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Supporting Evidence from the Primates Keith R Oliver1* and Wayne K Greene2

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Supporting Evidence from the Primates Keith R Oliver1* and Wayne K Greene2 Oliver and Greene Mobile DNA 2011, 2:8 http://www.mobilednajournal.com/content/2/1/8 REVIEW Open Access Mobile DNA and the TE-Thrust hypothesis: supporting evidence from the primates Keith R Oliver1* and Wayne K Greene2 Abstract Transposable elements (TEs) are increasingly being recognized as powerful facilitators of evolution. We propose the TE-Thrust hypothesis to encompass TE-facilitated processes by which genomes self-engineer coding, regulatory, karyotypic or other genetic changes. Although TEs are occasionally harmful to some individuals, genomic dynamism caused by TEs can be very beneficial to lineages. This can result in differential survival and differential fecundity of lineages. Lineages with an abundant and suitable repertoire of TEs have enhanced evolutionary potential and, if all else is equal, tend to be fecund, resulting in species-rich adaptive radiations, and/or they tend to undergo major evolutionary transitions. Many other mechanisms of genomic change are also important in evolution, and whether the evolutionary potential of TE-Thrust is realized is heavily dependent on environmental and ecological factors. The large contribution of TEs to evolutionary innovation is particularly well documented in the primate lineage. In this paper, we review numerous cases of beneficial TE-caused modifications to the genomes of higher primates, which strongly support our TE-Thrust hypothesis. Introduction extent of evolution on the different clades within that Building on the groundbreaking work of McClintock [1] lineage. and numerous others [2-14], we further advanced the proposition of transposable elements (TEs) as powerful The TE-Thrust Hypothesis facilitators of evolution [15] and now formalise this into The ubiquitous, very diverse, and mostly extremely ‘The TE-Thrust hypothesis’.Inthispaper,wepresent ancient TEs are powerful facilitators of genome evolu- much specific evidence in support of this hypothesis, tion, and therefore of phenotypic diversity. TE-Thrust which we suggest may have great explanatory power. acts to build, sculpt and reformat genomes, either We focus mainly on the well-studied higher primate actively by TE transposition and integration (active TE- (monkey, ape and human) lineages. We emphasize the Thrust), or passively, because after integration, TEs part played by the retro-TEs, especially the primate-spe- become dispersed homologous sequences that facilitate cific non-autonomous Alu short interspersed element ectopic DNA recombination (passive TE-Thrust). TEs (SINE), together with its requisite autonomous partner can cause very significant and/or complex coding, spli- long interspersed element (LINE)-1 or L1 (Figure 1A). cing, regulatory and karyotypic changes to genomes, In addition, both ancient and recent endogenizations of resulting in phenotypes that can adapt well to biotic or exogenous retroviruses (endogenous retroviruses environmental challenges, and can often invade new (ERVs)/solo long terminal repeats (sLTRs) have been ecological niches. TEs are usually strongly controlled in very important in primate evolution (Figure 1A). The the soma, where they can be damaging [16,17], but they Alu element has been particularly instrumental in the are allowed some limited mobility in the germline and evolution of primates by TE-Thrust. This suggests that, early embryo [18-20], where, although they can occa- at least in some mammalian lineages, specific SINE- sionally be harmful, they can also cause beneficial LINE pairs have a large influence on the trajectory and changes that can become fixed in a population, benefit- ing the existing lineage, and sometimes generating new * Correspondence: [email protected] lineages. 1School of Biological Sciences and Biotechnology, Faculty of Science and There is generally no Darwinian selection for indivi- Engineering, Murdoch University, Perth W. A. 6150, Australia Full list of author information is available at the end of the article dual TEs or TE families, although there may be © 2011 Oliver and Greene; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Oliver and Greene Mobile DNA 2011, 2:8 Page 2 of 17 http://www.mobilednajournal.com/content/2/1/8 A. B. Domestication C.C. Passive (8%) Other Gene Disruption (12%) Brain/ (2%) Metabolic/ (8%) other sensory (16%) Retrotransposition Exonisation (19%) (16%) (8%) Alu Immune LTR/ERV (44%) defense (33%) (17%) Reproduction/ Regulatory development L1 (54%) (47%) (15%) Figure 1 Summary of the effect of TEs on primate evolution. (A) Transposable elements (TEs) implicated in the generation of primate- specific traits. (B) Types of events mediated by TEs underlying primate-specific traits. Passive events entail TE-mediated duplications, inversions or deletions. (C) Aspects of primate phenotype affected by TEs. Based on the published data shown in Tables 3 to 6. exceptions, such as the primate-specific Alu SINEs in recombination, if the TE population is large, with the gene-rich areas [21,22]. Instead, according to the TE- potential for periodic punctuation events, or 2) stasis Thrust hypothesis, there is differential survival of those with the potential for periodic punctuation events if the lineages that contain or can acquire suitable germline TE population is small. repertoires of TEs, as these lineages can more readily • Mode 3: non-viable heterogeneous populations of adapt to environmental or ecological changes, and can TEs, in the absence of new infiltrations, result in pro- potentially undergo, mostly intermittently, fecund radia- longed stasis, which can sometimes result in extinctions tions. We hypothesize that lineages lacking a suitable and/or ‘living fossils’. repertoire of TEs are, if all else is equal, are liable to sta- • Mode 4: non-viable homogenous populations of TEs, sis, possibly becoming ‘living fossils’ or even becoming in the absence of new infiltrations, can result in: 1) gra- extinct. dualism as a result of ectopic recombination, if the TE TE activity is usually intermittent [23-27], with peri- population is large or 2) stasis if the TE population is odic bursts of transposition due to interplay between small. various cellular controls, various stresses, de novo synth- These modes of TE-Thrust are in agreement with the eses, de novo modifications, new infiltrations of DNA- findings of palaeontologists [29] and some evolutionary TEs (by horizontal transfer), or new endogenizations of biologists [30] that punctuated equilibrium is the most retroviruses. However, the vast majority of viable TEs common mode of evolution, but that gradualism and usually undergo slow mutational decay and become stasis also occur. Many extant ‘living fossils’ are also non-viable (incapable of activity), although some super- known. families have remained active for more than 100 Myr. We acknowledge that TE-Thrust acts by enhancing Episodic TE activity and inactivity, together with differ- evolutionary potential, and whether that potential is ential survival of lineages, suggests an explanation for actually realized is heavily influenced by environmental, punctuated equilibrium, evolutionary stasis, fecund ecological and other factors. Moreover, there are many lineages and adaptive radiations, all found in the fossil other ‘engines’ of evolution besides TE-Thrust, such as record, and for extant ‘fossil species’ [15,28]. point mutation, simple sequence repeats, endosymbiosis, TE-Thrust is expected to be optimal in lineages in epigenetic modification and whole-genome duplication which TEs are active and/or those that possess a high [31-35], among others. These often complement TE- content of homogeneous TEs, both of which can pro- Thrust; for example, point mutations can endow dupli- mote genomic dynamism [15]. We hypothesize four cated or retrotransposed genes with new functions main modes of TE-Thrust (Table 1), but as these are [36,37]. There may also be other, as yet unknown, or extremes of continuums, many intermediate modes are hypothesized but unconfirmed, ‘engines’ of evolution. possible. • Mode 1: periodically active heterogeneous popula- Higher primate genomes are very suited to TE- tions of TEs result in stasis with the potential for inter- Thrust as they possess large homogeneous mittent punctuation events. populations of TEs • Mode 2: periodically active homogenous populations Human and other extant higher primate genomes are of TEs result in: 1) gradualism as a result of ectopic well endowed with a relatively small repertoire of TEs Oliver and Greene Mobile DNA 2011, 2:8 Page 3 of 17 http://www.mobilednajournal.com/content/2/1/8 Table 1 Hypothesized major modes of transposable element (TE)-thrust Mode TE activity TE homogeneity TE population size Evolutionary outcome Type of TE thrust 1 Viable and intermittently active Heterogeneous Large Stasis with punctuation events Active Small Stasis with punctuation events Active 2 Viable and intermittently active Homogeneous Large Gradualism with punctuation events Active and passive Small Stasis with punctuation events Active 3 Non-viable/Inactive Heterogeneous Large Stasisa,b Minimalc Small Stasisa,b Minimalc 4 Non-viable/Inactive Homogeneous Large Gradualisma Passivec Small Stasisa,b Minimalc aUnless new infiltrations or reactivation of TEs occur. bFossil taxa are a possible outcome of prolonged stasis.
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