Evolution & Biodiversity

DOMAINS: All organisms are classified into three domains

1) Archaea; members known as archaeans (no membrane bound organelles, proteins similar to histones with DNA, only one to have I-form glycerole in membrane, with other 2 having d-form.) 2) Eubacteria; members known as bacteria. (only one to have peptidoglycan cell walls) 3) Eukaryota; members known as eukaryotes. (have membrane-bound organelles, histones associated with DNA) (all have unbranched side chains in membrane) •Original evidence of this came from base sequences of rRNA which is found in all organisms and evolves slowly, so suitable for studying the earliest evolutionary events. •Viruses are not classifies into domains as they aren't considered living organisms.

NATURAL SELECTION: "Adaptations are characteristics that make an individual suited to its environment and way of life." "Species tend to produce more offspring than the environment can support." "Individuals that are better adapted tend to survive and produce more offspring while the less well adapted tend to die or produce fewer offspring" "Individuals that reproduce pass on characteristics to their offspring" "Natural selection increases the frequency of characteristics that make individuals better adapted and decreases the frequency of other characteristics leading to changes within the species."

1) Species tend to produce more offspring than environment can support. Struggle for existence in which some individuals survive and some die. •(e.g. plants and fish make loads, mammals tend to make less because they care more for young. Carrying capacity is max density environment can support and too many organisms means demand for limited resources increases so more competition) 2) In natural populations there is variation, and some individuals are better adapted that others (adaptation: characteristic that makes individual suited to its environment and way of life) 3) Better adapted individuals tend to survive and produce more offspring (vise-versa for less adapted) because better able to compete, so each generation contains more offspring of better adapted individuals 4) Individuals that reproduce pass on characteristics to their offspring, so the frequency of genes that make individuals better adapted increases (vise-versa). Species changes and becomes better adapted. •Acquired characteristics during lifetime aren't heritable, so can't increase in a species by natural selection. e.g. large muscles can grow through exercise, but genes influencing size haven't been altered. •(Where and how an organism lives is due to specific adaptations that allow it to survive and reproduce in particular area, develop over time through natural selection.) •(For another species to develop genetically different individuals must become reproductively isolated and reproduce with individuals with similar traits)

Essential idea: The diversity of life has evolved and continues to evolve by natural selection. -VARIATION- "Natural selection can only occur if there is variation among members of the same species." "Mutation, meiosis and sexual reproduction cause variation between individuals in a species."

3 sources of variation: 1) Mutation: original source of variation as new alleles produced through mutation which enlarges population gene pool 2) Meiosis: produces new combinations of alleles by breaking up existing combinations in diploid cell (every cell likely to have different) because of independent orientation of bivalents/assortment of chromosomes, resulting in 2n possible variations of chromosomes and crossing-over. 3) Sexual reproduction: fusion of gametes (random fertilization), which (usually) come from different parents so offspring has combination of alleles from 2 individuals. •Within a species, different individuals of that species show genetic variation. •Individuals that are best suited for their environment will survive and reproduce. •If there was no variation within a species, then all individuals would be the same and no individual would be favoured over the other and natural selection would not take place

"Application: Recognition features of porifera, cnidaria, platylhelmintha, annelida, mollusca, arthropoda and chordata." Guidance: Recognition features expected for the selected animal phyla are those that are most useful in distinguishing the groups from each other and full descriptions of the characteristics of each phylum are not needed.

7 largest phyla of animals: PORIFERA (e.g. sponge): -no clear symmetry -attached to surface -pores through body -no mouth/anus CNIDARIA (e.g. jellyfish): -Radially symmetric -tentacles -stinging cells -mouth (no anus) PLATYHELMINTHS (flatworms): -bilaterally symmetric -flat bodies, no skeleton -unsegmented -mouth (no anus) ANNELIDA (e.g. centipede): -bilaterally symmetric -segmented -bristles (usually) -mouth and anus ARTHROPODA (e.g. insects, crabs shrimp etc., also butterflies): -bilaterally symmetric -(hard) exoskeleton -segmented -joint appendages MOLLUSCA (e.g. snail, squid): -muscular foot and mantle (fold of body) -shell (usually) -segmentation not visible -mouth & anus CHORDATA (all vertebrae and a few non-vertabrae) (these features in embryo): -notochord (cartilagenous spine ish) -dorsal nerve chord -pharyngeal gill slit -post-anal tail (tetrapods are first 4 legged animals)

"Recognition features of bryophyta, filicinophyta, coniferophyta and angiospermophyta" (Students should know which plant phyla have vascular tissue, but other internal details are not required.)!!

Bryophyta (mosses): -No roots but rhizoids (similar to root hairs) -No vascular tissue (only phyla without) -Simple leaves and stems, no flowers or seeds -Liveworts have flattened thallus (main body) -Reproductive structure: spores in capsules at the end of a stalk Filicinophytes (ferns): - Short, non-woody stems - Have roots - Leaves curled up in bud, often divided into pairs of leaflets -Reproductive: spores produced in sporangia (usually on underside of leafs) Coniferophytes (conifers -shrubs or trees): -Roots, leaves, woody stems. -Leaves often narrow, thick waxy cuticle -Reproductive: seeds (develop from ovules on the surface of the scales of female cones), and pollen (produced in male cones) Angiospermophytes (flowering plants): -(usually, because variable): roots, leaves, stems (which are woody if shrubs or trees). -Reproductive: seeds develop in ovules of ovaries in flowers, anthers for pollen. Fruits develop from ovaries to disperse seeds.

"Application: Cladograms including humans and other primates"

Cladistics and Human classification: Mitochondrial DNA from 3 humans and 4 related primates has been completely sequences to construct a cladogram. Using differences in base sequence as evolutionary clock, the approximate dates for splits are: 5m years: human-chimpanzee split 140,000 y: African - European/Japanese split 70,000: European-Japanese split . . . . . . .

"Application: Evolution of antibiotic resistance in bacteria."

Increasing problem with resistance, similar trend with many diseases. 1) microorganisms that naturally make antibiotic have genes that give it resistance to it 2) Transferred to bacterium through plasmid or other way (or mutation), and there is then variation in the bacterium: some resistant, some not. 3) antibiotics will kill bacteria (directly or weaken it so immune system can fight) if susceptible but not those that are resistant, which is an example of natural select never though selection pressure caused by humans using antibiotics 4) Antibiotic-resistant bacterias reproduce and pass on gene to offspring, bacteria spread by cross-infection between people (and can pass on resistance to others) 5) the more antibiotics used the more bacteria resistant, fewer non-resistant, so as a result of excessive antibacterial use most bacteria may eventually become resistant.

"Application: Development of melanistic insects in polluted areas."

Melanistic (dark variety of light insects) moth was rare, but in areas where industry developed it became much more common and peppered became rarer. Explanation: 1) Adult moths fly at night to find mate, during the day they sit on branches of trees 2) In unpolluted areas the trees are covered in lichens (pale colored) so peppered camouflage. 3) In areas that became industrial sulphur dioxide pollution kills lichens, and (soot from) coal burning blackens them, so melanistic camouflaged. 4) Birds that hunt in daylight predate moths, so melanistic were more likely to breed and pass on dark wing while peppered more likely to be eaten. Therefore population evolved from peppered to melanic.

"Taxonomists classify species using a hierarchy of taxa" "The principal taxa for classifying eukaryotes are kingdom, phylum, class, order, family, genus and species." "Application: Classification of one plant and one animal species from domain to species level."

Species classified into series of taxa (groups of species based on similar characteristics). Hierarchy is that each includes a wider range of species than previous one. (Damn King Philip Came Over From Great Spain): ANIMAL - HUMAN D: Eukaryota K: Animalia P: Chordata C: Mammalia O: Primate F: Hominidae G: Homo S: sapiens PLANT - GIANT REDWOOD D: Eukaryota K: Plantae P: Coniferophyta C: Pinopsida O: Pinales F: Cupressaceae G: Sequoia S: giganteum

BINOMIAL SYSTEM "The binomial system of names for species is universal among biologists and has been agreed and developed at a series of congresses." "When species are discovered they are given scientific names using the binomial system."

Species given scientific names with binomial system, which is universal (developed at international congresses) to avoid confusion if many names and to ensure every species has unique name. Features: 1) First name is genus (group of closely related species). Uppercase. 2) Second name is species, lowercase. 3) Italics in print. •(Carlos Linnaeus)

"Skill: Construction of dichotomous keys for use in identifying specimens"

Species identification is done with a dichotomous key which has: 1) a series of numbered stages which consist of a pair of alternative characteristics 2) Some alternatives give the next numbered stage of the key to go to 3) Eventually the identification of the species will be reached •The most useful key characteristics are easy to observe and are ere liable because they're present in every member of the species.

"Application: Recognition of features of birds, mammals, amphibians, reptiles and fish."

Vertabrates are subphylum of chordata which have a backbone with vertebrae. Besides fish, all are tetrapods (first 4 legged animals) with pentadactyl limbs, though modified or lost through evolution. (BONY-RAY FINNED) FISH: •Scales from skin •Gills with single gill-slit •Fins supported by rays •Swim bladder for buoyancy •External fertilization AMPHIBIANS: •Soft, moist, permeable skin •Lungs with small internal folds •External fertilization in water •Protective gel around eggs •Larval stages in water (e.g. tadpoles) REPTILES: •Dry, scaly, impermeable skin •Lungs with extensive folding •Internal fertilization •Soft shells around eggs •One type of teeth BIRDS: •Feathers from skin •Lungs with parabronchial tubules •Wings instead of front legs (though still tetrapods) •Hard shells around eggs •Beaks, no teeth MAMMALS: •Hairs growing from kin •Lungs with alveoli •Birth to live young •Mammary glands secrete milk •Teeth of different types

Mr Power's evolution checklist

e.g for peppered moths/antibiotics •Selection pressure: avoid predators in polluted area/antibiotics presence •Variation: Most white, small number of melanistic/most killed by antibiotics, some resistant. Determined by genes. •Competition: Moths produce more offspring than can survive, which compete to avoid predators/bacteria produce more, compete to survive in humans. •Adaptation: black moths less likely to be seen... & eaten/bacteria with resistance better adapted... •Survive & reproduce: ...so more likely to survive and reproduce, passing on genes (for black color/resistance to antibiotic) to offspring •Natural Selection: Black moths became more common over generations/bacteria population changes to include more resistant to penicillin. Have evolved by natural selection. (SVCASN)

CLADES "A clade is a group of organisms that have evolved from a common ancestor." "Evidence for which species are part of a clade can be obtained from the base sequences of a gene or the corresponding amino acid sequence of a protein." "Sequence differences accumulate gradually so there is a positive correlation between the number of differences between two species and the time since they diverged from a common ancestor" "Cladograms are tree diagrams that show the most probable sequence of divergence in clades"

•A clade is a group of organisms that evolved from a common ancestor. Can be large groups with a common ancestor far back, or smaller groups with a more recent common ancestor. •Evidence can be looked at through characteristics though hard to distinguish analogous and homologous traits from anatomical features so not used as much. Instead evidence comes from base sequence of gene or corresponding AA sequence. •Sequence differences (a result of mutation) accumulate gradually. Evidence that these occur at a constant rate, so there's a positive correlation between the number of differences between 2 species and the time since they diverged (AKA molecular clocks). •Cladograms are tree diagrams that show most probable sequence of divergence in clades. On cladograms nodes (branching points) show groups of organisms which are related and therefore presumably had common ancestry (degree of divergence between branches represent the differences that have developed between the two taxa since they diverged). Cladograms can be analyzed to find out how closely organisms are related to each other and indicate probable sequence in which groups split. •(Cladograms started being produced once base and AA sequence determined + analytical powers of computers grew) •Cladograms have been used to re-evaluate the classification of many organisms. Because this is a procedure different to previously used, this method of classification is called cladistics (which is different to natural classification which relies on morphology). ((Amino acids also have either right-handed or left-handed orientation The majority of organisms on earth use left-handed amino acids to build their proteins and only a small number use right-handed amino acids (mostly certain bacteria). This implies common ancestry for these life forms with the same amino acid orientation)) ((Another example comes from immunological studies, which is an way to detect differences in specific proteins of species, indirectly showing how closely two species are related: Human blood serum (blood minus cells and fibrinogens) is obtained and injected into a rabbit Later a sample of the rabbits blood that contains anti-human antibodies to human proteins is taken Serum from other mammals is mixed with the anti-human antibodies. The more the precipitation the more closely the animal is related to humans))

"Application: Changes in beaks of finches on Daphne Major."

•Daphne Major is an island in the Galapagos, where population of (medium ground) finches feed of different sized seeds. Larger seeds are harder to crack open, finches with large beaks better adapted to feeding on them. Variation in beak size is a heritable characteristic. •From 1973 finches trapped so beak sizes (mean length and width) have been measured. •Climate variable because of oscillation between warm ocean temps (El Nino, brings heavy rain which has small seeds) and cold ocean temps (La Nino, brings droughts which has few small seeds). •1974-77 cold temps (drought) experienced so population dropped from 1300-300, and those who died has smaller mean beak size = natural selection. •When population bred after drought, mean beak size remained higher because offspring inherited larger beak size from survivor parents. •In 1983 El Nino (warm, heavy rain) brought lots of soft small seeds, so mean beak size dropped as small beak sizes are better adapted to feeding on small seeds.

"Evolution occurs when heritable characteristics of a species change"

•Evolution: Changes that occur in a living organism over many generations in populations of organisms. Evidence for evolution: 1) fossil record 2) Homologous structures 3) Biogeography (variation in speciation) 4) Artificial selection

EVIDENCE FOR EVOLUTION: THE FOSSIL RECORD "The fossil record provides evidence for evolution."

•Fossils are the remains of organisms embedded in rock and preserved in petrified form. •Discovered of many organisms that no longer exist and in most cases no fossils for organisms today, suggesting organisms change over time. •Rocks can be dated to allow age of fossils to be deduced, sequence of appearances matches sequence expected to evolve in/complexity (bacteria & simple algae -> fungi & worms -> land vertebrates). •Many species of fossils exist which link together existing organisms with their likely ancestors. •(Acanthostega has similarities to vertebrates but has 8 fingers, 7 toes so not identical to any existing organism. Has 4 legs like most amphibians, reptiles and mammals but also gills and fish tail, lived in water. This shows land vertebrates could have evolved from fish via aquatic animal with legs)

EVIDENCE FOR EVOLUTION: ADAPTIVE RADIATION/HOMOLOGOUS STRUCTURES "Evolution of homologous structures by adaptive radiation explains similarities in structure when there are differences in function." "Traits can be analogous or homologous." "Application: Comparison of the pentadactyl limb of mammals, birds, amphibians and reptiles with different methods of locomotion."

•Homologous structures are similar in form and function and seem to be related. Underlying anatomical commonalities demonstrate descendence from common ancestor. Explained by adaptive radiation. •Adaptive radiation is a type of evolution where groups migrated to different locations with different challenges for survival which results in modified structure/because they adopted different locomotion, limbs developed in different ways to suit type. •Basic bone structure & position of pentadactyl limb in amphibians, reptiles, birds and mammals is the same, though have different shape, size, function. 1) AMPHIBIANS: Frogs (jumping) 2) MAMMALS: Humans (manipulation), bats (flying), horse it's thick legs/hooves (for running), mole (digging) 3) BIRDS: wings (flying) 4) REPTILES: lizard (crawling) •Analogous structures are similar in form or function as a result of convergent evolution (independent evolution of similar features in species of different lineages usually living in similar environments), meaning they were not present in the last common ancestor of those groups.

EVIDENCE FOR EVOLUTION: SELECTIVE BREEDING "Selective breeding of domesticated animals shows that artificial selection can cause evolution."

•Humans use animal/plant breeding to selectively develop particular traits by choosing which will sexually reproduce (originating from wild species, which explains obvious similarities and in some cases ability to still interbreed). •This results in changes to heritable characteristics of organisms, and is observed evolution, gives evidence that species can evolve rapidly by artificial selection. •(e.g. cows that make more milk)

"Skill: Analysis of cladograms to deduce evolutionary relationships

•Scale above cladogram if present can show % difference in AA sequence, which is used to add an estimated time scale below. •Nodes represent the time when two species are estimated to have split. •Just because a species like C split earlier than from B, it does not mean that B has evolved more. All the species at the top are present D species. The ones that have died out or changed would be at the nodes. Examples of clades vs not clades: . . . . .

"Taxonomists sometimes reclassify groups of species when new evidence shows that a previous taxon contains species that have evolved from different ancestral species." "Evidence from cladistics has shown that classifications of some groups based on structure did not correspond with the evolutionary origins of a group or species." "Application: Reclassification of the figwort family using evidence from cladistics."

•Since evidence from base and amino acid sequences only became possible in the mid to late 1900's, some changes have occurred in traditional classifications of certain plants and animals based solely on morphology •Sometimes new evidence shows scientists that members of a particular group do not share a common ancestor, sometimes other species are more similar than thought. •Ongoing process •Evidence from cladistics (genes from their chloroplast) showed that classification of some groups based on structure didn't correspond with evolutionary origins, falsified old classification. Cladograms showed that species in the figwort family didn't share a recent common ancestors. •Originally large family with 250 genera, now: 1) some genera reclassified as plantains or broomrapes. 2) 2 new family classifications developed (lindernia and calceolaria) 3) 2 existing families reclassified/merged as figworts (buddleja and myoporum)

EVIDENCE FOR EVOLUTION: BIOGEOGRAPHY "Populations of a species can gradually diverge into separate species by evolution." "Continuous variation across the geographical range of related populations matches the concept of gradual divergence."

•Speciation: populations of a species can become separated and unable to breed with each other, evolve differently and diverge in characteristics. •Difficult for taxonomies to classify often if species in different areas are same because continuous variation from slight to great (not clear enough to be distinct species but still in stages of speciation. Continuous variation across the geographical range of related population matches the concept of gradual divergence (and not of species being created)

NATURAL CLASSIFICATION: "Natural classifications help in identification of species and allow the prediction of characteristics shared by species within a group." "Taxonomists sometimes reclassify groups of species when new evidence shows that a previous taxon contains species that have evolved from different ancestral species."

•Taxonomists: specialize in classification of species, which is important because without it it would be hard to store/access information about them. •Artificial classification: based on similar characteristic e.g. wings vs no wings, though they're not similar enough in other ways to be grouped together, and wings can be analogous and evolved separately (e.g. wings of insects is not the same as wings of birds or bats, which are pentadactyl because they evolved separately) •Biologists try to devise natural classification, which assumed that all members of the group evolved from a shared common ancestor at some point in their history and therefore share inherited characteristics. This allows: 1) prediction of characteristics shared by species within a group 2) Identification of species. •Not always obvious what patterns of evolution and therefore their natural classification. Taxonomists sometimes reclassify groups of species when new evidence showed that previous taxon contains species that evolved from different ancestral species. •E.g. all living organisms were divided into 5 kingdoms, where all prokaryotes placed in one and eukaryotes across four. However when base sequence of nucleic acids was compared, 2 very different prokaryotes were identified (which were as different to each other as to eukaryotes) so higher grade of taxonomic group was added: domain. •((Dichotomous key would not work well for artificial classification (e.g. color of flower petals)))