---
title: "qpAdm models for Middle Eastern ancestry: four streams and the collinearity discipline"
description: "The Middle East is where qpAdm's sources crowd closest together: Natufian, Anatolian, Iranian and Caucasus ancestries all interrelated. The working recipe, the right set that splits them, failure modes and a worked reading."
canonical: https://www.ancestrify.io/blog/qpadm-models-middle-eastern-ancestry
date: 2026-09-01T09:36:00+00:00
updated: 2026-09-24
author: "Andi Thomaj"
---

# qpAdm models for Middle Eastern ancestry: four streams and the collinearity discipline

[Europe teaches the standard recipe](/blog/qpadm-models-european-ancestry);
[South Asia teaches the proxy problem](/blog/qpadm-models-south-asian-ancestry); the Middle East
teaches **collinearity** — what happens when the candidate sources are themselves relatives. The
region's four founding streams share deep structure, exchange gene flow from the Neolithic
onward, and produce the classic pathology:
[wild weights, huge errors, models that pass while meaning little](/blog/why-qpadm-models-get-rejected#errors-and-odd-outputs).
Modelling here is a discipline of *making* the streams distinguishable before asking about them.

## The four streams

The Epipalaeolithic-to-Neolithic Near East resolves into four deeply divergent but
**interrelated** ancestries:

- **Natufian / Levant_N** — the Epipalaeolithic Levant and its early farmers.
- **Anatolia_N** (Barcın) — northwest Anatolian farmers,
  [Europe's EEF source](/blog/qpadm-models-european-ancestry).
- **Iran_N** (Ganj Dareh) — early Zagros farmers.
- **CHG** (Kotias/Satsurblia) — Caucasus hunter-gatherers, Iran_N's closest deep relative.

Iran_N and CHG are the notorious pair — close enough that
[naive models cannot split them](/blog/is-qpadm-still-reliable) — with Natufian↔Anatolia_N the
second-tightest edge. Later prehistory then stirs the pot continuously, which is why this region,
more than any other, runs on the [distal discipline](/blog/qpadm-distal-vs-proximal): all four
sources predate the mixing they explain.

## The standard recipe

**Left:** target + two to four of `Levant_N` (or `Natufian`), `Anatolia_N`, `Iran_GanjDareh_N`
and `Georgia_CHG` — chosen by geography, and *never* Iran_N and CHG together in a first model:
[lowest rank first](/blog/qpadm-best-practices) means starting two-source (Levantine targets:
Levant_N + Iran_N; Anatolian/Mesopotamian: Anatolia_N + Iran_N or + CHG) and letting
[the rank test](/blog/qpwave-explained) decide, relative to the right set, whether a further
source is needed. Testing the lowest rank first is statistical parsimony: the simplest model that
fits, relative to the right set used; it is not a head count of the migrations in anyone's history.

**Right:** the region's models live or die on the **o9a-style extension** of
[the O9 spine](/blog/how-to-choose-qpadm-sources-and-outgroups#the-standard-right-sets): `Mbuti.DG`, `Ust_Ishim.DG`,
`Mota.DG`, `MA1`, `Ami.DG`, `Onge.DG`, plus the discriminators — `Russia_EHG`, `WHG`,
`Morocco_Iberomaurusian` (the North African edge, essential for Levantine and Egyptian-adjacent
targets), and where the source list allows it, whichever of the four streams sits *out* of the
left set. This is the published case where the machinery visibly rewards craft: the Bronze Age
Levant work found one added differentially-related outgroup **cut standard errors roughly
threefold** — the exact anti-collinearity lever, applied.

Later-era targets (Bronze Age onward, and all moderns) usually need a **steppe-related** fourth
column (`Yamnaya`/`Sintashta`-related, for Anatolian, Iranian-plateau and Levantine-diaspora
targets) and, for the Arabian peninsula and Horn-adjacent targets, an African stream
(`Mota.DG`-related or `Egypt`-adjacent proxies) — each addition paid for by
[a nested-model rejection](/blog/qpadm-model-record-explained), never added on vibes.

## The named failure modes

- **The Iran/CHG seesaw.** Both in the left set with a generic right set: weights trade against
  each other run to run, SEs balloon, sometimes
  [one goes negative](/blog/why-qpadm-models-get-rejected#negative-weights). Fix from the right (EHG,
  steppe-related and Anatolia contrasts split them best), or accept the honest merged reading —
  "Iranian/Caucasus-related" as one stream — when
  [the data sit below the resolution floor](/blog/is-qpadm-still-reliable).
- **Missing North Africa.** Levantine and coastal targets modelled without an
  Iberomaurusian-related term fail — or worse, pass with distorted Natufian weights (Natufians
  themselves relate to North African lineages; the right set must be able to see that edge).
- **Umbrella labels.** `Iran_N` pooling Ganj Dareh with later Chalcolithic plateau samples, or
  Levant labels pooling PPNB with Bronze Age —
  [check the .anno](/blog/aadr-sample-labels-sg-dg-ho-explained); era-pure source labels are
  worth more here than anywhere.
- **Modern reference temptation.** Using present-day populations as sources for other moderns,
  the proximal shortcut, gives up temporal order: on simulated admixture-graph histories
  (Flegontova et al. 2025), [proximal screens on the rotating protocol](/blog/qpadm-distal-vs-proximal)
  had median false-discovery rates of 72.5 to 100%. On the same study's simulated stepping-stone
  landscapes the protocols compared did not differ significantly, and neither result is an error
  rate for real studies. The region's dense ancient record makes the distal frame available; use it.

## A worked reading

A Lebanese-ancestry target: p = 0.24, Levant_N 0.58 ± 0.027, Iran_N 0.28 ± 0.031, Anatolia_N
0.09 ± 0.025, Yamnaya-related 0.05 ± 0.014; nested three-source models rejected; ~680k SNPs;
Iran_N/CHG swap re-run shifts weights within one SE (stability check passed). Reading: compatible
and consonant with the published Bronze-Age-Levant-plus-steppe-trickle picture; the Anatolia term
sits [barely two SEs from zero](/blog/how-to-read-qpadm-p-value-z-score-standard-error), so the
honest report flags it as the model's softest claim; and the swap test is the region's signature
move — [a result that survives proxy rotation](/blog/qpadm-best-practices) is the only kind worth
publishing here.

Terms used here are defined in the [glossary](/glossary).

## References

- Lazaridis, I. et al. (2016). Genomic insights into the origin of farming in the ancient Near
  East. *Nature*, 536, 419–424. (The four-stream framework and O9.)
- Agranat-Tamir, L. et al. (2020). The genomic history of the Bronze Age Southern Levant. *Cell*,
  181(5), 1146–1157. (o9a and the threefold SE reduction.)
- Feldman, M. et al. (2019). Late Pleistocene human genome suggests a local origin for the first
  farmers of central Anatolia. *Nature Communications*, 10, 1218.
- Haber, M. et al. (2017). Continuity and admixture in the last five millennia of Levantine
  history. *American Journal of Human Genetics*, 101(2), 274–282.
- Flegontova, O. et al. (2025). [Performance of qpAdm-based screens for genetic admixture on graph-shaped histories and stepping stone landscapes](https://doi.org/10.1093/genetics/iyaf047). *Genetics*, 230(1), iyaf047.