Biology Reference
In-Depth Information
regulation [reviewed in Maksakova
et al.
, 2006; Sverdlov, 2000]. Also, see Cohen
et al.
(2009) for a more critical examination of the use of LTRs from endogenous
retroviruses as functional human promoters (Cohen
et al.
, 2009).
E. Brief evolutionary history
Despite the fact that a spectacularly diverse set of TE lineages proliferated during
the course of metazoan evolution, only a handful of families remain active within
modern humans (Furano
, 2004; Pritham and Feschotte, 2007). It has been
noted, for example, that mammals in general retain far fewer ancient L1 lineages
compared to the fish species that have been examined thus far, and, in primates,
this number has been whittled down to a single L1 family during the course of
human evolution (Furano
et al.
, 2004). The bulk of ancient transposon diversity
appears to have been lost during the evolution of tetrapods, possibly during
synapsid evolution (Kordis
et al.
, 2006). The forces leading to this shift in TE
genomic ecology remain unclear. Both demographic processes (e.g., population
bottlenecks) and molecular changes are likely to have played their part in the
transition. Evidence that only a handful of members of the L1 elements—so called
“hot” elements—exhibit the highest levels of activity (Brouha
et al.
et al.
, 2003; Seleme
et al.
, 2006), suggest that random demographic fluctuations could have profound
impacts on the persistance of TE diversity. As ecological sustainable population
sizes generally decrease within higher trophic levels, loss of TE diversity could
result from the fact that the loss of active lineages due to genetic drift occurs more
rapidly than new lineages are emerging. If drift were the predominant force driving
the loss of TE diversity, however, we would arguably find more examples of
lineages that have lost their entire L1 complement (Cantrell
et al.
, 2008;
Casavant
, 2000). The adaptive evolution of TE nucleotide and protein
sequences, possibly to evade host repression mechanisms, likely play a substantial
role in determining levels of TE diversity. Boissinot and Furano (2001) provided
convincing evidence, based on the ratio of nonsynonymous to synonymous amino
acid changes, that adaptive evolution occurred in the L1 lineage during the last
25 myrs of human evolution (Boissinot and Furano, 2001), although the evolu-
tionary pressures driving these changes have not been definitively established.
Alu elements arrived considerably later on the evolutionary scene than L1
and have enjoyed spectacular success, reaching approximately 1 million copies in
the haploid human genome. Thought to have evolved from the human
et al.
7SLRNA
gene during early primate radiation, Alus have far outperformed their L1, SVA, and
HERV counterparts. Examination of sequence data does suggest, however, that the
overall amplification rate of both Alu and L1 elements has attenuated over time
from a peak rate approximately 40-50 mya (Ohshima
,2003). The cause of the
amplification burst and subsequent attenuation has not been established, although
changes in host molecular biology and/or demographic effects, such as population
et al.
