The complete mitochondrial genome of the lobe coral <i>Porites lobata</i> (Anthozoa: Scleractinia) sequenced using ezRAD

Tisthammer, Kaho H.; Forsman, Zac H.; Sindorf, Victoria; Massey, Tayler L.; Bielecki, Coral R.; Toonen, Robert J.

doi:10.1080/23802359.2016.1157770

Cited by 14 publications

(12 citation statements)

References 19 publications

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“…The mean coverage of the mitochondrial reference genome was 94% of the reference sequence with 50 x ± 133 (mean ± SD) coverage per library (Table S1), resulting in an 18,742 bp alignment with 6% missing data. Consistent with previous studies 10,38 , the mitochondrial genome had very low levels of polymorphism; only 130 bp were variable with 89 parsimony informative characters across all species. There were no fixed mitochondrial differences between the P. lobata and P. compressa morphotypes, which shared 100% identical whole mitochondrial genome haplotypes for the majority of individuals ( Fig.…”

Section: Resultssupporting

confidence: 87%

“…Forward and reverse reads were grouped into a paired list and quality trimmed to allow no more than a 0.1% chance of error and adaptor trimmed from both ends of reads allowing no mismatch and a minimum overlap of 8 bp. Each library was then mapped to the whole mitochondrial reference genome for Porites lobata 38 , using default parameters. The assemblies were visually inspected and appeared to be very high quality with very low levels of polymorphism with the exception of several ends of reads with consecutive polymorphisms that differed from other reads, which were manually trimmed.…”

Section: Sample Collection and Dna Sequencing Coral Samples Were Colmentioning

confidence: 99%

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Host-symbiont coevolution, cryptic structure, and bleaching susceptibility, in a coral species complex (Scleractinia; Poritidae)

Forsman

Ritson‐Williams

Tisthammer

et al. 2020

Sci Rep

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The ‘species’ is a key concept for conservation and evolutionary biology, yet the lines between population and species-level variation are often blurred, especially for corals. The ‘Porites lobata species complex’ consists of branching and mounding corals that form reefs across the Pacific. We used reduced representation meta-genomic sequencing to examine genetic relationships within this species complex and to identify candidate loci associated with colony morphology, cryptic genetic structure, and apparent bleaching susceptibility. We compared existing Porites data with bleached and unbleached colonies of the branching coral P. compressa collected in Kāneʻohe Bay Hawaiʻi during the 2015 coral bleaching event. Loci that mapped to coral, symbiont, and microbial references revealed genetic structure consistent with recent host-symbiont co-evolution. Cryptic genetic clades were resolved that previous work has associated with distance from shore, but no genetic structure was associated with bleaching. We identified many candidate loci associated with morphospecies, including candidate host and symbiont loci with fixed differences between branching and mounding corals. We also found many loci associated with cryptic genetic structure, yet relatively few loci associated with bleaching. Recent host-symbiont co-evolution and rapid diversification suggests that variation and therefore the capacity of these corals to adapt may be underappreciated.

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Section: Resultssupporting

confidence: 87%

Section: Sample Collection and Dna Sequencing Coral Samples Were Colmentioning

confidence: 99%

Host-symbiont coevolution, cryptic structure, and bleaching susceptibility, in a coral species complex (Scleractinia; Poritidae)

Forsman

Ritson‐Williams

Tisthammer

et al. 2020

Sci Rep

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“…For the samples from O'ahu, the following three regions of coral host DNA were PCRamplified: (1) ∼400 bp coral mitochondrial putative control region (CR) with primers CRf and CO3r (Vollmer & Palumbi, 2002), (2) ∼700 bp coral nuclear ITS1-5.8S-ITS2 region (ITS) with primers ITSZ1 and ITSZ2 (Forsman et al, 2009), and (3) ∼1,500 bp coral nuclear histone region spanning H2A to H4 (H2) with novel primers zH2AH4f (5 -GTGTACTTGGCTGCYGTRCT-3 ) and zH4Fr (5 -GACAACCGAGAATGTCCGGT-3 ). H2 was developed to create a genetic marker that allow direct sequencing of post PCR products to efficiently assess small-scale population genetic structure, because (1) the mitochondrial genome of P. lobata exhibits very little sequence variability (<0.02% polymorphic sites (Tisthammer et al, 2016)) due to its extremely slow evolutionary rate (Shearer et al, 2002), and (2) even though high polymorphism in ITS is a desirable trait, sequencing of ITS requires time-consuming cloning, and analyzing the multicopy gene poses analytical challenges, as it deviates from a standard diploid model. H2 consists of partial coding region of H2A, approximately 1000 bp introns and part coding region of H4.…”

Section: Pcrmentioning

confidence: 99%

Genetic structure is stronger across human-impacted habitats than among islands in the coralPorites lobata

Tisthammer

Forsman

Toonen

et al. 2020

PeerJ

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We examined genetic structure in the lobe coral Porites lobata among pairs of highly variable and high-stress nearshore sites and adjacent less variable and less impacted offshore sites on the islands of Oahu and Maui, Hawaii. Using an analysis of molecular variance framework, we tested whether populations were more structured by geographic distance or environmental extremes. The genetic patterns we observed followed isolation by environment, where nearshore and adjacent offshore populations showed significant genetic structure at both locations (AMOVA FST = 0.04∼0.19, P < 0.001), but no significant isolation by distance between islands. Strikingly, corals from the two nearshore sites with higher levels of environmental stressors on different islands over 100 km apart with similar environmentally stressful conditions were genetically closer (FST = 0.0, P = 0.73) than those within a single location less than 2 km apart (FST = 0.04∼0.08, P < 0.01). In contrast, a third site with a less impacted nearshore site (i.e., less pronounced environmental gradient) showed no significant structure from the offshore comparison. Our results show much stronger support for environment than distance separating these populations. Our finding suggests that ecological boundaries from human impacts may play a role in forming genetic structure in the coastal environment, and that genetic divergence in the absence of geographical barriers to gene flow might be explained by selective pressure across contrasting habitats.

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“…While this approach has proven useful in other taxa such as molluscs and cnidarians [54,55], here we provide the first complete mitochondrial genomes obtained from size-selected reduced representation genomic libraries of sponges. For all six libraries, we obtained more than 2 Mio.…”

Section: Mitochondrial Genome Organisation -A General Comparisionmentioning

confidence: 99%

Divergence times in demosponges (Porifera): first insights from new mitogenomes and the inclusion of fossils in a birth-death clock model

Schuster¹,

Vargas²,

Knapp

et al. 2017

Preprint

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Approximately 80% of all recent sponge species belong to the class Demospongiae. Yet, despite their diversity and importance, accurate divergence times are still unknown for most demosponge clades. The estimation of demosponge divergence time is key to answering fundamental questions like e.g. the origin of Demospongiae, their diversification and historical biogeography. Molecular sequence data alone is not informative on an absolute time scale, and therefore needs to be "calibrated" with additional data such as fossils. Here, we apply the fossilized birth-death model (FBD), which has the advantage, compared to strict node dating with the oldest fossil occurrences, that it allows for the inclusion of young and old fossils in the analysis of divergence time. We use desma-bearing sponges, a diverse group of demosponges that form rigid skeletons and have a rich and continuous fossil record dating back to the Cambrian (⇠500 Ma), aiming to date the demosponge radiation and constrain the timing of key evolutionary events, like the transition from marine to freshwater habitats. To do so, we assembled mitochondrial genomes of six desma-bearing demosponges from size-selected reducedrepresentation genomic libraries and apply a fossilized birth-death model including 30 fossils and 33 complete demosponge mitochondrial genomes to infer a dated phylogeny of Demospongiae. Our study supports a Neoproterozoic origin of Demospongiae. Novel age estimates for the split of freshwater and marine sponges dating back to the Carboniferous and the previously assumed Recent (⇠18 Ma) diversification of freshwater sponges is supported. Moreover, we provide detailed age estimates for a possible diversification of Tetractinellidae (⇠315 Ma), the Astrophorina (⇠240 Ma), the Spirophorina (⇠120 Ma) and the family Corallistidae (⇠188 Ma) all of which are considered as key groups for dating the Demospongiae, due to their extraordinary rich and continuous fossil history.

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The complete mitochondrial genome of the lobe coral Porites lobata (Anthozoa: Scleractinia) sequenced using ezRAD

Cited by 14 publications

References 19 publications

Host-symbiont coevolution, cryptic structure, and bleaching susceptibility, in a coral species complex (Scleractinia; Poritidae)

Host-symbiont coevolution, cryptic structure, and bleaching susceptibility, in a coral species complex (Scleractinia; Poritidae)

Genetic structure is stronger across human-impacted habitats than among islands in the coralPorites lobata

Divergence times in demosponges (Porifera): first insights from new mitogenomes and the inclusion of fossils in a birth-death clock model

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