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BIOS 209 Week 6 Ch. 8&9 Notes

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BIOS 209 Week 6 Ch. 8&9 Notes Bios 209

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This set of notes covers Chapter 8 on Development and Chapter 9 of Phylogeny. These notes go in depth of the concepts and the importance of these 2 concepts.
Organismal Biology
Bethia King
Class Notes
BIOS209, Organismal Biology
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This 6 page Class Notes was uploaded by De'Zhane' Notetaker on Thursday September 29, 2016. The Class Notes belongs to Bios 209 at Northern Illinois University taught by Bethia King in Fall 2016. Since its upload, it has received 42 views.


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Date Created: 09/29/16
 BIOS 209 Ch. 8 Development  Evolution and development   EVO­DEVO  1. Levels   2. Organism  3. morphogenesis= shape formation   4. Egg+ sperm= zygote  5. Formation of major body parts (eyes, limbs)  6. Location ( head vs, tail, back vs, belly , eyes, limbs)  7. repetition= segmentation  (legs, teeth, ribs, petals)  8. Rate at which body parts grow RELATIVE to each other in an individual may be isometric  Allometric  size of head when as you grow  5. Difference among species in timing or rate of development = heterochrony e.g allometry (jaw  grows faster  than top of skull for both species.)  Stripes initiated on zebra its the timing of growth Heterochrony  B. Molecular  9. Genes turn on/off (actually , make more or less, or none at all) = up regulated or down  regulate  10.HOW?  DNA­> RNA­> amino acids­> protein­> traits is chemical reaction so an signal that can affect a  chemical reaction can affect gene expression   11.Signal for upregulation or downregulation of gene expression may come from within same  cell  12.The genes that make these signals, i.e. these transcription factors , are called transcriptional regulatory genes  13.Signal may come from nearby cells or fluid ( RNA, protein, hormone)  14.Receptor is inside cell or on cell surface  15.Genes upregulate and downregulate in individual cells at different times  Upregulation for lens genes   “Simple cell signaling pathways”  C. Cell level mechanisms  16.Cell division (faster­> that part grow bigger) ex. Early animal embryo  17..Cell migration: seen with time­lapse photos  18.Stem cells can­> more stem cells or can undergo cell differentiation   How can stem cells daughter cells look different no mutation? Diff environment ­> diff genes  expressed  Often followed by organization into tissues  Tissues into organs   4. Programmed cell death  Signals from own or the cells set off reaction that activates nucleus and protease, which are  enzymes ­> cell shrinks then fragments  Fragments= surrounded by membranes.  Nearby cell engulf and break (phagocytosis)  D. gene loci:  19.Techniques to identify  genes controlling development. = types seen most frequently in  nature wild types  A. collect mutants based on phenotype then compare DNA base pair sequence, make sure  there are no difference in environment that might be affecting phenotype  20. Genes are grouped /named/ defined based on similarity in 21.The function or respect of phenotype 22.Base pair sequence  Any locus with a big effect on location and arrangement of body parts is called a homeotic gene (early discoveries of these loci were in Drosophila – fruit flies) + These loci's sequences were called Hox. Similar sequences were found in other parts of the fruit fly genome B. Hox genes 23.In what taxa? Animals 24.Often expressed in the same order that they are arranged on the given chromosome (Same order both temporally & spatially) Among different species, the Hox genes are highly conserved I.e. homologous, sequence of DNA is identical {color} or nearly identical {black} (2) Order of Hox gene clusters matches (3)Which body regions are regulated matches  Expressing Hox genes in the wrong segments can cause serious of phenotype Antennapedia mutant: legs where normally antennae 25.Eye development 26.[ Pax6] gene occurs in different animal species 27.If 1 of the alleles is nonfunctional 28.If scientist put a Pax6 from a sighted human in an insect in place of the insect's, what, happens? Insect eye develops in insects 29.Other gene also affect eye development I.e, eye development is polygenic BIOS 209 Ch. 9 Phylogeny What are Phylogenies? 1. Phylogenies are considered to be like family trees, but coming from MUCH farther back in time. + so look at taxa's (groups of related individuals) vs. Individuals to make manageable + Ex. Gibbons are humans 1 millionth cousin, 0ver 400,000 times removed Along with dogs are considered to be 27 millionth cousin, many times removed 2. Reading a phylogeny: focus on MRCA + when reading the phylogeny you must trace the given pairs back to the pivot point( most recent common ancestor) MRCA + based on the exact shape of a line wire via Left vs. Right is MEANINGLESS ( just convenient for diagramming) Unless an axis w/ units is given. + 2 trees are the same if 1 can be duplicated making another one without having to cut, remodel or reattach. + The twisting, rotating, bending or shrinking of lines is OK + The y axis is time , and only can be used in finding MRCA The taxa will end in a row always unless it is extinct (by ending sooner via. Extinct) 3. A clade is a monophyletic taxon = " a group of species which include an ancestral species & all its descendants" EX. Reptiles are not considered monophyletic since the bird was cut out 4. Taxonomy is a clue to Phylogeny Naming=Taxonomy + The diagram of evolutionary relatedness is called a phylogeny + Always remember to focus of the MRCA not the tips +The Classification level that indicates being most closely related is being in the same Species + The next closest is being from the same genus Ex. The Mangrove finch and the Woodpecker finch are of the same genus + When coming from the same genus should mean that they have a more recent common ancestor than a species of a different genera. 5. When considering a phylogenetic tree it is chosen by: Identifying monophyletic grouping(= Clade) by using computers to analyze the particular character types 6. The ideal use of a character can be: 7. Homologous not analogous 8. Have shared derived characters ( I.e NOT IN EVERY TAXON only the group that is being analyzed in 1 taxon.) < I.e not of ancestral> Derived = not a ancestor Do NOT use just for overall similarities + Rooted trees always show patterns of MRCA ( the distances between the lines are only meaningful sometimes.  Species we want to know evolutionary relationship is = ingroup  Groups we are confident is less closely related than all species in the ingroup;= reference point for analysis = outgroup  The rooted tree show location of most distant common ancestor (the root is what includes the in/out groups)  Trees if you cant find its rooting is called a unrooted tree When many taxa & characters, then to generate trees & pick best one via ( computer programming algorithms ) E.g., maximum parsimony method: assumes tree that requires fewest evolutionary changes Parsimony= idea that simpler hypotheses are preferable to more complicated ones  Applying Parsimony to DNA sequences each DNA nucleotide base pair is considered a separate character. Characters used in cladistics can include: 1. DNA bases (aligning the bases of the different taxa) EX. Species 1. CCAT CA Species 2. CCAT GT If species 1&2 had common ancestry, then DNA sequences were identical initially, they are homologous although they are not the same. 2 DNA products DNA->= transcribed into RNA->= translated into Amino acids->proteins-> traits PubMed: online, publicly available source of Scientific literature Sequences of DNA, function e.g, "GenBank" Computer program, e.g., BLAST to find & align your sequence with what's in the "Bank"  Uses statistical theory  Assesses probability that the observed similarity is due to having the same mutations by homology and evolution VI Rooted trees always show pattern of MRCA lines distances are meaningful if units are given E.g lengths from 1 most recent common ancestor [ pivot point] to the next, can indicate , since divergence :  # of nucleotide bp changes or amino acid changes  Time  Can convert from # to time if know time per # (or #per time) If DNA sequence are used as characters to create a phylogeny, how do we decide which gene loci to sequence? 9. Some gene loci evolve slowly [E.g DNA that codes for rRNA] so used for investigating evolutionary events I.e, branching points, of very long ago 10. Some gene loci evolve faster [e.g mtDNA] so used to explore evolutionary events sent to recent


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