Transcript TE-Thrust
Drivers of Evolution? Beholden to Environment? Transposable Elements Genomes and Genome Evolution 4 May 2016 Hypotheses Discussed • TE-Thrust (Oliver and Greene 2009 & 2012) • Bioessays • Ecology and Evolution • Epi-transposon (Zeh et al. 2009) • Bioessays • EC-TE Molecular Machine (Rey et al. 2016) • Trends in Ecology and Evolution Transposable Elements Phyletic Gradualism v. Punctuated Equilibrium Part I TE-THRUST Agents of Speciation - TEs • Mobile • Class I and Class II • Universal • From bacteria to mammals • Ancient • Traced to prokaryotes • Abundant • Larger genome, more TEs • Beneficial • Mutagens, conserved by selection Active Mechanisms • Direct contribution to genes and genome structure • “Neogenes” • V(D)J immune system • TEs within coding regions • Direct contribution to gene regulation • Tissue specific gene expression • Carriers of promoters and enhancers • Regulatory (micro) RNAs • Indirect retrotransposition/transduction of gene sequences • Retrogenes Passive Mechanisms • DNA duplication (or loss) by unequal recombination • Have repeats, have recombination. • Exon duplications • Gene duplications • Segmental duplications • Karyotypic changes • Prone to ectopic recombination • Intra-chromosomal DNA arrangements • Inter-chromosomal DNA arrangements TEs: Prerequisite for Evolutionary Radiation • Why are some lineages diverse and others less so? • Without TEs, species are trapped at adaptive peaks. • Presence of TEs permits: • New genes, modification of expression, rearrangement of chromosomes • Lineage or species-specific traits TE Accumulation Under Stress • Cost / Benefit of TE-facilitated variability in a host under stress. • Progeny inherit favorable adaptations. • Stressors that “activate” TEs • Oxidative stress • Viral infection • Heat shock • Genetic damage • Translational inhibition • Part of the normal physiological stress response? TE-Thrust (2012) • “…powerful facilitators of evolution that can act to generate genetic novelties in both an active mode and a passive mode.” • Expanded. Testable. Explicit. • Intragenomic potential of two flavors • Adaptive and Evolutionary • Standing variation • Realization of potential • Insecticides – adaptive • Radiations as in rats and bats – evolutionary Two Criteria for Speciation • Actual mechanism of speciation is still unclear. • Reproductive Isolation • Environment, ecology, hybridization, polyploidy, karyotypic changes • Intragenomic potential • TEs Horizontal Transposon Transfer • Important in TE “life cycle” • Transposons • P-element in Drosophila • Mariner in other insects • Less well documented in retro-TEs • BOV-B LINE • Gypsy-like retro-TEs • In 2010, 200 documented cases – 12 between phyla • Viruses, bacteria, endoparasites, intracellular parasites all likely vectors • TE amplification occurs immediately after HTT of a viable TE. Retroviruses • Most mobile of all mobile elements • Exist exogenously or endogenously • Restricted to vertebrates • Bornavirus viral sequences appear to have a function. From Retrovirus to Placenta • Major innovation over 160 Mya • Fusogenic ERVs of premammals resulted in the placenta • The platypus has no ERVs, but thousands of ancient Gypsy-class LTR retro-TEs • Numerous genes expressed in the placenta derived from retro-TEs and ERVs • Retroviruses abundant around head of sperm and coat the placenta • 5000+ species of placental mammals, less than 300 marsupials Four Modes of TE-Thrust • Mode 1: Stasis with Punctuation • Viable and heterogeneous TE population • Mode 2: Gradualism with Punctuation • Viable and homogenous TE population • Mode 3: Stasis • All quiet… • Mode 4: Gradualism • Nonviable and homogenous • Neutral to mildly deleterious subject to drift • Caveat: All else is equal. Testing the Hypothesis • Null • TE Thrust is not causal to adaptation, speciation, punctuation events, or evolution. • Alternate • TE Thrust is causal to adaptation, speciation, punctuation events, or evolution. Vesper Bats • Vespertilionidae • Active DNA transposons – nonviable in most other mammals for 37 Myr • Early radiation around 30-36 Mya by Helitron transposon Helibat • 3.4% in Myotis • Possible HTT of Helitrons? • Invertebrates, plants, and zebrafish • Further diversification 12-13 mya, corresponding with activity period of DNA transposons • What mechanisms are needed to generate such diversity? • (Mode 1 or 2) Murid Rodents • True mice and rats • Suite of rodent specific traits • Homogenous populations of TEs suited for passive TE-Thrust • (Mode 2) Naked Mole Rat • Most mammals have 35-50% of genome comprised of TEs. • Mole rat about 25% • “small mobilesome consortium” • Highly divergent TEs • Old and inactive • (Mode 3 or 4) Platypus • Bat and rats are small. • So are monotremes. • Conservative evolution – 120 Myr • Old and inactive elements • Truncated LINES • No ERVs • Never have been ERVs, HTT • No lineage specific TEs • (Mode 4) Green Anole / Tuatara • Anolis – Neotropical creatures • 400 species • 30% active TEs • DNA transposons are young and diverse • 68 families of 5 superfamilies • (Mode 1) • Tuatara – Less than 3% TE • In stasis (Mode 3) Final Remarks on TE-Thrust • Could be circumstantial. • More investigation • Cheaper sequencing • Other facilitators of evolution Part II EPI-TRANSPOSON HYPOTHESIS Epigenetics / Epigenomics • Epigenetics – heritable gene expression with no modification to underlying DNA sequence • Different phenotype, same genotype • Epigenomics – study of the arrangement and distribution of epigenetic patterns at the wholegenome level Epigenetic Regulators • Histone modifications • DNA methylation • Non-coding RNAs Elements of the Hypothesis • TEs have been a driving force in the evolution of epigenetic silencing mechanisms. • TEs are a source of novel genes. • Molecular domestication • Epigenetic repression of TEs breaks down due to stress. Breakdown of Silence • Many TEs were discovered in plants due to stress-induced phenotypes. • Drosophila – heat shock; TE-Dm412 increased • Shrimp – stress elevated TE expression • Epigenome is sensitive to stressful environment. • Air pollution, temperature extremes, famine, psychological stress, endocrine disruption, diet Agouti Signaling Protein in Mice • Avy allele of ASP • Retrotransposition silenced • Regular agouti coat expression • Retrotransposition active • Expression of yellow coat, obesity, Type II diabetes, predisposition to tumors • Passed to offspring Epi-Transposon Predictions • TE mobilization seeds the genome with noncoding elements that are conserved in evolution. • TE history follows a punctuated pattern. • New lineages are associated with bursts of TE activity. • Lineage specific patterns • Adaptive radiations should be triggered by TE mobilization. Last, but not least… EC-TE MACHINE Main Ideas • Having an understanding of the molecular trajectories that lead to phenotypic variation is central to evolutionary and conservation biology. • Epigenetic components (EC) and TEs strongly interact with one another and with the environment. • This EC-TE engine has been overlooked. • Same epigenetic components Future Study Organisms • Organisms chosen must: • • • • Be sensitive to global change Respond phenotypically Can be manipulated under experimental conditions Dispose genomic resources to facilitate monitoring Future Studies • Biotechnology and databases • Experimental evolution • Modify phenotype and monitor the genome • Molecular engineering can help demonstrate the link • Scabiosa columbaria • Demethylation restored depressed traits in inbred strains Conclusions • The EC-TE machine allows organisms to respond to contemporary environmental change by: • Tweaking phenotype • Adjusting heritable phenotype and genetic variation • Producing heritable phenotypes with differing levels of fidelity • Global environmental change may trigger (or have already triggered) this environmentally sensitive molecular engine. Questions?