DOI: 10.5061/dryad.pj620
title: Data from: Genomic architecture of habitat-related divergence and signature of directional selection in the body shapes of Gnathopogon fishes

description: Evolution of ecomorphologically relevant traits such as body shapes is
 important to colonize and persist in a novel environment. Habitat-related
 adaptive divergence of these traits is therefore common among animals. We
 studied the genomic architecture of habitat-related divergence in the body
 shape of Gnathopogon fishes, a novel example of lake–stream
 ecomorphological divergence, and tested for the action of directional
 selection on body shape differentiation. Compared to stream-dwelling
 Gnathopogon elongatus, the sister species Gnathopogon caerulescens,
 exclusively inhabiting a large ancient lake, had an elongated body,
 increased proportion of the caudal region and small head, which would be
 advantageous in the limnetic environment. Using an F2 interspecific cross
 between the two Gnathopogon species (195 individuals), quantitative trait
 locus (QTL) analysis with geometric morphometric quantification of body
 shape and restriction-site associated DNA sequencing-derived markers (1622
 loci) identified 26 significant QTLs associated with the interspecific
 differences of body shape-related traits. These QTLs had small to moderate
 effects, supporting polygenic inheritance of the body shape-related
 traits. Each QTL was mostly located on different genomic regions, while
 colocalized QTLs were detected for some ecomorphologically relevant traits
 that are proxy of body and caudal peduncle depths, suggesting different
 degree of modularity among traits. The directions of the body shape QTLs
 were mostly consistent with the interspecific difference, and QTL sign
 test suggested a genetic signature of directional selection in the body
 shape divergence. Thus, we successfully elucidated the genomic
 architecture underlying the adaptive changes of the quantitative and
 complex morphological trait in a novel system.
description: Centroid sizes of the
 mapping familyCentroid sizes of the
 samples from the mapping family and the populations of the founder's
 origin in NTS format. The numbers and the population codes (see
 supplementary Table S1) of the analysed populations are: 1 granddam, 8
 E2H, 1 grandsire, 12 CN, 40 F1, and 195 F2, in this
 order.Gnathopogon_GM_mapping_family_centroid_sizes.ntsShape variables of the mapping familyPartial warps and uniform components of the samples from the mapping family and the populations of the founder's origin in NTS format. The numbers and the population codes (see supplementary Table S1) of the analysed populations are: 1 granddam, 8 E2H, 1 grandsire, 12 CN, 40 F1, and 195 F2, in this order.Gnathopogon_GM_mapping_family_shape_variables.ntsCentroid sizes of the samples from natural populationsCentroid sizes of the samples from the natural populations in NTS format. The numbers and the population codes (see supplementary Table S1) of the analysed populations are: 11 E1T, 20 E1S, 34 E1D, 32 E1M, 8 E2H, 18 E2R, 10 E2K, 6 E2I, 14 E3K, 10 E3I, 3 S, 28 CM, and 12 CN, in this order.Gnathopogon_GM_natural_populations_centroid_sizes.ntsShape variables of the samples from the natural populationsPartial warps and uniform components of the samples from the natural populations in NTS format. The numbers and the population codes (see supplementary Table S1) of the analysed populations are: 11 E1T, 20 E1S, 34 E1D, 32 E1M, 8 E2H, 18 E2R, 10 E2K, 6 E2I, 14 E3K, 10 E3I, 3 S, 28 CM, and 12 CN, in this order.Gnathopogon_GM_natural_populations_shape_variables.ntsInput file for QTL analysisPhenotypic and genotypic data of the F2 offsprings for QTL analysis in R/qtl format. Missing values are coded as "-".Gnathopogon_rqtl.txtVertebral numbersVertebral numbers and standard lengths of the samples from the natural populations and the mapping family. Individual IDs, names and the codes (see supplementary Table S1) of the populations are also included. Missing values are coded as "-".Gnathopogon_vertebral_numbers.txt