Biology: Systematic, Phylogenies, and Comparative Biology PDF

Chapter 23: Systematic, Phylogenies, and Comparative Biology ============================================================ **Systematics** - All organisms share many characteristics - Cell(s) - DNA - Physical traits - Metabolism - ATP - Difficult to find who...

Chapter 23: Systematic, Phylogenies, and Comparative Biology ============================================================ **Systematics** - All organisms share many characteristics - Cell(s) - DNA - Physical traits - Metabolism - ATP - Difficult to find who is closely related **Branching Diagrams** - Show relatedness among things - Can be drawn in different ways, but show the same things - Who is more closely related to whom **Similarity does not necessarily predict evolutionary relationship s** - Question: The greater the time since divergence, the more different species should be right - Ehhhhh - Rates of evolutionary vary (skin color genes may evolve faster than a gene that is important and could cause problems if there is a mutation) - Evolution may not be unidirectional (manatees evolved backwards; started in water evolved to land, then went back to water) - Evolution is not always divergent - Convergent evolution **Cladistics** - Looking at ancestorial traits and derived traits - Ancestrial characteristics - Inherited from the most recent common ancestor of an entire group - May not help distinguish between one person and another - Derived characteristics - Help distinguish one organism from another - Shared only by a subset of the group - Most important: shared derived characters **Cladistics Methods** - Ancestral vs. Derived characters - Examples - Presence of hair is a shared derived feature of mammals - No traits are always derived or ancestral: it could change depending on what the organisms that are being referred to - Presence of lungs in mammals is an ancestral feature (showing that there is a common ancestor that is it) - Characters can be any aspect of the phenotype - Morphology - Physiology - Behavior - Ecology - Need recognizable character states - Example: "tail" in vertebrates has two states-presence/absence - Can make character matrixes with presence/absence - Lamprey is an outgroup, something to compare it too - Outgroup - Related to, but not a member of the group - Does not always exhibit the ancestral condition - Synapomorphy - Special derived trait found only in one small group of organisms - Still context dependent - For slide hair is a synapomorphy; it is only shared by the small group of mammals here Cladogram Terminology - Synapomorphy - Pleiomorphism: ancestral states (also in outgroup) (example: everyone in this room is a UT student, but does not separate us) - Symplesiomorphies: Shared ancestral traits in some organism but not all descendants, (not all descendants need it) - From distant ancestors - Not in outgroup, but in ancestor and some descendants - Presence of gills in both fish and amphibians. - Homoplasy - Shared character state, not from common ancestor - Examples: convergent evolution, evolutionary reversal - Produce problems, because two things may not be closely related, evolved independently - Matrixes and Cladograms can be made with DNA sequences, what letter is at what position **But it Comes with Problems** - Not all genetic characters evolve at the same speed - Some characters evolve rapidly - Only 4 character states are possible (A, T, G, C) so high probability that two species will independently evolve the same derived character state - If organism goes from A to T to G back to A. This change cannot be seen or known because it is back at A. - If we can estimate speed, we can calculate branching events - Molecular clock (when human and chimps had a common ancestor) - Know when a mutation has occurred **Species Concepts** - There are multiple definitions of species - We do not have a definition of species - Biological species concept (BSC) - Defines species as groups of interbreeding populations that are reproductively isolated - Phylogenetic Species Concept (PSC) - Species is a population or set of populations characterized by one or more shared derived characters - PSC solves two BSC problems - BSC cannot be applied to allopatric populations naturally separated (a great dame in the US and a great Dane in France cannot know if they can reproduce so do not know) - PSC looks to the past to see if they have been separated long enough to develop their own derived characters - BSC can be applied only to sexual species (bacteria and other things reproduce asexually, but according to BSC they are not a species because it is asexually - PSC can be applied to both sexual and asexual species **PSC still controversial** - Slightly different=different species - Example: flowers that are different colors are looked at as different species under PSC **Phylogenetics** - Basis for all comparative biology - Homologous structures (homo=same) - Derived from the same ancestorial source - But the descendants change it - Bone structure of human, bat hand, and whale fin use the same bones and structures (these species have evolved to use them for different purposes) - Phylogenetic analysis determines homologies **Homoplastic Convergence** - Similar traits have evolved independently in different clades - Structures look similar but the species are not related - Flight evolved independently, it does not come from a common ancestor - Echolocation convergence trait does not mean species are related - Giant pandas having opposable thumbs, evolved independently 1/27/25 Chapter 20 ========== **Many processes lead to evolutionary change** - Natural selection causes changes in allele frequencies - Need different genes to look different, then natural selection decides what genetics are better to survive depends on allele frequencies **Population Genetics** - Study of properties of genes in a population - Evolution results in a change in the genetic composition of a population - Natural populations contain substantial genetic variation - Is the population changing for the better? - Genetic variation is required for evolution to occur **Hardy-Weinburg Principle** - This is why populations don\'t only contain the dominant phenotypes - Hardy-Weinburg Equilibrium - Proportions of genotypes do not change in a population as long as - 1\. No mutation takes place (this is not correct; mutations do take place) - 2\. No genes are transferred to or from other sources (no immigration or emigrations) (People at UT are not from Florida, this is transferring genes) - 3\. Random mating is occurring (male birds do dances to attract females, however the females have a particular type they are looking for) (it is not random) - 4\. The population size is very large - 5\. no selection occurs (no forms of natural selection occur, this is not truthful. Natural selection is always happening in wild populations) - We see Hardy-Weinberg over time the allele frequency changing, it shows when change is occurring; it does not say why - Showing when change is occurring is the benefit **Agents of Evolutionary Change** - Mutation - Fundamental unit of change - Rates generally low - Without mutations there would be no differences - Ultimate source of genetic variation - Makes evolution possible - Gene Flow - Movement of alleles (genes) from one population to another - I was born and raised in Massachusetts but now have moved my alleles to Florida. Bringing my unique genes here - Animals physically move into new population - Drifting of gametes or immature stages of plants or animals into an area - Plants are capable of using gene flow in themselves (increasing pollen rate) - Mating of individuals from adjacent populations - Populations meet different populations - Nonrandom Mating - This is the standard - You have a type (very common in species) - Assortative mating - You look like me lets mate - Phenotypically similar individuals mate - Increases proportion of homozygous individuals (AA)(aa) - Disassortative mating - You look different - Phenotypically different individuals mate - Produces excess of heterozygotes (Aa) - Nothing in nature happens by accident - Genetic Drift - All by chance - In small populations, allele frequency may change by chance alone - Population must be large to be in H-W equilibrium - Founder and bottleneck effects - Founder: butterflies were blown to an island, but only orange and black not white. Natural selection may favor black color because there are two black and one orange. This may eventually make a new species. - Organisms on islands - Self-pollinating plants - Gene pools are not different from original population - Bottleneck: drastic reduction in population size - This is from natural disasters, drought, disease, natural forces - Hurricane wiping out short plants, so only tall plants are left, they will produce tall plants - Survivors may constitute a random genetic sample - Results in loss of genetic variability **Evolution by Natural Selection** - Three Conditions to be met - 1\. Variation must exist among individuals in a population - 2\. Variation among individuals must result in differences in the number of offspring surviving in the next generation - Must have genes that make you goof at finding food, shelter, mate, etc. - 3\. Variation must have a genetic basis - What you do to your body changes your genetics even if you may not notice it - If you have a scar, your child would not have the same scar because there is no genetic component **Evolution by Natural Selection** - Natural Selection and evolution are not the same - Natural Selection is the reason you changed - Natural selection is a process - Only one of several processes that can result in evolution - Evolution is the historical record, ot outcome, of change through time - Evolution+natural selection=well adapted populations - Evolution is the result of natural selection **Fitness and its measurement** - Fitness - Most "fit" =leaves the most offspring - Fitness has many components - Survival - Sexual selection- some individuals more successful at attracting mates - Number of offspring per mating - Traits favored for one component may be a disadvantage for others - A pregnant woman needs a lot of things to keep her and baby healthy **Sexual Selections** - Intrasexual selection - Same gender - Male elephant seals fight other males for the females - Intersexual selection - Bird of paradise doing the dance for the female to get her to mate with them - Different gender - Peacocks - Sexual dimorphism - Difference in size among genders - Usually in human\'s males tend to be larger than females - In whales females are large, and males try to find the largest female because she will grow a healthy offspring - Sperm competition - A lot of sperm race to the egg - The sperm that rotates faster have advantage to get to egg first **Maintenance of variation** - Frequency-dependent selection - Fitness of a phenotype depends on its frequency within the population - Negative frequency-dependent selection - Rare phenotypes favored by selection - The ones that are not common - Rare forms may be preyed upon less frequently - Positive frequency-dependent selection - Favors common form - Tends to eliminate variation **Oscillating Selection** - Evolution can change - May want one thing (large beak) but in five years may want something else (small beak), then another five years may want the original thing (large beak) - Selection favors one phenotype at one time and another phenotype at another **Selection acting on traits affected by multiple genes** - Many traits affected by more than one gene - Selection operates on all the genes for the trait - Changes the population depending on which genotypes are favored **Disruptive Selection** - Acts to eliminate intermediate types - Either really tall or really short no in between - Different beak sizes of African, black-bellied seed cracker finch - Available seeds fall into 2 categories (big and small) - Favors big beak for big seeds and small beak for small seeds - Birds with intermediate-sized beaks **Directional Selection** - Acts to eliminate one extreme - Often occurs in nature when the environment changes - Only wanting dark beetles, not light colored. Only dark colored **Stabilizing Selection** - Acts to eliminate both extremes - Example: In humans, infants with intermediate weight at birth have the highest survival rate - Too big could cause problems with development and birth and too small could also cause health problems **Limits of Selection** - Multiple phenotypic effects of alleles - Same gene affects size of hen's comb and rate at which she lays-selection for hens that lay many eggs but have a small comb would be difficult - This means that if you change one the other is definitely changing because it is controlled by the same gene - Lack of genetic variation - Gene pool of thoroughbred horses limited, and performance times have not improved for more than 50 years - It has not changed because they mate the fast horses, they use the small gene pool that cannot evolve - Phenotypic variation may not have genetic basis - Interactions between genes-epistasis Chapter 21: The Evidence for Evolution ====================================== **Beaks of Darwin\'s Finches** - Darwin collected 31 specimens from 3 islands in the Galapagos Islands - Holotype: first organism found of that species, the original, they are kept in jars to be able to compare to see if an organism belonged to a specific species - Finches eat a diversity of food - Maybe beak shape has to do with food - Darwin wrote "\...one might really fancy that\...one species has been taken and modified for different ends" **Artificial Selection** - Change initiated by us - Choosing certain phenotypes over others - Examples: dogs, we call them breeds not species different dogs were bred for different reasons **Agricultural Selection** Mustard plant is artificially selected for different traits in foods like: - Kale (selection for leaves) - Broccoli - Cabbage - Cauliflower - Brussel sprouts - Kohlrabi **Fossil Evidence for Evolution** Background - Organism buried in sediment - Calcium in bone or other hard tissue mineralizes - Surrounding sediment hardens to form rock Process of fossilization is a rare event - Majority of animals on this planet do not have bones (invertebrates, do not have bones from them 87% of animals) - Imprints are left from invertebrates, but it is very rare, process takes a long time **Estimating the age of fossils** - Just relative position initially-further up is younger fossils than the fossils that are further in the ground that are older - Erosion and plate shifting can cause issues with this - Isotopic dating (looking at number of neutrons) - Old events - Potassium (K) isotope - 40K half-life is 1.25 billion years - Recent Events - Carbon (C) isotope - 14C half-life is 5700 years **Evolutionary Transitions** - Intermediate forms have been found that demonstrate how major transitions occurred, there are small steps that occur to get to and from EX. Lizard, intermediate, bird - Oldest Known bird fossil is the Archaeopteryx - Clearly intermediate between bird and dinosaur - Possesses some ancestral traits and some traits of present-day birds **Anatomical Evidence for Evolution** - Homologous Structures - Structures with different appearances and functions, derived from the same body part in a common ancestor - It is all the same structure with the same parts - Human arm, cat arm, bat wing, whale fin, horse leg **Early Embryonic Development** - Strongest anatomical evidence supporting evolution comes from comparisons of how organisms develop - Ontogeny (development process) reflects phylogeny (who you are related to) - Early vertebrae embryos possess pharyngeal pouches that develop into - In humans: glands and ducts - In fish: gill slits - Humans have gills and tails in the womb then are changed to glands and ducts **Some organisms not perfectly adapted** - Imperfections- some organisms do not appear perfectly adapted - Most animals with long necks have many vertebrae for flexibility - Geese: 25 vertebrae - Plesiosaurs: 76 vertebrae - Mammals: 7 vertebrates - Giraffes only have 7 vertebrae, so they are unable to bend their necks in certain ways that makes it vulnerable, they were only given 7, they had to work with it, their vertebrae are very large in size - Eyes of Vertebrates-not perfect - Photoreceptors face backwards - Nerve fibers slightly obscure light and create a blind spot - Natural selection has not "fixed" this because it would harm us, if the eyes are turned around, a bunch of generations would be blind for the process to work **Vestigial Structures** - Vestigial structures have no apparent function, but resemble structures ancestors possessed - Many examples - Manatees-have fingernails because they started in the water, then evolved to go onto land with fingernails, but are back in the water. But have kept the fingernails - Whales- they have pelvises, but they do not need them. Pelvises are used to support legs and body weight; this structure was useful to their ancestors because they started on land then went to the water. But they no longer have the need for a pelvis - Blind cave fish- they have genes to make eyes, but the dark caves they do not need eyes. It is too much time, resources, and energy to make the eyes if they do not have a purpose **Pseudogenes** - 'Fossil' genes; traces of previously functioning genes - Example-Icefish - Live in Antarctic in below freezing water, they have a unique pseudogene that they do not freeze. An incomplete Hemoglobin gene is used in icefish, and their blood is copper based. This lowers the freezing point of their blood, allowing them to live in below freezing water. If it used normal hemoglobin it would die because hemoglobin is used in warmer waters. They had warm water ancestors **Biogeography** - Different geographical areas sometimes exhibit plants and animals of strikingly similar appearance, even though the organisms may be distantly related - Natural selection favors parallel evolutionary adaptations in similar environments - Organisms that are very far away from each other can look similar because of convergent evolution **Biogeographical Studies** - Darwin noted on his voyage: - Islands are often missing plants and animals common on continents - Can live there if introduced - Species present on islands often diverges from continental relatives - Occupy niches used by other species on continents - Exactly like Darwin's finches - Island species usually are more closely related to species on nearby continents - Darwin Concluded: - Many islands have never been connected to the mainland - They are volcanic, created by volcanic eruptions over hot spots during plates converging - Species arrive on islands by dispersing across the water - Dispersal from nearby areas is more likely than distant sources - Reef Fish only found in Japan after nuclear explosion floated across pacific in a tire and made it all the way to Oregon - Colonizers often evolve into many species - Evolve to fill different niches - Creating a town, there are no dentist, police officer, firefighter-need to fill these jobs