How to Resurrect a
160-Million-Year-Old Genomic Fossil
A two-axis functional and mitochondrial-origin annotation of 189 ancient human NUMTs, and an ancestral-reconstruction test showing SLAIN1's lost cross-species alignment eroded rather than vanished.
Jayden · Life Sciences & Computer Science, NUS · Frith Lab, UTokyo · UTSIP 2026
You carry two separate sets of DNA
the big set, in the nucleus
a tiny, separate loop in the mitochondria
Every one of your cells keeps two completely separate sets of DNA, in two different places.
Sometimes one gets pasted into the other
mito DNA now sitting inside the nuclear DNA
Once in a while, a scrap of mitochondrial DNA gets pasted into the nuclear DNA. That stray copy is a NUMT: a genomic fossil, because many were pasted in long ago and carried ever since.
The copy starts identical, then it drifts
Right after the copy-paste, the nuclear copy is letter-for-letter identical to the mitochondrial original.
How we find a NUMT
We line up two stretches of DNA and see how well they match.
Two ways to find them: direct alignment (mitochondria vs nucleus) and cross-species alignment (nucleus vs nucleus). Together, all 189.
Prof. Frith's lab already found 189 of these ancient NUMTs in our DNA. The big question: are they just random junk, or do any still matter?
Three questions
- 1. Where did each NUMT come from: random, or chosen?
- 2. Where did they land: does any of it matter?
- 3. Can we bring a faded one back?
We'll answer each one as we go. (Numbers and details are in my back pocket for questions.)
Objective 1
Where did each fossil come from?
I built a pipeline that finds each NUMT's origin point in the mitochondria, then labels which gene it came from, matched against the reference annotation of the mitochondrial genome.
Spin the wheel: every spin lands on a part of the mitochondria. Keep spinning, your tally (top) fills in to match what we actually found (bottom).
Objective 1 · the answer
Where did each come from: random, or chosen?
Random: no plan.
Bigger genes are just bigger targets, so which parts become NUMTs is pure chance, exactly the spread the wheel gave.
Objective 2
Where did they land in our own DNA?
The pipeline also records where each NUMT sits in the nuclear DNA and classifies what's there (a gene, a control switch, or quiet DNA) from the genome's annotation.
found directly (mito vs nucleus) found cross-species (through other animals)
About half land in DNA that does something: regulatory, active, even exons. Both ways of finding them give the same split, so it's a real pattern, not a method bias.
Covered at the mid-presentation and in your handout, so I'll keep this brief and focus on Objective 3.
Objective 2 · the answer
Objective 2 asked where all 189 landed, and whether it matters. Here's the catch: most of our genome is junk DNA, the long stretches between and inside genes that don't do a job.
So by the same random logic as the spin-wheel, most NUMTs should land in that junk, shouldn't they?
Yet ours keep landing where DNA is working.
Objective 2 · the answer
So why would that happen?
In DNA, important parts change slowly, unimportant parts change fast. Like a country's laws versus a time you agreed to meet a friend: the important one is harder, and rarer, to change.
Objective 3 · the hero
Can we bring a faded fossil back?
Meet SLAIN1: of all 189 NUMTs, one of the oldest (traceable back ~160 My) and one of the slowest-changing.
The mouse carries the same NUMT, but it has mutated so much it no longer lines up with other animals' copies. The question is: did they ever match, were they the same to begin with?
Rewinding the fossil
SLAIN1’s mouse copy, lined up against our oldest cousins: the opossum and platypus, ~160 My away. (Nuclear DNA vs nuclear DNA.)
Today’s mouse copy, lined up against the oldest cousin.
Objective 3 · the answer
Can we bring a faded NUMT back?
Yes: it was never lost, just mutated out of sight.
The match the mouse had lost came back the moment we reconstructed its ancestor. And you carry SLAIN1 too: faded, but still there.
What comes next
Could we use this to find new NUMTs?
Rebuild the ancestral mitochondrial genome, run direct alignment with it against our DNA (the way we first found NUMTs), then check against Prof. Huang's known set. A first test says promising:
| animal | found by both | only the ancestral search found | only today's search found |
|---|---|---|---|
| human | 978 (94%) | ~74 ← new leads | 80 |
| mouse | 229 | 39 | 64 |
| sloth | 295 | 42 | 50 |
In us, it re-found 94% of the known NUMTs (so it works) and flagged ~74 spots today's genome misses.
Three questions, three answers
- 1. Where did each come from? → Random chance, no plan.
- 2. Where did they land? → Mostly in working DNA (a hint they might matter, not proof).
- 3. Can we bring a faded one back? → Yes, SLAIN1: never lost, just mutated out of sight.
Along the way: a labelled catalogue of all 189 ancient NUMTs, and a way to tell true loss from mere fading.
A 160-million-year-old genomic fossil, brought back into focus.
Your questions
Audience questions appear here live.