Transposons in Eukaryotes (Part
B
): Genomic Consequences of Transposition
Authors: Lönnig Wolf‐Ekkehard 
Published: August 2015

The present contribution focuses on the known consequences of active transposition for the individual (∼100 human disease‐causing retrotransposon insertions have been recorded) and subsequently on the effects of
TEs
on populations over time (evolution), particularly on the arguments on
TEs
as ‘selfish
DNA
’ versus the ‘pacemakers of evolution’ inference (among them the effects of
Helitrons
in maize, the acclaimed V(D)J/
RAG1
transposon hypothesis and also putative cases of transposon domestications in the history of the angiosperms as well as plant and animal breeding). Basic problems involved in the
TE
domestication hypothesis are elucidated (chicken‐or‐egg dilemma, key point: ‘Is the host gene really derived from the
TE
, or did the
TE
capture the host gene?’). Moreover, a proposition for a synthesis of the different views is offered on the basis of the hierarchy of gene redundancies (the variable part) and the importance of loss‐of‐function mutations for regressive evolution, the origin of ecotypes and cultivated plants and animals. Last not least, open problems of
TE
research are addressed.

Key Concepts

TEs are causes of heritable and somatic diseases in humans and are also involved in the aging of mammalian tissues.

TEs display an immense detrimental potential by mutagenesis in individuals and populations.

The celebrated RAG1 transposon hypothesis is unproven, several scientific alternatives are available.

As there are no immediate phenotypic benefits of TE integrations in almost all cases described, there cannot be immediate selective advantages for the organisms harbouring them (evolution is not anticipatory).

TEs can spread even if they constitute a slight energetic burden for their hosts.

The enormous genetic differences in inbred maize lines (up to 75% noncolinearity mostly due to TEs; hundreds of complete genes and 10 000 gene fragments not shared, more than 1 000 000 SNPs, 30 000 indel polymorphisms) do not display correspondingly different phenotypes.

The C‐value paradox (even found in closely related species) cannot be explained by functional genetic advantages of the hosts thus affected.

The chicken‐or‐egg dilemma (which came first: the host gene or the more or less similar sequence in the TE?) raises doubts for the majority of the putative TE domestications supposed to be key events in evolution and breeding research.

The hypothesis that TEs belong to the most important factors in the origin of species in general and of higher systematic categories (
baupläne
) in particular is most probably false.

Nevertheless, losses‐of‐function mutations are important in regressive evolution, the origin of ecotypes, cultivated plants and animal husbandry. Gene inactivations by TEs have been assumed and in part already detected to be of particular relevance for these areas of research.

The documented segment of site‐specific positive TE (like LINE1 and
Alu
‐) functions in humans (and other organisms) could either be of primary origin (the deleterious effects due to new insertions thus being secondary) or in part belong to the category of substitutions of earlier gene functions perhaps comparable to the
syncytin
genes.