Table 1.

Analogies between community ecology and genetic of transposable elements

Ecology	Genome
A species	*A TE species: a TE family or sub-familly
Ecological niche	Genomic niche: parameters defining interactions between a TE species and its environment
An individual	*A copy of a TE
Population	TE population: set of TE copies of the same species in the genome of the host
Community	TE community: set of TE copies in the genome of the host
Species richness	TE species richness: diversity (or number) of TE species in a given genome
Relative species abundance	Relative TE species abundance (derived from the number of copies of each TE species in a given genome)
Birth rate	*Transposition rate
Death rate	*Deletion rate
Demographic stochasticity	Demographic stochasticity of TE species: variation of the number of TE copies (or growth rate variation) of TE species arising from random differences among TE copies in transposition and excision
Ecological drift	Genomic drift: random loss of TE species diversity associated to demographic stochasticity in all TE species
Migration	Mixing of host populations or horizontal transfers between species
Speciation	Divergence in TE sequences from the reference sequence leading to another TE species
Stable coexistence	Coexistence of TE species resulting from their genomic niche partitioning
Neutral coexistence	Coexistence of TE species resulting from random loss (genomic drift) offset by speciation or migration
Ecosystem	The host- zygote
Ecosystem phenotype	The host-zygote phenotype and by extension the host-individual phenotype
Population of integrated ecosystem	Host population

^*Defined as in Le Rouzic et al [25].