Confocal micrograph of evolved snowflake yeast: elongated cells with cyan-stained cell walls and amber nuclei, branching outward from central attachment points against a black field.

Multicellularity Long-Term Evolution Experiment

Welcome to the MuLTEEverse

Fifteen populations of snowflake yeast, five in each of three metabolic environments, selected daily for how fast they settle. Running since 2018, past 9,000 generations, and still going.

How the experiment works

Generations: 9,000+
Populations: 15
Treatments: 3
Frozen samples: 3,000+
First transfer: 2018

Status maintained by the lab. Transfers continue daily.

The origin of multicellular life was one of the most profound transitions in the history of life on Earth, allowing for the evolution of the large, complex organisms we see today. Understanding how it happened has been extremely challenging, largely because the earliest steps occurred hundreds of millions of years ago and left almost no direct record. Here, we take the opposite approach: rather than reconstructing the transition from fossils and phylogenies, we run it forward under conditions we control. Each day, fifteen populations of snowflake yeast grow for 24 hours and are then selected for how fast they settle through liquid, which depends mainly on cluster size. The growth phase is also selective, and it favours the opposite: small clusters that divide quickly. Everything that has evolved since, from millimetre-scale bodies visible to the naked eye to whole-genome duplication, has come out of the tension between these two phases.

What the experiment has shown

Key results

01

Evolution of macroscopic size through cell elongation and branch entanglement

After 600 rounds of daily settling selection, roughly 3,000 generations, all five anaerobic populations evolved millimetre-scale bodies. Mean cluster radius rose from 16 µm to 434 µm, about a 20,000-fold increase in volume. Cells first evolved to be more elongate, lowering packing density and delaying fracture, and that elongation then let adjacent branches entangle so groups held together even after many mother-daughter bonds had broken. As a material, these organisms went from weaker than gelatin to as tough as wood.

Bozdag et al. 2023 · Nature 617:747–754
02

Convergent whole-genome duplication driven by size selection

Diploid snowflake yeast under size selection became tetraploid within the first 50 days and fixed tetraploidy by day 100 in all ten anaerobic and mixotrophic populations, then held it for the next 950 days. We hypothesize that tetraploidy arose because it brings immediate phenotypic effects, generating larger, longer cells that yield larger clusters. Relax that selection and the evolved tetraploids readily shed ploidy, so it is selection rather than genome stability holding the state in place.

Tong et al. 2025 · Nature 639:691–699
03

Stable coexistence of small and large lineages through frequency-dependent selection

In the obligately aerobic treatment, three of five populations split from a monomorphic ancestor into coexisting small and large lineages that persisted together for about 4,300 generations. Competitions started from many different frequencies converge on the same equilibrium, roughly 9% Large and 91% Small, which is negative frequency dependence rather than an unfinished sweep. The axis is dissolved oxygen: small clusters compete better during growth, large clusters survive settling better. Group size alone, with no differentiated tissues, was enough to partition a niche.

Pineau et al. 2024 · Nature Ecology & Evolution 8:1010–1020
04

Metabolically driven fluid flows sustain exponential growth at macroscopic scale

Diffusion should limit exponential growth to bodies about 50 µm across, yet evolved anaerobic clusters keep growing exponentially in static liquid up to about a centimetre. Above a threshold size, their own metabolism generates density gradients that drive persistent buoyant circulation, at speeds comparable to the flows extant organisms produce with cilia. The flows stop in dead or starved clusters and reverse when the chamber is flipped, confirming they are metabolically driven. Transport arrives before any transport organ evolves, providing a clear case of biophysical scaffolding.

Narayanasamy et al. 2025 · Science Advances 11:eadr6399
05

Convergent Hsp90 down-regulation underlies the evolution of cell elongation

All five anaerobic lineages that became macroscopic converged on reduced Hsp90 expression; the mixotrophic line that stayed microscopic did not. Less Hsp90 destabilises its client Cdc28, delaying mitosis and prolonging polarized growth, which is what makes cells longer. Restoring either gene shortened cells, shrank clusters and lowered fitness. A protein-folding system conserved across eukaryotes was therefore modified by selection acting on a group-level trait.

Montrose et al. 2024 · Science Advances 10:eadn2706
06

Loss of the first-division delay and the emergence of coordinated cell division

The anaerobic ancestor divides asynchronously because daughter cells take about 25% longer to complete their first division than later ones. That delay builds more branched topologies, which concentrate mechanical stress and fracture sooner. Synchrony is favoured twice over, improving growth during the 24-hour phase and survival during settling, so one cell-level timing change is visible to selection at both levels. Anaerobic populations had lost the delay by day 200 and stayed synchronous through day 1,000.

Cedeño-Pérez et al. 2025 · PLOS Computational Biology
07

Morphological entanglement is generic to growing branched organisms

Segmented 3-D electron-microscopy reconstructions showed evolved branches caged by two or more neighbours, in configurations that rigid-body translation and rotation cannot undo. Simulations found that the narrow geometric window familiar from non-living entangled materials applies only at short times; given continued growth, most permissible geometries eventually entangle. Timescale, not geometry, is the control variable, which means tough, fracture-resistant bodies can arise early and generically, before any developmental control evolves.

Day et al. 2024 · Physical Review X 14:011008

Before the MuLTEE

Two earlier results are often grouped with the ones above, but they come from separate work. In 2012, Ratcliff and colleagues showed that ten replicate populations of unicellular S. cerevisiae all evolved clonal snowflake clusters within 60 transfers of settling selection, and the genetic basis was loss of a single transcription factor, ACE2. In 2021, Bozdag and colleagues published the first 145 transfers of a 20-population experiment testing how oxygen affects size evolution, and found the relationship is not monotonic: intermediate oxygen suppressed size evolution, while both anaerobic and high-oxygen conditions permitted it. Fifteen of those twenty populations were kept running and became the MuLTEE. See the full history →

Three metabolic environments

Fifteen populations, five per treatment

Dense field of elongated snowflake yeast cells with teal cell walls, green interiors and magenta highlights.

PA1–5 Anaerobic

The only lines that became macroscopic

Metabolism: Obligate fermentation
Mitochondria: Petite; cannot respire

Because they cannot respire, these populations pay no oxygen-diffusion cost for large size. All five evolved millimetre-scale bodies, then tetraploidy, lost the ancestral first-division delay, converged on reduced Hsp90, and at large size began generating their own fluid flows.

A single microscopic snowflake yeast cluster rendered in depth-coded colour, blue through green to amber, against black.

PM1–5 Mixotrophic

Stayed microscopic, but not a control

Metabolism: Fermentation and respiration
Mitochondria: Intact

These lines stayed microscopic, but they underwent the same rapid whole-genome duplication as the anaerobic populations while remaining largely euploid afterwards. All five have since evolved hollow toroidal morphologies whose central opening drives rapid flow without cilia or flagella (unpublished).

Fluorescence micrograph of rounder yeast cells with red membrane and green cell-wall labelling.

PO1–5 Obligately aerobic

Size-based niche diversification under oxygen limitation

Metabolism: Obligate respiration
Carbon source: Glycerol; cannot be fermented

Growth requires dissolved oxygen, which makes oxygen a directly contested resource. Three of the five populations diversified into coexisting small growth specialists and large survival specialists, maintained for thousands of generations by negative frequency-dependent selection.

Images show cells from evolved populations. Line and timepoint attributions are drawn from our imaging archive and are listed on the Populations page.

Open science

Strains, data, and protocols

Strains & sequences

Welcome to the MuLTEEverse

Key results

Evolution of macroscopic size through cell elongation and branch entanglement

Convergent whole-genome duplication driven by size selection

Stable coexistence of small and large lineages through frequency-dependent selection

Metabolically driven fluid flows sustain exponential growth at macroscopic scale

Convergent Hsp90 down-regulation underlies the evolution of cell elongation

Loss of the first-division delay and the emergence of coordinated cell division

Morphological entanglement is generic to growing branched organisms

Before the MuLTEE

Fifteen populations, five per treatment

The only lines that became macroscopic

Stayed microscopic, but not a control

Size-based niche diversification under oxygen limitation

Strains, data, and protocols

Data & Strains

Publications

Glossary

Press