DOI: 10.5061/dryad.qbzkh18pr
title: Data from: Evolutionary radiation strategy revealed in the Scarabaeidae with evidence of continuous spatiotemporal morphology and phylogenesis

description: Evolutionary biology faces the important challenge of determining how to
 interpret the relationship between selection pressures and evolutionary
 radiation. The lack of morphological evidence on cross-species research
 adds to difficulty of this challenge. We proposed a new paradigm for
 evaluating the evolution of branches through changes in characters on
 continuous spatiotemporal scales, for better interpreting the impact of
 biotic/abiotic drivers on the evolutionary radiation. It reveals a causal
 link between morphological changes and selective pressures: consistent
 deformation signals for all tested characters on timeline, which provided
 strong support for the evolutionary hypothesis of relationship between
 scarabs and biotic/abiotic drivers; the evolutionary strategies under
 niche differentiation, which were manifested in the responsiveness degree
 of functional morphological characters with different selection pressure.
 This morphological information-driven integrative approach sheds light on
 the mechanism of macroevolution under different selection pressures and is
 applicable to more biodiversity research.
description: Four homologous traits of scarabs under various selection
 pressures were chosen: the mandible and hindwing are related to the
 feeding and migration of scarabs and have been corroborated to be
 associated with the development of diversity, and the pronotum and
 elytron, regarded as important parts of the scarabs’ body, are closely
 related to the muscular system associated with digging and movement
 ability. This study was based on three datasets, which
 included 9,332 specimens of 5,900 species for the testing of the pronotum
 and elytron, 250 specimens of 216 species for the mandible, and 263
 specimens of 238 species for the hindwing. Most of the specimens were
 deposited in the Institute of Zoology, Chinese Academy of Sciences, and
 the Natural History Museum London. Additional photographs of species were
 taken from the literatures. The specimens were examined and dissected
 using a LEICA MZ 12.5 dissecting microscope, and all the photographs were
 taken using an Olympus EM5 (60mm) camera. Standard dorsal images were
 selected for this study. To facilitate accurate representation, images
 were only used when the testing characters were not covered or blurry, and
 the images possess adequate resolution (the smallest one was 90
 pixels). This study assumed that the morphological
 characters of test scarabs were symmetrical left and right. Three curves
 were extracted and resampled into 50/25/50 equally spaced semi-landmarks
 (SLMs) from the left contours of the mandible/pronotum/elytron through
 MorphoJ (Version: 1.06a), for representing the morphology, respectively.
 16 landmarks were taken from the right hindwing through MorphoJ for
 quantifying the structure of wing vein nodes.
description: # Data from: Evolutionary radiation strategy revealed in the Scarabaeidae
 with evidence of continuous spatiotemporal morphology and phylogenesis ##
 Description of the Data and file structure We proposed a new paradigm for
 evaluating the evolution of branches through changes in characters on
 continuous spatiotemporal scales, for better interpreting the impact of
 biotic/abiotic drivers on the evolutionary radiation. Four homologous
 traits of scarabs under various selection pressures were chosen: the
 mandible and hindwing are related to the feeding and migration of scarabs
 and have been corroborated to be associated with the development of
 diversity, and the pronotum and elytron, regarded as important parts of
 the scarabs' body, are closely related to the muscular system
 associated with digging and movement ability. It reveals a causal link
 between morphological changes and selective pressures: consistent
 deformation signals for all tested characters on timeline, which provided
 strong support for the evolutionary hypothesis of relationship between
 scarabs and biotic/abiotic drivers; the evolutionary strategies under
 niche differentiation, which were manifested in the responsiveness degree
 of functional morphological characters with different selection pressure.
 -This dataset includes 9,332 specimens of 5,900 species for the testing of
 the pronotum and elytron, 250 specimens of 216 species for the mandible,
 and 263 specimens of 238 species for the hindwing (Supplementary Table 4).
 Most of the specimens were deposited in the Institute of Zoology, Chinese
 Academy of Sciences, and the Natural History Museum London. Additional
 photographs of species were taken from the literatures. The specimens were
 examined and dissected using a LEICA MZ 12.5 dissecting microscope, and
 all the photographs were taken using an Olympus EM5 (60mm) camera.
 Standard dorsal images were selected for this study. To facilitate
 accurate representation, images were only used when the testing characters
 were not covered or blurry, and the images possess adequate resolution
 (the smallest one was 90 pixels). -Three curves were extracted and
 resampled into 50/25/50 equally spaced semi-landmarks (SLMs) from the left
 contours of the mandible/pronotum/elytron through MorphoJ (Version:
 1.06a), for quantitative analysing the morphology, respectively
 (Supplementary Data 2). The first curve was taken from the outer contour
 of mandible covered by the base of the left to the base of the right, a
 silhouette of dorsal view of mandible was used to avoid the partial
 asymmetry of the left and right mandible in three-dimensional space which
 could lead to instability in the results; the second curve was collected
 from the middle of the anterior margin of the pronotum and end up at the
 middle of the posterior margin of the pronotum; the third curve started
 from the anterior margin of the left elytron and stopped at the end of
 elytron. 16 landmarks were taken from the right hindwing through MorphoJ
 for quantifying the structure of wing vein nodes (Supplementary Data 2),
 in order of numbering of landmark points: the base of ScA, the
 intersection of the RA3+4 vein with the leading edge; the end of RA3+4;
 the end of RA3; the end of RA4; the base of RA1+2; the base of MP; the
 base of RP; the end of RP; the end of MP; the base of CuA; the end of CuA;
 the base of AA; the end of AA; the base of AP; the end of AP83. For the
 preprocessing of the mandible/pronotum/elytron dataset, all SLMs were
 digitized with tps-Dig (Version: 2.05). The format of data files used for
 morphological analysis were achieved by converting SLMs into LMs in text
 files for the subsequent analysis: the curve number and point number for
 each sample were deleted, then landmark numbers were replaced by point
 numbers. -19 subfamilies from eight families of Scarabaeoidea were
 selected for reconstructing the ancestral feeding types of Scarabaeidae:
 1) six subfamilies in Scarabaeidae were included in the inner group; 2) 13
 subfamilies from seven families of Scarabaeoidea were included in the
 outgroups. Test groups were divided according to the main test members or
 the typical representative feeding types of the test groups: 1) the
 omnivory: Aphodiinae-Rhyparini; Geotrupidae, Glaresidae, Hybosoridae,
 Trogidae; 2) the coprophagy: Aphodiinae-Aphodiini, Scarabaeinae; 3) the
 phytophagy: Cetoniinae, Dynastinae, Glaphyridae, Lucanidae, Melolonthinae,
 Passalidae, Rutelinae5. A phylogenetic relationship of Scarabaeoidea was
 revised by the published tree of 89 genes, then the feeding types of
 ancestor nodes were reconstructed through the feeding types of living taxa
 in Mesquite (Version: 2.72)(Supplementary Table 2). About the supplements:
 \[1] Supplementary Data 1: Deformation rate (DR) and sequential growth
 rate (SGR) of test characters; Description of Supplementary Data 1: This
 document contains 11 files, among which the files (No. 1-8) represent the
 original step graph of the DR of the test
 mandible/pronotum/elytron/hindwing, respectively (see Supplementary Table
 3 for values); the file No. 9 represents the Illustration of the DR step
 graph of the test characters (the Illustration has been inserted into the
 article titled 'Evolutionary radiation strategy revealed in the
 Scarabaeidae with evidence of continuous spatiotemporal morphology and
 phylogenesis', which has been accepted on 2024-04-10); the file No.
 10 represents the original curve of the SGR; the file No. 10 represents
 the Illustration of the SGR curve (see Supplementary Table 3 for values).
 The files (No. 1-8 and No. 10) contain all of the information necessary to
 support not only the illustrations (the Figure 3 and Figure 4 in the
 article 'Evolutionary radiation strategy revealed in the Scarabaeidae
 with evidence of continuous spatiotemporal morphology and
 phylogenesis') but also the research findings. \[2] Supplementary
 Data 2: Morphological dataset of test characters; Description of
 Supplementary Data 2: Three curves were extracted and resampled into
 50/25/50 equally spaced semi-landmarks (SLMs) from the left contours of
 the mandible/pronotum/elytron through MorphoJ (Version: 1.06a), for
 quantitative analysing the morphology, respectively. The first curve was
 taken from the outer contour of mandible covered by the base of the left
 to the base of the right, a silhouette of dorsal view of mandible was used
 to avoid the partial asymmetry of the left and right mandible in
 three-dimensional space which could lead to instability in the results
 (the specific data see the file 'SLMs in mandible test' in
 Supplementary Data 2); the second curve was collected from the middle of
 the anterior margin of the pronotum and end up at the middle of the
 posterior margin of the pronotum (the specific data see the file
 'SLMs in pronotum test' in Supplementary Data 2); the third
 curve started from the anterior margin of the left elytron and stopped at
 the end of elytron (the specific data see the file 'SLMs in elytron
 test' in Supplementary Data 2). 16 landmarks were taken from the
 right hindwing through MorphoJ for quantifying the structure of wing vein
 nodes, in order of numbering of landmark points: the base of ScA, the
 intersection of the RA3+4 vein with the leading edge; the end of RA3+4;
 the end of RA3; the end of RA4; the base of RA1+2; the base of MP; the
 base of RP; the end of RP; the end of MP; the base of CuA; the end of CuA;
 the base of AA; the end of AA; the base of AP; the end of AP83 (the
 specific data see the file 'LMs in hindwing test' in
 Supplementary Data 2). The order information (column variables) of all
 sampling data in the .tps file is consistent with the sample sequence
 information (column variables) of the corresponding test characters in
 Supplementary Table 4, which is convenient for readers to directly access
 the sample information from the Supplementary Table 4 and use it for
 subsequent grouping and analysis. \[3] Supplementary Data 3: Morphological
 dataset of ancestral nodes; Description of Supplementary Data 3: I
 quantified morphological changes across evolutionary nodes. The average
 shapes of the existing groups' test characters that were treated as
 the terminal taxa in the phylogenetic combined analysis were computed in
 MorphoJ. Then, the landmarks of the test characters were entered into
 Mesquite as a continuous matrix and linked to the topology of the
 phylogenetic tree. The ancestral forms of all nodes were reconstructed
 using the traces of all characters and the landmark drawings from the
 modules. \[4] Supplementary Table 1: Dispersion degree between test groups
 through confusion matrix analysis; Description of Supplementary Table 1:
 In Mathematica (Version: 12.1.0.0)97,100, the degree of dispersion between
 test groups was quantified based on confusion matrix analysis (CMA). \[5]
 Supplementary Table 2: Feeding types of ancestor nodes, phylogenetic
 topology map of Scarabaeoidea; Description of Supplementary Table 2:
 Reconstruction of the ancestral feeding types of Scarabaeidae: 19
 subfamilies from eight families of Scarabaeoidea were selected for
 reconstructing the ancestral feeding types of Scarabaeidae: 1) six
 subfamilies in Scarabaeidae were included in the inner group; 2) 13
 subfamilies from seven families of Scarabaeoidea were included in the
 outgroups. Test groups were divided according to the main test members or
 the typical representative feeding types of the test groups: 1) the
 omnivory: Aphodiinae-Rhyparini; Geotrupidae, Glaresidae, Hybosoridae,
 Trogidae; 2) the coprophagy: Aphodiinae-Aphodiini, Scarabaeinae; 3) the
 phytophagy: Cetoniinae, Dynastinae, Glaphyridae, Lucanidae, Melolonthinae,
 Passalidae, Rutelinae. A phylogenetic relationship of Scarabaeoidea was
 revised by the published tree of 89 genes, then the feeding types of
 ancestor nodes were reconstructed through the feeding types of living taxa
 in Mesquite (Version: 2.72). \[6] Supplementary Table 3:
 Mahalanobis/Euclidean distance of test characters, deformation rate of
 each lineage based on test characters (Mahalanobis/Euclidean distance),
 sequential growth rate of each lineage based on test characters
 (Mahalanobis/Euclidean distance); Description of Supplementary Table 3: -I
 quantified morphological changes across evolutionary nodes. The average
 shapes of the existing groups' test characters that were treated as
 the terminal taxa in the phylogenetic combined analysis were computed in
 MorphoJ. Then, the landmarks of the test characters were entered into
 Mesquite as a continuous matrix and linked to the topology of the
 phylogenetic tree. The ancestral forms of all nodes were reconstructed
 using the traces of all characters and the landmark drawings from the
 modules, and the Mahalanobis distance and Euclidean distance between each
 pair of test groups (including all the estimated ancestral nodes and
 terminal existing groups) were calculated based on canonical variate
 analysis (CVA) in MorphoJ and Mathematica, respectively (about the
 Mahalanobis distances and Euclidean distances, see the Sheet 1 and Sheet 2
 of this file, please); -I proposed two parameters to interpret the
 diversity mechanism of biological evolution at the spatiotemporal scale:
 1) the deformation rate (DR) was obtained by dividing the Mahalanobis
 distance and Euclidean distance of characters to the mean differentiation
 time of mean time between nodes; the sequential growth rate (SGR) was
 obtained by dividing the difference value between each DR by the previous
 DR (about the DR of Mahalanobis distances and Euclidean distances, see the
 Sheet 3-6 of this file, please); \[7] Supplementary Table 4: List of
 samples. Description of Supplementary Table 4: This study was based on
 three datasets for increasing the morphological information obtained from
 each test taxa to be more representative , which included 250 specimens of
 216 species for the mandible test (Supplementary Table 4-Sheet 1), 9,331
 specimens of 6,403 species for the testing of the pronotum and elytron
 (Supplementary Table 4-Sheet 2 and Sheet 3), and 263 specimens of 255
 species for the hindwing test (Supplementary Table 4-Sheet 4).