Data from: Vestigial organs alter fossil placements in an ancient group of terrestrial chelicerates
Cite this dataset
Gainett, Guilherme (2024). Data from: Vestigial organs alter fossil placements in an ancient group of terrestrial chelicerates [Dataset]. Dryad. https://doi.org/10.5061/dryad.m905qfv6q
Abstract
Vestigial organs provide a link between ancient and modern traits, and therefore have great potential to resolve the phylogeny of contentious fossils that bear features not seen in extant species. Here we show that extant daddy-longlegs (Arachnida, Opiliones), a group once thought to possess only one pair of eyes, in fact additionally retain a pair of vestigial median eyes and a pair of vestigial lateral eyes. Neuroanatomical gene expression surveys of eye-patterning transcription factors, opsins, and other structural proteins in the daddy-longlegs Phalangium opilio show that the vestigial median and lateral eyes innervate regions of the brain positionally homologous to the median and lateral eye neuropils, respectively, of chelicerate groups like spiders and horseshoe crabs. Gene silencing of eyes absent shows that the vestigial eyes are under the control of the retinal determination gene network. Gene silencing of dachshund disrupted the lateral eyes but not the median eyes, paralleling loss-of-function phenotypes in insect models. The existence of lateral eyes in extant daddy-longlegs bears upon the placement of the oldest harvestmen fossils, a putative stem-group that possessed both a pair of median eyes and a pair of lateral eyes. Phylogenetic analysis of harvestman relationships with an updated understanding of lateral eye incidence resolved the four-eyed fossil group as a member of an extant daddy-longlegs suborder, which in turn resulted in older estimated ages of harvestman diversification. This work underscores that developmental vestiges in extant taxa can influence our understanding of character evolution, placement of fossils, and inference of divergence times.
README: Vestigial organs alter fossil placements in an ancient group of terrestrial chelicerates
Supporting Text: Additional descriptions of the results and discussion. This supporting text is cited in the main manuscript as "Supporting text in [DOI].
**Dataset S1 (refers to STAR Methods): **two spreadsheets (Table S1-S4 as four sheets; and Table S5) containing:
(1) Data S1, Table S1: the list of accession numbers of the genes used in the HCR in situ hybridization experiments.
(2) Data S1, Table S2: the list of species and accession numbers of arachnid terminals included in the opsin phylogenetic analysis with metazoan opsins.
(3) Data S1, Table S3: the primer pairs and two sequenced plasmids with incorporated cloned fragments of Po-eya used in the RNAi experiments.
(4) Data S1, Table S4: fossils and age estimates implemented for node dating in PhyloBayes, with ages are in million years (Myr).
(5) Data S1, Table S5 (separate spreadsheet, containing several sheets): the reference sequences and probes sequences used in the HCR experiments.
**Dataset S2: **Raw (.czi) files of all the confocal scans presented in the paper. Files are named according to the figure numbers where they appear.
For instance: Figure1c_HCR15_tube4_Ptep_rh1_647_rh2_488_peropsin_546_embryo1.czi
This is the complete Z-stack of the image used in Figure 1C. HCR15_tube4 indicates the original naming of the experiment (not reported in the paper). Ptep is the code for Parasteatoda tepidariorum (species code). Next, the gene and channel used to image are indicated. Ex: gene rh1, channel 647.
We note that the naming reflects the original file name used by the authors. For orientation, please use the reference to the figures in the paper and information reported in the paper. In case of any doubt, please the corresponding author. I hope this will be a useful resource.
Other relevant names:
Popi: Phalangium opilio
Cscu: Centruroides sculpturatus
Ipus: Iporangaia pustulosa
Dataset S3: Zipped Folder containing raw data files of the phylogenetic analyses for the groundplan coding matrix, original matrix, and strict matrix, and dating analyses. The folders contain the morphological matrices (.nex files), alignments, molecular data analyses, and the description of morphological characters.
├── Maximum likelihood: Contains all the data for the total evidence analyses
│ ├── 1_Datasets for IQTREE: Contains the molecular matrix and the morphological matrices for each coding scheme.
│ │ ├── Molecules78.phy: Molecular matrix
│ │ ├── Morphology2023_groundplan.nex: Groundplan coding
│ │ ├── Morphology2023_groundplan_CyphoEyes.nex: Groundplan coding with Cyphophthalmi median eyes coded as "Absent"
│ │ ├── Morphology2023_original.nex: Original coding
│ │ ├── Morphology2023_strict.nex: Strict coding
│ │ └── Morphology2023_strict_CyphoEyes.nex: Strict coding with Cyphophthalmi median eyes coded as "Absent"
│ │ └── Morphology2023_strict_polystate.nex: New coding for the lateral eye reduction added, see Supplementary Results and Discussion.
│ ├── 2_Command files for total evidence ML searches with IQTREE
│ │ ├── TE.Opis2023_groundplan.txt
│ │ ├── TE.Opis2023_groundplan_polystate.txt: polystate analysis refers to the matrix with the new lateral eye reduction character, see Supplementary Results and Discussion.
│ │ ├── TE.Opis2023_original.txt
│ │ └── TE.Opis2023_strict.txt
│ │ └── TE.Opis2023_strict_polystate.txt: polystate analysis refers to the matrix with the new lateral eye reduction character, see Supplementary Results and Discussion.
│ └── 3_Tree files from IQTREE
│ ├── Molecules only tree
│ │ ├── Opi78genes.log
│ │ └── Opi78genes.tree
│ ├── Morphology only tree
│ │ ├── GroundplanMorphology.tree
│ │ ├── OriginalMorphology.tree
│ │ └── StrictMorphology.tree
│ └── Total evidence trees
│ ├── Groundplan.bionj
│ ├── Groundplan.ckp.gz
│ ├── Groundplan.contree
│ ├── Groundplan.iqtree
│ ├── Groundplan.log
│ ├── Groundplan.mldist
│ ├── Groundplan.parstree
│ ├── Groundplan.splits.nex
│ ├── Groundplan.tree
│ ├── Groundplan.tree.pdf
│ ├── Groundplan_CyphoEyes.bionj
│ ├── Groundplan_CyphoEyes.ckp.gz
│ ├── Groundplan_CyphoEyes.contree
│ ├── Groundplan_CyphoEyes.iqtree
│ ├── Groundplan_CyphoEyes.log
│ ├── Groundplan_CyphoEyes.mldist
│ ├── Groundplan_CyphoEyes.parstree
│ ├── Groundplan_CyphoEyes.splits.nex
│ ├── Groundplan_CyphoEyes.tree
│ ├── Groundplan_polystate.bionj
│ ├── Groundplan_polystate.ckp.gz
│ ├── Groundplan_polystate.contree
│ ├── Groundplan_polystate.iqtree
│ ├── Groundplan_polystate.log
│ ├── Groundplan_polystate.mldist
│ ├── Groundplan_polystate.parstree
│ ├── Groundplan_polystate.splits.nex
│ ├── Groundplan_polystate.tree
│ ├── Original.tree.pdf
│ ├── Strict.bionj
│ ├── Strict.ckp.gz
│ ├── Strict.contree
│ ├── Strict.iqtree
│ ├── Strict.log
│ ├── Strict.mldist
│ ├── Strict.parstree
│ ├── Strict.splits.nex
│ ├── Strict.tree
│ ├── Strict.tree.pdf
│ ├── Strict_CyphoEyes.bionj
│ ├── Strict_CyphoEyes.ckp.gz
│ ├── Strict_CyphoEyes.contree
│ ├── Strict_CyphoEyes.iqtree
│ ├── Strict_CyphoEyes.log
│ ├── Strict_CyphoEyes.mldist
│ ├── Strict_CyphoEyes.parstree
│ ├── Strict_CyphoEyes.splits.nex
│ └── Strict_CyphoEyes.tree
│ ├── Strict_polystate.bionj
│ ├── Strict_polystate.ckp.gz
│ ├── Strict_polystate.contree
│ ├── Strict_polystate.iqtree
│ ├── Strict_polystate.log
│ ├── Strict_polystate.mldist
│ ├── Strict_polystate.parstree
│ ├── Strict_polystate.splits.nex
│ └── Strict_polystate.tree
└── Node dating with PhyloBayes: Contains all the data for the Dating analyses
├── 1_Dataset
│ └── Molecules78.phy
├── 2_Calibration data
│ ├── calib_new.txt
│ └── calib_original.txt
├── 3_Outgroup
│ └── Ar.outgroup.txt
├── 4_Constraint tree
│ └── Opi78.tree
└── 5_Results
├── Dated.New_calibrations.tre
└── Dated.Original_calibrations.tre
Methods
czi. files of confocal stacks of whole mount HCR in situ hybridization, multichannel.
Taken on a Zeiss Confocal 780.
Usage notes
Supporting Text. Relates to STAR Methods.
Additional descriptions of the results and discussion. This supporting text is cited in the main manuscript as "Supporting text in [DOI].
Data S1 (available in Dryad). Relates to STAR Methods.
Spreadsheets containing (1) the list of genes used in the HCR in situ hybridization experiments (Data S1, Table S1); (2) the list of species and accession numbers of arachnid terminals included in the opsin phylogenetic analysis with metazoan opsins (Data S1, Table S2); (3) the primer pairs and two sequenced plasmids with incorporated cloned fragments of Po-eya used in the RNAi experiments (Data S1, Table S3); (4) fossils and age estimates implemented for node dating in PhyloBayes, with ages are in million years (Myr) (Data S1, Table S4); (5) the reference sequences and probes sequences used in the HCR experiments (Data S1, Table S5).
Data S2 (available in Dryad). Relates to STAR Methods.
Raw .czi files of the confocal scans presented in the paper. Files are named according to the figure numbers where they appear.
Data S3 (available in Dryad). Relates to STAR Methods.
Zipped Folder containing raw data files of the phylogenetic analyses for the ground plan coding matrix, original matrix, and strict matrix, and dating analyses. The folders contain the morphological matrices (.nex files), alignments, molecular data analyses, and the description of morphological characters. Folder information is in the Readme.txt file enclosed.
Detailed instructions for the phylogenetic and dating analysis are available in the STAR Methods.
Funding
National Science Foundation, Award: IOS-2016141
National Science Foundation, Award: IOS-1552610
United States-Israel Binational Science Foundation, Award: BSF-2019216
United States-Israel Binational Science Foundation, Award: NSF-BSF-2019823