DOI: 10.5061/dryad.qbzkh18p9
title: Genetic variation in the brooding brittle-star: A global hybrid polyploid complex?

description: The widespread and abundant brooding brittle-star (Amphipholis squamata)
 is a simultaneous hermaphrodite with a complex mitochondrial
 phylogeography of multiple divergent overlapping mtDNA lineages, high
 levels of inbreeding or clonality and unusual sperm morphology. We use
 exon-capture and transcriptome data to show that the nuclear genome
 comprises multiple (&gt;3) divergent (π &gt; 6%) expressed
 components occurring across samples characterised by highly divergent
 (~20%)  mitochondrial lineages, and encompassing several other
 genera, including diploid dioecious species. We report a massive sperm
 genome size in A. squamata, an order of magnitude larger than that present
 in other brittlestars, and consistent with our SNP-based measure of
 greatly elevated ploidy. Similarity of these genetic signatures to
 well-known animal systems suggests that A. squamata (and related taxa) is
 a hybrid polyploid asexual complex of variable subgenome origins, ploidy
 and reproductive mode. We discuss enigmatic aspects of A. squamata biology
 in this light. This putative allopolyploid complex would be the first to
 be reported from the phylum Echinodermata.
description: Exon capture next-generation DNA sequence data, including
 mitochondrial genes Bioinformatic scripts (R and Bash)
 and data tables
description: # Amphipholis squamata hybrid polyploid swarm data This dyrad submission
 contains the DNA next generation Illumina raw reads, aligned nuclear and
 mitochondrial sequences, and tables of analytical results from our study
 on the genomic architecture of the brooding brittle star Amphipholis
 squamata. Manuscript citation: Hugall, Byrne, OHara (submitted) Brooding
 brittle-star is a global hybrid polyploid swarm. BioRxiv ## Description of
 the data and file structure Figure numbers below refer to the submitted
 paper. SQUAMATA_RAW: Zipped folder containing the original raw Illumina
 Next-Gen sequences read files, with table listing the sample identities.
 SRalign: Zipped folder containing single read analysis sequence variants,
 in fasta format. Exon alignment file name follows the structure (project
 label)_(exon name)_grouprepsCL.fasta. Alignments for 1255 exons. Missing
 data is coded by tilde (~). Note the number of samples - and sequences per
 sample, varies between exons. Individual sequence labels comprise sample
 (genus_species_sample ID), followed by codes for the clustering level (dc#
 where # is the number of differences allowed in a cluster), a unique
 identifier for a sample variant at a particular clustering level (grp#),
 and the total read coverage for that sequence variant (c#). MRalign:
 Zipped folder containing the merged read equivalent of SRalign. RHACK:
 Zipped folder containing the Bash scripts for the sequence variant read
 mapping system (RHACK3cp.sh) and attendant accessory files: 1552exons.txt
 position table of the total ophiouroid exon capture system exons (columns:
 exon name, length, start position, end position); RevTable.txt for
 sequence reverse compliment translation. See Hugall et al. (2016)
 (doi:10.1093/molbev/msv216) for further details on exon capture system,
 pipeline and target. HETTER2.sh for calculating minor state frequencies
 (see Figure 5). Amphipholis_COI_16S_aln_v2.fasta: Mitochondrial COI and
 16S alignment used to generate a mitochondrial phylogeny (Figure 3a).
 Fasta format. Amphipholis_16Sv10_mftX.fasta: Fasta format alignment of
 partial mitochondrial 16S from GenBank and our samples, used to generate
 16S phylogeny Figure S1. GenBank samples label starts with accession
 number. Amphipholis32_Trin_across_x5bin_50TX.zip: Exon capture pipeline
 sample-specific reference concatenated sequence, trimmed to remove sites
 where less than 50% of samples have a defined base (ACGT). Fasta format
 compressed. Used to generate Figure 3b.
 Amphipholis32_Trin_across_x5bin_50T_genelist.txt: The matching exon
 capture partition file for the concatenated exon capture alignment. Format
 as for the 1552exons.txt list but the exons have been grouped into genes.
 Amphi32b_GTrees.nwk: Newick format file of the gene trees made from the
 individual gene partitions in the concatenated alignment. Gene trees
 (n=234) used to generate ASTRAL summary tree (Figure S2)
 Amphi32b_GTset.txt: Text format table listing the genes used to create the
 gene trees with four columns: name of gene, number of samples, total
 number of sites, and number of variable sites.
 Amphi26_360e0.50dc1_rgsUPGMA.nwk: P-distance UPGMA trees generated from
 360 single read analysis exon sequence variant alignments (SRaligns),
 using the dc1 clustering level sequences.
 Amphipholis22MR_200e0.50dc1_rgsUPGMA.nwk: P-distance UPGMA tree generated
 from 200 merged read analysis exon sequence variant alignments (MRaligns),
 using the dc1 clustering level sequences. Figure 2 is an example of one of
 these trees. ## Sharing/Access information Novel mitochondrial COI and 16S
 sequences are deposited in NCBI/nucleotide Previous dryad submission(s)
 with the exon-capture methodology include All data is included in this
 dryad submission ## Code/Software This submission includes some UNIX bash
 code for analysing the Illumina raw DNA paired end reads, and R code for
 producing the figures.