Slow Mitochondrial COI Sequence Evolution at the Base of the Metazoan Tree and Its Implications for DNA Barcoding

Huang, Danwei; Meier, Rudolf; Todd, Peter A.; Chou, Loke Ming

doi:10.1007/s00239-008-9069-5

Cited by 289 publications

(215 citation statements)

References 60 publications

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“…The average genetic distance between the six molecular groups was 1.6 ± 0.4%, ranging from 2.5 ± 0.5% between clades II and V to 0.6 ± 0.2% between clades III and IV (Table S3). These results represent a further demonstration that, even though the mitochondrial DNA of scleractinian corals is characterized by slow evolution rates and a resulant low number of nucleotide variations among species (Shearer et al, 2002;Hellberg, 2006;Huang et al, 2008), some intergenic non-coding regions can be highly informative in resolving species boundaries. Indeed, the utility of these IGRs as phylogenetic variable markers has been already proven in different scleractinian families and genera (reviewed by Kitahara et al, in press).…”

Section: Molecular Considerationsmentioning

confidence: 75%

Species delimitation in the coral genus Goniopora (Scleractinia, Poritidae) from the Saudi Arabian Red Sea

Terraneo

Benzoni

Arrigoni

et al. 2016

Molecular Phylogenetics and Evolution

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Variable skeletal morphology, genotype induced plasticity, and homoplasy of skeletal structures have presented major challenges for scleractinian coral taxonomy and systematics since the 18 th century. Although the recent integration of genetic and micromorphological data is helping to clarify the taxonomic confusion within the order, phylogenetic relationships and species delimitation within most coral genera are still far from settled. In the present study, the species boundaries in the scleractinian coral genus Goniopora were investigated using 199 colonies from the Saudi Arabian Red Sea and sequencing of four molecular markers: the mitochondrial intergenic spacer between CytB and NAD2, the nuclear ribosomal ITS region, and two single-copy nuclear genes (ATPsβ and CalM). DNA sequence data were analyzed using a variety of methods and exploratory species-delimitation tools.The results were broadly congruent in identifying five distinct molecular lineages within the sequenced Goniopora samples: G. somaliensis/G. savignyi, G. djiboutiensis/G. lobata, G. stokesi, G. albiconus/G. tenuidens, and G.minor/G. gracilis. Although the traditional macromorphological characters used to identify these nine morphospecies were not able to discriminate the obtained molecular clades, informative micromorphological and 2 microstructural features (such as the micro-ornamentation and the arrangement of the columella) were recovered among the five lineages. Moreover, unique in vivo morphologies were associated with the genetic-delimited lineages, further supporting the molecular findings. This study represents the first attempt to identify species boundaries within Goniopora using a combined morpho-molecular approach. The obtained data establish a basis for future taxonomic revision of the genus, which should include colonies across its entire geographical distribution in the Indo-Pacific.

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Section: Molecular Considerationsmentioning

confidence: 75%

Species delimitation in the coral genus Goniopora (Scleractinia, Poritidae) from the Saudi Arabian Red Sea

Terraneo

Benzoni

Arrigoni

et al. 2016

Molecular Phylogenetics and Evolution

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“…These are haploid, and thus unambiguous sequences can be obtained generally without cloning. While mitochondrial genes typically evolve faster than nuclear genes in metazoans, anthozoans show an opposite pattern (van Oppen et al 1999;Shearer et al 2002;Fukami and Knowlton 2005;Tseng et al 2005;Hellberg 2006;Huang et al 2008;Chen et al 2009). Therefore, these genes are more informative for reconstructing deep coral phylogenies.…”

Section: The Rise Of Molecular Phylogenetic Methodsmentioning

confidence: 99%

The New Systematics of Scleractinia: Integrating Molecular and Morphological Evidence

Kitahara

Fukami

Benzoni

et al. 2016

The Cnidaria, Past, Present and Future

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100

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The taxonomy of scleractinian corals has traditionally been established based on morphology at the "macro" scale since the time of Carl Linnaeus. Taxa described using macromorphology are useful for classifying the myriad of growth forms, yet new molecular and small-scale morphological data have challenged the natural historicity of many familiar groups, motivating multiple revisions at every taxonomic level. In this synthesis of scleractinian phylogenetics and systematics, we present the most current state of affairs in the field covering both zooxanthellate and azooxanthellate taxa, focusing on the progress of our phylogenetic understanding of this ecologically-significant clade, which today is supported by rich sets of molecular and morphological data. It is worth noting that when DNA sequence data was first used to investigate coral evolution in the 1990s, there was no concerted effort to use phylogenetic information to delineate problematic taxa. In the last decade, however, the incompatibility of coral taxonomy with their evolutionary history has become much clearer, as molecular analyses for corals have been improved upon technically and expanded to all major scleractinian clades, shallow and deep. We describe these methodological developments and summarise new taxonomic revisions based on robust inferences of the coral tree of life. Despite these efforts, there are still unresolved sections of the scleractinian phylogeny, resulting in uncertain taxonomy for several taxa. We highlight these and propose a way forward for the taxonomy of corals.

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“…For angiosperms alone there is a 5,000-fold range in the absolute rate of synonymous site substitutions (d S ) among explored mitochondrial genomes (104), and up to a 340-fold range among genes within a single mtDNA (109). The mitochondrial synonymous substitution rate range is almost as staggering for cnidarians (103), sponges (110), and other animals (111), as well as for various protists, including alveolates (112,113) and amoebozoans (114). Plastid genome mutation rate estimates, on the other hand, are less variable within and across lineages and do not display such extreme values as those for mtDNAs (115,116).…”

Section: Mitochondrial Mutation Rates Are More Variable and Often Mucmentioning

confidence: 99%

Mitochondrial and plastid genome architecture: Reoccurring themes, but significant differences at the extremes

Smith

Keeling

2015

Proc. Natl. Acad. Sci. U.S.A.

355

344

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Mitochondrial and plastid genomes show a wide array of architectures, varying immensely in size, structure, and content. Some organelle DNAs have even developed elaborate eccentricities, such as scrambled coding regions, nonstandard genetic codes, and convoluted modes of posttranscriptional modification and editing. Here, we compare and contrast the breadth of genomic complexity between mitochondrial and plastid chromosomes. Both organelle genomes have independently evolved many of the same features and taken on similar genomic embellishments, often within the same species or lineage. This trend is most likely because the nuclear-encoded proteins mediating these processes eventually leak from one organelle into the other, leading to a high likelihood of processes appearing in both compartments in parallel. However, the complexity and intensity of genomic embellishments are consistently more pronounced for mitochondria than for plastids, even when they are found in both compartments. We explore the evolutionary forces responsible for these patterns and argue that organelle DNA repair processes, mutation rates, and population genetic landscapes are all important factors leading to the observed convergence and divergence in organelle genome architecture.E ndosymbiosis can dramatically impact cellular and genomic architectures. Mitochondria and plastids exemplify this point. Each of these two types of energy-producing eukaryotic organelle independently arose from the endosymbiosis, retention, and integration of a free-living bacterium into a host cell more than 1.4 billion years ago. Mitochondria came first, evolving from an alphaproteobacterial endosymbiont in an ancestor of all known living eukaryotes, and still exist, in one form or another (1), in all its descendants (2). Plastids came later, via the "primary" endosymbiosis of a cyanobacterium by the eukaryotic ancestor of the Archaeplastida, and then spread laterally to disparate groups through eukaryote-eukaryote endosymbioses (3). Consequently, a significant proportion of the identified eukaryotic diversity has a plastid.With few exceptions (1, 4), mitochondria and plastids contain genomes-chromosomal relics of the bacterial endosymbionts from which they evolved (2, 5). Mitochondrial and plastid DNAs (mtDNAs and ptDNAs) have many traits in common, which is not surprising given their similar evolutionary histories. Both are highly reduced relative to the genomes of extant, free-living alphaproteobacteria and cyanobacteria (2, 5), and both have transferred most of their genes to the host nuclear genome and are therefore reliant on nuclear-encoded, organelle-targeted proteins for the preservation of crucial biochemical pathways and many repair-, replication-, and expression-related functions (6). Both also show a wide and perplexing assortment of genomic architectures (7,8), which has spurred various evolutionary explanations, ranging from ancient inheritance from the RNA world to selection for greater "evolvability" (9, 10).At first glance, genomic complexity w...

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Slow Mitochondrial COI Sequence Evolution at the Base of the Metazoan Tree and Its Implications for DNA Barcoding

Cited by 289 publications

References 60 publications

Species delimitation in the coral genus Goniopora (Scleractinia, Poritidae) from the Saudi Arabian Red Sea

Species delimitation in the coral genus Goniopora (Scleractinia, Poritidae) from the Saudi Arabian Red Sea

The New Systematics of Scleractinia: Integrating Molecular and Morphological Evidence

Mitochondrial and plastid genome architecture: Reoccurring themes, but significant differences at the extremes

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