DOI: 10.5061/dryad.jsxksn0gr
title: Data for: Adaptive tail-length evolution in deer mice is associated with differential Hoxd13 expression in early development

description: Variation in the size and number of axial segments underlies much of the
 diversity in animal body plans. Here, we investigate the evolutionary,
 genetic, and developmental mechanisms driving tail-length differences
 between forest and prairie ecotypes of deer mice (Peromyscus maniculatus).
 We first show that long-tailed forest mice perform better in an arboreal
 locomotion assay, consistent with tails being important for balance during
 climbing. We then identify six genomic regions that contribute to
 differences in tail length, three of which associate with caudal vertebra
 length and the other three with vertebra number. For all six loci, the
 forest allele increases tail length, indicative of the cumulative effect
 of natural selection. Two of the genomic regions associated with variation
 in vertebra number contain Hox gene clusters. Of those, we find an
 allele-specific decrease in Hoxd13 expression in the embryonic tail bud of
 long-tailed forest mice, consistent with its role in axial elongation.
 Additionally, we find that forest embryos have more presomitic mesoderm
 than prairie embryos, and that this correlates with an increase in the
 number of neuromesodermal progenitors (NMPs), which are modulated by Hox13
 paralogs. Together, these results suggest a role for Hoxd13 in the
 development of natural variation in adaptive morphology on a
 microevolutionary timescale.
description: Please see Methods in the main text
description: # Data for: Adaptive tail-length evolution in deer mice is associated with
 differential Hoxd13 expression in early development
 **File descriptions**
 *NB_BW_F1_xray.csv* Data for Figures 1D,E; 3D; S1A,B. Measurements from
 radiographs of adult *P. maniculatus*. "NA" indicates no
 measurement for that element. Columns names indicate: * subspp: *P.m.
 nubiterrae* ("NB"), *P. m. bairdii* ("BW") or NBxBW F1
 ("F1") * sex: determined by presence of uterus/testes * s01–s04:
 sacral vertebral lengths (mm) * ca01–ca28: caudal vertebral lengths (mm) *
 ca_total: summed length of all caudal vertebrae (mm) * count: number of
 caudal vertebrae * maxvert: length of longest caudal vertebra (mm) *
 s_total: summed length of all sacral vertebrae (mm) * total: total animal
 length measured by ruler at necropsy (mm) * body: total – ca_total (mm)
 *NB_BW_voluntary_cross_data.csv* Data for Figure 2C. Results of
 rod-crossing assays performed on adult *P. maniculatus* (see Methods).
 "NA" indicates that a mouse fell and therefore did not have the
 opportunity to complete a cross. * strain: *P.m. nubiterrae*
 ("NB") or *P. m. bairdii* ("BW") * ID: individual
 mouse ID * cross: number of crosses * sex: determined by external genital
 morphology * fell: did the mouse fall? * fell_numeric: 1 = fell; 0 = did
 not fall * pfs_visited: number of platforms visited * crossed_complete:
 did the mouse complete a cross? 0 = no; 1 = yes
 *NBxBW_F2_Hoxd13_NBH_genotypes.csv* Data for Figure 4A. Genotypes are
 "N", homozygous *nubiterrae*; "B", homozygous
 *bairdii*; "H", heterozygous * F2_ID: individual mouse ID *
 Hoxd13_5: marker genotype 5' of *Hoxd13* * Hoxd13_3: marker genotype
 3' of *Hoxd13* *Mus_Hoxd13_CRISPR-HDR_counts.csv* Data for Figure 4F.
 Counts of P0 caudal vertebrae from CRISPR-Cas9 modified laboratory mice.
 P0 mice were offspring of two mating pairs (each pair indicated by
 "Family"); each parent was heterozygous for the Hoxd13A109
 CRISPR HDR allele. Genotypes determined by PCR and PstI digestion as
 described in the Methods. * ID: individual mouse ID * count: number of
 caudal vertebrae * Family: described above * Genotype: "wt",
 +/+; "het", +/*Hoxd13*A109; "homo",
 *Hoxd13*A109/*Hoxd13*A109 *NB_BW_embryo_PSM-S1.csv* Data for Figures 5B,C;
 S9. * subspp: *P.m. nubiterrae* ("NB") or *P. m. bairdii*
 ("BW") * psm: length of presomitic mesoderm (µm) * s1: length of
 most-recently-formed somite (µm) * postHLcount: number of post-hindlimb
 somites * binned1: bins of post-hindlimb somites ("lt6", n &lt;
 6; "six12", 6 ≤ n &lt; 12; "twel18", 12 ≤ n &lt; 18;
 "gt18", 18 ≤ n) *NB_BW_Sox2-T.csv* Data for Figure 5E. Numbers
 of cells counted from tailbud tissue immunostains (see Methods). * subspp:
 *P.m. nubiterrae* ("NB") or *P. m. bairdii* ("BW") *
 T: number of T-positive cells * sox2: number of Sox2-positive cells *
 sox2-t_ratio: ratio of Sox2 count to T count * colab: number of cells with
 Sox2 and T signal * cnh_total: total number of cells in the chordoneural
 hinge region * colab_fract: colab/cnh_total
 *NB_BW_explant_somite_timing.csv* Data for Figure S8. Number of minutes
 between somite formation events in tail explant cultures (see Methods).
 *NB_BW_p0.csv* Data for Figure S5. Number of caudal vertebrae at birth. *
 subspp: *P.m. nubiterrae* ("NB") or *P. m. bairdii*
 ("BW") * count: number of caudal vertebrae ***QTL files in
 'csvs' format. See rqtl.org for file specifications.*** Data for
 Figures 3; S1D; S2; S4. *NBxBW_F2_QTL_gen.csv* Genotype file for NBxBW F2
 QTL analysis. Dash ("-") indicates a missing genotype.
 *NBxBW_F2_QTL_phe.csv* Phenotype file for NBxBW F2 QTL and phenotype
 analyses. Column labels are the same as *NB_BW_F1_xray.csv*, except: *
 ID,altID: individual mouse IDs * pgm: paternal grandmother, i.e., cross
 direction * age: age in days * ca6to18: summed length of caudal vertebrae
 6–18 (mm)