Between the Fish Backbone and the Mammalian Branch
The birds, reptiles and amphibians hold the middle of the tetrapod tree. Birds and reptiles together form the sauropsid amniotes, while amphibians stand as the living link between water and land that genomic studies flag as pivotal for the water-to-land transition. The BrainStorm atlas samples them at cell-type resolution, exposing how lineage-specific circuits, glia and activity programs were assembled on deeply conserved ancestral frameworks.
Birds and Reptiles Together
Birds and reptiles are sister amniote lineages, 10 birds and 8 reptiles in the atlas. Together they reveal how maternal care, vocal learning and thermoregulation are patterned on shared sauropsid brain architecture.
The Amphibian Bridge
Three amphibians, the axolotl, the ribbed newt and the African clawed frog, represent the last non-amniote tetrapods in the atlas, sampling the earliest tetrapod configuration of the brain.
Cells in the Atlas
The 100-species analysis layer holds 49,052 bird cells, 38,486 reptile cells and 15,000 amphibian cells, capped at 5,000 cells per species for cross-species comparison.
Interneurons Tuned to Lineage-Specific Circuits
Inhibitory neurons in this part of the tree diversify not by inventing new programs but by redeploying conserved ones: ARX-centered GABAergic specification is pervasively conserved, while its downstream states are distributed according to lineage-specific circuit demands.
In_05_ARX
The interneuron subcluster In_05_ARX is enriched in birds, an example of independent tuning of inhibitory control to the demands of song-learning and vocal circuitry.
In_12_ARX
A second ARX-positive population, In_12_ARX, is enriched in amphibians, suggesting that distinct inhibitory branches were separately amplified in the bird and amphibian lineages.
In_18_BACH2
BACH2-positive interneurons (In_18_BACH2) are found in birds and reptiles, implying amniote-specific innovations in inhibitory modulation that predate the mammalian branch.
Regional Specialization in the Pallial Astrocyte
Astrocyte subclustering across the five major lineages reveals a stratified taxonomy: the most ancient clusters predominate in fishes and amphibians with progenitor-like SOX2 and PAX6 states, reptile and bird clusters diverge toward regionally specialized regulators, and mammal-restricted clusters reach the highest regulatory divergence.
HES5 · NKX2.2 · LHX2
Reptile- and bird-enriched astrocyte clusters show increased expression of HES5, NKX2.2 and LHX2, indicating enhanced regional specialization within the pallial and subpallial domains.
TBR1 · EMX2
Avian- and reptile-specific clusters express the unique regulators TBR1 and EMX2, further distinguishing the sauropsid astrocyte program from the mammalian one.
Ast_03_TRPS1
Among the resolution-0.5 astrocyte subclusters, Ast_03_TRPS1 is enriched in birds with a fold change of 4.29, a striking signal of a bird-specific astrocyte state.
A Graded Maturity Landscape Across Sauropsids
A complete oligodendrocyte lineage with a basic myelin program is already assembled in early jawed vertebrates. Across lineages, the core OPC-to-oligodendrocyte axis is conserved, but where in that axis cells accumulate differs strikingly: mammals lean toward mature states with a low transitional fraction, teleosts keep a higher progenitor share, and the birds and reptiles take this to an extreme.
Birds, Highest Progenitor Proportion
Among all lineages, birds show the highest progenitor (OPC) proportion in the oligodendrocyte lineage, a developmental strategy distinct from the mature-bias of mammals.
Reptiles, Transitional and Progenitor Bias
Reptiles show a markedly reduced mature-state fraction: turtle lineages are transitional-biased while lizard lineages are progenitor-biased, resolving two distinct glial configurations within reptiles.
Stated with Caution
These proportions are reported as descriptive biases; they are not controlled for brain region, study batch or phylogenetic relatedness, and are not treated as estimates of evolutionary rate.
Activity-Dependent States and a Regenerative Model
Amphibians carry both ancient neuronal programs and the axolotl, one of the most studied regenerative vertebrates. The amphibian samples root the tetrapod side of the atlas in the water-to-land transition.
EGR2 States
EGR2-marked populations, both the excitatory Ex_14_EGR2 and the inhibitory In_17_EGR2, are found in fishes and amphibians, pointing to a conserved activity-dependent regulatory state that predates the amniote brain.
Axolotl · Ambystoma mexicanum
The axolotl is one of the most studied vertebrates for regeneration research. Here it is newly profiled across four libraries in the BrainStorm atlas, its amphibian cell types forming part of the 15,000 amphibian cells in the analysis layer.
All 21 Species
Ten birds, eight reptiles and three amphibians from the 100-species atlas, listed by class following the species library table.
Birds · 10 Species
| Common Name | Latin Name | Type |
|---|---|---|
| Mallard | Anas platyrhynchos | Newly sequenced |
| Rock pigeon | Columba livia | Newly sequenced + public |
| Japanese quail | Coturnix japonica | Newly sequenced |
| Chicken | Gallus gallus | Public dataset |
| Bengalese finch | Lonchura striata domestica | Public dataset |
| Turkey | Meleagris gallopavo | Newly sequenced |
| Budgerigar | Melopsittacus undulatus | Newly sequenced |
| Atlantic canary | Serinus canaria | Newly sequenced |
| Common ostrich | Struthio camelus | Newly sequenced |
| Zebra finch | Taeniopygia guttata | Public dataset |
Reptiles · 8 Species
| Common Name | Latin Name | Type |
|---|---|---|
| Green anole | Anolis carolinensis | Public dataset |
| Painted turtle | Chrysemys picta | Newly sequenced |
| Yellow pond turtle | Mauremys mutica | Newly sequenced |
| Chinese pond turtle | Mauremys reevesii | Newly sequenced |
| Corn snake | Pantherophis guttatus | Public dataset |
| Chinese softshell turtle | Pelodiscus sinensis | Newly sequenced + public |
| Lizard | Pogona vitticeps | Public dataset |
| Turtle | Trachemys scripta elegans | Newly sequenced |
Amphibians · 3 Species
| Common Name | Latin Name | Type |
|---|---|---|
| Axolotl | Ambystoma mexicanum | Newly sequenced |
| Ribbed newt | Pleurodeles waltl | Public dataset |
| African clawed frog | Xenopus laevis | Public dataset |
Dive Deeper
All 100 Vertebrates
Browse the complete species catalog across all lineages.
Mammals
See how sauropsid programs compare with the mammalian branch.
Fish
Trace the basal jawed-vertebrate backbone beneath the tetrapods.
Cell Browser
Explore bird, reptile and amphibian cells interactively.