Population analysis of retrotransposons in giraffe genomes supports RTE decline and widespread LINE1 activity in Giraffidae

Some self-copying DNA inside giraffes appears to be losing its ability to spread. These sequences reproduce by inserting copies into new positions in the genome. Giraffes inherited two major families of such DNA, but a large genetic comparison suggests that one remains active while the other is approaching inactivity.

Malte Petersen and colleagues examined three genome assemblies and sequencing data from 48 giraffes spanning the four species recognised in their analysis. They identified recent insertions, checked whether copies retained the machinery needed to reproduce, and compared patterns across populations. They also tested whether these markers recovered the population relationships identified in an earlier whole-genome study.

Of roughly 139,500 recent insertions identified, about 87% belonged to the still-active LINE1 family. The other family, RTE, had very few new full-length copies, while shorter sequences dependent on it had barely spread during the last two million years. Those genomic patterns support declining activity, rather than directly observing copying stop in living cells. The insertion markers also broadly supported four giraffe groups and reflected differences in their population histories. A giraffe genome therefore preserves more than inherited genes: it records which self-copying sequences are still spreading, and which are becoming evolutionary remnants.