Indo-West Pacific

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Fourteen species of hermit crab families Coenobitidae, Diogenidae and Paguridae are reported from the terrestrial, littoral and shallow subtidal habitats in Anambas and Natuna Islands, Indonesia. Almost all species are widely distributed in the Indo-West Pacific. Only Diogenes spinicarpus Rahayu & Forest, 1995, has limited distribution, so far reported only from Indonesian waters.

— Cardiids or marine cockles are one of the best known families of marine bivalves in the world, with a long history of study and collection given their large and accessible shells, a tractable level of biodiversity globally (~290 species) and a solid fossil record extending to the late Triassic. In Western Australia, the cardiids are well known relative to other marine bivalve families, having been the subject of focussed treatment and consist of 31 species. However, given the proximity to the Indo-West Pacific, sheer size of the state and almost unparalleled number of habitats, the diversity is likely underestimated. Over the last 40 years, ongoing expedition work coupled with taxonomic study by the authors, has resulted in a doubling of the cardiid fauna of Western Australia (WA). Current cardiid diversity now stands at 68 species, including seven species of giant clams (Tridacninae). Subfamilial representation has changed little (except for the addition of Tridacninae previously in its own family, the Tridacnidae), and key genera in Cardiinae (e.g. Fulvia), Fraginae (e.g. Fragum) and Trachycardiinae (e.g. Acrosterigma and Vasticardium) still deliver much of the diversity. This updated biodiversity census has implications within and beyond Western Australia, with 16 new species records for the state and 14 new records for Australia, including four new species: Acrosterigma extremattenuatum sp. nov., Ctenocardia pilbaraensis sp. nov., Microcardium scabrosum sp. nov. and Pratulum occidentale sp. nov. Further taxonomic decisions include recognition of Vasticardium serricostatum (Melvill & Standen, 1899) and Lunulicardia tumorifera (Lamarck, 1819) as distinct species. Vasticardium swanae Maxwell, Congdon & Rymer, 2016 is considered a new synonym of Cardium variegatum G.B. Sowerby II, 1840; Vasticardium lomboke Vidal, 2003 is considered a new synonym of Cardium mindanense Reeve, 1844 and Acrosterigma abrolhense Vidal, 1999 is considered a new synonym of Cardium cygnorum Deshayes, 1855. All subspecies in the Vasticardium elongatum (Bruguière, 1789) complex are raised to species level.

New acquisitions arising from tropical survey work in the north have yielded all of the newly added species and all newly described species in the Western Australian Museum (WAM) cardiid collections. This is in contrast to the relatively stable biodiversity of southwestern Western Australia. In the north, diversity is highly structured with sixteen taxa found restricted to offshore islands and shoals (e.g. Vasticardium philippinense (Hedley, 1899), V. elongatum (Bruguière, 1789), Corculum cardissa (Linnaeus, 1758), Ctenocardia fornicata (G.B. Sowerby II, 1840), C. gustavi Vidal & Kirkendale, 2007), and a smaller cohort found exclusively inshore (e.g. A. extremattenuatum sp. nov., V. wilsoni (Voskuil & Onverwagt, 1991), C. pilbaraensis sp. nov.). Biodiversity comparisons are made with other tropical states in northern Australia, including the Northern Territory (NT) and Queensland (Qld), and considered together these records support recognition of a vast Dampierian Province. Regional biogegraphic comparisons are also made to examine whether cardiids in northern Australia are as diverse as other central Indo West Pacific (IWP) areas. To improve management of the commercially important Tridacninae (giant clams), we provide the first formal records of species diversity and distribution in this group for WA. While cardiids are relatively well characterised, persistent gaps remain that are not unique to this family. Our knowledge of small and/or cryptic species, as well as the deep water fauna broadly, lags behind our understanding of shallow water macromolluscs.

Ranunculus is a large genus with a worldwide distribution. Phylogenetic analyses of c. 200 species of Ranunculus s.l. based on sequences of the nrITS using maximum parsimony and Bayesian inference yielded high congruence with previous cpDNA restriction site analyses, but strongly contradict previous classifications. A large core clade including Ranunculus subg. Ranunculus, subg. Batrachium, subg. Crymodes p.p., Ceratocephala, Myosurus, and Aphanostemma is separated from R. subg. Ficaria, subg. Pallasiantha, subg. Coptidium, subg. Crymodes p.p., Halerpestes, Peltocalathos, Callianthemoides, and Arcteranthis. Within the core clade, 19 clades can be described with morphological and karyological features. Several sections are not monophyletic. Parallel evolution of morphological characters in adaptation to climatic conditions may be a reason for incongruence of molecular data and morphology-based classifications. In some mountainous regions, groups of closely related species may have originated from adaptive radiation and rapid speciation. Split decomposition analysis indicated complex patterns of relationship and suggested hybridization in the apomictic R. auricomus complex, R. subg. Batrachium, and the white-flowering European alpines. The evolutionary success of the genus might be due to a combination of morphological plasticity and adaptations, hybridization and polyploidy as important factors for regional diversification, and a broad range of reproductive strategies.

Most of the 29 living species of Potamididae show a close association with mangroves. The trees provide the snails with shelter, protection from predators, a solid substrate and sometimes food. Using sequences from three genes (nuclear 18S rRNA and 28S rRNA, mitochondrial COI) we derive a molecular phylogeny and recognize six living genera (Terebralia, Telescopium, Tympanotonos, Cerithidea, Cerithideopsis, Cerithideopsilla). The oldest modern genera (Terebralia, Cerithideopsis) appeared in the Tethyan realm in the Middle Eocene, shortly after the origin of mangrove trees. Whereas most potamidid genera are now restricted to either the Indo-West Pacific (IWP) or to the eastern Pacific plus Atlantic (EPA), sister clades of Cerithideopsis survive in both realms. Based on a reinterpretation of the fossil record (particularly of the monotypic Tympanotonos and extinct Potamides), and parsimonious reconstruction of ancestral habitats, we suggest that the living potamidids are an adaptive radiation that has always been closely associated with mangroves. The specialized tree-climbing groups Cerithidea and Cerithideopsis were independently derived from mud-dwelling ancestors. Cerithideopsilla cingulata (a species complex in the IWP) and 'Potamides' conicus (in the Mediterranean and Indian Ocean) form a single clade within the genus Cerithideopsilla. This refutes the hypothesis that 'P.' conicus is the sole relict of the Tethyan Potamides that has occurred in the Mediterranean region since the Palaeocene. Instead, the phylogeny and fossil record suggest that an ancestor of Cerithideopsilla conica with planktotrophic larvae dispersed from the IWP to the Mediterranean in the Middle Miocene, that its direct development evolved in the Mediterranean during the Pliocene, and that it reinvaded the Indian Ocean during the Plio-Pleistocene.

Mud crabs of the genus Scylla are commercially important mangrove residents that are extensively fished throughout their range in the Indo-West Pacific. Despite this high level of exploitation very little is known about the population dynamics of any of the Scylla species. The present study concentrated on an exploited population of Scylla paramamosain in a natural estuarine mangrove on Can Coc Island in the mouth of the Hau River, Mekong Delta, Vietnam. A total of 6,114 juvenile crabs captured on the seaward mangrove fringe were internally tagged by injection of coded microwire tags and released over a period of 29 days. Recaptures were monitored over the following 144 days. There was little migratory movement within the estuary; of 285 recaptured crabs, 93% were recovered within the island mangrove study area and only two individuals were recovered from mangroves lining the opposite mainland riverbanks. A von Bertalanffy growth function was fitted to growth increment data from recaptured crabs, with L max = 150 mm to derive a growth constant, k = 2.39 year -1 . The theoretical age at which carapace width is zero (t 0 ) was derived from known size at recruitment at instar 1, giving a value of -0.0095 years. Previous studies of the same population have shown that female S. paramamosain reach maturity at a mean size of 102 mm carapace width. The present study indicates that they attain this size at around 160 days from first settlement in the mangrove fringe. Abundance of juvenile crabs in the study area was estimated by the Petersen method as 1,101,500 (95% CI 4,17,300-1,785,800, representing 1,102 crabs ha -1 of mangrove. Estimation of mortality from tag returns and from the age-catch curves during a period of constant recruitment were comparable (Z = 1.11 and 1.04 month -1 , respectively). Fishing only accounted for 14% of total mortality, suggesting that at the time exploitation was not at a critical level despite the apparent high level of fishing activity.

Following recent systematic revisions of , seven species of the viviparous genus Microbrotula (Teleostei: Bythitidae) have been described, all from the Indo-west Pacific Ocean. Six of these species are here recognised as valid: M. bentleyi, M. greenfieldi, M. punicea, M. queenslandica, M. randalli and M. rubra. Microbrotula polyactis is regarded as a junior synonym of M. bentleyi. Two additional new species, M. andersoni and M. hamata, obtained from Christmas Island (eastern Indian Ocean) and New Caledonia, respectively, are described herein. The main specific characters distinguishing the new species are the number of precaudal vertebrae, numbers of pectoral, caudal and dorsal fin rays, number and distribution of head pores, number and distribution of sensory papillae on the head and lateral line, presence or absence of a (mostly hidden) curved spine at the lower angle of the preopercle, and otolith morphology. The limits of the genus Microbrotula are redefined and the genus is compared with other shallow water bythitine genera. Calamopteryx is regarded as the genus that is most closely related to Microbrotula. As a result of the redefinition of Microbrotula, one of its previously assigned species, M. randalli, is placed in a new genus, Ematops, characterised by the head pore pattern, unique presence of scales partly covering the eye, number of precaudal vertebrae, number of pectoral and caudal fin rays and the otolith proportion.

The damselfishes (Perciformes, Pomacentridae) are an important family of marine reef fishes that occupy a range of ecological positions in the world's oceans. In order to determine the evolutionary pattern of their radiation, we used multiple methods to examine molecular data from 104 species representing all extant genera. The analysis of 4291 DNA nucleotides (1281 bp were parsimony informative) from three nuclear genes (rag-1, rag-2 and bmp-4) and three mitochondrial genes (12s, 16s and nd3), produced well-resolved phylogenies with strong evidence for a monophyletic Pomacentridae, and support for five major damselfish clades. We found that the monotypic subfamily Lepidozyginae evolved early in the pomacentrid radiation. The placement of the genus Altrichthys indicates that brood care has evolved at least twice among the damselfishes. The subfamilies Chrominae and Pomacentrinae, and the genera Abudefduf, Chromis, Chrysiptera, Plectroglyphidodon, and Stegastes, were always found to be polyphyletic, and monophyly was rejected for the genus Amphiprion by almost every analysis. All phylogenetic studies of the Pomacentridae have indicated that their taxonomy is in need of revision at multiple levels. We provide a new classification scheme wherein each subfamily is now monophyletic, and this reorganization is consistent with all previous molecular studies of the damselfishes. The Chrominae are restricted to the genera Chromis and Dascyllus; the Pomacentrinae now represent a lineage of 16 genera that constitute a major, and relatively recent, radiation of coral reef fishes throughout the Indo-West Pacific; we erect the new subfamlies Abudefdufinae and Stegastinae; we relegate the anemonefishes (the Amphiprioninae sensu Allen) to the tribe Amphiprionini within the Pomacentrinae, and synonomize the genus Azurina with Chromis.

In the present study, a trapezoid crab, Quadrella reticulata was found for the first time in the north of Kish Island, the Persian Gulf, Iran. Diagnostic characters of the species are figured and its world geographical distribution in the Indo-West Pacific region is considered.

Members of the subfamily Priceinae are gastrocotylinean monogeneans of the gills of scombrid fishes of the genus Scomberomorus (and perhaps the genera Acanthocybium, Rastrelliger and Katsuwonus) from warm to warmtemperate seas of the world. We revise the diagnosis of the subfamily and regard the Mexicotylinae Lebedev, 1984 as a synonym. Two monotypic genera are accepted as valid. Pricea multae Chauhan, 1945 is recorded from seven species of Scomberomorus from the Indo-west Pacific, from off eastern South Africa north to the Persian Gulf and as far east as Fiji. New synonyms we recognise include P. minimae Chauhan, 1945 (described from India, reportedly on Katsuwonus pelamis), P. solandri Gupta & Chanana, 1977 (a single specimen was described from India, reportedly on Acanthocybium solandri) and P. microcotylae Chauhan, 1945 (also described from India, reportedly on Rastrelliger kanagurta). Mexicotyle mexicana ) Lebedev, 1984 is recorded on four species of Scomberomorus from the western Atlantic Ocean (United States to Brazil), two in the eastern Pacific (California to Peru) and one from the eastern Atlantic (Ghana).

Seagrasses of the Great Barrier Reef predominantly occur in coastal regions where terrestrial inputs modify water quality and photosynthetic light is highly variable. Responses to shading were tested for Cymodocea serrulata, Halodule uninervis, Thalassia hemprichii and Zostera muelleri. In aquaria, four light treatments – high (66% surface light), moderate (31%), low (14%) and very low light (1%) treatments – were

Misophrioid copepods are described from anchialine caves on Palau, Western Caroline Islands and on Lanzarote, Canary Islands. A new species of Misophria, M. kororiensis sp. nov., is described, based on material found in a submerged cave on Koror Island, Palau. A new genus, Expansophria gw. nov., characterized by a distensible but unenclosed first pedigerous somite, is established for two new species. The type species, E. dimorpha sp. nov., was collected from a flooded lava tube (Jameos del Agua) on Lanzarote and the second species, E. apoda sp. nov., from a sinkhole on Ngeruktabel Island, Palau. Two other new genera are erected for new species collected in Jameos del Agua on Lanzarote, Pdpophria gen. nov. and Dimisophria gen. nov. The former is characterized by extremely long, uniramous mandibular palps, the latter by the 6 . reduced number of spines on the swimming legs. In addition, a fourth genus and species, represented only by an unnamed copepodid 1V stage, was recorded from Jameos del Agua. It is suggested that at least some of the cave-dwelling misophrioids represent descendants of deep-sea 3 forms which became separated by vertical vicariance events.

The article argues that India and the United States are poised to strengthen their bilateral strategic convergences, not only in the Indian Ocean but also in Pacific-Asia that lies eastwards of the Malacca Straits, and wherein India’s geo-strategic stakes as well as its military-strategic footprint are likely to increase in the coming years. This would progressively enhance the complementarities between their navies in the western Pacific and its contiguous seas, thereby enabling substantive naval cooperation towards ensuring security and stability in the broader Indo-Pacific region. Introducing the theoretical concept of ‘geo-strategic frontier’, the article examines the various factors at play and conceives the likely future scenarios of ‘high-end’ India–US naval cooperation in Pacific-Asia, in the short-, medium- and long-term time-frames.

Litterfall consumption and predation on propagules is high in Indo-west-Pacific mangroves and low in Atlantic-east-Pacific ones. However, data for the latter area comes only from Caribbean and subtropical North American mangroves. South American data on litterfall consumption contradicts this view but data on predation on propagules are scarce. We measured predation on Rhizophora mangle, Avicennia schaueriana and Laguncularia racemosa propagules and seedlings and related to densities of large ([1.5 m high) and small (1-1.5 m) plants in mature and regenerating mangroves in Ceará state, Brazil. Predation on propagules was the highest among American mangroves (R. mange,[47%; A. schaueriana, [97%; L. racemosa, [83%), especially in the regenerating area. Predation on seedlings was low (maximum of 14% for R. mangle) and did not hamper growth. The dominance of large R. mangle trees in the mature mangrove is consistent with the lower predation on its propagules but the high proportions of small plants of other species indicate that dominance is achieved by mechanisms other than predation. In the regenerating mangrove, dominance of large and small L. racemosa and A. schaueriana plants is not consistent with the high predation on their propagules. Therefore, predation is not the main determinant of the species composition in this mangrove system.

Abalone taxonomy and systematics have remained unresolved: neither stable species-level nomenclature nor a cladistic hypothesis of relationships among species have been established. To infer the phylogeny of the genus Haliotis and to identify species using molecular data, we compared complementary DNA (cDNA) sequences of sperm lysin from 27 speciesgroup taxa from

The narrow-barred Span- ish mackerel (Scomberomorus com- merson) is widespread throughout the Indo-West Pacific region. This study describes the reproductive biology of S. commerson along the west coast of Australia, where it is targeted for food consumption and sports fishing. Development of testes occurred at a smaller body size than for ovaries, and more than 90% of males were sexually mature by the minimum legal length of 900 mm TL compared to 50% of females. Females dominated overall catches although sex ratios within daily catches vary consider- ably and females were rarely caught when spawning. Scomberomorus commerson are seasonally abundant in coastal waters and most of the commercial catch is taken prior to the reproductive season. Spawning occurs between about August and November in the Kimberley region and between October and January in the Pilbara region. No spawning activity was recorded in the more southerly West Coast region, and only in the north Kimberley region wer...

Members of the subfamily Thoracocotylinae are gastrocotylid monogeneans of Spanish mackerels (scombrid fishes of the genus Scomberomorus) from warm to warm-temperate seas around the world. We revise the diagnosis of the subfamily and recognise two genera and three species as valid. The genus Paradawesia Bravo

Six species of the alpheid genus Salmoneus Holthuis, 1955, including five new species, are reported from Nhatrang Bay, southern Vietnam. Salmoneus nhatrangensis, new species, S. auroculatus, new species, S. falcidactylus, new species, and S. pusillus, new species, were collected under rocks on sand-mud bottoms at depths of 6-40 m. Salmoneus alpheophilus, new species and S rostratus were collected on tidal flat from burrows of Alpheus with gobies. The affinities of the new species to other Indo-West Pacific and Atlantic species are discussed. All species are illustrated. Salmoneus is preliminarily divided into seven species groups.

The significant decrease in wild mud crab population highlights the need to manage the resources and domesticate crabs. This paper presents the initial results of the domestication of mud crab Scylla serrata aimed at producing good-quality captive broodstock. The analysis of the genetic structure of the base population was done as a prerequisite for domestication. Adult S. serrata from the northern to southern parts of the Philippines (Cagayan, Camarines, Samar, and Surigao) were obtained for genetic diversity analysis and domestication. Analysis of molecular variance showed that differences in the genetic variability between the four populations were not significant. Moreover, no significant deviation from Hardy–Weinberg Equilibrium was observed in each sample population and even in pooled populations. Body weight was positively correlated with the carapace width. Second spawning occurred 41–46 days after the first spawning and 34 days from second to third spawning. However, there was a decrease in the number of zoea in repeat spawnings. Twenty-four first-generation (F1) families were produced from the four sites. The duration from spawning of the base population (P0) to attainment of broodstock size F1 was 10–14 months. Four second-generation (F2) families were produced after 11–12 months. Up to the F2, crabs tested negative for six viruses: white spot syndrome virus, infectious hypodermal and hematopoietic necrosis virus, gill-associated virus, yellow head virus, Taura syndrome virus, and infectious myonecrosis virus. The reproductive performance of P0 was comparable to the succeeding generations. Several families were obtained from one population in a year. However, due to the cannibalistic behavior of crabs, more space is required for the nursery and grow-out phase. The domestication of S. serrata is the first study done on any mud crab species in the Indo-west Pacific region. The initial results would serve as guide to understand and eliminate the barriers to mud crab domestication. The breeding technology developed from this study will support the production of good-quality seedstock for farming.

The phylogeographical and systematic relationships among species in the tropical marine fish genus Dascyllus were inferred using mitochondrial DNA (mtDNA) sequence data. Although our results were generally consistent with previously published phylogenies based on both morphological and mitochondrial data, our broad taxonomic and geographical sampling design revealed novel insights into the phylogenetic history of Dascyllus that had escaped previous notice. These results include: (a) the polyphyletic nature of D. reticulatus mtDNAs, representing two divergent and geographically separated lineages, one shared with D. flavicaudus and the second forming the sister lineage of D. carneus; (b) the paraphyly of D. trimaculatus relative to the closely related D. abisella; and (c) phylogeographical structure within the widespread taxa D. aruanus and D. trimaculatus. Application of a molecular clock permits us to posit a causative role for tectonic and oceanic changes regarding some Dascyllus speciation events. Finally, we mapped body size and the presence or absence of protogynous sex change on the mtDNA tree, and tested published hypotheses regarding determinants of the evolution of mating system and protogyny in the genus. Our data rejected a model based on body size but not one based on phylogenetic inertia. The ability to change sex arose once in the ancestor to the entire genus, and was lost once in the ancestor of the D. trimaculatus complex. For taxa that are as geographically widespread as many Indo-Pacific genera, this study highlights the importance of adequate geographical sampling when inferring patterns of species diversification and life history evolution.

The presence of boundaries to dispersal has been recently documented for many Indo-West Pacific (IWP) species with planktonic propagules and a widespread distribution. We studied the phylogeography of the mangrove crab Neosarmatium meinerti (Brachyura: Sesarmidae) and the phylogenetic relationship to its presumed sister species N. fourmanoiri in the IWP in order to compare intraspecific with interspecific diversity. Portions of the mitochondrial genes 16S and CoxI were sequenced for 23 specimens of N. meinerti and 5 N. fourmanoiri, while a fragment of the 28S was obtained for a subset of specimens. Genetic data are supplemented by morphometric and based on 37 adult males of N. meinerti and 9 males of N. fourmanoiri.

In the present study, a trapezoid crab, Quadrella reticulata was found for the first time in the north of Kish Island, the Persian Gulf, Iran. Diagnostic characters of the species are figured and its world geographical distribution in the Indo-West Pacific region is considered.

To date, only one species of Erythrean stomatopod, Erugosquilla massavensis (Kossmann), has been reported from the Mediterranean Sea. We report the first appearance of a second Erythrean stomatopod species from the Mediterranean coast of Israel, Clorida albolitura Ahyong & Naiyanetr, on 24 May 2006.

Anaporrhutine gorgoderids (Digenea: Gorgoderidae: Anaporrhutinae) found in the body cavity of six species of elasmobranchs from the orders Carcharhiniformes, Myliobatiformes and Orectolobiformes from Australian waters were found to belong to the genus Staphylorchis. Although these specimens were morphologically variable, sequences of ITS2 and 28S ribosomal DNA from specimens from three host families and two host orders were identical. Based on morphological and molecular data these specimens were identified as the type-species of the genus, Staphylorchis cymatodes. New measurements are provided for S. cymatodes, and for the first time genetic data are presented for this species. In addition to providing new morphological and molecular data for S. cymatodes, the previously described species S. gigas, S. parisi and S. scoliodonii, are here synonymised with S. cymatodes. This implies that S. cymatodes, as conceived here, has remarkably low hostspecificity, being recorded from eight elasmobranch species from four families and three orders, has a wide geographical distribution in the Indo-west Pacific from off India, in the Bay of Bengal, to Moreton Bay in the Coral Sea, and is morphologically plastic, with body size, size of specific organs and body shape differing dramatically between specimens from different host species. The genus Staphylorchis now contains only two valid species, S. cymatodes and S. pacifica.

New, large-scale collections have been made of marine benthic macroalgae (seaweeds) on the east coast of South Africa, and the distributions of shallow-water species were analyzed in detail by multivariate, clustering and b-diversity methods. The two northernmost sites are distinct, with a predominance of tropical species, and it is concluded that the changeover from a tropical Indian Ocean flora to a temperate South African flora occurs most rapidly in the vicinity of St. Lucia, 135 km south of the Mozambique border. It is imperative that all future biogeographical studies on the South African inshore marine biota include detailed collections north of St. Lucia. The remaining 440 km of the South African east coast (southern and central Kwazulu-Natal Province) is populated by a mixture of tropical and temperate elements, with only 2% endemism in this data set. This, thus, represents a true overlap region, with relatively equal numbers of species with affinities in the temperate Agulhas and tropical Indo–West Pacific floras, rather than a distinctive sub-tropical marine province, as the South African east coast is considered to be by most previous authors. The distinction between this overlap region and the south coast (Agulhas) region proper is not as clearly distinct. The change from a temperate to a tropical flora shows a relative increase in green algae from 15% to 25% of the species present. Criteria for the delineation of marine biogeographical regions are critically discussed, and it is concluded that the monitoring of distributions of all species, including rare species, is necessary. This is particularly relevant with regard to using these data to assess effects of potential changes in seawater temperature, including those which may be caused by global warming. Criteria for the delimitation of biogeographic entities such as ‘‘marine provinces’’ need to be clearly spelt out in all investigations.

The Indo-Pacific is an area of intense ecological interest, not least because of the region's rich biodiversity. Important insights into the origins, evolutionary history, and maintenance of Indo-Pacific reef faunas depend upon the analysis of faunal occurrences derived from detailed stratigraphic sections. We investigated Neogene origination and extinction patterns derived from a combination of new coral occurrences and previously published records from the central Indo-West Pacific Ocean (cIWP, Indonesia, Papua New Guinea and Fiji). Two faunal turnover events were observed. In the first, an increase in generic richness of Scleractinia from the cIWP during the middle Miocene (17-14 Ma) coincided with both large-scale sea level fluctuations and the great Mid-Miocene collision event. We raise the hypothesis that Mid-Miocene origination was facilitated by habitat and population fragmentation associated with tectonism and sea level fall. The second, subsequent, turnover event was characterized by an overall lowering of generic diversity throughout the late Miocene and Pliocene (7-3 Ma), and was followed by a pronounced pulse of extinction at the Pliocene-Pleistocene boundary (*2.6 Ma). With the exception of the onset of Pleistocene sea-level cycles and the onset of northern hemisphere glaciation around 2.5 Ma, which might explain increased extinction during this time interval, there are no tectonic, eustatic, climatic or oceanographic events that neatly coincide with this second episode of Neogene coral taxonomic turnover. Our results reveal a total of 62 genera, including synonyms, from the Miocene to the Pleistocene. Neither episode of turnover among coral genera is exactly coincident with turnover in the Atlantic thus regional environmental change is found to drive Neogene reef dynamics.

The tropical Indo-West Pacific is the biogeographic region with the highest diversity of marine shallow water species, with its centre in the Indo-Malay Archipelago. However, due to its high endemism, the Red Sea is also considered as an important centre of evolution. Currently, not much is known about exchange among the Red Sea, Indian Ocean and West Pacific, as well as connectivity within the Indo-Malay Archipelago, even though such information is important to illuminate ecological and evolutionary processes that shape marine biodiversity in these regions. In addition, the inference of connectivity among populations is important for conservation. This study aims to test the hypothesis that the Indo-Malay Archipelago and the Red Sea are important centres of evolution by studying the genetic population structure of the giant clam Tridacna maxima. This study is based on a 484-bp fragment of the cytochrome c oxidase I gene from 211 individuals collected at 14 localities in the Indo-West Pacific to infer lineage diversification and gene flow as a measure for connectivity. The analysis showed a significant genetic differentiation among sample sites in the Indo-West Pacific (Φst = 0.74, P < 0.001) and across the Indo-Malay Archipelago (Φst = 0.72, P < 0.001), indicating restricted gene flow. Hierarchical AMOVA revealed the highest fixation index (Φct = 0.8, P < 0.001) when sample sites were assigned to the following regions: (1) Red Sea, (2) Indian Ocean and Java Sea, (3) Indonesian throughflow and seas in the East of Sulawesi, and (4) Western Pacific. Geological history as well as oceanography are important factors that shape the genetic structure of T. maxima in the Indo-Malay Archipelago and Red Sea. The observed deep evolutionary lineages might include cryptic species and this result supports the notion that the Indo-Malay Archipelago and the Red Sea are important centres of evolution.

Here the population genetic structure of an ecologically and economically important coral reef fish, the coral trout Plectropomus leopardus, is investigated in the context of contemporary and historical events. Coral trout were sampled from four regions (six locations) and partial mtDNA D-loop sequences identified six populations (Fst = 0.89209, P  0.0001): Scott Reef and the Abrolhos Islands in west Australia; the Great Barrier Reef (GBR), represented by northern and southern GBR samples; New Caledonia and Taiwan, with Taiwan containing two genetic lineages. Furthermore, this study identified source and sink populations within and among regions. Specifically, the northern population in west Australia (Scott Reef) was identified, as the source for replenishment of the Abrolhos population, whilst New Caledonia was a source for recruitment to the GBR. Based on these insights from a single mtDNA marker, this study will facilitate the development of rational management plans for the conservation of P. leopardus populations and therefore mitigate the risk of population declines from anthropogenic influences.

Members of the Holothuriidae, found globally at low to middle latitudes, are often a dominant component of Indo-West Pacific coral reefs. We present the first phylogeny of the group, using 8 species from the 5 currently recognized genera and based on approximately 540 nucleotides from a polymerase chain reaction-amplified and conserved 3¢ section of 16S mitochondrial ribosomal DNA. Parsimony and likelihood analyses returned identical topologies, permitting several robust inferences to be drawn. Several points corroborated the Linnean classification. Actinopyga and Bohadschia each appear monophyletic and Pearsonothuria is sister to Bohadschia. Other aspects of our phylogeny, however, were not in accord with the taxonomy of Holothuriidae or previous speculations about the group's evolutionary history. Most notably, the genus Holothuria appears paraphyletic. Actinopyga and Bohadschia, sometimes held to be closely related to one another because of certain morphologic similarities, are only distantly related. The morphologically distinct Labidodemas, even thought to warrant separation at the family level, is nested well within Holothuria. A maximum parsimony reconstruction of ancestral ossicle form on the phylogeny indicated that, in addition to a probable bout of elaboration in ossicle form (the modification of rods or rosettes to holothuriid-type buttons), at least 2 rounds of ossicle simplification also transpired in which buttons reverted to rods or rosettes. Cuvierian tubules, defensive organs unique to numerous members of Holothuriidae, were probably present before the initial radiation of the family, but the reconstruction is ambiguous as to their ancestral function.

A survey of the cryptogonimid trematode fauna infecting Indo-West Pacific Lutjanidae (Perciformes) revealed the presence of four new species whose morphological and genetic differences relative to all other known cryptogonimids warrants the proposal of a new genus, Varialvus gen. nov. Species of this new genus were recovered from sites off Heron and Lizard Islands on the Great Barrier Reef, Australia, New Caledonia and Rasdhoo Atoll, Maldives. Varialvus gen. nov. is distinguished from all other cryptogonimid genera by the combination of a fusiform to oval body, the relatively small number of large oral spines, a median ovary which is relatively condensed and highly lobed, opposite to slightly oblique testes, uterine loops that are restricted to the hindbody and extend well posterior to the testes, and vitelline follicles that are mainly in the forebody but may extend from the anterior margin of the ovary to anterior to the intestinal bifurcation. Bayesian inference analysis of partial large subunit (LSU) rDNA sequence data for these species revealed that they formed a monophyletic clade, despite V. charadrus sp. nov. having a distinctly muscular gonotyl, which based on morphological characters alone may have warranted placement in a separate genus in the absence of DNA sequence data. At least one species of Varialvus gen. nov. is apparently widespread in the Indo-West Pacific. Three species, V. lacertus sp. nov., V. jenae sp. nov. and V. angustus sp. nov. have each been found at only one locality, but V. charadrus sp. nov. was recovered from lutjanids off the Great Barrier Reef, New Caledonia and the Maldives, demonstrating a biogeographic range of at least 10,000 kilometres. Siphoderina lutjani ) Miller et Cribb, 2008 is transferred here as V. lutjani n. comb. based on morphological and host group agreement with species of Varialvus gen. nov.

Seascapes are complex environments, and populations are often isolated by factors other than distance. Here we investigate the role of coastal habitat preference and philopatry in shaping the distribution and population structure of lemon sharks. The genus Negaprion comprises the amphiatlantic lemon shark (N. brevirostris), with a relict population in the eastern Pacific, and its Indo-West Pacific sister species, the sicklefin lemon shark (N. acutidens). Analyzing 138 individuals throughout the range of N. brevirostris (N = 80) and N. acutidens (N = 58) at microsatellite loci (nine and six loci, respectively) and the mitochondrial control region, we find evidence of allopatric speciation corresponding to the Tethys Sea closure (10–14 million years ago) and isolation of the eastern Pacific N. brevirostris population via the emergence of the Isthmus of Panama (~3.5 million years ago). There is significant isolation by oceanic distance (R2 = 0.89, P = 0.005), defined as the maximum distance travelled at depths greater than 200 m. We find no evidence for contemporary transatlantic gene flow (m, M = 0.00) across an oceanic distance of ~2400 km. Negaprion acutidens populations in Australia and French Polynesia, separated by oceanic distances of at least 750 km, are moderately differentiated (FST = 0.070–0.087, P≤ 0.001; ΦST = 0.00, P = 0.99), with South Pacific archipelagos probably serving as stepping stones for rare dispersal events. Migration between coastally linked N. brevirostris populations is indicated by nuclear (m = 0.31) but not mitochondrial (m < 0.001) analyses, possibly indicating female natal site fidelity. However, philopatry is equivocal in N. acutidens, which has the lowest control region diversity (h = 0.28) of any shark yet studied. Restricted oceanic dispersal and high coastal connectivity stress the importance of both local and international conservation efforts for these threatened sharks.

The Kemp's ridley sea turtle (Lepidochelys kempi) is restricted to the warm temperate zone of the North Atlantic Ocean, whereas the olive ridley turtle (L. olivacea) is globally distributed in warm-temperate and tropical seas, including nesting colonies in the North Atlantic that nearly overlap the range of L. kempi. To explain this lopsided distribution, Pritchard (1969) proposed a scenario in which an ancestral taxon was divided into Atlantic and Pacific forms (L. kempi and L. olivacea, respectively) by the Central American land bridge. According to this model, the olive ridley subsequently occupied the Pacific and Indian Oceans and recently colonized the Atlantic Ocean via southern Africa. To assess this biogeographic model, a 470 bp sequence of the mtDNA control region was compared among 89 ridley turtles, including the sole L. kempi nesting population and 7 nesting locations across the range of L. olivacea. These data confirm a fundamental partition between L. olivacea and L. kempi (p=0.052-0.069), shallow separations within L. olivacea (p=0.002-0.031), and strong geographic partitioning of mtDNA lineages. The most divergent L. olivacea haplotype is observed in the Indo-West Pacific region, as are the central haplotypes in a parsimony network, implicating this region as the source of the most recent radiation of olive ridley lineages. The most common olive ridley haplotype in Atlantic samples is distinguished from an Indo-West Pacific haplotype by a single nucleotide substitution, and East Pacific samples are distingushed from the same haplotype by two nucleotide substitutions. These shallow separations are consistent with the recent invasion of the Atlantic postulated by Pritchard (1969), and indicate that the East Pacific nesting colonies were also recently colonized from the Indo-West Pacific region. Molecular clock estimates place these invasions within the last 300,000 years.

Seagrasses of the Great Barrier Reef predominantly occur in coastal regions where terrestrial inputs modify water quality and photosynthetic light is highly variable. Responses to shading were tested for Cymodocea serrulata, Halodule uninervis, Thalassia hemprichii and Zostera muelleri. In aquaria, four light treatments -high (66% surface light), moderate (31%), low (14%) and very low light (1%) treatmentswere applied for 102 d. Stress responses in the low and very low light treatments occurred in the following sequence: metabolic and physiological changes (reduced growth, increased pigment concentrations and photosynthetic efficiency); shedding (leaf loss, shoot loss) and production of new, altered tissue (leaves with reduced length, width and thickness). Complete shoot loss was projected after 76 (Z. muelleri) to 130 d (T. hemprichii). Responses were slower in the low than in the very low treatment, therefore, efforts to minimize water quality degradation will be rewarded with delayed impacts to seagrasses.