Comparative genomics sheds light on mammalian and avian gene regulation and phenotypic evolution

Anabella P. Trigila, Paula Beati, Dante Montini, Camila Jovicic, Paula de la Vega and Lucía F. Franchini ()
Additional contact information
Anabella P. Trigila: Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET)
Paula Beati: Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET)
Dante Montini: Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET)
Camila Jovicic: Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET)
Paula de la Vega: Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET)
Lucía F. Franchini: Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET)

Nature Communications, 2025, vol. 16, issue 1, 1-19

Abstract: Abstract The discovery of the genetic mechanisms underlying the emergence of phenotypic novelties is a cornerstone of evolutionary biology. To identify sequences in vertebrate genomes leading to the emergence of clade defining traits, we uncover genomic regions conserved across vertebrates that accumulated substitutions in a faster than neutral rate in the Avian or in the Mammalian basal lineages. We identify 2888 and 3476 noncoding avian and mammals accelerated regions, respectively, accumulating in key developmental genes in each lineage. Interestingly, we find that the neuronal transcription factor NPAS3, that carries the largest number of human accelerated regions, also accumulates the largest amount of noncoding mammals accelerated regions. We also detect that four NPAS3 noncoding mammals accelerated regions overlap previously identified human accelerated regions. Thus, we show that noncoding regions of particular large-effect genes are repeatedly targets of accelerated evolution, suggesting the existence of evolutionary hotspots underlying phenotypic innovation in different lineages.

Date: 2025
References: Add references at CitEc
Citations:

Downloads: (external link)
https://www.nature.com/articles/s41467-025-64134-2 Abstract (text/html)

Related works:
This item may be available elsewhere in EconPapers: Search for items with the same title.

Export reference: BibTeX RIS (EndNote, ProCite, RefMan) HTML/Text

Persistent link: https://EconPapers.repec.org/RePEc:nat:natcom:v:16:y:2025:i:1:d:10.1038_s41467-025-64134-2

Ordering information: This journal article can be ordered from
https://www.nature.com/ncomms/

DOI: 10.1038/s41467-025-64134-2

Access Statistics for this article

Nature Communications is currently edited by Nathalie Le Bot, Enda Bergin and Fiona Gillespie

More articles in Nature Communications from Nature
Bibliographic data for series maintained by Sonal Shukla () and Springer Nature Abstracting and Indexing ().