Scleractinian corals are affected by environment-induced phenotypic plasticity and intraspecific morphological variation caused by genotype. In an effort to identify new strategies for resolving this taxonomic issue, we applied a molecular approach for species evaluation to two closely related genera, Echinophyllia and Oxypora, for which few molecular data are available. A robust multi-locus phylogeny using DNA sequence data across four loci of both mitochondrial (COI, ATP6-NAD4) and nuclear (histone H3, ITS region) origin from 109 coral colonies was coupled with three independent putative species delimitation methods based on barcoding threshold (ABGD) and coalescence theory (PTP, GMYC). Observed overall congruence across multiple genetic analyses distinguished two traditional species (E. echinoporoides and O. convoluta), a species complex composed of E. aspera, E. orpheensis, E. tarae, and O. glabra, whereas O. lacera and E. echinata were indistinguishable with the sequenced loci. The combination of molecular species delimitation approaches and skeletal character observations allowed the description of two new reef coral species, E. bulbosa sp. n. from the Red Sea and E. gallii sp. n. from the Maldives and Mayotte. This work demonstrated the efficiency of multi-locus phylogenetic analyses and recently developed molecular species delimitation approaches as valuable tools to disentangle taxonomic issues caused by morphological ambiguities and to re-assess the diversity of scleractinian corals.

PAPUA NIUGINI

Scleractinian corals (i.e. hard corals) play a fundamental role in building and maintaining coral reefs, one of the most diverse ecosystems on Earth. Nevertheless, their phylogenies remain largely unresolved and little is known about dispersal and survival of their planktonic larval phase. The small subunit ribosomal RNA (SSU rRNA) is a commonly used gene for DNA barcoding in several metazoans, and small variable regions of SSU rRNA are widely adopted as barcode marker to investigate marine plankton community structure worldwide. Here, we provide a large sequence data set of the complete SSU rRNA gene from 298 specimens, representing all known extant reef coral families and a total of 106 genera. The secondary structure was extremely conserved within the order with few exceptions due to insertions or deletions occurring in the variable regions. Remarkable differences in SSU rRNA length and base composition were detected between and within acroporids (Acropora, Montipora, Isopora and Alveopora) compared to other corals. The V4 and V9 regions seem to be promising barcode loci because variation at commonly used barcode primer binding sites was extremely low, while their levels of divergence allowed families and genera to be distinguished. A time-calibrated phylogeny of Scleractinia is provided, and mutation rate heterogeneity is demonstrated across main lineages. The use of this data set as a valuable reference for investigating aspects of ecology, biology, molecular taxonomy and evolution of scleractinian corals is discussed.

PAPUA NIUGINI

Abstract The family Euphylliidae consists of reef-building zooxanthellate scleractinian corals distributed across the Indo-Pacific. Seven extant genera comprising a total of 22 valid species are currently recognised. Recent studies have re-organised the taxonomy of the family at the genus level based on molecular and morphological data, including a comprehensive revision of Euphyllia and the resurrection of Fimbriaphyllia . Here, three mitochondrial loci ( coi , 12S rRNA, and 16S rRNA) were sequenced and morphological examinations were conducted at three scales (macro/micromorphology and microstructure of the skeleton, and polyp morphology) to study the phylogeny and taxonomy of Euphylliidae. We analysed a total of 11 valid species collected from seven Indo-Pacific localities. The monotypic genus Coeloseris , currently in Agariciidae, was also investigated since previous molecular data suggested a close relationship with the Euphylliidae. Molecular and morphological phylogenetic trees were broadly concordant in the definition of genus-level clades. All analysed genera, i.e., Ctenella, Euphyllia, Fimbriaphyllia, Galaxea , and Gyrosmilia , were reciprocally monophyletic based on molecular results. Coeloseris was nested within the family and, therefore, is formally moved into Euphylliidae. Updated morphological diagnoses are provided for each investigated genus. This study further demonstrated that a phylogenetic classification of scleractinian corals can be achieved by applying a combined morpho-molecular approach. Finally, we encourage phylogenetic and taxonomic studies of the euphylliid taxa not yet analysed molecularly, such as the monotypic genera Montigyra and Simplastrea .

KAVIENG 2014, PAPUA NIUGINI

We investigated the globally distributed red algal genus Pterocladiella , comprising 24 described species, many of which are economically important sources of agar and agarose. We used DNA-based species delimitation approaches, phylogenetic, and historical biogeographical analyses to uncover cryptic diversity and infer the drivers of biogeographic patterns. We delimited 43 species in Pterocladiella , of which 19 are undescribed. Our multigene time-calibrated phylogeny and ancestral area reconstruction indicated that Pterocladiella most likely originated during the Early Cretaceous in the Tethys Sea. Ancient Tethyan vicariance and long-distance dispersal have shaped current distribution patterns. The ancestor of Eastern Pacific species likely arose before the formation of the formidable Eastern Pacific Barrier—a first confirmation using molecular data in red algae. Divergences of Northeast and Southeast Pacific species have been driven by the Central American Seaway barrier, which, paradoxically, served as a dispersal pathway for Atlantic species. Both long- and short-distance dispersal scenarios are supported by genetic relationships within cosmopolitan species based on haplotype analysis. Asymmetrical distributions and the predominance of peripatry and sympatry between sister species suggest the importance of budding speciation in Pterocladiella . Our study highlights the underestimation of global diversity in these crucial components of coastal ecosystems and provides evidence for the complex evolution of current species distributions.

ATIMO VATAE, KARUBENTHOS 2012, MADIBENTHOS, PAPUA NIUGINI

A multi‐gene ( SSU , LSU , psb A, and COI ) molecular phylogeny of the family Corallinaceae (excluding the subfamilies Lithophylloideae and Corallinoideae) showed a paraphyletic grouping of six monophyletic clades. Pneophyllum and Spongites were reassessed and recircumscribed using DNA sequence data integrated with morpho‐anatomical comparisons of type material and recently collected specimens. We propose Chamberlainoideae subfam. nov., including the type genus Chamberlainium gen. nov., with C. tumidum comb. nov. as the generitype, and Pneophyllum . Chamberlainium is established to include several taxa previously ascribed to Spongites , the generitype of which currently resides in Neogoniolithoideae. Additionally we propose two new genera, Dawsoniolithon gen. nov. (Metagoniolithoideae), with D. conicum comb. nov. as the generitype and Parvicellularium gen. nov. (subfamily incertae sedis ), with P. leonardi sp. nov. as the generitype. Chamberlainoideae has no diagnostic morpho‐anatomical features that enable one to assign specimens to it without DNA sequence data, and it is the first subfamily to possess both Type 1 ( Chamberlainium ) and Type 2 ( Pneophyllum ) tetra/bisporangial conceptacle roof development. Two characters distinguish Chamberlainium from Spongites : tetra/biasporangial conceptacle chamber diameter (<300 μm in Chamberlainium vs. >300 μm in Spongites ) and tetra/bisporangial conceptacle roof thickness (<8 cells in Chamberlainium vs. >8 cells in Spongites ). Two characters also distinguish Pneophyllum from Dawsoniolithon : tetra/bisporangial conceptacle roof thickness (<8 cells in Pneophyllum vs. >8 cells in Dawsoniolithon ) and thallus construction (dimerous in Pneophyllum vs. monomerous in Dawsoniolithon ).

KAVIENG 2014

LIFOU 2000, MONTROUZIER

ATIMO VATAE, KARUBENTHOS 2, KAVIENG 2014, PAPUA NIUGINI, SANTO 2006

The systematics of the Laurencia complex was investigated using a taxon-rich data set including the chloroplast ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit (rbcL) gene only and a character-rich data set combining mitochondrial cytochrome oxidase 1 (COI-5P), the rbcL marker, and the nuclear large subunit of the ribosomal operon (LSU). Bayesian and ML analyses of these data sets showed that three species hitherto placed in the genus Laurencia J.V.Lamour. were not closely related to Laurencia s. str. Laurencia caspica Zinova & Zaberzhinskaya was the sister group of the remaining Osmundea Stackh. species, L. crustiformans McDermid joined Palisada and L. fl exilis Setch. consisted of an independent lineage. In light of these results a new genus, Ohelopapa F.Rousseau, Martin-Lescanne, Payri & L.Le Gall gen. nov., is proposed to accommodate L. fl exilis. This new genus is morphologically characterized by four pericentral cells in each vegetative axial segment; however, it lacks ‘corps en cerise’ in cortical cells and secondary pit connections between cortical cells, which are characteristic of Laurencia. Three novel combinations are proposed to render the classifi cation closer to a natural system: Ohelopapa fl exilis (Setch.) F.Rousseau, Martin-Lescanne, Payri & L.Le Gall comb. nov., Osmundea caspica (Zinova & Zaberzhinskaya) Maggs & L.M.McIvor comb. nov. and Palisada crustiformans (McDermid) A.R.Sherwood, A.Kurihara & K.W.Nam comb. nov.

KARUBENTHOS 2012

ATIMO VATAE

PAPUA NIUGINI

Abstract The calcified encrusting brown-algal genus Newhousia was collected in 2012 from two sites in Madang Lagoon, northern Papua New Guinea. This is the first report of that enigmatic genus since its original description in 2004 from Oahu in the Hawaiian Islands. Morphologies of thalli from both Papuan localities agree with the original diagnosis and the published figures of the Hawaiian Newhousia imbricata . Ribulose-1,5-biphosphate carboxylase large subunit ( rbc L) sequences of Papuan specimens were 96% identical to those of N. imbricata , and although there were no outstanding morphological differences between the Hawaiian and the Papuan specimens, the genetic divergence between the two strongly indicates they are not conspecific. A formal description of the new species, Newhousia yhaga , is provided and the phylogenetic implications of concatenated cox 3, psb A and rbc L sequences evaluated. A multi-marker phylogeny was generated in the hope to establish the precise phylogenetic position of Newhousia within the order Dictyotales. Even though both Bayesian inference (BI) and maximum likelihood (ML) analysis point to Newhousia being sister to Lobophora , these results are not supported by ML bootstrap values. The present documentation of Newhousia in a southwest Pacific locality considerably extends the geographical range of this unusual genus.

PAPUA NIUGINI

Abstract The calcified encrusting brown-algal genus Newhousia was collected in 2012 from two sites in Madang Lagoon, northern Papua New Guinea. This is the first report of that enigmatic genus since its original description in 2004 from Oahu in the Hawaiian Islands. Morphologies of thalli from both Papuan localities agree with the original diagnosis and the published figures of the Hawaiian Newhousia imbricata . Ribulose-1,5-biphosphate carboxylase large subunit ( rbc L) sequences of Papuan specimens were 96% identical to those of N. imbricata , and although there were no outstanding morphological differences between the Hawaiian and the Papuan specimens, the genetic divergence between the two strongly indicates they are not conspecific. A formal description of the new species, Newhousia yhaga , is provided and the phylogenetic implications of concatenated cox 3, psb A and rbc L sequences evaluated. A multi-marker phylogeny was generated in the hope to establish the precise phylogenetic position of Newhousia within the order Dictyotales. Even though both Bayesian inference (BI) and maximum likelihood (ML) analysis point to Newhousia being sister to Lobophora , these results are not supported by ML bootstrap values. The present documentation of Newhousia in a southwest Pacific locality considerably extends the geographical range of this unusual genus.

PAPUA NIUGINI

PAPUA NIUGINI

The existence of massive cryptic diversity in algae makes linking DNA-based lineages to existing taxa exceedingly difficult. A better integration of historical collections into modern taxonomic research is therefore highly desirable. Using the brown algal genus Lobophora as a test case, we explore the feasibility of linking taxonomic names to clades in modern phylogenies. Despite Lobophora being a pantropical genus with probably more than 100 species, traditionally only a handful of species have been recognized. In this study we reevaluated the identity of 17 historical taxa thought to belong to Lobophora by attempting DNA amplification of herbarium material as well as specimens recently collected from the type localities (epitypes). In an attempt to assign them to Molecular Operational Taxonomic Units, the obtained sequences were integrated in a global Lobophora phylogeny based upon data derived from more than 650 specimens. Our results indicate that although five sequences were obtained from type specimens, exclusive reliance on information preserved in type specimens is problematic. Epitype material proved a more successful way forward, but this route often comes with a considerable degree of uncertainty, especially in tropical regions where the extent of sympatry among Lobophora lineages is often considerable. More problematic from a broader perspective is the fact that for 35% of historical taxa, either the type could not be traced or permission was not granted to extract DNA from the types. Such a low accessibility rate may reduce our reliance on type material and jeopardize future efforts to integrate historical taxa into a framework of a modern DNA-based taxonomy.

KAVIENG 2014, PAPUA NIUGINI

Aim: Historical processes that shaped current diversity patterns of seaweeds remain poorly understood. Using Dictyotales, a globally distributed order of brown seaweeds as a model, we test if historical biogeographical and diversification patterns are comparable across clades. Dictyotales contain some 22 genera, three of which, Dictyota, Lobophora and Padina, are exceptionally diverse. Specifically, we test whether the evolutionary processes that produced the latitudinal diversity patterns in these clades are in line with the tropical conservatism, out-of-the-tropics or diversification rate hypotheses.

KAVIENG 2014, PAPUA NIUGINI

We re-evaluated the diversity of Lobophora using an integrative taxonomic approach based on a broad sampling across French Polynesian archipelagos. Our results show that French Polynesia supports at least 37 Lobophora species of which ~57% (21) are endemic. This level of endemicity is comparable to that presently known in the Caribbean and the western Indian Ocean, while French Polynesian coastlines cover a much smaller length. With a third of the species in common, French Polynesia shares considerable biogeographic affinities with the Melanesian Islands, situated over 4000 km to the west. Distribution ranges of a few species reach the western Indian Ocean, and two species also occur in the Atlantic. We hypothesize that Lobophora species in French Polynesia have mainly evolved into endemic species from colonizers originating from the Central Indo-Pacific. These rare dispersal events to ocean archipelagos followed by a long period of isolation and speciation represent an important process responsible for the high level of endemism in remote archipelagos. While south-eastern Pacific Islands could be considered an ‘evolutionary graveyard’ for the genus Lobophora as little local radiation occurred, this may simply be due to recent evolutionary history. Based on these new data, the diversity of Lobophora represents ~10% of French Polynesian seaweed diversity. Eighteen new species of Lobophora are here described from French Polynesia.

KAVIENG 2014