 0.25

7 Conditions for Hardy Weinberg 5 1. No mutations: allelic changes do not occur, or any changes that do occur have to be balanced out in the opposite direction (no gene duplication, no exon shuffling, no horizontal gene transfer) 2. No gene flow: migration of alleles into or out of the population cannot occur 3. Random Mating: individuals have to pair entirely by chance, never by genotypes 4. No genetic drift: the population is very large, so that changes in allele frequencies in allele frequencies due to change alone are insignificant 5. No selection: no selective agents that favor one genotype over another, all genotypes are equally adapted Hardy Weinberg Equilibrium VERY RARELY occurs So why study it? - If p or q is changed from one generation to another, evolution has occurred - Hardy Weinberg identifies factors that cause evolution: evolution detected by noting any deviation from Hardy- Weinberg equilibrium of allele frequencies in gene pool of a population - Equilibrium Population: hypothetical population in which evolution does not occur Its a way to study and measure evolution Microevolution: accumulation of small changes in the gene pool of a population of a population over a relatively short period of time Causes of Microevolution 1. Genetic Mutations - The raw material for evolutionary change, the original source of genetic variability - Source of new alleles, new combinations of alleles, what evolution acts on - Not goal- oriented, not a result of environmental necessity - Random events (good bad or neutral) depending on environmental conditions - Other forces act to either maintain the variation or remove it from the population 2. Gene Flow Gene Migration - Movement of alleles between populations when - Gametes of seeds (in plants ) are carried into another population - Breeding individuals migrate into or out of population - Continual gene flow reduces genetic divergences between populations

8 - Populations of relatively sedentary organisms are more isolated from one another then populations of very mobile organisms (subspecies: isolated organisms that can still reproduce but are separated naturally and becomes 2 different species) 3. Nonrandom Mating: when individuals do not choose their mates randomly - Assortative mating - Individuals select mates with their phenotype - Individuals reject mates with different phenotype - Non- assortative mating is the opposite: it increases homozygousity - Sexual selection - Males compete with each other for the right to reproduce (intrasexual) Ex. Crabs fighting with each other - Females choose males possessing a particular phenotype (intersexual) Ex. Peacocks choosing males based on feathers 4. Genetic Drift - Occurs by disproportionate random sampling from population - Can cause the gene pools of two isolated populations to become dissimilar - Some alleles are lost and others become fixed (unopposed) and occur at higher frequencies - Likely to occur - After severe inbreeding or a bottleneck (random event that prevents a majority from entering the next population, next generation composed of the alleles that just happened to make it - Ex. Squirrels become separated in the Grand Canyon, 2 different populations - Ex. Cheetahs have very low genetic variability, monomorphic through most of genes due to severe inbreeding, trying to diversify - Ex. Northern elephant seal: Low genetic variability when hunted down to 20, which bred with each other to 100,000 ) - Ex. Founders start a new population (ex. Amish community moved from Germany, no new alleles come in. 1/14 in Lancaster, PA have polydactyl (extra fingers), 1/1000 in the world) - Stronger effect on smaller populations 6

9 January 12 th, Natural Selection: Major cause of Microevolution Adaptation of a population to the biotic and abiotic environment Abiotic: Climate, water availability, and minerals Biotic: Competition, predation, sexual selection - Requires - Variation: the members of a population differ from one another - Inheritance: many differences are heritable genetic differences - Differential Adaptiveness: Some differences affect survivability - Differential Reproduction: Some differences affect likelihood of successful reproduction - Results in: - A change in allele frequencies in the gene pool - Improved fitness of the population Types of Selection 1. Directional selection - Extreme phenotype is favored - Curve shifts in the extreme direction; bell curve adjusts to turn the extreme into the majority Ex. Size of the modern horse, industrial melanism (moths became darker, favored throughout all the pollution and soot), antibiotic resistant bacteria, DDT resistant Mosquitos

10 8 2. Stabilizing Selection - The peak of the curve increases, and the tails decrease - Intermediate phenotype is favored Ex. Human high or low birth weight are less likely to survive, 4 to 5 eggs in birds is favorable, more or less is not - Usually produces more heterozygotes, with homozygous extremes slowly decreasing Ex. Sickle cell anemia: 1 sickle cell is more favorable over 2 sickle cells or 2 hemoglobin cells, and more likely to survive both malaria and sickle cell anemia (heterozygote advantage) 3. Disruptive (Diversifying) Selection - Two or more extreme phenotypes are favored over intermediates: bimodal distribution - Middle of bell curve disappears, and two separate phenotypes are created - If this continues due to some sort of separation, they could become different species and may not be able to reproduce with each other Ex. Snails vary because in some areas, its better to be one extreme (light). In other areas, other extreme (dark). Middle snails die off, and only extremes remain in separate areas.

11 9 Maintenance of Variations - Genetic Variability - Populations with limited variation may not be able to adapt to new conditions (cheetahs, seals, founder populations) - Maintenance of variability is advantageous to population - Only exposed alleles are subject to natural selection - Natural Selection doe not cause genetic changes - Natural selection acts on individuals - Population evolves as gene frequencies change What is a Species? Speciation: the splitting of one species into two (cladogenesis) or the transformation of one species into a new species over time (anagenesis) Macroevolution: evolutionary changes that create new species and groups of species; accumulations of macroevolutionary changes; long periods of time Typographical (Morphological) Species Concept (Pre- Darwin): - Species are defined by fixed, essential species - Each species has a unique structure that makes it distinct

12 Biological Species Concept: 10 - A species is a reproductive community of populations (reproductively isolated from others) that occupies a specific niche in nature: must be able to successfully reproduce with each other, share a common gene pool - Drawbacks: species have dimensions in space and time (become extinct sometimes, cant know who they were interbreeding with), sexual and asexual reproduction; species is both a unit of evolution and a taxonomic category Ecological Species Concept: - Using the ability of organisms to successfully occupy their own ecological niche or habitat, including their use of resources and impact on the environment, to distinguish species Phylogenetic (Evolutionary) Species Concept (Most recent): - A species is an irreducible group of organisms diagnosable distinct from other such groupings and within which there is parental pattern of ancestry and descent (morphological, chromosomal, and molecular characters used) Reproductive Isolating Mechanisms: inhibit gene flow between species and maintain distinctiveness of species (two general categories) - Prezygotic Mechanisms: discourage attempts to mate - Habitat isolation (live in different habitats) - Temporal isolation (time isolation, don t reproduce all at the same time of year, seasonal) - Behavioral isolation (different mating rituals, bird songs only attract birds of same species) - Mechanical isolation (sex organs don t fit together) - Gamete isolation (gametes may not survive in the reproductive parts of other species) - Postzygotic Mechanisms: prevent hybrid offspring from developing or breeding - Zygotes mortality (zygote doesn t survive, doesn t develop) - Hybrid sterility (mules are sterile, cant reproduce, ligers/tyglons) - Reduced F2 Fitness (doesn t know which developmental pattern to follow)

13 Modes of Speciation: 11 - Allopatric Speciation - Two geographically isolated populations of one species - Becomes different species over time - Can be due to differing selection pressures in differing environment January 18 th, 2012 Adaptive Radiation - When members of a species invade several new geographically separate environments - The populations become adapted to different environments - Many new species from the single ancestral species - This is considered allopatric speciation Ex. Hawaiian Honeycreepers arrived in Hawaiian Islands 3-7 million years ago, founder effect, 54 different species developed, many new extinct Darwin s Finches: - When Darwin travelled to different islands on the Galapagos, he found many different kinds of finches, all differently adapted to the kinds of food they preferred and the conditions that food was found in Modes of Speciation - Sympatric Speciation - One population develops into two or more reproductively isolated groups - No prior geographic isolation - Autoploidy: 2n plant - > 2n gametes (+n) = triploid (sterile, seedless) - Alloploidy: Tetraploid Hybridization plants How did life begin? - 4 Overlapping Stages - Results in self fertile species - Reproductively isolated from either parental species 1. Nucleotides and amino acids produced prior to existence of cells 2. Nucleotides and amino acids became polymerized to form DNA, RNA and proteins 3. Polymers became enclosed in membranes 4. Polymers enclosed in membranes evolved cellular properties

14 Primitive Earth 12 - Originally too hot for liquid water - As earth cooled, water vapor condensed to liquid water Alternative Mechanisms - Extraterrestrial Hypothesis (Theory of Panspermia) - Organic carbon from asteroids and comets stocked prebiotic soup - Meteorite Studies: Carbonaceous chondrites, lots of organic carbon, amino acids, nucleic acid bases - Controversy: meteorites are often destroyed by intense heat of impact - Deep- Sea Vent Hypothesis Key organics arose at deep- sea vents - Superheated water (300F) rich metal ions mixes with cold seawater - Organics formed in temperature gradient around vents January 19 th, 2012 Origin of the 1 st cell - Clay hypothesis - Simple organics polymerize on solid surface (clay, mud, inorganic crystals) into more complex organisms - Stromatolites: mats of mineralized cyanobacteria - Cell- like structures protobiont - Boundary (membrane) - Polymers inside contain info - Polymer s inside with enzymatic functions - Self- replication - Chemical Selection RNA World - RNA in Protobionts - Can store info - Capacity for replication - Enzymatic functions (ribozymes), DNA does not have enzymatic properties, proteins cant store information - Reverse transcriptase makes RNA into DNA

15 Fossil Dating - Relative 13 - Fossils: Remains and traces of past life - Paleontology is the study of the fossil record - Most fossils are traces of organisms embedded in sediments - Sediments converted to rock - Becomes recognizable stratum in stratigraphic sequence of rocks - Strata of the same age tend to contain similar fossils - Helps geologists determine relative dates of embedded fossils despite upheavals - Different layers (strata) signify different ages and different fossils - More abundant organisms are more likely to leave fossils behind Fossil Dating Absolute (one method relies on radioactive dating) - Half- Life - The length of time require for have the atoms to change into something else - Unaffected by temperature, light, pressure, etc - All radioactive isotopes have a dependable half like ranges from seconds to billions of years - Many isotopes are used, and they re combined half like lives make them useful over all periods of interest Examples Isotope Half life Useful dating range - Carbon 14 - > N <50,000 - K40 - > Ar billion 100, billion - U235 - > Pb million 10 million to 4.5 billion Geological Time Scale: Time line of Earths History, origin to present Changes in organisms result from 1. Genetic Changes 2. Environmental Changes Eras Paleozoic (Ancient Life), Mesozoic (Middle life), Cenozoic (New life) Boundaries are mass extinctions

16 Precambrian Time - Includes 87% of geological timescale 14 - Little to no atmospheric oxygen - Lack of ozone shield allowed UV radiation to bombard Earth - First Cells came into existence in aquatic environments (600-4,500 mya) - Prokaryotes - Cyanobacteria left many ancient stromatolites fossils - Added first oxygen to the atmosphere - Eukaryotic Cells arise 2 Billion years ago - Multi- cellularity arises 1.4 billion years ago Ediacaran Fossils - Vendian Period million years ago - First concrete evidence of multicellular organisms - Mudflat animals, unusual forms, no internal organs, sponges appear Paleozoic Era ( million years ago) - Includes three major mass extinctions - Cambrian Explosion ( million years ago) - Warm, wet climate (no ice at poles) - Many invertebrates - All existent phyla developed (at least 30 different present in fossils) - Many marine inverts with shells - Burgeon Shale: large amount of fossils from this period - High diversity of the Cambrian may be due to the evolution of outer skeletons - Increase in oxygen, some change from anaerobic to aerobic - More CaCO3 in water, which contributes to evolution of shells - Invasion of land - Plants - Seedless vascular plants - Later flourished in carboniferous period - Invertebrates - Arthropods were first animals on land - Outer skeleton and jointed appendages pre- adapted them to live on land, or Arial existence

17 - Vertebrates 15 - Fishes first appeared - Amphibian s diversified in the carboniferous period (much larger) - First reptiles appeared Mesozoic Era Age of Reptiles ( million years ago) - Triassic Period - Nonflowering seed plants became dominant - Jurassic Period - Dinosaurs achieved enormous sizes - Mammals remained small and insignificant - Cretaceous Period - Dinosaurs began precipitous decline - Mammals - Began adaptive radiation - Moved into habitats left vacated by dinosaurs - Flowering plants start to evolve Cenozoic Era Age of Mammals (65 million years ago to today) - Tertiary period ( million years ago) - Mammals continued adaptive radiation (birds and insects diversified) - Flowering plants already diverse and plentiful - Primate evolution began Quaternary period (1.8 million years ago to now- Age of Man) Factors influencing evolution 1. Climate/Temperature 2. Atmosphere 3. Land Masses moving 4. Glaciation 5. Volcanic Eruptions 6. Meteorites