Genetic variation in the brooding brittle-star: A global hybrid polyploid complex?

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 (>3) divergent (π > 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 enig..., Exon capture next-generation DNA sequence data, including mitochondrial genes
Bioinformatic scripts (R and Bash) and data tables, , # 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 sequen...