DOI: 10.5061/dryad.573n5tbdv
title: Data from: Heterochronic shifts in a timing-keeping microRNA are associated with multiple instances of neoteny in plants

description: 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.
description: Double digest restriction associated DNA sequencing libraries
 were prepared with HindII and MfeI on 201 individual samples.
 Pyrad was used to generate supermatrices based on minimum sample
 and paralog thresholds. RAxML was used for generating
 phylogenies.
description: # Data from: Heterochronic shifts in a timing-keeping microRNA are
 associated with multiple instances of neoteny in plants --- 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.