Click
here to close Hello! We notice that
you are using Internet Explorer, which is not supported by Echinobase
and may cause the site to display incorrectly. We suggest using a
current version of Chrome,
FireFox,
or Safari.
???displayArticle.abstract???
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 (greater than 3) divergent (π > 6%) expressed components occurring across samples characterized by highly divergent (greater than 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 brittle-stars, 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.
Figure 1. . (a) Amphipholis squamata, dorsal disc and arm bases, (b) Amphistigma minuta, arrow indicates examples of the tubercle-shaped plates on the disc margin, (c) Ophiodaphne formata, arrows indicate the arms of the male emerging from underneath the disc, (d) A. squamata, dorsal disc removed to reveal brooded juveniles, (e) Amphipholis pugetana, dorsal disc removed to reveal dioecious gonads of male (upper left) and female (lower right), (f) A. squamata entire testis with only a few mature sperm (arrow) at a time, (g) A. pugetana testis with abundant sperm (arrow) dominating the lumen and (h–i) enlarged A. squamata and A. pugetana testis. Scale bars (a–e) 1 mm, (f–i) 0.02 mm.
Figure 2. . Example of an exon sequence variant phylogeny. UPGMA p-distance tree of a merged-read exon (ZGC73290 exon 1) colour-coded by highly divergent mito-group (figure 3). Note some samples missing due to inadequate coverage. Sample labels with numbers (1–4) indicate examples with that number of sequence variants. Putative diploid samples have one (homozygous, e.g. IE.2013.10780 and the Ophiosphaera-complex) or two (heterozygous, SIO.E7449) sequence variants. Putative allopolyploid examples have three (Misaki029) or four (F211339) sequence variants, some of which are non-monophyletic with respect to other mito-groups. We use the median number of these non-monophyletic lineages (NMLs) across exons to quantify hybridization within each sample (table 1). In this example exon, both Misaki029 and F211339 have an NML of 3, as two of the four variants in F211339 fall into a clade comprising only one mito-group (A, at top of tree). Note some sequence variants are identical across samples in different mito-groups, e.g. between Misaki029 (C) and Misaki011 (E).
Figure 3. . Summary phylogenetic patterns: (a) mitochondrial DNA (16S + COI) representing the maternal subgenome, (b) standard concatenated 252 kb IUPAC-coded exon data—with numbers in brackets indicating median number of sequence variants across exons (see figure 4), (c) shared sequence variant cluster lineage Jaccard pairwise distance from 70 data-rich exons as nMDS, X = outgroups. Panels (b–c) provide alternative ways of representing the amalgam of parental subgenomes. Samples are colour-coded according to squamata complex mito-group classification. Trees (a) and (b) are IQ-Tree ML with bootstrap node support. Some samples are missing from some trees due to data limitations. The ASTRAL-II tree version of (b) is essentially the same (electronic supplementary material, figure S2).
Figure 4. . Heat-map of sample sequence variant (a) richnessand (b) mean within-exon pairwise p-distance (nucleotide diversity π) between sequence variants from our 360-single-read exon dataset. Last column is the median across exons for each sample. Note the consistency between exons within a sample and between samples within mito-groups (including group E that contains a transcriptome MVF214040).
Figure 5. . Minor state frequency (MSF) distribution of SNPs plotted in 0.02 (2%) bins for selected exon-capture and transcriptome (MVF214040) samples. Minor state is calculated as the ratio of coverage of the second most common base at a site divided by the most common, for all sites with more than one base state recorded. All sites with coverage greater than 40th and less than 95th percentile. SNP frequencies less than 0.04 are not shown. MSF distributions with a peak around 0.5 (50%) conform to diploid expectations (group S, outgroups and the group C sample IE.2013.10780), other samples have MSF distributions indicative of elevated ploidy [13].
