L27-Molecular Evolution +Evolution in Geological Time

Transcription

1 L27-Molecular Evolution +Evolution in Geological Time

2 Mutations Frameshift mutations can cause major amino acid changes, resulting in genetic diseases -anemia due to unbalanced globin protein production (thalassemia)

3 Mutations Chromosomal mutations that affect copy number ( ploidy ) and rearrangements Arise frequently during meiosis generally lethal trisomy 21-Down s

4 Gene duplications

5 Gene duplications enzyme A - supplies raw material for biological evolution B C duplication & divergence -Jianzhi Zhang, TREE substrate 1 2 -redundant functions facilitate emergence of new functions through the acquisition of mutations (1 gene /100 My in verts.) --leucine biosynthesis + TCA cycle --red + green sensitive opsins in humans

6 Gene duplications and new functions Subfunctionalizationparalogous division of labor Neofunctionalization-paralogs evolve novel attributes RNASE -> RNASE1 + RNASE1B -facilitates persistence on plant material -N acquired from cellulolytic gut bacteria

7 Gene duplications enzyme A -retention of ancestral functions balanced by acquisition of mutations B C duplication & divergence Duplicate genes acquire deleterious mutations and are pseudogenized substrate enzyme 1 2 A B C gene loss

8 Evolutionary forces behind gene duplication Dykhuisen-Hartl theory: random mutations are fixed in one gene under relaxed purifying selection, which is the result of reduced functional constraint provided by the redundancy >no need for positive selection

9 Evolutionary forces behind gene duplication Dykhuisen-Hartl theory: random mutations are fixed in one gene under relaxed purifying selection, which is the result of reduced functional constraint provided by the redundancy >no need for positive selection Multifunctional specialization: positive selection drives a multifunction-encoding gene to specialize, as enabled by the redundancy.

10 Mutations in nonprotein coding DNA Transcriptional regulation mutations can interfere with appropriate temporal or conditional expression Mobile genetic elements (transposons) likely not under selection, and can change, as well as introduce indel mutations (Micro)satellites repetitive sequences dispersed throughout the genome -Huntington s (>35 CAG repeats) -useful for phylogenetic/forensic analyses

11 Measuring genetic change transitional states are not always available multiple substitutions can obscure evolutionary history

12 Measuring genetic change Models of sequence evolution used to correct for differences between observed and expected species divergence

13 DNA substitution models of evolution Jukes-Cantor (homologous) -equal probability of character change Kimura Two-Parameter -pur->pur changes more likely than pur->pyr

14 DNA substitution models of evolution Felsenstein 1981 (F81) -similar to JC and K2P -accounts for base composition (25-75%) -assumes even distribution of base composition Thermus and Deinococcus are closely related but trees using base composition may not group them

15 DNA substitution models of evolution Felsenstein 1981 (F81) -similar to JC and K2P -accounts for base composition (25-75%) -assumes even distribution of base composition Hasegawa-Kishino-Yano 1985 (HKY85) -merges K2P and F81 Likelihood tests are used to evaluate the appropriateness of the model.

16 Frequencies of substitutions by nucleotide feature Empirical evidence about rates of change in different regions can parameterized to inform models sequence evolution

17 Nonuniform nucleotide site variation Limitations on sites that can vary can impact the rate of sequence divergence (A) can vary at 80% of sites at a rate of 0.5%/My but (B) varies at 50% of sites at a rate of 2%/My While site changes saturate more rapidly in (B) than (A), one might incorrectly infer that (B) is evolving more quickly.

18 Models of molecular evolution Haemoglobin alpha-globin present in most verts Comparison of a.a. changes between increasing different species shows a proportional increase in seq. distance Steady rate of change suggests that a-globin behaves in like a molecular clock

19 Models of molecular evolution Natural selection acts to remove deleterious mutations (purifying) while fixing those that confer fitness benefits (positive) -experimental evidence showed that at many loci up to an average of 30% polymorphism exist with an average heterozygosity of 11% If most mutations are deleterious, how can so much variation be maintained in populations

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21 Models of molecular evolution If most mutations are deleterious, how can so much variation be maintained in populations? Neutral mutations are those that do not confer selective costs

22 What type of mutation would most A. synonymous B. frameshi1 C. nonsynonymous D. 4 nucleo7de indel likely be neutral?

23 Models of molecular evolution If most mutations are deleterious, how can so much variation be maintained in populations? Neutral mutations are those that do not confer selective costs Motoo Kimura 1 st proposed the neutral theory of evolution in deleterious and selectively removed -neutral and slight chance of fixation

24 Models of molecular evolution Functional constraint strongly impacts the frequency of deleterious and neutral mutations and the rate of substitutions. Alpha-globins (essential for hemoglobin function) are under considerable functional constraint.

25 L27-Molecular Evolution +Evolution in Geological Time

26 AGE (Ma) MAGNETIC POLARITY HIST. ANOM. 1 C1 2 2A 3 3A 4 4A 5 5A 5B 5C 5D 5E 6 6A 6B 6C 7 7A CHRON. C2 C2A C3 C3A C4 C4A C5 C5A C5B C5C C5D C5E C6 C6A C6B C6C C7 C7A C8 C9 C10 C11 C12 C13 C15 C16 C17 C18 C19 C20 C21 C22 C23 C24 C25 C26 C27 C28 C29 30 C30 CENOZOIC PERIOD EPOCH HOLOCENE QUATER- NARY PLEISTOCENE* PALEOGENE NEOGENE PLIOCENE MIOCENE OLIGOCENE EOCENE PALEOCENE AGE CALABRIAN GELASIAN PIACENZIAN ZANCLEAN MESSINIAN TORTONIAN SERRAVALLIAN LANGHIAN BURDIGALIAN AQUITANIAN CHATTIAN RUPELIAN PRIABONIAN BARTONIAN LUTETIAN YPRESIAN THANETIAN SELANDIAN DANIAN GSA GEOLOGIC TIME SCALE v. 4.0 PICKS (Ma) MAGNETIC AGE POLARITY (Ma) HIST ANOM M0r M1 M3 M5 M10 M12 M14 M16 M18 M20 M22 M25 M29 CHRON. 30 C30 34 MESOZOIC C31 C32 C33 C34 RAPID POLARITY CHANGES PERIOD EPOCH TRIASSIC JURASSIC CRETACEOUS LATE EARLY LATE MIDDLE EARLY LATE MIDDLE EARLY AGE MAASTRICHTIAN CAMPANIAN SANTONIAN CONIACIAN TURONIAN CENOMANIAN ALBIAN APTIAN BARREMIAN HAUTERIVIAN VALANGINIAN BERRIASIAN TITHONIAN KIMMERIDGIAN OXFORDIAN CALLOVIAN BATHONIAN BAJOCIAN AALENIAN TOARCIAN PLIENSBACHIAN SINEMURIAN HETTANGIAN RHAETIAN NORIAN CARNIAN LADINIAN ANISIAN OLENEKIAN INDUAN PICKS (Ma) AGE (Ma) PALEOZOIC PERIOD EPOCH CARBONIFEROUS PERMIAN PENNSYL- VANIAN ORDOVICIAN SILURIAN DEVONIAN MISSIS- SIPPIAN CAMBRIAN LATE MIDDLE EARLY LATE MIDDLE EARLY LATE MIDDLE EARLY PRIDOLI LUDLOW WENLOCK Lopingian Guadalupian Cisuralian LLANDO- VERY LATE MIDDLE EARLY FURON- GIAN Epoch 3 Epoch 2 TERRE- NEUVIAN AGE CHANGHSINGIAN WUCHIAPINGIAN CAPITANIAN WORDIAN ROADIAN KUNGURIAN ARTINSKIAN SAKMARIAN ASSELIAN GZHELIAN KASIMOVIAN MOSCOVIAN BASHKIRIAN SERPUKHOVIAN VISEAN TOURNAISIAN FAMENNIAN FRASNIAN GIVETIAN EIFELIAN EMSIAN PRAGIAN LOCHKOVIAN LUDFORDIAN GORSTIAN HOMERIAN SHEINWOODIAN TELYCHIAN AERONIAN RHUDDANIAN HIRNANTIAN KATIAN SANDBIAN DARRIWILIAN DAPINGIAN FLOIAN TREMADOCIAN AGE 10 JIANGSHANIAN PAIBIAN GUZHANGIAN DRUMIAN AGE 5 AGE 4 AGE 3 AGE 2 FORTUNIAN PICKS (Ma) AGE (Ma) PRECAMBRIAN EON PROTEROZOIC ARCHEAN HADEAN ERA NEOPRO- TEROZOIC MESOPRO- TEROZOIC PALEOPRO- TEROZOIC NEOARCHEAN MESO- ARCHEAN PALEO- ARCHEAN EOARCHEAN PERIOD EDIACARAN CRYOGENIAN TONIAN STENIAN ECTASIAN CALYMMIAN STATHERIAN OROSIRIAN RHYACIAN SIDERIAN BDY. AGES (Ma) *The Pleistocene is divided into four ages, but only two are shown here. What is shown as Calabrian is actually three ages Calabrian from 1.8 to 0.78 Ma, Middle from 0.78 to 0.13 Ma, and Late from 0.13 to 0.01 Ma. Walker, J.D., Geissman, J.W., Bowring, S.A., and Babcock, L.E., compilers, 2012, Geologic Time Scale v. 4.0: Geological Society of America, doi: /2012.CTS004R3C The Geological Society of America. The Cenozoic, Mesozoic, and Paleozoic are the Eras of the Phanerozoic Eon. Names of units and age boundaries follow the Gradstein et al. (2012) and Cohen et al. (2012) compilations. Age estimates and picks of boundaries are rounded to the nearest whole number (1 Ma) for the pre-cenomanian, and rounded to one decimal place (100 ka) for the Cenomanian to Pleistocene interval. The numbered epochs and ages of the Cambrian are provisional. REFERENCES CITED Cohen, K.M., Finney, S., and Gibbard, P.L., 2012, International Chronostratigraphic Chart: International Commission on Stratigraphy, (last accessed May 2012). (Chart reproduced for the 34th International Geological Congress, Brisbane, Australia, 5 10 August 2012.) Gradstein, F.M, Ogg, J.G., Schmitz, M.D., et al., 2012, The Geologic Time Scale 2012: Boston, USA, Elsevier, DOI: /B

27 Evolutionary trends patterns of directional change over time Cope s rule-mammals get larger the longer they exist passive: constraint on size active: selection for size

28 Evolutionary trends Active trends through parallel change or species selection

29 Phyletic Gradualism New species arise through gradual transformation of ancestral species Darwin accepted gradualism as the primary means for species diversification - gaps in the fossil record were confounding 11

30 Phyletic Gradualism New species arise through gradual transformation of ancestral species 11

31 Punctuated Equilibria Niles Eldredge and Stephen J. Gould (1972) Prolonged stasis of well-adapted forms (not to exclusion of less well-adapted forms ) interrupted by rapid shifts from one state to another. May explain rapid evolutionary changes observed during Cambrian explosion 11

32 Punctuated Equilibria Niles Eldredge and Stephen J. Gould (1972) Prolonged stasis of well-adapted forms (not to exclusion of less well-adapted forms ) interrupted by rapid shifts from one state to another. Punctuated anagenesis: loss of ancestral state 11

33 Punctuated Equilibrium Pattern of change in the fossil record Long periods of little or no change (stasis) followed by rapid change Stasis is punctuated by rapid change A hypothesis about the evolutionary process Evolutionary change accompanied speciation which occurred off stage in small (allopatric) populations (i.e., subpopulations of a species). 10