Atypically low rate of cytochrome b evolution in the scleractinian coral genus Acropora.
ABSTRACT Unexpectedly low levels of mitochondrial DNA (mtDNA) cytochrome b sequence divergence are found between species of the scleractinian coral genus Acropora. Comparison of 964 positions of the cytochrome b gene of two out of the three Caribbean Acropora species with seven of their Pacific congeners shows only 0.3-0.8% sequence difference. Species in these biogeographic regions have been evolving independently for at least three million years (since the rise of the Isthmus of Panama) and this geological date is used to estimate nucleotide divergence rates. The results indicate that the Acropora cytochrome b gene is evolving at least 10-20 times slower than the 'standard' vertebrate mtDNA clock and is one of the most slowly evolving animal mitochondrial genes described to date. The possibility is discussed that, unlike higher animals, cnidarians may have a functional mtDNA mismatch repair system.
Full-textDOI: · Available from: Madeleine van Oppen, Mar 12, 2014
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ABSTRACT: The identification of coral recruits has been problematic due to a lack of definitive morphological characters being available for higher taxonomic resolution. In this study, we tested whether fluorescent detection of coral recruits used in combinations of different DNA-barcoding markers (cytochrome oxidase I gene [COI], open reading frame [ORF], and nuclear Pax-C intron [PaxC]) could be useful for increasing the resolution of coral spat identification in ecological studies. One hundred and fifty settlement plates were emplaced at nine sites on the fringing reefs of Kenting National Park in southern Taiwan between April 2011 and September 2012. A total of 248 living coral spats and juveniles (with basal areas ranging from 0.21 to 134.57 mm2) were detected on the plates with the aid of fluorescent light and collected for molecular analyses. Using the COI DNA barcoding technique, 90.3% (224/248) of coral spats were successfully identified into six genera, including Acropora, Isopora, Montipora, Pocillopora, Porites, and Pavona. PaxC further separated I. cuneata and I. palifera of Isopora from Acropora, and ORF successfully identified the species of Pocillopora (except P. meandrina and P. eydouxi). Moreover, other cnidarian species such as actinarians, zoanthids, and Millepora species were visually found using fluorescence and identified by COI DNA barcoding. This combination of existing approaches greatly improved the taxonomic resolution of early coral life stages, which to date has been mainly limited to the family level based on skeletal identification. Overall, this study suggests important improvements for the identification of coral recruits in ecological studies.PLoS ONE 09/2014; 9(9):e107366. DOI:10.1371/journal.pone.0107366 · 3.53 Impact Factor
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ABSTRACT: A key tool in evolutionary ecology is information about the temporal dynamics of species over time. Paleontology has long been the major source of this information, however, a very different source of temporal data resides in the variation of genes within and between species. These data provide an independent way to date species divergence but can also uniquely reveal processes such as gene introgression between species and demographic isolation within species. Genetic tools are particularly useful for understanding genera with closely related species that can potentially hybridize, such as reef building corals. Here we use genetic data from four loci (3 introns and 1 mitochondrial) to assay divergence and gene flow in Caribbean corals. The data show that there is persistent gene flow between species in the genus Acropora, but that this gene flow is unidirectional and highly variable among loci. Selection against introgressed alleles is high enough at one locus, Mini-collagen, to prevent gene flow between species. By contrast, selection against mitochondrial introgression appears much weaker, with 40–80 times higher rates of inter-specific gene flow than for any nuclear locus we examined. The same loci also show that gene flow among locations within species is locally restricted, but is nevertheless much higher between populations than between species. Interpretation of population data is complicated by the variable nature of selection on introgressed alleles, and some patterns of genetic differentiation might be driven by local introgression and selection. The combination of inter-specific and intra-specific data using the same loci treated in a genealogical framework helps resolve complications due to introgression and helps paint a picture of the evolution and maintenance of species in a complex spatial and temporal framework.Evolutionary Ecology 03/2011; 26(2). DOI:10.1007/s10682-011-9517-3 · 2.37 Impact Factor
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ABSTRACT: We investigated phylogeography, demography, and population connectivity of the dugong (Dugong dugon) in Australian waters using mitochondrial control region DNA sequences from 177 Australian dugongs and 11 from elsewhere. The dugong is widespread in shallow Indo-West Pacific waters suitable for growth of its main food, seagrass. We hypothesized that the loss of habitat and creation of a land barrier (the Torres Strait landbridge) during low sea level stands associated with Pleistocene glacial cycles have left a persisting genetic signature in the dugong. The landbridge was most recently flooded about 7,000 yr ago. Individual dugongs are capable of traveling long distances, suggesting an alternative hypothesis that there might now be little genetic differentiation across the dugong's Australian range. We demonstrated that Australian dugongs fall into two distinct maternal lineages and exhibit a phylogeographic pattern reflecting Pleistocene sea-level fluctuations. Within each lineage, genetic structure exists, albeit at large spatial scales. We suggest that these lineages diverged following the last emergence of the Torres Strait landbridge (ca. 115 kya) and remained geographically separated until after 7 kya when passage through Torres Strait again became possible for marine animals. Evidence for population growth in the widespread lineage, especially after the last glacial maximum, was detected.Marine Mammal Science 01/2014; 30(1). DOI:10.1111/mms.12022 · 1.82 Impact Factor