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

Cowman, Peter F.; Quattrini, Andrea M.; Bridge, Tom C. L.; Watkins‐Colwell, Gregory J.; Fadli, Nur; Grinblat, Mila; Roberts, Thomas E.; McFadden, Catherine S.; Miller, David J.; Baird, Andrew H.

doi:10.1016/j.ympev.2020.106944

Cited by 81 publications

(67 citation statements)

References 61 publications

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“…The copyright holder for this preprint this version posted November 4, 2021. ; https://doi.org/10.1101/2021.11.03.467181 doi: bioRxiv preprint designations that are currently being revised (Cowman et al, 2020). We used typical abundance of species data from Veron (2000) and geographic distribution data from Hughes et al (2013) downloaded for the 396 species from the Coral Trait Database (Madin et al, 2016).…”

Section: Methodsmentioning

confidence: 99%

“…Ecological persistence-For the second part of the triage process we focused on three characteristics (ecological abundance, geographic range size and thermal bleaching susceptibility) broadly defined as factors contributing to ecological persistence of reef building coral species. We acknowledge that these characteristics will depend on current taxonomic designations that are currently being revised (Cowman et al, 2020). We used typical abundance of species data from Veron (2000) and geographic distribution data from Hughes et al (2013) downloaded for the 396 species from the Coral Trait Database (Madin et al, 2016).…”

Section: Methodsmentioning

confidence: 99%

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Selecting coral species for reef restoration

Madin

McWilliam

Quigley

et al. 2021

Preprint

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Humans have long sought to restore species but little attention has been directed at how best to do so for rich assemblages of foundation species that support ecosystems, like rainforests and coral reefs that are increasingly threatened by environmental change.We developed a two-part triage process for selecting optimized sets of species for restoration. We demonstrated this process using phenotypic traits and ecological characteristics for reef building corals found along the east coast of Australia. Without clear linkages between phenotypic traits and ecosystem functions, the first part of the triage hedges against function loss by ensuring an even spread of life history traits. The second part hedges against future species losses by weighting species based on characteristics that are known to increase their ecological persistence to current environmental pressures—abundance, species range and thermal bleaching tolerance— as well as their amenability to restoration methods.We identified sets of ecologically persistent and restorable species most likely to protect against functional loss by examining marginal returns in occupancy of phenotypic trait space per restored species.We also compared sets of species with those from the southern-most accretional reef as well as a coral restoration program to demonstrate how trait space occupancy is likely to protect against local loss of ecosystem function.Synthesis and applications. A quantitative approach to selecting sets of foundational species for restoration can inform decisions about ecosystem protection to guide and optimize future restoration efforts. The approach addresses the need to insure against unpredictable losses of ecosystem functions by investing in a wide range of phenotypes. Furthermore, the flexibility of the approach enables the functional goals of restoration to vary depending on environmental context, stakeholder values, and the spatial and temporal scales at which meaningful impacts can be achieved.

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Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Selecting coral species for reef restoration

Madin

McWilliam

Quigley

et al. 2021

Preprint

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“…Standardized morphological and molecular taxonomic practices are not equally available for all coral holobiont entities, nor equally well tried-and-tested. For instance, coral skeletal-based taxonomy has a long history (Veron, 2000), but is not without discrepancies if compared against molecular-based analyses (Fukami et al, 2004;Kitahara et al, 2016;Terraneo et al, 2019a;Cowman et al, 2020). But therein lies the conundrum: while molecular analyses commonly achieve superior taxonomic resolution, they rely on initial expert review and annotation to prevent error-propagation through incorrect phylogenetic annotations of sequence database entries (Tripp et al, 2011).…”

Section: Consensus Guidelines -Assessment and Recommendationsmentioning

confidence: 99%

“…It is important to acknowledge that taxonomic identification 7 https://www.sanger.ac.uk/collaboration/aquatic-symbiosis-genomics-project/ is challenging because morphological characteristics that differentiate species in one genus may not be applicable to other genera, and the same is true for molecular markers (Veron, 2000;Shearer et al, 2002;Stolarski et al, 2021). In the case of many coral lineages, species-level molecular markers are simply not (yet) available (Quattrini et al, 2018;Cowman et al, 2020;Erickson et al, 2021), partially due to ongoing taxonomic revisions, but also due to corals exhibiting low levels of congeneric divergence for commonly employed (mitochondrial) gene markers, effectively hampering specieslevel resolutions (Shearer et al, 2002; Supplementary Table 2). Both circumstances support the necessity of skeletal voucher specimens as a reference to validate, synchronize, or update ascribed taxonomic annotations and allow later re-evaluation in case of taxonomic revisions.…”

Section: Consensus Guidelines -Assessment and Recommendationsmentioning

confidence: 99%

Consensus Guidelines for Advancing Coral Holobiont Genome and Specimen Voucher Deposition

et al. 2021

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Coral research is being ushered into the genomic era. To fully capitalize on the potential discoveries from this genomic revolution, the rapidly increasing number of high-quality genomes requires effective pairing with rigorous taxonomic characterizations of specimens and the contextualization of their ecological relevance. However, to date there is no formal framework that genomicists, taxonomists, and coral scientists can collectively use to systematically acquire and link these data. Spurred by the recently announced “Coral symbiosis sensitivity to environmental change hub” under the “Aquatic Symbiosis Genomics Project” - a collaboration between the Wellcome Sanger Institute and the Gordon and Betty Moore Foundation to generate gold-standard genome sequences for coral animal hosts and their associated Symbiodiniaceae microalgae (among the sequencing of many other symbiotic aquatic species) - we outline consensus guidelines to reconcile different types of data. The metaorganism nature of the coral holobiont provides a particular challenge in this context and is a key factor to consider for developing a framework to consolidate genomic, taxonomic, and ecological (meta)data. Ideally, genomic data should be accompanied by taxonomic references, i.e., skeletal vouchers as formal morphological references for corals and strain specimens in the case of microalgal and bacterial symbionts (cultured isolates). However, exhaustive taxonomic characterization of all coral holobiont member species is currently not feasible simply because we do not have a comprehensive understanding of all the organisms that constitute the coral holobiont. Nevertheless, guidelines on minimal, recommended, and ideal-case descriptions for the major coral holobiont constituents (coral animal, Symbiodiniaceae microalgae, and prokaryotes) will undoubtedly help in future referencing and will facilitate comparative studies. We hope that the guidelines outlined here, which we will adhere to as part of the Aquatic Symbiosis Genomics Project sub-hub focused on coral symbioses, will be useful to a broader community and their implementation will facilitate cross- and meta-data comparisons and analyses.

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“…). Identification was confirmed by Dr Tom Bridge, Senior Curator of Corals at the Queensland Museum Network (QMN), based on morphology from the field photos alongside phylogenetic methods (ultraconserved elements (UCEs) via hybrid capture(Quattrini et al 2017, Zhang et al 2019, Cowman et al 2020 …”

mentioning

confidence: 99%

Complete mitochondrial genomes of three reef forming Acropora corals (Acroporidae, Scleractinia) from Chagos Archipelago, Indian Ocean

Colin¹,

Yesson²,

Head³

2021

BDJ

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We present the first mitochondrial genomes from Chagos Archipelago, Indian Ocean, of three putative species of reef forming Acropora (Acropora aff. tenuis, Acropora aff. cytherea and Acropora aff. orbicularis). The circular genome consists respectively of 18,334 bp, 18,353 bp and 18,584 bp. All mitochondrial genomes recovered comprise 13 protein-coding genes, two transfer RNA genes and two ribosomal RNA genes, with an overall GC content ranging from 37.9% to 38.0%. These new genomic data contribute to our increased understanding of genus Acropora and its species boundaries, ultimately aiding species monitoring and conservation efforts.

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

Cited by 81 publications

References 61 publications

Selecting coral species for reef restoration

Selecting coral species for reef restoration

Consensus Guidelines for Advancing Coral Holobiont Genome and Specimen Voucher Deposition

Complete mitochondrial genomes of three reef forming Acropora corals (Acroporidae, Scleractinia) from Chagos Archipelago, Indian Ocean

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