Lecture 20 figs - A Species 1 Species 2 Species 3 1AlB 2AZB...

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Unformatted text preview: A Species 1 Species 2 Species 3 1AlB 2AZB 3A3B 1A 2A 3A 3B 2B 13 O I O I I I I I I I I I Orthologs are genes diverging due to species lineages separating. Gene trees Species tree Paraiogs are genes evolving in parallel within species _ _ 1—Duplication after a duplication- 4—— Duplication 3 Eu ka ryotes E A B B A E Eu karyotes Archaea Bacteria TU Tu Tu Tu {3 G G Tu G Tu G Tu G I I C O I I I I I I I I I Archaea .Tu Rooter/T ‘K RRoot of ' ' Bacteria EF-Tu tree Duplication EF—G tree T—Dupllcauon FIGURE 5.20. Orthologs, paralogs, and rooting the tree of life. (A) Evolutionary trees of species and genes representing gene duplication events. (Left) The tree includes a species tree (thick gray lines) and gene trees (blue and red lines). A gene duplication event, leading to the coexistence of the blue and red paralogs in the root of the species tree, is labeled. The species tree subsequently splits twice, pro— ducing three species, each Of which has inherited the blue and red paraIOgs. (Righfi The gene tree is extracted from the species tree and untanglecl. The red forms of the gene, which are orthologs of each other, are mOre clOsely related to each other than to any Of the blue fOrms. The same is true fOr the blue forms of the gene. Note that the species relationships among the two groups of orthologs (red and blue) are the same. (5’) The same types of trees as in A, but these correspond to the evolution of elon— gation factors Tu and G across the three domains of life. The red and blue branches in the rightmost tree each correspond to a Tree of Life, and each is rooted by the paralogous elongation factor. 5.20A,B, redrawn from Eisen ].A., GenomeRes. 8: 163—167, © 1998 CSHLP,WWW.cshlpress. com Evolution © 2007 Cold Spring Harbor Laboratory Press Eukarya A B Animals Fungi Plants 1 2 3 4 ' Bacteria Archaea Other bacteria Cyanobacteria Crenarchaeota Euryarchaeota Algae Proteobacteria b /\r Q I C'I' t “ a / -“averisetoch “3 e5 " u ‘ _ Other single-cell eukaryotes Hyperthermophilic bacteria Common ancestral community of primitive cells FIGURE 5.23. Lateral gene transfer and the tree of life. (A) Gene transfer diagrammed on a hypo- thetical tree of four species. The horizontal red line shows the transfer of genes from the lineage of species 4 to that of species 3. The transferred genes then merge with the endogenous genes in the lineage of species 3, creating a chimera, where some genes have the "blue" ancestry and oth— ers have the "red" ancestry. (B) Gene transfer in the Tree of Life. The figure shows a reticulated network following the same general scheme as the rooted Tree of Life in Fig 5.21 with the bacte- ria as the deepest branching domain. However, many branch-crossing events (e.g., gene transfer from organelles to the nuclear genomes of eukaryotes) create a network, not a tree. Note that there is no single LUCA shown, i.e., no single common ancestor of all modern organisms, because gene transfer prevents the species tree from tracing back to a single organism. However, individual gene trees may still have a single LUCA. w I Y w Y V X X b Prob WXY WKYZ w x a PPP PPPP h PPA PPAP >L< C PAP PAPP d APP APPP / Z Y e PAA PAAP w Y E APB. APRIL g a HP Fr?” 1: AAA AAAA x z c W Z Y X W Z l_l;l_l Z Y X W l_lLl_| Y X W Z I_I;l_l X FIG. 3. The fusion of two genomes produces a cycle graph. In the left side of (a), three genomes, W, X, and Y, and the conditioning genome, C, ale represented as an unlooted tree just before descendants of W and Y fuse. In the right side of {a}, the immediate ancestors ofW and Y, represented by dots, have divided and ploduced W, Y, and their progeny, which fuse to ploduce the new organism Z. The probabilities of the genome alignment patterns found in the three-genome (W, X, Y) tree and in the four-genome (W, X, Y, Z) graph are shown at the left side of {h}. The two four-taxon trees that are simultaneously supported by the four genome patterns are shown on the right side of {h}. (c) The two simultaneously supponed four-[axon trees ale consistent with a repeating arrangement of genomes W Z Y X W Z Y X, which corresponds to the cycle glaph shown at the bottom ofthe figure. Eukaryetee Preteebaeteria Eepyta Gyenebaetetie Baeilli Euryereheea Figure 3 fiteehernetie diagram ef the ring pf life. The eulterpetee plus the twp eultenretie reet erpenierne {the eperetienel entl inferrnetienel enpeetere} eernpriee the eukaryetie reel rn [see Supplementary Dleeueelenl. Flneeetere defining rnejergreu pe in the preheryetle TERI l'l'l ENE if‘ldiflfltfld by eme II CiTCIES fll'l the ring. The flfflhflflflw, Shiller fll'l the bflflfll‘l‘l right, if‘lCIIJEf-ES the EUWfllflhflEfl, the Eflflflfl Eil'ld the if‘lfflfl‘f‘lfltifll‘lfll eukaryetie Eif'lCEEtflT. The Kareem-’5, ehewn en the upper right ef the ri hp, inelueee the Eeeyte and the inferrnetienel eukaryetie eneeeter. The upper left eirele includes the Preteebeetenefg and the eperetienel eukaryetie eneeeter. The meet heeel netle en the left repreeente the pheteepnthetie prelteryetee end the eperetienel eukerpetie eneeeter. Nehezna r # “Emma I , ’ Mier-eep-eridie Enigma”; 3.4; g .- " _ I-T“ .-' 1;; g m Hete'elelaeseans .l 'I I: Eu xi Parabaaalcls 3% % E Nchamnebae II' n = j _ - l-l- Ell I. A -% g 'g Myeetezcla . "-E'a E s I :- 93' I. 19%; Ea MIWMF'IEIBI'IS Dipllarr'nnadfi 'in Ciliates E ‘3} I Rhedephyles '. a {she -. 12.; Swing Emwn algae -I E” Demyne’ces I richly? I Createmenas Crs'PlfiPhil'tfl .' Efifi ' China: s r Eukaryete met 5 Fl - Miteeheedrial Cd. "3E4? pm I“ aeqaisiijnn '3' Animals .r' / '“a I .I' Fungi #3 Preke “yetes 4' ; 'Crclwn' grclups Figure 1 The general eutline ef eukaryete eyelutien preyided by rented rRHA trees. The tree has been redrawn and lTlflLlifiELl fI‘fllTl ref. 92. Until recently, lineages branching near the rent were thnught tn primitiyely lack lTlil'flCl'lfll'llLlI‘iEl and were termed fircheana". Exactly which archeanans branched first is nnt clearly resnlyed rlih'fl datal, hence the [Jnlytnniy {nmre than twn branches frnm the same nnde] inynlying diplnnlnnads, parabasalids and niicrn-spn-ridia at the rnnt. Plastid-bearing lineages are indicated in cnlnurs apprtnciniating their respectiye pigmentatinn. Lineages furthest away frnm the rnnt, including thnse with multicellularity, were thnught tn- be the latest-branching harms and were snmetimes misleadingly {see ref. till] called the ‘crnwn’ grnups. GhEHI'IEI Nudurlid ammhaa Fungl Hlnmpuridla Fungl Opiafl'buknrrta nnzqr—uzc \ Lubes-«a menu “MIMIiEII “ya-emu Wham: mum" Amhanmbm 1' G ?Ill-lllllllIlllIIIIIIIIIIIIIIIllllllllllllllllllll ) (D Dlplonmnads C) Flat:anan Hust GWMS 0 Pamhmdim E rate tax-El Trypanmrnafldi “5 Euglunids Tnmasb‘ '1: Dunmnads WE Jalmhlds Ciliataa Dlnuflagalu’naa }Numlm Aplmmplmn: Brawn algae Dlatums }51rammupllu “mum—naz—naafirn m—an—m Flhudphy'tan Arthuplullda Plum — Radlalarlans mammal" melnlrara Hfilfllmpmidiana Plasma-dinnfmridn Cflnmmnhphyms Emmanadi Euglyphld amoeba Gamma b-I-I'MH—J'J: ®?Cuflaflfly dabalad pmitian of ma rant 2‘“ Sawflawanduawnhiuah ® Hydmganunmas ® Hitmurnans or ran-1511’: ni‘tud1m1dria Acamhamueha ipp. ' Masfigamueha Miami-rm Phrsflfum PDWFEF’HWN‘ AMDEB UZDA (96¢ Dmtyuitehum disuurdeum "inn" Eli'sthde app. Usfliaga mam}: Fratemspungia 5p. Munasiga spp. flPIETHD “.0 “TA Dmsuphflfl mammal-aster Ham sap-fans 'Maiawimnnas cafifnrnialna' Mara win! ans-s jakabifu rmu‘s Hmcercummuides 5p. Trimasrf: pyrjmrmis METfi-M DHAEIA Hahn-manuals waginafis Spiro-nqu barhhanus Gfardia Fnresfinafia ".Efufiilfifi.‘ Andmwia Murmur: 'Jflhaha hahamensfs' Jflmm Imam 'Secuiflmvanas ecuadudensr's‘ Hfsflnna amid” Rech'numunas amerfcana DISCDBA Memorial 5p. Sawyeri‘a marylafldansis Erachyamneba flpaphnra Euymna yracms Tamar-Imam: 3p. Lefshmania 5p- Glaucucystis nasmchineamm Cyannphura pal-radars {Myra safiva Mmmmanafi SP; ,_ ARC HAEPLASTIDA Chis-m ydnnmnas remhard f1: Chanfl'rus tfispufi Famhym spp. I Péflfifinflfi’fififlmy 'CHRGMALVEDLATEE' “WM?” “3"” RHIZARIA L‘s-mammal: Magma-ada- Elfasmcys “'5 h nmfm's Thafl‘a SEiIJ-sfira pseudonana F'hp'mphmara spp. DIWWW'“ 'CHHDMALVEDLATEE' Tetrahymena 5|]. Tompflasma gut-n cm Alexandria”! tamarense Arnpmdmmm wrung EXCAVATA 35H: "‘1 .I mxlmUM support a Mitochondria b Hydmgenoscmes I: Mitusomas Py'uvatc E Pyruvato Py'uvate Plan-warn \i l \ o2 : PDH : F'FG PEG : ‘5 Fa --QF‘1 HDR mo : Q Fr Analyst-5A E O Acetyl-Cc-A H HspEO CD: ’ “$70 PF" ADP : O ADHE _ . Pl - MCF - ATE‘JCGIHNQ : © ASC Euccmars ACE mop] ' SWWI'COA E Succinyl-Crm ‘ STK 1‘ : Summit Funerals A P AP; I lch.ls¢S E (1an P' . Ich,lsc:S é —'II- - O : Re 63 : 2‘ Krebs cycle and 5 PFC: Eugiena AI except PFL: Trichomonas MCF complex I. II, III and : HYD; Nyctofhems PFL: Naooaflfmasi‘fx Enlamoeba IV in most forms E ADH E Chlamydomonas : PFL. Chiamydomonas : ASC: Trypanosoma : FRD: Fascioia : RC1: Fascioia and Eugiena g Fe—S clusters Figure 2 Enzymes and pathways found in various manifestations of mitochondria. Proteins sharing more sequence similarity to eubacterial than to archaebacterial homologues are shaded blue; those with converse similarity pattern are shaded red; those whose presence is based only on biochemical evidence are shaded grey; those lacking clearly homologous counterparts in prokaryotes are shaded green. a, Schematic summary of salient biochemical functions in mitochondria‘r‘”, including some anaerobic forms”'”. In, Schematic summary of salient biochemical functions in hydrogenosomesu'w. C, Schematic summary of available findings for mitosomes and ‘remnant’ mitochondria31 “'93. The asterisk next to the Trachipleistophom and Cgptosporidium mitosomes denotes that these organisms are not anaerobes in the sense that they do not inhabit Oz-POUI' (cnfaciors of electron transport) niches, but that their ATP supply is apparently lSig-independent. UQ, ubiquinone; CI, mitochondrial complex] {and II, III and IV, respectively}; NAD, nicotinamide adenine dinucleotide; MCF, mitochondrial carrier family protein transporting ADP and ATP; STK, succin ate thiokinase; PFC}, pyruvateferredoxin oxidoreductase; PDH, pyruvate dehydrogenase; CoA, coenzyme A; Fd, ferredoxin; HDR, iron—only hydrogenase; PFL, pyruvate:formate lyase; ASC, acetate-succinate CoA transferase; ADI-IE, bi—functional alcohol acetaldehyde dehydrogenase; FRD, fumarate reductase; RQ, rhodoquinone; Hsp, heat shock protein; Ich, iron—sulphur cluster assembly scaffold protein; IscS; cysteine desulphurase; ACS {ADP}, acetyl—CoA synthase (ADP—forming}. Eukaryate diversificatiOn 1- .I. I Mitochondriata ._'I eukaryote Gig-consuming _. __ a—proiaebacterium 'F _ -' Amitochondriate ' eukaryote I I a b _ _ c d __ /_<:-. E a f g .-” ‘-.-. v’ 1 - .J'-. . :‘h-‘fi‘e- 'I .—-—-. \ _"“/ ' “Fir. : a I II 1‘ ._ I t I I” - FE:- " “~- I I I I II .J >" ‘x i E a ' a 1 a a r = ilk/bf.) E E E u Archaebaclen'ai Kit-iv E E k/XI I \h—F : I I : II‘m“EIEttEl‘-'3’EE"'ial him With E Arfifiejfimfiflaflprt E Archaebaeterial host with : : : ‘ - E the common ancestcrr : w Egg: “'3 : mitochondrial symbiont . I _. ~ I : : of mitochondria and : y : (sulphur cycling} _ ' I —'|_|— I I , "-\ : hydmgennsomes E _ E I I I I ‘ ,.- : : : I . : : : e _- : . - . U . —I_I— - Methanogens - - “Emma” , - . . Thermoplasma : : : - I—'_ I I H S_ d I I I _ : I _ I pl’O Llciflg . . . . . HZ-cnnsurnlng - Archaebaclenum- 9h b . I I I I I I I I C: F]? I I : U - atchebaclerlum: fl : am fie a mum LN : : I i I i '. | : _ _. : : U : — ._ : i : x.) : "er" : : : *---r - k2” : t"... : Spimchaete rig-producing I‘v‘ Grampaeitive : 'i.;_*:-|._' are: :Hfflififlhacwfia :Gram-nagaliva . : Eybacifinurn I " _ : 02-Dansuming : stgnsuming I : eubacterium {:3 : lacnnabaflfirlum} I Hz'PmdUC‘”Q : u—preteebacterium : [1—prgiepbac13flum - - Em . : u—protechaetertum . . I ' we ' I I I I I {crenarchaec-te}: : : : Figure 4 |Modelsfor eukaryote origins that are, in principle, testable |with genome data. a—d, Models that prupuse the origin of a nucleus-bearing but arnitochnndriate cell first, followed the acquisition of mitachundria in a enkaryutic host. e—g, Models that prupuse the origin ufrnitnchundria in a prnkaryntic host, followed by the acquisition of eukaryutic-specific features. Panels a—g are redrawn tram refs 57 {a}, 58 {h}, 59 {El}, 6!} and 6] {d}, 62 {e}, 53 {f} and 64 {g}. The relevant microbial players in each model are labelled. Archaebacterial and en bacterial lipid membranes are indicated in red and blue, respectively. ...
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Lecture 20 figs - A Species 1 Species 2 Species 3 1AlB 2AZB...

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