An enhanced target-enrichment bait set for Hexacorallia provides phylogenomic resolution of the staghorn corals (Acroporidae) and close relatives

Abstract

The phylogenetic utility of targeted enrichment methods has been demonstrated in 34 taxa that often have a history of single gene marker development. These genomic capture 35 methods are now being applied to resolve evolutionary relationships from deep to shallow 36 timescales in clades that were previously deficient in molecular marker development and 37 lacking robust morphological characters that reflect evolutionary relationships. Effectively 38 capturing 1000s of loci, however, in a diverse group across a broad time scale requires a bait 39 set that incorporates multiple baits per locus. We redesigned a custom bait set for the 40 cnidarian class Anthozoa to target 1,436 UCE loci and 1,572 exon regions within the subclass 41 Hexacorallia. We test this redesigned bait set on 99 specimens of hard corals (Scleractinia) 42 spanning both the "complex" (Acroporidae, Agariciidae) and "robust" (Fungiidae) clades. 43With focused sampling in the staghorn coral genus Acropora we explore the ability of capture 44 data to inform the taxonomy of a clade deficient in molecular resolution. A mean of 1850 (± 45 298) loci were captured per taxon (955 UCEs, 894 exons). A 75% complete concatenated 46 alignment included 1792 loci (991 UCE, 801 exons) and ~1.87 million base pairs. Parsimony 47 informative sites varied from 48% for alignments including all three families, to 1.5% among 48 samples within a single Acropora species. Maximum likelihood and Bayesian analyses 49 recover highly resolved topologies and robust molecular relationships not previously found 50 with traditional markers within the Acroporidae. Species level relationships within the 51 Acropora genus do not support traditional morphological groups or morphological 52 phylogenies. Both UCE and exon datasets delineated six well-supported clades within 53 Acropora. The enhanced bait set for Hexacorallia will allow researchers to survey the 54 evolutionary history of important groups of reef building corals where previous molecular 55 marker development has been unsuccessful.56 57 58 3 104 photosymbiotic relationship with dinoflagellates of the family Symbiodiniaceae, which 105 mainly restricts both hermatypic corals and coral reefs to shallow tropical and sub-tropical 106 regions (Kleypas et al., 1999). In recent years, molecular phylogenetics has fundamentally 107 altered our understanding of the systematics and evolution of the Scleractinia, revealing that 108 5most morphological characters traditionally used to identify families, genera and species do 109 not reflect their evolutionary history (Fukami et al., 2008(Fukami et al., , 2004 Romano and Palumbi, 1996). 110 This has led to taxonomic revisions of the Scleractinia at every taxonomic level (Kitahara et 111 al., 2016). 112 Within Scleractinia, the family Acroporidae is the most speciose family, accounting 113 for approximately one-third of all reef-building coral species (Madin et al., 2016). Despite 114 their ecological importance and use as a model system to understand coral biology and 115 symbi...

Genomic signatures in the coral holobiont reveal host adaptations driven by Holocene climate change and reef specific symbionts

“…All genome sequencing was based on DNA extracted from sperm collected from a single A. tenuis colony collected on 10th of December 2014 from Orpheus Island. The species examined in this paper is widely referred to as A. tenuis on the GBR; however, we note that the taxonomy of this species is likely to change in light of recent molecular phylogenetic research indicating that traditional morphological taxonomy does not accurately reflect species boundaries or evolutionary relationships (54). The identity of the species is currently under examination using an integrated taxonomic approach, with preliminary analysis suggesting the species is most likely not A. tenuis (Dana 1846) but A. kenti (Brook 1892), a species described from the Torres Strait but synonymized with A. tenuis (Dana 1848) by Veron and Wallace (1984).…”

New approaches to species delimitation and population structure of anthozoans: Two case studies of octocorals using ultraconserved elements and exons

“…This target‐capture approach was also able to confirm species boundaries, known from reproductive and allozyme data, that were only weakly supported by the widely used DNA barcodes for octocorals (e.g., McFadden et al., 2010). Our enhanced octocoral bait set combined with the companion hexacoral bait set (Cowman et al, 2020) are now available to help resolve the anthozoan tree of life across deep to shallow evolutionary timescales.…”

“…data). Also, this newly designed bait set can be combined with the hexacoral‐v2 bait set (Cowman et al, 2020) to address deep‐ to shallow‐level evolutionary questions across the anthozoan tree of life. We retained the use of “UCE” and “exon” in this study because of how the targeted loci were designed (i.e., exon loci from transcriptomes and UCE loci from genomes).…”

“…(2018), we added more octocoral‐specific baits to (a) improve target‐capture performance of the anthozoa‐v1 loci in octocorals and (b) target additional loci, which were not included in the anthozoa‐v1 bait set. A similar procedure was followed for hexacorals, as reported elsewhere (Cowman et al, 2020). Methods are outlined in Appendix S1, but more details can also be found in both Quattrini et al.…”

“…By targeting the same individuals used in these previous studies, we address whether species and population boundaries delimited with target‐capture of UCEs and exons are congruent with findings from other methods. Specifically, we redesigned our original anthozoa‐v1 bait set (Quattrini et al., 2018) to capture more loci with a higher capture rate in both subclasses of anthozoans, including octocorals (herein) and hexacorals (Cowman et al, 2020). In this study, we then target‐captured these loci within two exemplar genera of alcyonacean soft corals and examined phylogenetic and phylogeographical relationships.…”