Drivers of Evolution?
Beholden to Environment?
Genomes and Genome Evolution
4 May 2016
• TE-Thrust (Oliver and Greene 2009 & 2012)
• Ecology and Evolution
• Epi-transposon (Zeh et al. 2009)
• EC-TE Molecular Machine (Rey et al. 2016)
• Trends in Ecology and Evolution
Phyletic Gradualism v.
Agents of Speciation - TEs
• Class I and Class II
• From bacteria to mammals
• Traced to prokaryotes
• Larger genome, more TEs
• Mutagens, conserved by selection
• Direct contribution to genes and genome structure
• 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
• 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
• Why are some lineages diverse and others less
• Without TEs, species are trapped at adaptive
• 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
• 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?
• “…powerful facilitators of evolution that can act to
generate genetic novelties in both an active mode and a
• 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
Horizontal Transposon Transfer
• Important in TE “life cycle”
• 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.
• Most mobile of all mobile elements
• Exist exogenously or endogenously
• Restricted to vertebrates
• Bornavirus viral sequences appear to have a
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
• 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
• TE Thrust is not causal to adaptation,
speciation, punctuation events, or evolution.
• TE Thrust is causal to adaptation, speciation,
punctuation events, or evolution.
• Active DNA transposons – nonviable in most other mammals
for 37 Myr
• Early radiation around 30-36 Mya by Helitron transposon
• 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)
• True mice and rats
• Suite of rodent specific traits
• Homogenous populations of TEs suited for
• (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)
• 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
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
• Histone modifications
• DNA methylation
• Non-coding RNAs
Elements of the Hypothesis
• TEs have been a driving force in the
evolution of epigenetic silencing
• 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
• 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
• Regular agouti coat
• Expression of yellow
coat, obesity, Type II
• Passed to offspring
• 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
• Lineage specific patterns
• Adaptive radiations should be triggered by TE
Last, but not least…
• 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
• This EC-TE engine has been overlooked.
• Same epigenetic components
Future Study Organisms
• Organisms chosen must:
Be sensitive to global change
Can be manipulated under experimental conditions
Dispose genomic resources to facilitate monitoring
• Biotechnology and databases
• Experimental evolution
• Modify phenotype and monitor the genome
• Molecular engineering can help demonstrate the
• Scabiosa columbaria
• Demethylation restored depressed traits in inbred strains
• 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
• Global environmental change may trigger (or have
already triggered) this environmentally sensitive