Vestigial organs alter fossil placements in an ancient group of terrestrial chelicerates

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, paralleli..., czi. files of confocal stacks of whole mount HCR in situ hybridization, multichannel.
Taken on a Zeiss Confocal 780., 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 a..., # 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 seque...