An Age-of-Allele Test of Neutrality for Transposable Element Insertions

Blumenstiel, Justin P.; Chen, Xi; He, Mei; Bergman, Casey M.

doi:10.1534/genetics.113.158147

Cited by 69 publications

(110 citation statements)

References 63 publications

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“…Our assumption that TE insertions are mostly deleterious is also well supported (Yukuhiro et al, 1985;Mackay, 1989;Mackay et al, 1991;Houle and Nuzhdin, 2004;Blumenstiel et al, 2014;Pasyukova et al, 2004). Moreover it seems highly unlikely that a complex host defence mechanisms, such as the piRNA pathway; could have evolved if TEs were not deleterious.…”

Section: Discussionsupporting

confidence: 79%

piRNA clusters need a minimum size to control transposable element invasions

Kofler¹

2019

Preprint

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piRNA clusters are thought to repress transposable element activity in mammals and invertebrates. Here we show that a simple population genetics model reveals a constraint on the size of piRNA clusters: the total size of the piRNA clusters of an organism ought to exceed 0.2% of a genome. Larger piRNA clusters accounting for up to 3% of the genome may be necessary when populations are small, transposition rates are high and TE insertions recessive. If piRNA clusters are too small the load of deleterious TE insertions accumulating during a TE invasion may drive populations extinct before an effective piRNA based defence against the TE can be established. Our finding is solely based on three well supported assumptions: i) TEs multiply withing genomes, ii) TEs are mostly deleterious and iii) piRNA clusters act as transposons traps, where a single insertion in a cluster silences all TE copies in trans. Interestingly, piRNA clusters of some species meet our minimum size requirements while clusters of other species don't. Species with small piRNA clusters, such as humans and mice, may experience severe fitness reductions during invasions of novel TEs, possibly even threatening the persistence of some populations. This work also raises the important question of how piRNA clusters evolve. We propose that the size of piRNA clusters may be at an equilibrium between evolutionary forces that act to expand and contract piRNA clusters.

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Section: Discussionsupporting

confidence: 79%

piRNA clusters need a minimum size to control transposable element invasions

Kofler¹

2019

Preprint

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“…However, if this were true then some of the TR elements studied here may have once been FL inserts that became fixed but subsequently accumulated deletions over time. To confirm that TR and FL elements are indeed separate classes and not simply at varying stages of the drift-deletion process due to differences in age (Blumenstiel et al 2012), we compared the population frequencies of TR and FL insertions of similar age (<1% divergent from their consensus sequence) in the Central Florida green anole population. We determined the population frequency distributions of these age-matched sets of insertions to be significantly different ( P < 0.05, Mann–Whitney U test), thus strengthening our conclusion that TR elements can reach fixation relatively quickly and are subsequently removed by large deletions.…”

Section: Discussionmentioning

confidence: 99%

Lizards and LINEs: Selection and Demography Affect the Fate of L1 Retrotransposons in the Genome of the Green Anole (Anolis carolinensis)

Tollis

Boissinot

2013

Genome Biology and Evolution

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Autonomous retrotransposons lacking long terminal repeats (LTR) account for much of the variation in genome size and structure among vertebrates. Mammalian genomes contain hundreds of thousands of non-LTR retrotransposon copies, mostly resulting from the amplification of a single clade known as L1. The genomes of teleost fish and squamate reptiles contain a much more diverse array of non-LTR retrotransposon families, whereas copy number is relatively low. The majority of non-LTR retrotransposon insertions in nonmammalian vertebrates also appear to be very recent, suggesting strong purifying selection limits the accumulation of non-LTR retrotransposon copies. It is however unclear whether this turnover model, originally proposed in Drosophila, applies to nonmammalian vertebrates. Here, we studied the population dynamics of L1 in the green anole lizard (Anolis carolinensis). We found that although most L1 elements are recent in this genome, truncated insertions accumulate readily, and many are fixed at both the population and species level. In contrast, full-length L1 insertions are found at lower population frequencies, suggesting that the turnover model only applies to longer L1 elements in Anolis. We also found that full-length L1 inserts are more likely to be fixed in populations of small effective size, suggesting that the strength of purifying selection against deleterious alleles is highly dependent on host demographic history. Similar mechanisms seem to be controlling the fate of non-LTR retrotransposons in both Anolis and teleostean fish, which suggests that mammals have considerably diverged from the ancestral vertebrate in terms of how they interact with their intragenomic parasites.

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“…On top of holding most of the predictions of the ectopic recombination model, this model also predicts a positive correlation between the TE age (another family feature) and the TE frequency as observed for some TE families [56,57,58 ]. However, the equilibrium model still better explains the genome-wide TE dynamics as strong evidence of purifying selection was identified (reviewed in [60]).…”

Section: Te Dynamics In Insectsmentioning

confidence: 80%