Deep genetic divergences among Indo-Pacific populations of the coral reef sponge Leucetta chagosensis (Leucettidae): founder effects, vicariance, or both?

Sponge diversification in marine lakes: Implications for phylogeography and population genomic studies on sponges

The relative influence of geography, currents, and environment on gene flow within sessile marine species remains an open question. Detecting subtle genetic differentiation at small scales is challenging in benthic populations due to large effective population sizes, general lack of resolution in genetic markers, and because barriers to dispersal often remain elusive. Marine lakes can circumvent confounding factors by providing discrete and replicated ecosystems. Using high-resolution double digest restriction-site-associated DNA sequencing (4826 Single Nucleotide Polymorphisms, SNPs), we genotyped populations of the sponge Suberites diversicolor (n = 125) to test the relative importance of spatial scales (1-1400 km), local environmental conditions, and permeability of seascape barriers in shaping population genomic structure. With the SNP dataset, we show strong intralineage population structure, even at scales <10 km (average F ST = 0.63), which was not detected previously using single markers. Most variation was explained by differentiation between populations (AMOVA: 48.8%) with signatures of population size declines and bottlenecks per lake. Although the populations were strongly structured, we did not detect significant effects of geographic distance, local environments, or degree of connection to the sea on population structure, suggesting mechanisms such as founder events with subsequent priority effects may be at play. We show that the inclusion of morphologically cryptic lineages that can be detected with the COI marker can reduce the obtained SNP set by around 90%. Future work on sponge genomics should confirm that only one lineage is included. Our results call for a reassessment of poorly dispersing benthic organisms that were previously assumed to be highly connected based on low-resolution markers.

Low genetic diversity and predation threaten a rediscovered marine sponge

Discovered in 1819 in the tropical waters off Singapore, the magnificent Neptune's cup sponge Cliona patera (Hardwicke, 1820) was harvested for museums and collectors until it was presumed extinct worldwide for over a century since 1907. Recently in 2011, seven living individuals were rediscovered in Singapore with six relocated to a marine protected area in an effort to better monitor and protect the population, as well as to enhance external fertilisation success. To determine genetic diversity within the population, we sequenced the complete mitochondrial genomes and nuclear ribosomal DNA of these six individuals and found extremely limited variability in their genes. The low genetic diversity of this rediscovered population is confirmed by comparisons with close relatives of C. patera and could compromise the population's ability to recover from environmental and anthropogenic pressures associated with the highly urbanised coastlines of Singapore. This lack of resilience is compounded by severe predation which has been shrinking sponge sizes by up to 5.6% every month. Recovery of this highly endangered population may require ex situ approaches and crossbreeding with other populations, which are also rare.

A paradigm for the recognition of cryptic trematode species in tropical Indo-west Pacific fishes: the problematic genus Preptetos (Trematoda: Lepocreadiidae)

Molecular data have transformed approaches to trematode taxonomy by providing objective evidence for the delineation of species. However, although the data are objective, the interpretation of these data regarding species boundaries is subjective, especially when different markers conflict. Conserved markers can lead to an underestimation of richness and those used for finer species delineation have the capacity to inflate species recognition, perhaps unrealistically. Here we examine molecular and morphological evidence for species recognition in an especially confusing system, the lepocreadiid genus Preptetos Pritchard, 1960 in acanthuriform fishes of the tropical Indo-west Pacific. We consider species boundaries within this genus based on combined data (ITS2 and 28S rDNA; cox1 mtDNA and morphometrics) for substantial new collections. Delineation of species using only morphological data suggest fewer species than analysis of the sequence data; the latter suggests the presence of potential cryptic species and analysis of different markers suggests the presence of differing numbers of species. We conclude that an integrative interpretation creates the most satisfying taxonomic hypothesis. In the light of the new data, we have chosen and propose a model of trematode species recognition that demands reciprocal monophyly in the most discriminating available molecular marker plus distinction in morphology or host distribution. By invoking these criteria, we distinguish eight species in our new tropical Indo-west Pacific collections. Six of these are new (Preptetos allocaballeroi n. sp., Preptetos paracaballeroi n. sp., Preptetos pearsoni n. sp., Preptetos prudhoei n. sp., Preptetos quandamooka n. sp. and Preptetos zebravaranus n. sp.) and we continue to recognise Preptetos cannoni Barker, Bray & Cribb, 1993 and Preptetos laguncula Bray and Cribb, 1996. Notably; two of the new species, P. allocaballeroi n. sp. and P. paracaballeroi n. sp., are morphologically cryptic relative to each other. Our criteria lead us to recognise, as species, populations with unvarying morphology and similar host relationships but which may have a complex population structure over their range. In our view, this paradigm has the capacity to render tractable the interpretation of the species status of the huge trematode fauna of the tropical Indo-west Pacific.

Integrative taxonomy of calcareous sponges (Porifera: Calcarea) from Réunion Island, Indian Ocean

The Western Indian Ocean Province is reckoned for its rich marine diversity; however, sponges of the Mascarene Islands ecoregion are still poorly known. In La Réunion, only three species of class Calcarea have been registered. Hence, calcareous sponges were searched in seven sites representing various habitats of the Western coast of La Réunion, but found in only three of them. A total of 23 sponge samples was identified using morphological and molecular taxonomy. This sampling represents 11 species, all new records for the region, and seven of them are new to science: Ascandra mascarenica sp. nov., A. oceanusvitae sp. nov., Janusya indica gen. et sp. nov., Leucascus tenuispinae sp. nov., Lelapiella tertia sp. nov., Soleneiscus intermedius sp. nov. and Leucandra ornata sp. nov.; and a new genus, Janusya gen. nov.. Based on results from this and from previous studies, we propose the synonymization of the order Murrayonida with Clathrinida. A very low sampling effort has thus increased the number of calcareous sponge species from the Mascarenes Islands ecoregion by 69 % and from La Réunion by 367%.

Population genetics of the brooding coral Seriatopora hystrix reveals patterns of strong genetic differentiation in the Western Indian Ocean

Coral reefs provide essential goods and services but are degrading at an alarming rate due to local and global anthropogenic stressors. The main limitation that prevents the implementation of adequate conservation measures is that connectivity and genetic structure of populations are poorly known. Here, the genetic diversity and connectivity of the brooding scleractinian coral Seriatopora hystrix were assessed at two scales by genotyping ten microsatellite markers for 356 individual colonies. S. hystrix showed high differentiation, both at large scale between the Red Sea and the Western Indian Ocean (WIO), and at smaller scale along the coast of East Africa. As such high levels of differentiation might indicate the presence of more than one species, a haploweb analysis was conducted with the nuclear marker ITS2, confirming that the Red Sea populations are genetically distinct from the WIO ones. Based on microsatellite analyses three groups could be distinguished within the WIO: (1) northern Madagascar, (2) south-west Madagascar together with one site in northern Mozambique (Nacala) and (3) all other sites in northern Mozambique, Tanzania and Kenya. These patterns of restricted connectivity could be explained by the short pelagic larval duration of S. hystrix, and/or by oceanographic factors, such as eddies in the Mozambique Channel (causing larval retention in northern Madagascar but facilitating dispersal from northern Mozambique towards south-west Madagascar). This study provides an additional line of evidence supporting the conservation priority status of the Northern Mozambique Channel and should inform coral reef management decisions in the region.

Morphological diversity in the foraminiferal genus Marginopora

Benthic foraminifera, and certainly symbiont-bearing (large) benthic foraminifera are generally considered to have large geographic ranges in combination with significant ecomorphological variation. With the advance of molecular phylogenetic approaches, supported or preceded by detailed morphological studies, it was demonstrated that this view needs to be reevaluated. In this paper I evaluate the morphology of five Marginopora populations from around the Coral Sea by microCT-scanning. I argue that ecomorphological and ontogenetic variation is smaller than geographic variation in morphology. This forms the basis for the description of three new species, M. santoensis nov. spec., M. charlottensis nov. spec., M. orpheusensis nov. spec. Quantitative morphological variation between M. rossi, M. orpheusensis nov. spec. and M. charlottensis nov. spec. is overlapping, but each species has unique morphological characters supporting recognition as new species. Support to distinguish the deep living (M. rossi, M. charlottensis nov. spec., M. orpheusensis nov. spec.) and shallow living (M. vertebralis) Marginopora populations as separate species is strong, but not enough molecular phylogenetic data are available to test the three new deep-living species on the Great Barrier Reef hypothesis. However, detailed understanding of ecophenotypic variation in M. santoensis nov. spec. supports the conclusion that it is unlikely that ecophenotypic variation can explain the morphological variation between the three species. I argue that the number of species in this genus is underestimated, and that there are at least five species in the Coral Sea area alone.

Implications of population connectivity studies for the design of marine protected areas in the deep sea: An example of a demosponge from the Clarion-Clipperton Zone

The abyssal demosponge Plenaster craigi inhabits the Clarion-Clipperton Zone (CCZ) in the northeast Pacific, a region with abundant seafloor polymetallic nodules with potential mining interest. Since P. craigi is a very abundant encrusting sponge on nodules, understanding its genetic diversity and connectivity could provide important insights into extinction risks and design of marine protected areas. Our main aim was to assess the effectiveness of the Area of Particular Environmental Interest 6 (APEI-6) as a potential genetic reservoir for three adjacent mining exploration contract areas (UK-1A, UK-1B and OMS-1A). As in many other sponges, COI showed extremely low variability even for samples ~900 km apart. Conversely, the 168 individuals of P. craigi, genotyped for 11 microsatellite markers, provided strong genetic structure at large geographical scales not explained by isolation by distance (IBD). Interestingly, we detected molecular affinities between samples from APEI-6 and UK-1A, despite being separated ~800 km. Although our migration analysis inferred very little progeny dispersal of individuals between areas, the major differentiation of OMS-1A from the other areas might be explained by the occurrence of predominantly northeasterly transport predicted by the HYCOM hydrodynamic model. Our study suggests that although APEI-6 does serve a conservation role, with species connectivity to the exploration areas, it is on its own inadequate as a propagule source for P. craigi for the entire eastern portion of the CCZ. Our new data suggest that an APEI located to the east and/or the south of the UK-1, OMS-1, BGR, TOML and NORI areas would be highly valuable.

Hidden diversity in the genus Tethya: comparing molecular and morphological techniques for species identification

Correctly determining species' identity is critical for estimating biodiversity and effectively managing marine populations, but is difficult for species that have few morphological traits or are highly plastic. Sponges are considered a taxonomically difficult group because they lack multiple consistent diagnostic features, which coupled with their common phenotypic plasticity, makes the presence of species complexes likely, but difficult to detect. Here, we investigated the evolutionary relationship of Tethya spp. in central New Zealand using both molecular and morphological techniques to highlight the potential for cryptic speciation in sponges. Phylogenetic reconstructions based on two mitochondrial markers (rnl, COI-ext) and one nuclear marker (18S) revealed three genetic clades, with one clade representing Tethya bergquistae and two clades belonging to what was a priori thought to be a single species, Tethya burtoni. Eleven microsatellite markers were also used to further resolve the T. burtoni group, revealing a division consistent with the 18S and rnl data. Morphological analysis based on spicule characteristics allowed T. bergquistae to be distinguished from T. burtoni, but revealed no apparent differences between the T. burtoni clades. Here, we highlight hidden genetic diversity within T. burtoni, likely representing a group consisting of incipient species that have undergone speciation but have yet to express clear morphological differences. Our study supports the notion that cryptic speciation in sponges may go undetected and diversity underestimated when using only morphology-based taxonomy, which has broad scale implications for conservation and management of marine systems.

Beneath the hairy look: the hidden reproductive diversity of the Gibsmithia hawaiiensis complex (Dumontiaceae, Rhodophyta)

The tropical alga previously recognized as Gibsmithia hawaiiensis (Dumontiaceae, Rhodophyta) was recently suggested to represent a complex of species distributed throughout the Indo-Pacific Ocean and characterized by a peculiar combination of hairy (pilose) gelatinous lobes growing on cartilaginous stalks. Phylogenetic reconstructions based on three genetic markers are presented here with the inclusion of new samples. Further diversity is reported within the complex, with nine lineages spread in four major phylogenetic groups. The threshold between intra- and interspecific relationships was assessed by species delimitation methods, which indicate the existence of 8-10 putative species in the complex. Two species belonging to the G. hawaiiensis complex are described here: Gibsmithia malayensis sp. nov. from the Coral Triangle and Gibsmithia indopacifica sp. nov., widely distributed in the Central and Eastern Indo-Pacific. Morphological differences in the vegetative and reproductive structures of the newly described species are provided and compared to the previously described species of the complex. Additional lineages represent putative species, which await further investigation to clarify their taxonomic status. Gibsmithia hawaiiensis sensu stricto is confirmed to be endemic to the Hawaiian Islands, and Gibsmithia eilatensis is apparently confined to the Red Sea, with an expanded distribution in the region. New records of the G. hawaiiensis complex are reported from Egypt, Saudi Arabia, Indonesia, Philippines, and the Federated States of Micronesia, indicating that the complex is more broadly distributed than previously considered. The isolated position of Gibsmithia within the Dumontiaceae is corroborated by molecular data.

Genomic signatures of evolution in Nautilus-An endangered living fossil

Living fossils are survivors of previously more diverse lineages that originated millions of years ago and persisted with little morphological change. Therefore, living fossils are model organisms to study both long-term and ongoing adaptation and speciation processes. However, many aspects of living fossil evolution and their persistence in the modern world remain unclear. Here, we investigate three major aspects of the evolutionary history of living fossils: cryptic speciation, population genetics and effective population sizes, using members of the genera Nautilus and Allonautilus as classic examples of true living fossils. For this, we analysed genomewide ddRAD-Seq data for all six currently recognized nautiloid species throughout their distribution range. Our analyses identified three major allopatric Nautilus clades: a South Pacific clade, subdivided into three subclades with no signs of admixture between them; a Coral Sea clade, consisting of two genetically distinct populations with significant admixture; and a widespread Indo-Pacific clade, devoid of significant genetic substructure. Within these major clades, we detected five Nautilus groups, which likely correspond to five distinct species. With the exception of Nautilus macromphalus, all previously described species are at odds with genomewide data, testifying to the prevalence of cryptic species among living fossils. Detailed F_ST analyses further revealed significant genome-wide and locus-specific signatures of selection between species and differentiated populations, which is demonstrated here for the first time in a living fossil. Finally, approximate Bayesian computation (ABC) simulations suggest large effective population sizes, which may explain the low levels of population differentiation commonly observed in living fossils.

Swept away: ocean currents and seascape features influence genetic structure across the 18,000 Km Indo-Pacific distribution of a marine invertebrate, the black-lip pearl oyster Pinctada margaritifera

BACKGROUND

Genetic structure in many widely-distributed broadcast spawning marine invertebrates remains poorly understood, posing substantial challenges for their fishery management, conservation and aquaculture. Under the Core-Periphery Hypothesis (CPH), genetic diversity is expected to be highest at the centre of a species' distribution, progressively decreasing with increased differentiation towards outer range limits, as populations become increasingly isolated, fragmented and locally adapted. The unique life history characteristics of many marine invertebrates such as high dispersal rates, stochastic survival and variable recruitment are also likely to influence how populations are organised. To examine the microevolutionary forces influencing population structure, connectivity and adaptive variation in a highly-dispersive bivalve, populations of the black-lip pearl oyster Pinctada margaritifera were examined across its ~18,000 km Indo-Pacific distribution.

RESULTS

Analyses utilising 9,624 genome-wide SNPs and 580 oysters, discovered differing patterns of significant and substantial broad-scale genetic structure between the Indian and Pacific Ocean basins. Indian Ocean populations were markedly divergent (F st = 0.2534-0.4177, p < 0.001), compared to Pacific Ocean oysters, where basin-wide gene flow was much higher (F st = 0.0007-0.1090, p < 0.001). Partitioning of genetic diversity (hierarchical AMOVA) attributed 18.1% of variance between ocean basins, whereas greater proportions were resolved within samples and populations (45.8% and 35.7% respectively). Visualisation of population structure at selectively neutral loci resolved three and five discrete genetic clusters for the Indian and Pacific Oceans respectively. Evaluation of genetic structure at adaptive loci for Pacific populations (89 SNPs under directional selection; F st = 0.1012-0.4371, FDR = 0.05), revealed five clusters identical to those detected at neutral SNPs, suggesting environmental heterogeneity within the Pacific. Patterns of structure and connectivity were supported by Mantel tests of isolation by distance (IBD) and independent hydrodynamic particle dispersal simulations.

CONCLUSIONS

It is evident that genetic structure and connectivity across the natural range of P. margaritifera is highly complex, and produced by the interaction of ocean currents, IBD and seascape features at a broad scale, together with habitat geomorphology and local adaptation at regional levels. Overall population organisation is far more elaborate than generalised CPH predictions, however valuable insights for regional fishery management, and a greater understanding of range-wide genetic structure in a highly-dispersive marine invertebrate have been gained.

Molecular biodiversity of Red Sea demosponges

Sponges are important constituents of coral reef ecosystems, including those around the Arabian Peninsula. Despite their importance, our knowledge on demosponge diversity in this area is insufficient to recognize, for example, faunal changes caused by anthropogenic disturbances. We here report the first assessment of demosponge molecular biodiversity from Arabia, with focus on the Saudi Arabian Red Sea, based on mitochondrial and nuclear ribosomal molecular markers gathered in the framework of the Sponge Barcoding Project. We use a rapid molecular screening approach on Arabian demosponge collections and analyze results in comparison against published material in terms of biodiversity. We use a variable region of 28S rDNA, applied for the first time in the assessment of demosponge molecular diversity. Our data constitutes a solid foundation for a future more comprehensive understanding of sponge biodiversity of the Red Sea and adjacent waters.

Host control of symbiont natural product chemistry in cryptic populations of the tunicate Lissoclinum patella

Natural products (secondary metabolites) found in marine invertebrates are often thought to be produced by resident symbiotic bacteria, and these products appear to play a major role in the symbiotic interaction of bacteria and their hosts. In these animals, there is extensive variation, both in chemistry and in the symbiotic bacteria that produce them. Here, we sought to answer the question of what factors underlie chemical variation in the ocean. As a model, we investigated the colonial tunicate Lissoclinum patella because of its rich and varied chemistry and its broad geographic range. We sequenced mitochondrial cytochrome c oxidase 1 (COXI) genes, and found that animals classified as L. patella fall into three phylogenetic groups that may encompass several cryptic species. The presence of individual natural products followed the phylogenetic relationship of the host animals, even though the compounds are produced by symbiotic bacteria that do not follow host phylogeny. In sum, we show that cryptic populations of animals underlie the observed chemical diversity, suggesting that the host controls selection for particular secondary metabolite pathways. These results imply novel approaches to obtain chemical diversity from the oceans, and also demonstrate that the diversity of marine natural products may be greatly impacted by cryptic local extinctions.

Phylogeography of the sponge Suberites diversicolor in Indonesia: insights into the evolution of marine lake populations

The existence of multiple independently derived populations in landlocked marine lakes provides an opportunity for fundamental research into the role of isolation in population divergence and speciation in marine taxa. Marine lakes are landlocked water bodies that maintain a marine character through narrow submarine connections to the sea and could be regarded as the marine equivalents of terrestrial islands. The sponge Suberites diversicolor (Porifera: Demospongiae: Suberitidae) is typical of marine lake habitats in the Indo-Australian Archipelago. Four molecular markers (two mitochondrial and two nuclear) were employed to study genetic structure of populations within and between marine lakes in Indonesia and three coastal locations in Indonesia, Singapore and Australia. Within populations of S. diversicolor two strongly divergent lineages (A & B) (COI: p = 0.4% and ITS: p = 7.3%) were found, that may constitute cryptic species. Lineage A only occurred in Kakaban lake (East Kalimantan), while lineage B was present in all sampled populations. Within lineage B, we found low levels of genetic diversity in lakes, though there was spatial genetic population structuring. The Australian population is genetically differentiated from the Indonesian populations. Within Indonesia we did not record an East-West barrier, which has frequently been reported for other marine invertebrates. Kakaban lake is the largest and most isolated marine lake in Indonesia and contains the highest genetic diversity with genetic variants not observed elsewhere. Kakaban lake may be an area where multiple putative refugia populations have come into secondary contact, resulting in high levels of genetic diversity and a high number of endemic species.

Lock, stock and two different barrels: comparing the genetic composition of morphotypes of the indo-pacific sponge Xestospongia testudinaria

The giant barrel sponge Xestospongiatestudinaria is an ecologically important species that is widely distributed across the Indo-Pacific. Little is known, however, about the precise biogeographic distribution and the amount of morphological and genetic variation in this species. Here we provide the first detailed, fine-scaled (<200 km(2)) study of the morphological and genetic composition of X. testudinaria around Lembeh Island, Indonesia. Two mitochondrial (CO1 and ATP6 genes) and one nuclear (ATP synthase β intron) DNA markers were used to assess genetic variation. We identified four distinct morphotypes of X. testudinaria around Lembeh Island. These morphotypes were genetically differentiated with both mitochondrial and nuclear markers. Our results indicate that giant barrel sponges around Lembeh Island, which were all morphologically identified as X. testudinaria, consist of at least two different lineages that appear to be reproductively isolated. The first lineage is represented by individuals with a digitate surface area, CO1 haplotype C5, and is most abundant around the harbor area of Bitung city. The second lineage is represented by individuals with a predominantly smooth surface area, CO1 haplotype C1 and can be found all around Lembeh Island, though to a lesser extent around the harbor of Bitung city. Our findings of two additional unique genetic lineages suggests the presence of an even broader species complex possibly containing more than two reproductively isolated species. The existence of X. testudinaria as a species complex is a surprising result given the size, abundance and conspicuousness of the sponge.

Phylogenetic diversity and community structure of the symbionts associated with the coralline sponge Astrosclera willeyana of the Great Barrier Reef

The coralline sponge Astrosclera willeyana, considered to be a living representative of the reef-building stromatoporoids of the Mesozoic and the Paleozoic periods, occurs widely throughout the Indo-Pacific oceans. We aimed to examine, for the first time, the phylogenetic diversity of the microbial symbionts associated with A. willeyana using molecular methods and to investigate the spatial variability in the sponge-derived microbial communities of A. willeyana from diverse sites along the Great Barrier Reef (GBR). Both denaturing gradient gel electrophoresis (DGGE) analyses of 12 Astrosclera specimens and sequencing of a 16S rRNA gene clone library, constructed using a specimen of A. willeyana from the Yonge Reef (380 clones), revealed the presence of a complex microbial community with high diversity. An assessment of the 16S rRNA gene sequences to the particular phylogenetic groups showed domination of the Chloroflexi (42 %), followed by the Gammaproteobacteria (14 %), Actinobacteria (11 %), Acidobacteria (8 %), and the Deferribacteres (7 %). Of the microbes that were identified, a further 15 % belonged to the Deltaproteobacteria, Alphaproteobacteria, and Nitrospirae genera. The minor phylogenetic groups Gemmatimonadetes, Spirochaetes, Cyanobacteria, Poribacteria, and the Archaea composed 3 % of the community. Over 94 % of the sequences obtained from A. willeyana grouped together with other sponge- or coral-derived sequences, and of these, 72 % formed, with nearest relatives, 46 sponge-specific or sponge-coral clusters, highlighting the uniqueness of the microbial consortia in sponges. The DGGE results showed clear divisions according to the geographical origin of the samples, indicating closer relationships between the microbial communities with respect to their geographic origin (northern vs. southern GBR).

Global diversity of sponges (Porifera)

With the completion of a single unified classification, the Systema Porifera (SP) and subsequent development of an online species database, the World Porifera Database (WPD), we are now equipped to provide a first comprehensive picture of the global biodiversity of the Porifera. An introductory overview of the four classes of the Porifera is followed by a description of the structure of our main source of data for this paper, the WPD. From this we extracted numbers of all 'known' sponges to date: the number of valid Recent sponges is established at 8,553, with the vast majority, 83%, belonging to the class Demospongiae. We also mapped for the first time the species richness of a comprehensive set of marine ecoregions of the world, data also extracted from the WPD. Perhaps not surprisingly, these distributions appear to show a strong bias towards collection and taxonomy efforts. Only when species richness is accumulated into large marine realms does a pattern emerge that is also recognized in many other marine animal groups: high numbers in tropical regions, lesser numbers in the colder parts of the world oceans. Preliminary similarity analysis of a matrix of species and marine ecoregions extracted from the WPD failed to yield a consistent hierarchical pattern of ecoregions into marine provinces. Global sponge diversity information is mostly generated in regional projects and resources: results obtained demonstrate that regional approaches to analytical biogeography are at present more likely to achieve insights into the biogeographic history of sponges than a global perspective, which appears currently too ambitious. We also review information on invasive sponges that might well have some influence on distribution patterns of the future.

Sponge ecology in the molecular era

Knowledge of the functioning, health state, and capacity for recovery of marine benthic organisms and assemblages has become essential to adequately manage and preserve marine biodiversity. Molecular tools have allowed an entirely new way to tackle old and new questions in conservation biology and ecology, and sponge science is following this lead. In this review, we discuss the biological and ecological studies of sponges that have used molecular markers during the past 20 years and present an outlook for expected trends in the molecular ecology of sponges in the near future. We go from (1) the interface between inter- and intraspecies studies, to (2) phylogeography and population level analyses, (3) intra-population features such as clonality and chimerism, and (4) environmentally modulated gene expression. A range of molecular markers has been assayed with contrasting success to reveal cryptic species and to assess the genetic diversity and connectivity of sponge populations, as well as their capacity to respond to environmental changes. We discuss the pros and cons of the molecular gene partitions used to date and the prospects of a plentiful supply of new markers for sponge ecological studies in the near future, in light of recently available molecular technologies. We predict that molecular ecology studies of sponges will move from genetics (the use of one or some genes) to genomics (extensive genome or transcriptome sequencing) in the forthcoming years and that sponge ecologists will take advantage of this research trend to answer ecological and biological questions that would have been impossible to address a few years ago.

Sponge systematics facing new challenges

Systematics is nowadays facing new challenges with the introduction of new concepts and new techniques. Compared to most other phyla, phylogenetic relationships among sponges are still largely unresolved. In the past 10 years, the classical taxonomy has been completely overturned and a review of the state of the art appears necessary. The field of taxonomy remains a prominent discipline of sponge research and studies related to sponge systematics were in greater number in the Eighth World Sponge Conference (Girona, Spain, September 2010) than in any previous world sponge conferences. To understand the state of this rapidly growing field, this chapter proposes to review studies, mainly from the past decade, in sponge taxonomy, nomenclature and phylogeny. In a first part, we analyse the reasons of the current success of this field. In a second part, we establish the current sponge systematics theoretical framework, with the use of (1) cladistics, (2) different codes of nomenclature (PhyloCode vs. Linnaean system) and (3) integrative taxonomy. Sponges are infamous for their lack of characters. However, by listing and discussing in a third part all characters available to taxonomists, we show how diverse characters are and that new ones are being used and tested, while old ones should be revisited. We then review the systematics of the four main classes of sponges (Hexactinellida, Calcispongiae, Homoscleromorpha and Demospongiae), each time focusing on current issues and case studies. We present a review of the taxonomic changes since the publication of the Systema Porifera (2002), and point to problems a sponge taxonomist is still faced with nowadays. To conclude, we make a series of proposals for the future of sponge systematics. In the light of recent studies, we establish a series of taxonomic changes that the sponge community may be ready to accept. We also propose a series of sponge new names and definitions following the PhyloCode. The issue of phantom species (potential new species revealed by molecular studies) is raised, and we show how they could be dealt with. Finally, we present a general strategy to help us succeed in building a Porifera tree along with the corresponding revised Porifera classification.

Species boundaries and phylogenetic relationships between Atlanto-Mediterranean shallow-water and deep-sea coral associated Hexadella species (Porifera, Ianthellidae)

Coral reefs constitute the most diverse ecosystem of the marine realm and an increasing number of studies are focusing on coral species boundaries, distribution, and on processes that control species ranges. However, less attention has been paid to coral associated species. Deep-sea sponges dominate cold-water coral ecosystems, but virtually nothing is known about their molecular diversity. Moreover, species boundaries based on morphology may sometimes be inadequate, since sponges have few diagnostic characters. In this study, we investigated the molecular diversity within the genus Hexadella (Porifera, Demospongiae, Verongida, Ianthellidae) from the European shallow-water environment to the deep-sea coral ecosystems. Three molecular markers were used: one mitochondrial (COI) and two nuclear gene fragments (28S rDNA and the ATPS intron). Phylogenetic analyses revealed deeply divergent deep-sea clades congruent across the mitochondrial and nuclear markers. One clade contained specimens from the Irish, the Scottish, and the Norwegian margins and the Greenland Sea (Hexadella dedritifera) while another clade contained specimens from the Ionian Sea, the Bay of Biscay, and the Irish margin (H. cf. dedritifera). Moreover, these deeply divergent deep-sea clades showed a wide distribution suggesting a connection between the reefs. The results also point to the existence of a new deep-sea species (Hexadella sp.) in the Mediterranean Sea and of a cryptic shallow-water species (Hexadella cf. pruvoti) in the Gorringe Bank. In contrast, low genetic differentiation between H. cf. dedritifera and H. pruvoti from the Mediterranean Sea was observed. All Hexadella racovitzai specimens from the Mediterranean Sea (shallow and deep) to the Atlantic formed a monophyletic group.

[Intra-individual allele heterozygotes in phylogenetic analysis]

The study of evolutionary relationships among organisms is vital in evolutionary biology. To reconstruct a reliable species phylogeny, one of the most important issues is to choose proper molecular markers and take full advantage of phylogenetic information contained in these markers. Intra-individual allele heterozygotes (IIAHs) have been commonly detected in intron phylogenetic studies. How to incorporate IIAHs into phylogenetic framework has been a focus in current studies. In this review, the conception, isolation, and analytic methods of IIAHs in phylogeny were summarized.

Development and characterization of microsatellite markers for analysis of population differentiation in the tree legume Acacia koa (Fabaceae: Mimosoideae) in the Hawaiian Islands

The aim of this research was to develop and use microsatellite markers to characterize the high-value timber tree Acacia koa (koa), which is endemic to the Hawaiian Islands. Genomic DNA fragments of 300-1000 bp were cloned and sequenced following enrichment for microsatellite motifs by PCR using 7 oligonucleotide repeat primers in separate reactions. Among 96 sequences analyzed, 63 contained unique microsatellite motifs flanked by variable sequences. A dual PCR method involving a primer walking step was used to develop 15 primer pairs. Another 16 primer pairs were developed directly from the variable sequences on both sides of the microsatellite motifs. These 31 primer pairs were tested on 172 koa plants representing 11 populations collected from 4 of the major Hawaiian Islands. Nine of the primers that identified polymorphic microsatellite loci and 3 that detected unique alleles exclusively in some populations were used for genetic diversity studies of koa. Cluster analysis and multidimensional scaling of the allelic phenotype data revealed that koa from Kauai formed a distinct group separate from koa of the neighboring islands of Oahu, Maui, and Hawaii. The oldest of the four islands, Kauai, also had the most diverse populations of koa.