Data for: Adaptive tail-length evolution in deer mice is associated with differential Hoxd13 expression in early development
Data files
Feb 07, 2024 version files 3.56 MB
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Mus_Hoxd13_CRISPR-HDR_counts.csv
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NB_BW_embryo_PSM-S1.csv
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NB_BW_explant_somite_timing.csv
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NB_BW_F1_xray.csv
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NB_BW_p0.csv
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NB_BW_Sox2-T.csv
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NB_BW_voluntary_cross_data.csv
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NBxBW_F2_Hoxd13_NBH_genotypes.csv
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NBxBW_F2_QTL_gen.csv
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NBxBW_F2_QTL_phe.csv
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README.md
Abstract
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.
README: Data for: Adaptive tail-length evolution in deer mice is associated with differential Hoxd13 expression in early development
https://doi.org/10.5061/dryad.jsxksn0gr
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 < 6; "six12", 6 ≤ n < 12; "twel18", 12 ≤ n < 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)
Methods
Please see Methods in the main text