Gene content and organization in a segment of the mitochondrial genome of the scleractinian coral Acropora tenuis: major differences in gene order within the anthozoan subclass zoantharia Citation]

Oppen, Madeleine Jh van; Hislop, Nikki R.; Hagerman, Paul J.; Miller, David J.

doi:10.1093/oxfordjournals.molbev.a026094

Cited by 24 publications

(23 citation statements)

References 14 publications

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“…The mt tRNA uptake systems of anthozoans clearly have specificity, as codon use differs between mitochondrial and nuclear genes in Acropora despite similar overall base composition; for example, TTT being the strongly favoured Phe codon in mt-genes but bias being much less apparent in the case of nuclear genes [79], [80].…”

Section: Resultsmentioning

confidence: 99%

The “Naked Coral” Hypothesis Revisited – Evidence for and Against Scleractinian Monophyly

et al. 2014

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The relationship between Scleractinia and Corallimorpharia, Orders within Anthozoa distinguished by the presence of an aragonite skeleton in the former, is controversial. Although classically considered distinct groups, some phylogenetic analyses have placed the Corallimorpharia within a larger Scleractinia/Corallimorpharia clade, leading to the suggestion that the Corallimorpharia are “naked corals” that arose via skeleton loss during the Cretaceous from a Scleractinian ancestor. Scleractinian paraphyly is, however, contradicted by a number of recent phylogenetic studies based on mt nucleotide (nt) sequence data. Whereas the “naked coral” hypothesis was based on analysis of the sequences of proteins encoded by a relatively small number of mt genomes, here a much-expanded dataset was used to reinvestigate hexacorallian phylogeny. The initial observation was that, whereas analyses based on nt data support scleractinian monophyly, those based on amino acid (aa) data support the “naked coral” hypothesis, irrespective of the method and with very strong support. To better understand the bases of these contrasting results, the effects of systematic errors were examined. Compared to other hexacorallians, the mt genomes of “Robust” corals have a higher (A+T) content, codon usage is far more constrained, and the proteins that they encode have a markedly higher phenylalanine content, leading us to suggest that mt DNA repair may be impaired in this lineage. Thus the “naked coral” topology could be caused by high levels of saturation in these mitochondrial sequences, long-branch effects or model violations. The equivocal results of these extensive analyses highlight the fundamental problems of basing coral phylogeny on mitochondrial sequence data.

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Section: Resultsmentioning

confidence: 99%

The “Naked Coral” Hypothesis Revisited – Evidence for and Against Scleractinian Monophyly

et al. 2014

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“…Population genetic analyses were conducted using the putative mitochondrial control region [56], a 941-bp fragment that has been shown to have high haplotype diversity and the ability to resolve population genetic structure in A. cervicornis across the Caribbean [21]. Three nuclear genes previously evaluated for A. cervicornis have few native alleles (2 in MiniCollagen and 1 in both Calmodulin and PaxC), and thus signatures of population structure are dominated by introgression [21].…”

Section: Methodsmentioning

confidence: 99%

Genetic Diversity and Connectivity in the Threatened Staghorn Coral (Acropora cervicornis) in Florida

Hemond

Vollmer

2010

PLoS ONE

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Over the past three decades, populations of the dominant shallow water Caribbean corals, Acropora cervicornis and A. palmata, have been devastated by white-band disease (WBD), resulting in the listing of both species as threatened under the U.S. Endangered Species Act. A key to conserving these threatened corals is understanding how their populations are genetically interconnected throughout the greater Caribbean. Genetic research has demonstrated that gene flow is regionally restricted across the Caribbean in both species. Yet, despite being an important site of coral reef research, little genetic data has been available for the Florida Acropora, especially for the staghorn coral, A. cervicornis. In this study, we present new mitochondrial DNA sequence data from 52 A. cervicornis individuals from 22 sites spread across the upper and lower Florida Keys, which suggest that Florida's A. cervicornis populations are highly genetically interconnected (FST = −0.081). Comparison between Florida and existing mtDNA data from six regional Caribbean populations indicates that Florida possesses high levels of standing genetic diversity (h = 0.824) relative to the rest of the greater Caribbean (h = 0.701±0.043). We find that the contemporary level of gene flow across the greater Caribbean, including Florida, is restricted ( = 0.117), but evidence from shared haplotypes suggests the Western Caribbean has historically been a source of genetic variation for Florida. Despite the current patchiness of A. cervicornis in Florida, the relatively high genetic diversity and connectivity within Florida suggest that this population may have sufficient genetic variation to be viable and resilient to environmental perturbation and disease. Limited genetic exchange across regional populations of the greater Caribbean, including Florida, indicates that conservation efforts for A. cervicornis should focus on maintaining and managing populations locally rather than relying on larval inputs from elsewhere.

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“…As is characteristic of the control region in other organisms (Brown 1985), the putative control region in some scleractinians is more variable than protein‐coding regions of the mitochondrial genome (Table 2, Fig. 3; van Oppen et al . 1999a, 2001; Vollmer & Palumbi 2002).…”

Section: Interspecific Mtdna Divergence In the Anthozoamentioning

confidence: 99%

“…1998; Beaton et al . 1998), thus most tRNAs must be imported for translation of mitochondrially encoded proteins (Wolstenholme 1992; Boore 1999; Schneider & Marechal‐Drouard 2000), and this import appears to be selective (van Oppen et al . 1999a).…”

Section: Factors Contributing To Slow Mitochondrial Evolutionmentioning

confidence: 99%

Slow mitochondrial DNA sequence evolution in the Anthozoa (Cnidaria)

et al. 2002

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Mitochondrial genes have been used extensively in population genetic and phylogeographical analyses, in part due to a high rate of nucleotide substitution in animal mitochondrial DNA (mtDNA). Nucleotide sequences of anthozoan mitochondrial genes, however, are virtually invariant among conspecifics, even at third codon positions of protein-coding sequences. Hence, mtDNA markers are of limited use for population-level studies in these organisms. Mitochondrial gene sequence divergence among anthozoan species is also low relative to that exhibited in other animals, although higher level relationships can be resolved with these markers. Substitution rates in anthozoan nuclear genes are much higher than in mitochondrial genes, whereas nuclear genes in other metazoans usually evolve more slowly than, or similar to, mitochondrial genes. Although several mechanisms accounting for a slow rate of sequence evolution have been proposed, there is not yet a definitive explanation for this observation. Slow evolution and unique characteristics may be common in primitive metazoans, suggesting that patterns of mtDNA evolution in these organisms differ from that in other animal systems.

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Gene content and organization in a segment of the mitochondrial genome of the scleractinian coral Acropora tenuis: major differences in gene order within the anthozoan subclass zoantharia Citation]

Cited by 24 publications

References 14 publications

The “Naked Coral” Hypothesis Revisited – Evidence for and Against Scleractinian Monophyly

The “Naked Coral” Hypothesis Revisited – Evidence for and Against Scleractinian Monophyly

Genetic Diversity and Connectivity in the Threatened Staghorn Coral (Acropora cervicornis) in Florida

Slow mitochondrial DNA sequence evolution in the Anthozoa (Cnidaria)

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