2008 Brugler, M.R. and S.C. France. The mitochondrial genome of a deep-sea bamboo coral (Cnidaria, Anthozoa, Octocorallia, Isididae): genome structure and putative origins of replication are not conserved among octocorals. Journal of Molecular Evolution in press
Octocoral mitochondrial (mt) DNA is subject to an exceptionally low rate of substitution, and it has been suggested that mt genome content and structure are conserved across the subclass, an observation that has been supported for most octocorallian families by phylogenetic analyses using PCR products spanning gene boundaries. However, failure to recover amplification products spanning the nad4L-msh1 gene junction in species from the family Isididae (bamboo corals) prompted us to sequence the complete mt genome of a deep-sea bamboo coral (undescribed species). Compared to the ''typical'' octocoral mt genome, which has 12 genes transcribed on one strand and 5 genes on the opposite (cox2, atp8, atp6, cox3, trnM), in the bamboo coral genome a contiguous string of 5 genes (msh1, rnl, nad2, nad5, nad4) has undergone an inversion, likely in a single event. Analyses of strand-specific compositional asymmetry suggest that (i) the light-strand origin of replication was also inverted and is adjacent to nad4, and (ii) the orientation of the heavy-strand origin of replication (OriH) has reversed relative to that of previously known octocoral mt genomes. Comparative analyses suggest that intramitochondrial recombination and errors in replication at OriH may be responsible for changes in gene order in octocorals and hexacorals, respectively. Using primers flanking the regions at either end of the inverted set of five genes, we examined closely related taxa and determined that the novel gene order is restricted to the deep-sea subfamily Keratoisidinae; however, we found no evidence for strand-specific mutational biases that may influence phylogenetic analyses that include this subfamily of bamboo corals.
2007 France, S.C. Genetic analysis of bamboo corals (Cnidaria: Octocorallia: Isididae): does lack of colony branching distinguish Lepidisis from Keratoisis? Bulletin of Marine Science 81: 323-333
Bamboo corals (family Isididae) are among the most easily recognized deep-water octocorals due to their articulated skeleton comprised of non-sclerite calcareous internodes alternating with proteinaceous nodes. Most commonly encountered in the deep-sea are species in the subfamily Keratoisidinae, including the genera Acanella Gray, 1870, Isidella Gray, 1857, Keratoisis Wright, 1869, and Lepidisis Verrill, 1883. Systematists have debated whether Lepidisis and Keratoisis should be defined on the basis of “colony branching.” Although recent taxonomic keys use “colonies unbranched” to distinguish Lepidisis, the original description of the genus included both branched and unbranched morphologies, with both forms also classified in Keratoisis. This study analyzed mitochondrial DNA sequence variation from isidids collected between 500–2250 m depth to address the following question: are unbranched, whip-like bamboo corals in the subfamily Keratoisidinae monophyletic? DNA sequences of the msh1 gene (1426 nucleotides) from 32 isidids were used to construct a phylogeny. Coding of gaps provided additional informative characters for taxon discrimination. The results show five well-supported clades, all grouping both branched and unbranched colony morphologies; there was no single monophyletic clade of unbranched Keratoisidinae. The msh1 phylogeny suggests that the distinction between the genera Lepidisis and Keratoisis should not be based on whether or not colonies branch.
2007 Brugler, M.R. and S.C. France. The complete mitochondrial genome of the black coral Chrysopathes formosa (Cnidaria:Anthozoa:Antipatharia) supports classification of antipatharians within the subclass Hexacorallia. Molecular Phylogenetics and Evolution 42: 776-788
Black corals comprise a globally distributed shallow- and deep-water taxon whose phylogenetic position within the Anthozoa has been debated. We sequenced the complete mitochondrial genome of the antipatharian Chrysopathes formosa to further evaluate its phylogenetic relationships. The circular mitochondrial genome (18,398 bp) consists of 13 energy pathway protein-coding genes and two ribosomal RNAs, but only two transfer RNA genes (trnM and trnW), as well as a group I intron within the nad5 gene that contains the only copies of nad1 and nad3. No novel genes were found in the antipatharian mitochondrial genome. Gene order and genome content are most similar to those of the sea anemone Metridium senile (subclass Hexacorallia), with differences being the relative location of three contiguous genes (cox2-nad4-nad6) and absence (from the antipatharian) of a group I intron within the cox1 gene. Phylogenetic analyses of multiple protein-coding genes support classifying the Antipatharia within the subclass Hexacorallia and not the subclass Ceriantipatharia; however, the sister-taxon relationships of black corals within Hexacorallia remain inconclusive.
2006 McFadden, C.S., S.C. France, J.A. Sánchez and P. Alderslade. A molecular phylogenetic analysis of the Octocorallia (Cnidaria: Anthozoa) based on mitochondrial protein-coding sequences (ND2, msh1). Molecular Phylogenetics and Evolution 41: 513-527
Despite their abundance and ecological importance in a wide variety of shallow and deep water marine communities, octocorals (soft corals, sea fans, and sea pens) are a group whose taxonomy and phylogenetic relationships remain poorly known and little studied. The group is currently divided into three orders (O: Alcyonacea, Pennatulacea, and Helioporacea); the large O. Alcyonacea (soft corals and sea fans) is further subdivided into six sub-ordinal groups on the basis of skeletal composition and colony growth form. We used 1429 bp of two mitochondrial protein-coding genes, ND2 and msh1 , to construct a phylogeny for 103 octocoral genera representing 28 families. In agreement with a previous 18S rDNA phylogeny, our results support a division of Octocorallia into two major clades plus a third, minor clade. We found one large clade (Holaxonia-Alcyoniina) comprising the sea fan sub-order Holaxonia and the majority of soft corals, and a second clade (Calcaxonia-Pennatulacea) comprising sea pens (O. Pennatulacea) and the sea fan sub-order Calcaxonia. Taxa belonging to the sea fan group Scleraxonia and the soft coral family Alcyoniidae were divided among the Holaxonia-Alcyoniina clade and a third, small clade ( Anthomastus-Corallium ) whose relationship to the two major clades was unresolved. In contrast to the previous studies, we found sea pens to be monophyletic but nested within Calcaxonia; our analyses support the sea fan family Ellisellidae as the sister taxon to the sea pens. We are unable to reject the hypothesis that the calcaxonian and holaxonian skeletal axes each arose once and suggest that the skeletal axis of sea pens is derived from that of Calcaxonia. Topology tests rejected the monophyly of sub-ordinal groups Alcyoniina, Scleraxonia, and Stolonifera, as well as 9 of 14 families for which we sampled multiple genera. The much broader taxon sampling and better phylogenetic resolution afforded by our study relative to the previous efforts greatly clarify the relationships among families and subordinal groups within each of the major clades. The failure of these mitochondrial genes as well as previous 18S rDNA studies to resolve many of the deeper nodes within the tree (including its root) suggest that octocorals underwent a rapid radiation and that large amounts of sequence data will be required in order to resolve the basal relationships within the clade.
2004 Smith, P. J. , S. M. McVeagh, J. T. Mingoia, and S. C. France. Mitochondrial DNA sequence variation in deep-sea bamboo coral (Keratoisidinae) species in the southwest and northwest Pacific Ocean. Marine Biology 144: 253-261
The Keratoisidinae are a poorly known, but phenotypically diverse group of deepwater corals. Recent developments in deepwater trawling in the southwest Pacific have provided many more specimens of bamboo corals. Two sub-regions of the mitochondrial genome were sequenced to test genetic relationships among specimens collected over a wide geographical range (27-50°S): a sub-region of the large-subunit rRNA (16S rRNA), characterized by a highly variable insertion/deletion (INDEL#2) region; and a non-coding region between COII and COI. Based on DNA haplotypes, 14 species of Keratoisidinae were recognized among 88 specimens from deep water in the southwest Pacific Ocean. The common haplotypes also appeared in specimens collected in the northwest Pacific Ocean and may indicate that some bamboo coral species are widespread in the Pacific, or that the mitochondrial markers are insensitive to recent speciation events. Many specimens were taken from flat bottom areas and, contrary to assumptions, the bamboo corals are not endemic to seamounts. The closure of some seamounts to trawling will protect bamboo corals from extinction, but not from local depletion.
2002 France, S. C., and L. L. Hoover. DNA sequences of the mitochondrial COI gene have low levels of divergence among deep-sea octocorals (Cnidaria: Anthozoa). Hydrobiologia 471: 149-155
Abstract. We are analyzing genetic diversity in deep-seamount octocorals with the ultimate goal of studying the effect of retention and dispersal of larvae on genetic population structure. Here we report on the sequence diversity of the mitochondrial cytochrome oxidase I (COI) gene among 11 species. Uncorrected pairwise sequence divergences ranged from 0.4% – 10.3% for comparisons among species spanning the intrageneric to interordinal levels. Relative to other invertebrates, these divergences are very low, suggesting that COI may not be useful as a genetic marker for studying dispersal among deep-sea octocoral populations. Possible explanations for the reduced rates of divergence observed include a lower rate of evolution for octocoral mitochondrial genomes and the presence of a gene, mtMSH, which may code for a mitochondrial DNA mismatch-repair system. We report the finding of mtMSH in three deep-sea octocorals (Acanthogorgia sp., Corallium ducale, and Paramuricea sp.), which brings the total published observations of this gene to six species, all in the subclass Octocorallia.
2001 France, S. C., and L. L. Hoover. Analysis of variation in mitochondrial DNA sequences (ND3, ND4L, MSH) among Octocorallia (=Alcyonaria) (Cnidaria: Anthozoa). Bulletin of the Biological Society of Washington 10:110-118
Abstract. We have sequenced a portion of the mitochondrial genome encompassing ND3, ND4L and mtMSH, and the two non-coding regions (NCRs) between the genes, from 15 species of Octocorallia. ND4L has a lower substitution rate than ND3, and mtMSH shows the highest rate of substitution, with approximately twice the percentage of variable sites as the NADH genes. There were no insertions or deletions in any of the protein-coding sequences, but the NCRs ranged from 4 bp to a maximum of 39 bp in length. In a limited sample, we observed no variation in NCR sequences among conspecific individuals, nor in some cases, in interspecific comparisons. This report now brings the total published observations of a mitochondrial mismatch repair gene homologue (mtMSH) to 18 species, all in the subclass Octocorallia (=Alcyonaria).
2001 Berntson, E. A., F. M. Bayer, A. G. Mcarthur, and S. C. France. Phylogenetic relationships within the Octocorallia (Cnidaria: Anthozoa) based on nuclear 18S rRNA sequences. Marine Biology 138:235-246.
Abstract. We determined the nuclear 18S rRNA sequences for 41 species of octocorals and used these to address the validity of the historical ordinal divisions and the current subordinal divisions within the Subclass Octocorallia. We also explored the phylogenetic affinities of the species Dendrobrachia paucispina, which was originally classified in the Order Antipatharia (subclass Ceriantipatharia) although polyp structure indicates it belongs in the Subclass Octocorallia. Trees constructed using maximum likelihood techniques are incongruent with the current and historical taxonomy of the Octocorallia. There appear to be three major clades of octocorals. The first clade included most but not all pennatulaceans as a monophyletic group. The second clade contained 21 species representing all major octocoral groups other than pennatulacenas. The third clade contained members from three suborders of the Alcyonacea and one member of the Pennatulacea. These data could not be used to distinguish the branching order of the three major clades. The species D. paucispina had a close affinity with the genera Corallium and Paragorgia (Alcyonacea: Scleraxonia) although its morphology suggests it is more similar to the genus Chrysogorgia (Alcyonacea: Calcaxonia). The morphological character of dimorphism (the presence of both autozooids and siphonozooids within a single colony) corresponded loosely with the topology of the most likely trees and a single origin of dimorphism could not be rejected. Despite sampling from the majority of families within the Octocorallia, many of the relationships within this group remain ambiguous.
1999 Rosel, P.E.., S. C. France, J.Y. Wang and T. D. Kocher. Genetic structure of harbour porpoise Phocoena phocoena populations in the Northwest Atlantic based on mitochondrial and nuclear markers. Molecular Ecology 8: S41-S54
Abstract. The harbour porpoise, Phocoena phocoena, experiences high levels of non-natural mortality due to interactions with commercial fisheries throughout its range. To accurately evaluate the significance of this bycatch, information on population structure is needed. We have examined the population structure of this species in the Northwest Atlantic Ocean using mitochondrial DNA sequence and nuclear microsatellite data. Samples from four previously proposed summer breeding populations - Gulf of Maine, eastern Newfoundland, the Gulf of St. Lawrence, and West Greenland - were analyzed. Control region sequences revealed a significant partitioning of genetic variation among most of these summer populations, indicating that Northwest Atlantic harbour porpoises should not be considered one panmictic population. Analysis of females alone yielded the highest levels of population subdivision, suggesting females are more philopatric than males. At least three management units may be defined for harbour porpoises in the Northwest Atlantic based on these data. Analysis of six microsatellite loci failed to detect significant population subdivision. Male-mediated gene flow may maintain homogeneity among nuclear loci, while female philopatry is sufficient to produce a signal of population subdivision in the maternally inherited mtDNA genome. MtDNA analyses also indicate that winter aggregations of harbour porpoises along the U.S. mid-Atlantic states are comprised of animals from more than one summer breeding population.
1999 France, S.C., N. Tachino, T.F. Duda, Jr., R.A. Shleser and S.R. Palumbi. Intraspecific genetic diversity in the marine shrimp Penaeus vannamei: multiple polymorphic elongation factor-1alpha loci revealed by intron sequencing. Marine Biotechnology 1: 261-268
Abstract. Intron sequences from the elongation factor 1alpha (EF1a) gene from the marine shrimp Penaeus vannamei reveal extensive variation even among inbred populations of hatchery-raised shrimp. Among 44 individuals analyzed, we found 13 alleles varying by up to 7.5% sequence differences, and including several allele-diagnostic insertions and deletions. High heterozygosity contrasts with low genetic variation at allozyme loci, but we observed up to 4 alleles per individual, suggesting that we have identified two separate, polymorphic loci. We partitioned the observed alleles into two groups representing hypothetical duplicated loci. However, the alleles are so similar to one another that a phylogenetic analysis does not cluster them into monophyletic groupings. A possible explanation is that concerted evolution is acting to homogenize genetic variation among these two putative loci.
1999 Berntson, E. A., S. C. France and L. S. Mullineaux. Phylogenetic Relationships within the Class Anthozoa (Phylum Cnidaria) Based on Nuclear 18S rDNA Sequence Information. Molecular Phylogenetics and Evolution 13(2): 417-433
Abstract. Taxonomic relationships within the corals and anemones (Phylum Cnidaria: Class Anthozoa) are based upon few morphological characters. The significance of any given character is debatable, and there is little fossil record available for deriving evolutionary relationships. We analyzed complete 18S ribosomal sequences to examine subclass-level and ordinal-level organization within the Anthozoa. We suggest that the Subclass Ceriantipatharia is not an evolutionarily relevant grouping. The Order Corallimorpharia appears paraphyletic, and closely related to the Order Scleractinia. The 18S rRNA gene may be insufficient for establishing robust phylogenetic hypotheses concerning the specific relationships of the Corallimorpharia and the Ceriantharia, and the branching sequence for the orders within the Hexacorallia. The 18S rRNA gene has sufficient phylogenetic signal, however, to distinguish among the major groupings within the Class Anthozoa, and we use this information to suggest relationships for the enigmatic taxa Dactylanthus and Dendrobrachia.
1996 France, S. C. & T. D. Kocher. DNA sequencing of formalin-fixed crustaceans from archival research collections. Molecular Marine Biology and Biotechnology 5 (4): 304-313
Abstract. Marine invertebrate collections have historically been maintained in ethanol following fixation in formalin. These collections may represent rare or extinct species or populations, provide detailed time-series samples, or come from presently inaccessible or difficult-to-sample localities. We have tested the viability of obtaining DNA sequence data from formalin-fixed, ethanol-preserved (FFEP) deep-sea crustaceans, and found that nucleotide sequences for mitochondrial 16S rRNA and COI genes can be recovered from FFEP collections of varying age, and that these sequences are unmodified compared to those derived from frozen specimens. These results were repeatable among multiple specimens and collections for several species. Our results indicate that in the absence of fresh or frozen tissues, archived, FFEP specimens may prove a useful source of material for analysis of gene sequence data by PCR and direct sequencing.
1996 France, S. C. & T. D. Kocher. Geographic and bathymetric patterns of mitochondrial 16S rRNA sequence divergence among deep-sea amphipods, Eurythenes gryllus. Marine Biology 126: 633-644
Abstract. The physical uniformity of the deep sea suggests a lack of absolute barriers to faunal dispersal and thus genetic homogeneity in broadly-distributed species is expected. The deep-sea amphipod Eurythenes gryllus Lichtenstein (Lysianassoidea, Crustacea) is considered a panoceanic, cold-water stenotherm, with a vertical depth distribution from 184 to 6500 m. We surveyed mtDNA sequence diversity in E. gryllus to assess genetic diversity and population structure in different oceans and across traditionally defined bathyal and abyssal zones. DNA sequences (437 nucleotides length) from the mitochondrial large-subunit ribosomal RNA gene (16S rRNA) of 95 individuals, collected between 1982 to 1990 from 14 locations in the central North Pacific (including multiple samples on the slope of a seamount), eastern and western North Atlantic, and the Arctic Ocean, were obtained. Our analysis of DNA sequence diversity indicates 1) genetic homogeneity among sites within the same depth zone at the scale of ocean basins; and 2) genetically-divergent, cryptic taxa distributed at different depths, with the greatest diversity in the bathyal zone. These observations suggest that ecological and physical conditions are important isolating mechanisms that may lead to speciation in this group.
1996 France, S. C., P. E. Rosel, J. E. Agenbroad, L.S. Mullineaux, & T. D. Kocher. DNA sequence variation of mitochondrial large-subunit rRNA provides support for a two subclass organization of the Anthozoa (Cnidaria). Molecular Marine Biology and Biotechnology 5 (1): 15-28
Abstract. We have sequenced a portion of the mitochondrial 16S rRNA gene from 29 species of Anthozoa, representing six orders of the subclasses Ceriantipatharia, Hexacorallia, and Octocorallia, with the focus on deep-seamount corals ( 500 meters depth). We have detected significant length variation in the gene, with homologous gene fragments ranging from 545 base pairs (bp) in a shallow-water scleractinian coral to 911 bp in a deep-sea antipatharian black coral. The aligned sequences were divided into five regions: three high-identity sequence blocks (HSBs) and two highly variable blocks (INDELs). Most of the length variation among species occurred as varying numbers of nucleotides in the two INDELs. Little or no intraspecific sequence variation was detected over spatial scales of up to Å150 km. Interspecific sequence variation was lowest among the octocorals and greatest among the ceriantipatharians. Our data indicate that the orders Ceriantharia and Antipatharia are highly divergent, and a phylogenetic reconstruction provides support for the two subclass system of the Class Anthozoa (Hexacorallia and Octocorallia).
1994 France, S. C. Genetic population structure and gene flow among deep-sea amphipods, Abyssorchomene spp., from six California Continental Borderland basins. Marine Biology 118: 67-77
Abstract. Studies of geographic population variation needed to estimate gene flow are lacking in deep-sea biology. Using allozyme electrophoresis, I have studied population-level geographic variation among scavenging lysianassoid amphipod populations (Abyssorchomene spp.) inhabiting deep-water basins of the Southern California Continental Borderland. Samples were collected from November, 1987 to November, 1990, using baited traps, from 6 basins whose bottom depths ranged from ~1000 - 2100 m. Five basins (San Diego Trough, Santa Catalina, San Nicolas, Santa Cruz, Tanner Basins) could be grouped together as "shallow-sill" basins, with physical conditions distinctly different from a single "deep-sill" basin (San Clemente Basin). Amphipods tentatively identified as Abyssorchomene sp. 1 collected from the shallow-sill basins were morphologically discriminated from those collected in the San Clemente Basin, which were identified as Abyssorchomene sp. 2. Results from 8 enzyme loci revealed significant genetic differentiation [Nei's genetic distance (D) > 0.155] of deep-sill basin-dwelling Abyssorchomene sp. 2 vs. Abyssorchomene sp. 1 from the shallow-sill basins and low levels of gene flow (migration rate, M < 1). Comparisons of benthic fauna suggest the presence of an abyssal-related assemblage in the deep-sill basin isolated from the northern shallow-sill basins. Genetic distance among the 5 shallow-sill basin populations of Abyssorchomene sp. 1 was very low (D < 0.003). Estimates of gene flow among these populations were very high (M ~ 24 - 170) and suggested weak isolation by distance.
1993 France, S. C. Geographic variation among three isolated populations of the hadal amphipod Hirondellea gigas (Crustacea: Amphipoda: Lysianassoidea). Marine Ecology Progress Series 92:277-287
Abstract. The relative homogeneity and continuity of the deep sea may provide a habitat in which species can maintain widespread, genetically homogeneous populations. This study examines the lysianassoid amphipod Hirondellea gigas (Birstein and Vinogradov 1955) to determine whether populations from spatially-disjunct habitats in the deep-sea maintain genetic homogeneity. H. gigas is a scavenger which rapidly responds to and consumes experimental baitfalls at depths of 10000 meters. It appears to be endemic to western Pacific trenches, having been collected only within the Kurile-Kamchatka, Japan, Izu-Bonin, Volcano, Yap, Mariana, Palau, and Philippine Trenches. To estimate the degree of isolation of populations from the last three trenches, morphological variation was quantified through a discriminant analysis of surficial morphometric characters. Discriminant classification results were compared to "null-populations," generated using a bootstrap randomization procedure, to determine the significance of the discrimination. Variation was sufficient to allow 68.4 - 84.5 % of individuals to be correctly reclassified into their population using discriminant functions. Bootstrapped randomizations of the data indicate that the classification success was significantly greater than random. The results indicate that these geographically-isolated trench populations may have reduced levels of gene flow between them, causing them to diverge morphologically.
1992 France, S. C., R. C. Vrijenhoek & R. R. Hessler. Genetic differentiation between spatially-disjunct populations of the deep-sea, hydrothermal vent-endemic amphipod Ventiella sulfuris. Marine Biology 114: 551-559
Abstract. Species endemic to deep-sea hydrothermal vent ecosystems have disjunct distributions imposed by the island-like arrangement of their specialized habitats. Using allozyme electrophoresis, we examined genetic population structure of the hydrothermal vent amphipod Ventiella sulfuris Barnard & Ingram, 1990. Samples from five sites along the East Pacific Rise (EPR) and two along the Galapagos Rift were collected in 1990 and 1988 respectively. Variability, based on 12 enzyme loci, was relatively high (P95 = 41.6%; H = 0.158) compared with shallow-water marine and freshwater amphipods, and similar to the deep-sea lysianassid Eurythenes gryllus. Genetic divergence among populations spread along a contiguous rift axis (i.e. EPR) was low (Nei's D ranged from > 0.001 - 0.018). Genetic structure analysis suggests that along a contiguous ridge axis migration occurs in a stepping stone manner and is unconstrained by distances as great as 1200 km (migration rate, M, ranged from 1.9 - 67.8 individuals per generation). However, genetic divergence between populations on disjunct ridge axes was extremely high (D ranged from 0.438 - 0.476). Most of the variance in gene frequencies was due to the differences between the major subpopulations inhabiting the two distinct ridge axes, EPR and Galapagos Rift. Apparently, very little migration and gene flow occur between these major subpopulations (M << 1). This level of genetic divergence may be sufficient to justify separation of EPR and Galapagos Rift populations at the species level. Further analyses of morphological characters is required before taxonomic status can be assigned.
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