Network inference at single-cell resolution reveals morphoregulatory divergence and multilayered buffering in limb evolution
- 1Centro Andaluz de Biologia del Desarrollo (CABD-CSIC), Sevilla, Spain
Abstract
How changes in conserved developmental genetic programs contribute to morphological evolution remains poorly understood, particularly in non-conventional model species. Here, we combine single-cell transcriptomic and chromatin-accessibility profiling with cross-species label transfer and gene regulatory network inference to compare mouse and pig limb development. Our analyses identify broadly conserved cellular organization but discrete divergence in HOX-, FGF- and SHH-regulated programs. FGFR inhibition in mouse limb buds phenocopies the distal expansion of pig GREM1 expression, while altered SHH responses and anterior-posterior polarity converge on the PTCH1 regulatory landscape. Its functional dissection reveals degeneration of a limb regulatory module in artiodactyls, conservation of an additional distal enhancer, and extensive redundancy among cis-regulatory inputs. Allele-specific analyses further show that reduced Ptch1 dosage is buffered by transcriptional compensation. Together, these findings reveal how cis-regulatory and pathway-level robustness can accommodate distributed regulatory change while preserving developmental function, providing a mechanistic framework for the evolution of artiodactyl limb morphology.
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BibTeX
@misc{alcainacaro2026network,
title = {{Network inference at single-cell resolution reveals morphoregulatory divergence and multilayered buffering in limb evolution}},
author = {A. Alcaina-Caro and I. Sospedra-Arrufat and V. Tissieres and I. Salvador-Martinez and L. Almorox and J. J. Pawluk and A. Diaz-Rueda and A. Fernandez-Minan and A. Hurtado and F. Martinez Real and D. Lupianez and B. Pernaute and A. Visel and M. Osterwalder and H. Heyn and J. J. Tena and G. Nusspaumer and J. Lopez-Rios},
howpublished = {bioRxiv},
year = {2026},
month = nov,
doi = {10.64898/2026.11.07.765081},
url = {https://www.biorxiv.org/content/10.64898/2026.11.07.765081v1},
note = {CC BY-NC-ND},
}
RIS
TY - UNPB
TI - Network inference at single-cell resolution reveals morphoregulatory divergence and multilayered buffering in limb evolution
AU - A. Alcaina-Caro
AU - I. Sospedra-Arrufat
AU - V. Tissieres
AU - I. Salvador-Martinez
AU - L. Almorox
AU - J. J. Pawluk
AU - A. Diaz-Rueda
AU - A. Fernandez-Minan
AU - A. Hurtado
AU - F. Martinez Real
AU - D. Lupianez
AU - B. Pernaute
AU - A. Visel
AU - M. Osterwalder
AU - H. Heyn
AU - J. J. Tena
AU - G. Nusspaumer
AU - J. Lopez-Rios
PY - 2026
DA - 2026/11/07
PB - bioRxiv
DO - 10.64898/2026.11.07.765081
UR - https://www.biorxiv.org/content/10.64898/2026.11.07.765081v1
AB - How changes in conserved developmental genetic programs contribute to morphological evolution remains poorly understood, particularly in non-conventional model species. Here, we combine single-cell transcriptomic and chromatin-accessibility profiling with cross-species label transfer and gene regulatory network inference to compare mouse and pig limb development. Our analyses identify broadly conserved cellular organization but discrete divergence in HOX-, FGF- and SHH-regulated programs. FGFR inhibition in mouse limb buds phenocopies the distal expansion of pig GREM1 expression, while altered SHH responses and anterior-posterior polarity converge on the PTCH1 regulatory landscape. Its functional dissection reveals degeneration of a limb regulatory module in artiodactyls, conservation of an additional distal enhancer, and extensive redundancy among cis-regulatory inputs. Allele-specific analyses further show that reduced Ptch1 dosage is buffered by transcriptional compensation. Together, these findings reveal how cis-regulatory and pathway-level robustness can accommodate distributed regulatory change while preserving developmental function, providing a mechanistic framework for the evolution of artiodactyl limb morphology.
ER -