Universal target-enrichment baits for anthozoan (Cnidaria) phylogenomics: New approaches to long-standing problems

Abstract

46Anthozoans (e.g., corals, anemones) are an ecologically important and diverse group of 47 marine metazoans that occur from shallow to deep waters worldwide. However, our 48 understanding of the evolutionary relationships among the ~7500 species within this class is 49 hindered by the lack of phylogenetically informative markers that can be reliably sequenced 50 across a diversity of taxa. We designed and tested 16,308 RNA baits to capture 720 51Ultraconserved Element loci and 1,071 exon loci. Library preparation and target enrichment was 52 performed on 33 taxa from all orders within the class Anthozoa. Following Illumina sequencing 53and Trinity assembly, we recovered 1,774 of 1,791 targeted loci. The mean number of loci 54 recovered from each species was 638 ± 222, with more loci recovered from octocorals (783 ± 55 138 loci) than hexacorals (475 ±187 loci). Phylogenetically informative sites ranged from 26-56 49% for alignments at differing hierarchical taxonomic levels (e.g., Anthozoa, Octocorallia, 57 Hexacorallia). The percent of variable sites within each of three genera (Acropora, Alcyonium, 58and Sinularia) for which multiple species were sequenced ranged from 4.7-30%. Maximum 59 likelihood analyses recovered highly resolved trees with topologies matching those supported by 60 other studies, including the monophyly of the order Scleractinia. Our results demonstrate the 61 utility of this target-enrichment approach to resolve phylogenetic relationships from relatively 62 old to recent divergences. Re-designing the baits with improved affinities to capture loci within 63 each sub-class will provide a valuable toolset to address systematic questions and further our 64

A next generation approach to species delimitation reveals the role of hybridization in a cryptic species complex of corals

“…One example of an intriguing question is whether the high diversity of Sinularia was generated in sympatry through mechanisms such as hybrid speciation or whether species have diverged in allopatry and then colonized the same reefs. With the advent of new genomic techniques such as RADSeq and target-capture genomics (e.g., Quattrini et al, 2018), we can begin to examine how pervasive hybridization is on coral reefs, particularly because F1 hybrids and their progeny may be more fit than the parent populations, and hybrid vigor may help in the maintenance and resilience of coral reef diversity (Slattery et al, 2008). Using a genomic approach can help to guide species delimitation while simultaneously shedding light on the processes generating diversity in this genus, just one of many hyperdiverse coral lineages (e.g., the scleractinians Acropora, Porites, Pocillopora and the octocorals Dendronephthya, Lobophytum and Sarcophyton ) in which ecologically similar congeners co-occur in high numbers on coral reefs throughout the Indo-Pacific.…”

New approaches to species delimitation and population structure of corals: two case studies using ultraconserved elements and exons

“…targeted, yet in analyses of specimens that were target-enriched with the new bait set and 544 sequenced on the NovaSeq platform, phyluce randomly discarded 200-500 "duplicate" loci per 545 specimen. These loci were removed because they either matched multiple contigs or contigs 546 contained multiple UCE/exon loci, which perhaps is a reflection of large contig sizes obtained as 547 compared to previous studies (e.g., Branstetter et al, 2017;Quattrini et al, 2018). Further 548 investigation is needed to determine whether or not these "duplicates" were discarded 549 unnecessarily.…”

“…This new temporary bait set was aligned back to the genomes of P. irene, P. stephencairnsi, and R. muelleri and UCE loci of Chrysogorgia tricaulis, Cornularia pabloi, and Parasphaerasclera valdiviae (see Quattrini et al, 2018) using phyluce_probe_run_multiple_lastzs_sqlite, with an identity value of 70% and a minimum coverage of 83% (default). From these alignments, baits that matched multiple loci were removed.…”

“…The temporary baits were re-aligned to the transcriptomes of C. rubrum, Eunicea flexuosa (unpubl. data, see Quattrini et al, 2018), Nephthyigorgia sp., Keratoisidinae (Zapata et al, 2015), P. biscaya, and UCE loci of A. digitatum, C. pabloi, C. tricaulis, and P. valdiviae (see Quattrini et al, 2018) using phyluce_probe_run_multiple_lastzs_sqlite, with an identity value of 70% and a minimum coverage of 83% (default). A list containing exon loci found in at least five of the taxa was created and a new exon bait set was designed by tiling 120-bp baits (3X density, middle overlap) and screening for high (>70%) or low (<30%) GC content, masked bases (>25%), and duplicates as described above.…”

“…In 166 this study, we then target-captured these loci within two exemplar genera of alcyonacean soft 167 corals and examined phylogenetic and phylogeographic relationships. In addition, we further 168 To have higher specificity for and target more loci in specific taxonomic groups, we re-202 designed a bait set (anthozoa-v1, Quattrini et al, 2018) that was produced to target-capture 720 203 UCE and 1,071 exon loci from across the sub-class Anthozoa. Target-capture results with the 204 original bait set from 235 anthozoans (unpubl.…”