Data from: Heterochronic shifts in a timing-keeping microRNA are associated with multiple instances of neoteny in plants

Published Sep 04, 2025 on Dryad. https://doi.org/10.5061/dryad.573n5tbdv

Abstract

The prolonged production of juvenile traits and an associated reduction or loss of adult traits during development (neoteny) can either arise from a change in genes that mediate the timing of the shift between juvenile and adult traits (timing genes) or from changes in genes that are necessary for the development of adult traits (target genes). To date, the relative contribution of each developmental mechanism to the origins of neoteny remain unclear. We examined this question in the plant genus, Acacia Mill., which contains species that undergo thejuvenile-to-adult vegetative transition (vegetative phase change) early in shoot development, as well as species that remain permanently juvenile, or have delayed vegetative phase change. Mapping the timing of vegetative phase change onto a molecular phylogeny of Acacia revealed that permanent juvenility has evolved multiple times and is sometimes associated with a delay in vegetative phase change in related species. In three cases, the absence or delay in vegetative phase change was associated with either higher amounts or a delayed decline in level of miR156, the master regulator of vegetative phase change in plants. These findings support the hypothesis that neoteny in Acacia has evolved not by a loss in the capacity to produce the adult leaf phenotype, but by a change in the timing of genes that promote juvenile leaf identity.

Data supporting the analysis of heterochrony in Acacia.

Description of the data and file structure

Phylip formated supermatrices, phenotypic data, and tree files. Associated ddRAD-seq libraries available at Bioproject PRJNA988539.

Sharing/Access information

This dataset contains the following:

fullsamples_30-3.phy DNA supermatrix from all libraries with minimum individuals of 30 (min) and max individuals with shared heterozygous sites of 3 (maxSH)
fullsamples_30-6.phy min=30, maxSH=6
fullsamples_60-3.phy min=60, maxSH=3
fullsamples_60-6.phy min=60, maxSH=6
fullsamples_90-3.phy min=90, maxSH=3
fullsamples_90-6.phy min=90, maxSH=6
fullsamples_120-3.phy min=120, maxSH=3
fullsamples_120-6.phy min=120, maxSH=6
fullsamples_150-3.phy min=150, maxSH=3
fullsamples_150-6.phy min=150, maxSH=6

besttree_fullsamples_30-3.tree Best-scoring ML tree with support values as branch labels, all libraries
besttree_fullsamples_30-6.tree Best-scoring ML tree with support values as branch labels, all libraries
besttree_fullsamples_60-3.tree Best-scoring ML tree with support values as branch labels, all libraries
besttree_fullsamples_60-6.tree Best-scoring ML tree with support values as branch labels, all libraries
besttree_fullsamples_90-3.tree Best-scoring ML tree with support values as branch labels, all libraries
besttree_fullsamples_90-6.tree Best-scoring ML tree with support values as branch labels, all libraries
besttree_fullsamples_120-3.tree Best-scoring ML tree with support values as branch labels, all libraries
besttree_fullsamples_120-6.tree Best-scoring ML tree with support values as branch labels, all libraries
besttree_fullsamples_150-3.tree Best-scoring ML tree with support values as branch labels, all libraries
besttree_fullsamples_150-6.tree Best-scoring ML tree with support values as branch labels, all libraries

phase_length.csv Phenotypic data for time to first phyllode in days post-germination (Figures S1 and S9).
discrete_states.csv Character states for species used for ancestral character state reconstruction in Figure 2.

Data from: Heterochronic shifts in a timing-keeping microRNA are associated with multiple instances of neoteny in plants

Data files

Abstract

README: Data from: Heterochronic shifts in a timing-keeping microRNA are associated with multiple instances of neoteny in plants

Description of the data and file structure

Sharing/Access information

Methods

Works referencing this dataset