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Cell type evolution reconstruction across species through cell phylogenies of single-cell RNA sequencing data

Nature Ecology & Evolution volume 8, pages 325–338 (2024)Cite this article

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Abstract

The origin and evolution of cell types has emerged as a key topic in evolutionary biology. Driven by rapidly accumulating single-cell datasets, recent attempts to infer cell type evolution have largely been limited to pairwise comparisons because we lack approaches to build cell phylogenies using model-based approaches. Here we approach the challenges of applying explicit phylogenetic methods to single-cell data by using principal components as phylogenetic characters. We infer a cell phylogeny from a large, comparative single-cell dataset of eye cells from five distantly related mammals. Robust cell type clades enable us to provide a phylogenetic, rather than phenetic, definition of cell type, allowing us to forgo marker genes and phylogenetically classify cells by topology. We further observe evolutionary relationships between diverse vessel endothelia and identify the myelinating and non-myelinating Schwann cells as sister cell types. Finally, we examine principal component loadings and describe the gene expression dynamics underlying the function and identity of cell type clades that have been conserved across the five species. A cell phylogeny provides a rigorous framework towards investigating the evolutionary history of cells and will be critical to interpret comparative single-cell datasets that aim to ask fundamental evolutionary questions.

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Fig. 1: Percentage of variance described per PC.
Fig. 2: The inclusion of more PCs in the character matrix leads to a prevalence of noise, obscuring the phylogenetic signal.
Fig. 3: The formation of cell type clades improves when the number of PCs is reduced.
Fig. 4: A cell phylogeny of aqueous humour cells.
Fig. 5: Averaging replicate cells stabilizes relationships between and within cell type clades.

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Data availability

A GitHub repository (https://github.com/dunnlab/cellphylo) is provided containing select input, intermediate and output files (‘cellphylo/analysis/’) sufficient to reproduce the analyses.

Code availability

All custom code is available in our GitHub repository: https://github.com/dunnlab/cellphylo.

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Acknowledgements

We express our gratitude to members of the Dunn lab, including S. Church, for their invaluable feedback throughout this project. We would also like to thank J. Musser, G. Wagner, D. Stadtmauer, A. Chavan, D. Adams and L. Revell for insightful comments that greatly improved our manuscript and analyses. We thank the Yale Center for Research Computing for guidance and the cloud resources provided as a part of the AWS Cloud Credit for Research Program at Yale. J.L.M. acknowledges funding from the Gruber Foundation (Gruber Science Fellowship) and the Natural Sciences and Engineering Research Council of Canada (NSERC PGS-D).

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Authors and Affiliations

  1. Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA

    Jasmine L. Mah & Casey W. Dunn

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  1. Jasmine L. Mah
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Contributions

J.L.M. and C.W.D. conceptualized this study and developed its methodology. J.L.M. designed and conducted the formal analyses, investigation and visualization, wrote the manuscript and performed revisions. C.W.D. additionally supervised the project and contributed text, feedback and edits.

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Correspondence to Jasmine L. Mah.

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Nature Ecology & Evolution thanks Xavier Grau-Bové and the other, anonymous, reviewer(s) for their contribution to the peer review of this work.

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Extended data

Extended Data Fig. 1 Matrices created at each step of the workflow.

Each grey box represents a matrix, with the number of cells indicated. Matrices were processed separately for each species (‘Within-Species Analysis’ - steps 1-4), then combined into a single multi-species matrix (‘Cross-Species Analysis’ - steps 5-6) and rotated (step 7) to produce a 919 cell 919 principal component matrix. The matrices used for Figures 2–5 were subsequently built by subsetting from a 919 cell 919 PC matrix. Note that the step 7 matrix is re-calculated for each figure. The PCA (via the R function ‘prcomp’) is reproducible, but small differences are possible due to machine rounding error. Because of this, all input files for each figure are provided in the git repo (https://github.com/dunnlab/cellphylo) to ensure reproducibility. A step-by-step walk through to produce the results described by Figures 2, 4 and 5 are provided in the repo. The animal silhouettes were from PhyloPic (https://www.phylopic.org).

Extended Data Fig. 2 Cells cluster into multi-species cell type clusters after cross-species integration.

A UMAP plot of cells, colored by A. species identity and B. cell type identity. macF, Macaca fascicularis, macM, Macaca mulatta, CollectorChn, collector channel cell, CollectorChnAqVein, collector channel aqueous vein cell, Endo, endothelium, Endo-Corneal, corneal endothelium, Endo-Schlemms, Schlemm’s canal endothelium, Endo-Vasc, vascular endothelium, Epi-CiliaryNonPigment, non-pigmented ciliary epithelium, Epi-CiliaryPigment, pigmented ciliary epithelium, Epi-Corneal, corneal epithelium, Epi-Pigment, pigmented epithelium, JCT, juxtacanalicular tissue, NKT, natural killer T cell, my, myelinating, nmy, non-myelinating.

Extended Data Fig. 3 A cell phylogeny of 92 aqueous humor cells.

This phylogeny was created using the same methods as the 54 cell phylogeny of Figure 4, but was inferred from the 92 cell 20 PC matrix (Extended Data Fig. 1, step C1.1) that included one cell per cell type group per species for all 92 cell type groups. This matrix is more encompassing than the 54 cell 20 PC matrix (Extended Data Fig. 1, step C1.2), as it includes the unstable cell type groups that were excluded from the final analysis (Methods). Jumble scores are plotted at the nodes. The scale bar indicates units of expected evolutionary change. H. sap., Homo sapiens, M. fas., Macaca fascicularis, M. mul., Macaca mulatta, M. mus., Mus musculus, Sus. scr., Sus scrofa, my, myelinating, nmy, non-myelinating, JCT, juxtacanalicular tissue, NKT, natural killer T cell.

Extended Data Fig. 4 Felsenstein’s bootstrap is not a suitable measure of biological repeatability for a cell phylogeny.

The 54 cell phylogeny (Fig. 4) is annotated with Felsenstein’s bootstrap scores calculated from scjackknife trees. While scjackknife trees still produced cell type clades, cell clades among scjackknife trees frequently varied by a few cells. This subtle variability is not well captured by traditional bootstrap scores, which mark clades as present/absent based on the presence of all tips, without acknowledging the degree of similarity. Species and cell type groups are labeled at the tips; numbers refer to the cluster number of the cell type group. Cell type clades are indicated by vertical bars. The scale bar indicates units of expected evolutionary change. H. sap., Homo sapiens, M. fas., Macaca fascicularis, M. mul., Macaca mulatta, M. mus., Mus musculus, Sus. scr., Sus scrofa, JCT, juxtacanalicular tissue, my, myelinating, nmy, non-myelinating, NKT, natural killer T cell.

Extended Data Fig. 5 Leaf stability index by cell type.

Leaf stability indices (LSI) calculated from the Fig. 4 phylogeny are highly concordant with negligible spread within each cell type clade, with the exception of immune cells (NKT and macrophages). Mean LSI for each cell type is plotted and vertical lines indicate standard deviation. The number of tips per cell type label is indicated along the bottom as ‘n tips’. The standard deviation for n tips < 3 is not shown. Cell type labels are labeled along the x-axis. Superclades are indicated with horizontal lines. Endo-Vasc, vascular endothelium, CollectorChn, collector channel cell, NKT, natural killer T cell, JCT, juxtacanalicular tissue, Endo-Corneal, corneal endothelium, my, myelinating, nmy, non-myelinating.

Extended Data Fig. 6 The averaged tree exhibits high tip stability.

The leaf stability index (LSI) is plotted as tip color onto the Fig. 5 tree. Most tips exhibit an LSI close to 1, the maximum score. Species and cell type groups are labeled at the tips, with numbers referring to the cluster number of the cell type group. Cell type clades are indicated by vertical bars. The scale bar indicates units of expected evolutionary change. Inset: Mean LSI for each cell type is plotted and vertical lines indicate standard deviation. The number of tips per cell type label is indicated along the bottom as ‘n tips’. The standard deviation for n tips < 3 is not shown. Cell type labels are labeled along the x-axis. Superclades are indicated with horizontal lines. H. sap., Homo sapiens, M. fas., Macaca fascicularis, M. mul., Macaca mulatta, M. mus., Mus musculus, Sus. scr., Sus scrofa, my, myelinating, nmy, non-myelinating, JCT, juxtacanalicular tissue, CC, collector channel, NKT, natural killer T cell, Endo-Vasc, vascular endothelium, CollectorChn, collector channel cell, Endo-Corneal, corneal endothelium.

Extended Data Fig. 7 Neighbour joining tree calculated from averaged expression levels.

The neighbour joining method was used to calculate a phenetic tree from the averaged matrix (Extended Data Fig. 1, step D1) used to infer the Fig. 5 cell phylogeny. Cell type clades are indicated with vertical bars. Species and cell type groups are labeled at the tips, with numbers indicating the cluster number of the cell type group. H. sap., Homo sapiens, M. fas., Macaca fascicularis, M. mul., Macaca mulatta, M. mus., Mus musculus, Sus. scr., Sus scrofa, my, myelinating, nmy, non-myelinating, JCT, juxtacanalicular tissue, CC, collector channel, VE, vascular endothelium, NKT, natural killer T cell.

Extended Data Fig. 8 UPGMA tree calculated from averaged expression levels.

UPGMA was used to calculate a phenetic tree from the averaged matrix (Extended Data Fig. 1, step D1) used to infer the Fig. 5 cell phylogeny. Species and cell type groups are labeled at the tips, with numbers indicating the cluster number of the cell type group. Cell type clades are indicated with vertical bars. Red dots highlight cells that failed to group with their corresponding cell type clade. The Schwann cells and immune cells superclades are paraphyletic, as indicated with dashed lines. H. sap., Homo sapiens, M. fas., Macaca fascicularis, M. mul., Macaca mulatta, M. mus., Mus musculus, Sus. scr., Sus scrofa, my, myelinating, nmy, non-myelinating, JCT, juxtacanalicular tissue, CC, collector channel, VE, vascular endothelium, NKT, natural killer T cell.

Extended Data Fig. 9 WPGMA tree calculated from averaged expression levels.

WPGMA was used to calculate a phenetic tree from the averaged matrix (Extended Data Fig. 1, step D1) used to infer the Fig. 5 cell phylogeny. Species and cell type groups are labeled at the tips, with numbers indicating the cluster number of the cell type group. Cell type clades are indicated with vertical bars. Red dots highlight cells that failed to group with their corresponding cell type clade. The vessel endothelia superclade is polyphyletic, as indicated with dashed lines. H. sap., Homo sapiens, M. fas., Macaca fascicularis, M. mul., Macaca mulatta, M. mus., Mus musculus, Sus. scr., Sus scrofa, my, myelinating, nmy, non-myelinating, JCT, juxtacanalicular tissue, CC, collector channel, VE, vascular endothelium, NKT, natural killer T cell.

Extended Data Fig. 10 The topologies of the cell phylogeny and neighbour joining tree are broadly similar.

Neighbour joining was used to create scjackknife trees. The resulting scjackknife scores were plotted onto the Fig. 5 cell phylogeny. There is broad agreement at nodes defining cell type clades and the relationships between them. H. sap., Homo sapiens, M. fas., Macaca fascicularis, M. mul., Macaca mulatta, M. mus., Mus musculus, Sus. scr., Sus scrofa, my, myelinating, nmy, non-myelinating, JCT, juxtacanalicular tissue, CC, collector channel, NKT, natural killer T cell.

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Mah, J.L., Dunn, C.W. Cell type evolution reconstruction across species through cell phylogenies of single-cell RNA sequencing data. Nat Ecol Evol 8, 325–338 (2024). https://doi.org/10.1038/s41559-023-02281-9

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