Evidence map›Paper›PMID 41846974›Full record

ArticlebioRxiv : the preprint server for biology2026

Recovering signatures of archaic introgression using ancestral recombination graphs.

Yulin Zhang, Arjun Biddanda, Sarah A Johnson, Colm O'Dushlaine, Priya Moorjani

Abstract readPreprint
PubMed Full text at PMC Publisher
In one paragraph

Article in bioRxiv : the preprint server for biology, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

0numbers the graph read from it
0cells of the map it votes in
0citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

0 citing papers in PubMed.

No citing paper in PubMed yet.

4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

5 authors.

Yulin ZhangCenter for Computational Biology, University of California Berkeley, Berkeley, CA, USA.ORCID 0009-0002-8899-5411
Arjun BiddandaDepartment of Biology, Johns Hopkins University, Baltimore, MD, USA.ORCID 0000-0003-1861-1523
Sarah A JohnsonCenter for Computational Biology, University of California Berkeley, Berkeley, CA, USA.ORCID 0000-0003-3034-0666
Colm O'Dushlaine54Gene, Inc. Washington, D.C., USA.ORCID 0000-0003-2858-3642
Priya MoorjaniCenter for Computational Biology, University of California Berkeley, Berkeley, CA, USA.ORCID 0000-0002-0947-5673

Funding

GENOMICST32HG000047 · NHGRI · UNIVERSITY OF CALIFORNIA BERKELEY · PI RASMUS NIELSEN, Daniel Soleyman Rokhsar · 2000 to 2026
$13.5M
NHGRI NIH HHS T32 HG000047
6 · The paper itself

Abstract

Neanderthal and Denisovan genomes have reshaped our understanding of archaic introgression. Yet, the limited number of archaic genomes sequenced and the reliance on unadmixed outgroups have left much of this history unresolved. We introduce TRACE, a method to identify archaic ancestry using features of ancestral recombination graphs inferred from contemporary genomes alone. Simulations show that TRACE reliably detects archaic introgression without requiring archaic genomes or unadmixed outgroups. Applied to 1000 Genomes data, TRACE recovers known Neanderthal and Denisovan introgression and reveals signals of ghost admixture from previously uncharacterized hominins in both Africans and non-Africans. Strikingly, ghost ancestry persists in Neanderthal and Denisovan ancestry deserts, challenging their interpretation as

Identifiers

PMID41846974
PMCPMC12991142

What Socratic holds

Textmetadata
LicenceCC BY-NC-ND
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the Socratic graph.