Evolution Exam Review PDF

Chapter 1 Classifica(on (Systema(cs): System of grouping species in a hierarchical classifica7on of groups nested within larger groups. Taxon (plural taxa): group of organisms assigned to any of the Linnean system Taxonomy: Discipline in charge of naming Taxa. Nomenclature: Rules...

Chapter 1 Classifica(on (Systema(cs): System of grouping species in a hierarchical classifica7on of groups nested within larger groups. Taxon (plural taxa): group of organisms assigned to any of the Linnean system Taxonomy: Discipline in charge of naming Taxa. Nomenclature: Rules to name taxa Evolu7on Change – 7me o In a popula7on over genera7ons o The central ideas of evolu7on are that life has a history — it has changed over 7me — and that different species share common ancestors. Phylogene7c tree = A hypothesis of the evolu7on of taxa. We use these phylogenies to support our biological classifica7on. Tips = things we observe (where the names are) Anagenesis – changes within a species  Cladogenesis – branching of a linage into two or more descendants o Have to include the split Cladogenesis is the branching of evolu7onary lineages, while anagenesis is the gradual change within a lineage Cladogram – topology Depicts only rela7onships The axis menas nothing o Basically, a cladogram uses lines that branch off in different direc7ons, represen7ng a group of organisms with a last common ancestor, ending at a clade model-based tree/addi7ve – changes between organisms from common ancestors branch length indicates evolu7onary distance the y axis means something branches from node to 7p have different lengths  lengths represent 7me change short = very similar between orgaisms scale bar = distance in the 7me/amount of change Dated Tree branch length indicates 7me of divergence 7me polytomy – unknown/par7ally resolved who are sisters & unrelated – cnt tell who separated from each other polyphyly – independent mul7ple ancestors – different lineages Monophyly – clades that has all descendant that share the most recent common ancestor  Paraphyle – does not include al descendat that share a most recent common ancestor – ones that share certain traits Homology – a trait present in an ancestor and its descendants Homoplasym – similari7es arrives via independent evolu7on Chapter 3 – building trees Homologue - The same organ in different animals under every variety of form and func7on Taxic homology – focuses on the similarity of physical structures or traits across different species, Molecular homology - molecular homology examines the similarity of molecules, particularly DNA and protein sequences.  o Sequence alignment o Insert gaps to get the same size Molecular data that can be aligned o DNA o RNA o Proteins/amino acids Morphology – need to study the organism Molecules – get the same gene and then get same sequence alignment OTUs (Opera7onal Taxonomical Units) = Terminals HTUs (Hypothe7cal Taxonomical Units) = Nodes, specia7on events Fully resolved vs unresolved  Hard polytomy – simultaneous divergence occurs So] polytomy – uncertainty of when divergence occurred Parsimony – only one that gives you cladograms o Simplest explana7on o The best hypotheses that required fewest evolu7onary changes o Uses the lowest number of changes because 7 required less of an explanta7on than others Modl based – require model of subs7tu7on 2 Maximum likelihood o Best probabilt of being true so eovluton can use it Bayesian o Needs to find tree wih higher exterior probability made by evolu7on § Prior informa7on Pr ( Data | Tree ) x Pr ( Tree ) ( Tree | Data ) = Pr ( Data )  Pr ( Data | Tree ) = Likelihood (calculated as before, but integra7ng the prior probability of all parameters) Pr ( Tree ) = The probability that our tree is the correct among all trees Pr ( Data ) = Summa7on of over all trees Molecular data 2 types of homology o Orthology – copies of the same gene across different animals o Paralogy - copies that exist within the same organisms/ different families § Gives incorrect phylogeny Molecular evolu7on Sequence evolu7on = changes in the nucleo7des / amino acids at a par7cular posi7on in that sequence Subs7tu7on = one base change into a different base at the same posi7on. Inser7on = one base appeared in the sequence without locally homologous posi7on Dele7on = one base disappeared in the sequence Mul7ple sequence alignemnet (MSA) - Progressive - calculates distance from sequences it decreases distance by making trees and new alignemnts - Itera7ve – subdivide alignemnst based on distanced bthen caulcualte the distance between subgroups and then merge and you keep repea7ng un7l you get a good tree Distance between two sequences - Transi7on A-G C-T - Transversions A-C, A-T, G-c, G-T Lineage sor7ng Horizontal gene transfer – not the same species so not due to evolu7on Introgression – Popula7on gene7cs Microevolu7on refers to small-scale changes within a popula7on or species over rela7vely short periods of 7me. This includes changes in allele frequencies, adapta7on to local environments, and the emergence of new traits within a specie Macroevolu7on refers to large-scale evolu7onary changes that occur over long periods, o]en leading to the forma7on of new species, genera, or higher taxonomic groups. It encompasses processes like specia7on, ex7nc7on, and the diversifica7on of life over vast 7mescales Microevolu7on = anagenesis o because it represents gradual changes within a single lineage over time, driven by the same microevolutionary processes that affect population Macroevolu7on = cladogenesis Cladogenesis, or branching evolution, is a fundamental mechanism driving macroevolutionary patterns and processes. It's the process where one ancestral species splits into two or more descendant species, leading to increased biodiversity and the formation of new lineages on the tree of life. Popula7on gene7cs o Study of the distribu7on of alleles in popula7ons and causes of allele frequency changes o In popula7on gene7cs, evolu7on is seen as a change in allele frequencies across genera7ons Allele frequencies o The propor7on of gene copies in a popula7on that are a given allele. Gene pool o The totality of genes of a popula7on Genotype o Genotype freq: Number of AA, Aa, aa/ total number of organism  Alleles o Allele freq: number of A or a / totl number of genotpes P = freq of dominant allele (one leaer) Q = freq of recessive allele (one leaer) P2 = freq of homozygous genotype (AA) Q2 = freq of homozygous recessive genotype (aa) Frequency of an allele (one leaer) = square root Microeveolu7onary mechanisms 1. natural selec7on environment puts pressure on certain alleles removed gene7c varia7on Selec7on occurs when individuals with different genotypes survive or make gametes at different rates 2. Muta7on VERY SLOWLY INCREASES gene7c varia7on in a popula7on Muta7on occurs when mistakes during meiosis turn copies of one allele into copies of another Subs7tu7on in nucleo7des 3. migra7on VERY FAST INCREASES gene7c varia7on into a popula7on occurs when individuals move into or out of the popula7on 4. dri] random events removed gene7c varia7on FASTER than natural selec7on dri] occurs when blind chance allows gametes with some genotypes to par7cipate in more fer7liza7ons than gametes with other genotypes  HWE= o NOOOO… Muta7on, gene flow, natural selc7on, o random ma7ng o infinite size popula7on o essen7ally no evolu7on Gene7c dri] Evolu7on results from chance events (survival, reproduc7on, inheritance) CHANCE PLAYS A KEY ROLE IN EVOLUTION For example, Meiosis. Unbiased Random fluctua7ons in allele frequencies are larger in smaller popula7ons Causes gene7c varia7on to be lost  Causes popula7ons that are ini7ally iden7cal to become different An allele can become fixed without natural selec7on Genealogy of genes Gene trees – Remember, we can reconstruct the evolu7onary history of genes too. Coalescence – When lineages of two gene copies merge we say they coalesce. Boaleneck effect Situa7on in which a popula7on is reduced to a small size for a small number of genera7ons Founder effects New popula7on is started from a small number of individuals Specific genes are carried into a new Zera finch in the lesser sundas islands was founded by 9 individuals Gene flow – the exchange of genes between two popula7ons Mixing of alleles from different popula7ons Can play two roles: Equalizes allele frequencies Introduce new alleles into a popula7on The result from dispersal: movement of individuals and gametes (migra7on  Muta7ons Central dogma o DNA à DNA (Self replicates) o DNA à RNA (transcrip7on) o RNA à PROTEIN (transla7on) Gene expression regula7on Genes are not expressed all the 7me, or not even in the same cells. Splicing: Removal of introns Alterna7ve splicing: removing exons too Exon shuffling: interchange of the exon posi7on at the mRNA strand Gene recombina7on Gene7c mixing results from gene(c recombina(on, a process that combines in a gamete a gene copy at one locus that was inherited from the maternal lineage, with a gene copy at a second locus inherited from the paternal lineage. Then, recombina(on rate (r) is the probability that recombina7on occurs between a given pair of loci. When an allele at one locus is found together in a popula7on more o]en than expected by chance with an allele at a second locus, we say these loci are in linkage disequilibrium. Meiosis – diplonema Crossing over Muta7ons Are the ul7mate source of varia7on Point muta7on – changes in single nucleo7des Structural muta7ons – inser7on of nucleo7des  JC69 (Jukes and Cantor 1969) = Assumes every nucleo7de has the same rate of changing into another nucleo7de. K80 (Kimura 1980) = Accounts different rates for transi7ons and transversions. HKY85 (Hasegawa et al. 1985) = unequal base composi7ons and asymmetrical subs7tu7on rates GTR (General reversible model) = each possible subs7tu7ons has its own probability Synonymous muta7on – change in nucleo7de from original but codes for the sam amino acid Nonsynonymous muta7on – change in nucleo7des codes for a different amino acid Nonsense muta7on – 3 stop codons Posi7ve/Darwinian- nega7ve/purifying selec7on Nonsynonymous/ synonymous > 1 > 1 = Muta7ons are favored – Posi7ve or Darwinian selec7on