DNA barcoding Indonesian Acanthopleurinae (Polyplacophora)

The approximately 14 recognized species of Acanthopleurinae worldwide include conspicuous and large tropical shore chitons of the genera Acanthopleura, Liolphura, and Squamopleura. They are well studied for their impressive homing behavior, shell eyes (ocelli), radular biomineralization, and bioerosion activities, but have a relatively shallow fossil record, not recorded from before the Miocene. The accessibility of these chitons on the shores of Indonesia made them an excellent test case for new efforts to DNA barcode biodiversity, training and employing Indonesians with the objective of initiating a more complete assessment of biodiversity throughout the Coral Triangle. The latest monographic treatment including Acanthopleurinae was published in 2006 and reports only three members of this taxon in the vicinity of Indonesia: Acanthopleura spinosa (Bruguière 1792), A. gemmata (De Blainville 1825), and Squamopleura miles (Carpenter in Plsbry 1893). Here we apply current and accepted DNA barcoding methods to assess biodiversity in Acanthopleurinae throughout Indonesia, also employing available published or unpublished relevant sequences. Because Indonesian marine research has been historically underrepresented in the international scientific community until recent years, we hypothesized that we would discover new operational taxonomic units (OTUs), which could represent previously-undescribed species. If the Coral Triangle acts as a center of origin of chiton biodiversity, we hypothesized that the phylogenetic positions of the Indonesian chitons will be more derived than described species. Our combined analysis of mitochondrial COI and 16S rDNA gene portions for over 200 Acanthopleurinae from Indonesia has confirmed this expectation. Our preliminary analyses have identified as many as 11 OTUs, indicating that either cryptic species or strong phylogeographic structure are to be expected in this region of known high endemism. We conclude by making recommendations for future intertidal research in Indonesia and the Coral Triangle

The recovery of coral genetic diversity in the Sunda Strait following the 1883 eruption of Krakatau

Surveys of microsatellite variation show that genetic diversity has largely recovered in two reef-building corals, Pocillopora damicornis and Seriatopora hystrix (Scleractinia: Pocilloporidae), on reefs which were decimated by the eruption of the volcano Krakatau in 1883. Assignment methods and gene flow estimates indicate that the recolonization of Krakatau occurred mainly from the closest upstream reef system, Pulau Seribu, but that larval input from other regions has also occurred. This pattern is clearer in S. hystrix, which is traditionally the more dispersal- limited species. Despite these observed patterns of larval dispersal, self-recruitment appears to now be the most important factor in supplying larvae to coral populations in Krakatau. This suggests that the colonization of devastated reefs can occur quickly through larval dispersal; however, their survival requires local sources of larvae for self-recruitment. This research supports the observation that the recovery of genetic diversity in coral reef animals can occur on the order of decades and centuries rather than millennia. Conservation measures aimed at sustaining coral reef populations in Krakatau and elsewhere should include both the protection of upstream source populations for larval replenishment should disaster occur as well as the protection of large adult colonies to serve as local larval source

Coral reefs Corals' adaptive response to climate change

The long-term response of coral reefs to climate change depends on the ability of reef-building coral symbioses to adapt or acclimatize to warmer temperatures, but there has been no direct evidence that such a response can occur. Here we show that corals containing unusual algal symbionts that are thermally tolerant and commonly associated with high-temperature environments are much more abundant on reefs that have been severely affected by recent climate change. This adaptive shift in symbiont communities indicates that these devastated reefs could be more resistant to future thermal stress, resulting in significantly longer extinction times for surviving corals than had been previously assumed

Ten polymorphic STR loci in the cosmopolitan reef coral, Pocillopora damicornis

We report the development of 10 polymorphic molecular markers containing short tandem repeats in the cosmopolitan reef‐building coral, Pocillopora damicornis, an important model species for coral health, physiology, ecology, and genetics. The availability of polymorphic DNA markers in P. damicornis can act as impetus for investigations into inheritance and population genetics, as well as novel investigations into host‐symbiont ecology and evolution. Coral bleaching and gene flow studies performed with these markers can have direct conservation implications

Strong genetic structure among coral populations within a conservation priority region, the Birds Head Seascape (Papua and West Papua, Indonesia)

Marine Protected Areas (MPAs) are widely considered to be one of the best strategies available for protecting species diversity and ecosystem processes in marine environments, particularly in developing, tropical nations. While data on connectivity and genetic structure of marine populations are critical to designing appropriately sized and spaced networks of MPAs, such data are rarely available. Here we present an assessment of genetic structure in reef-building corals from Papua and West Papua, Indonesia, among the most biologically diverse and least disturbed coral reef regions in the world, and the focus of the multi-institutional Birds Head Seascape initiative to design and implement a functional network of MPAs. Microsatellite variation was assessed within and among populations of Pocillopora damicornis (Linnaeus , 1758) and Seriatopora hystrix (Dana 1846) (family: Pocilloporidae) from three regions, each currently under a different conservation regime: Teluk Cenderawasih, Raja Ampat, and southwest Papua. Analyses of molecular variance, assignment tests, and genetical bandwidth mapping revealed significant local-scale structure in both species, and a lack of regional filters to gene flow. Overall, P. damicornis populations were less structured ( F ST = 0.139, p < 0.00001) than those of S. hystrix ( F ST = 0.357, p < 0.00001). In order to maintain connectivity within and among regions, coral reef conservation on the local scale is needed. These data have been directly applied to the design of a MPA network in the Bird’s Head Seascape

Christmas tree worms of Indo-Pacific coral reefs : untangling the Spirobranchus corniculatus (Grube, 1862) complex

Christmas tree worm is the common name of a group of colorful serpulid polychaetes from the genus Spirobranchus that are symbionts of hermatypic corals. As is increasingly common with reef-associated organisms, Spirobranchus is arranged as a complex of species with overlapping geographic ranges. Current species delimitations based largely on opercular morphology are problematic because of high intraspecific variation. Here, a multi-gene phylogeny of the Spirobranchus corniculatus complex, which tentatively includes S. corniculatus, S. cruciger, and S. gaymardi, sampled from the Coral Triangle, Australia, and Fiji, was reconstructed to test whether the complex includes three genetically distinct lineages identifiable by their opercula. Maximum-likelihood analyses of nuclear and mitochondrial markers revealed a single, monophyletic clade for the S. corniculatus complex. Furthermore, the genetic and morphological variation observed is not geographically based, indicating that the former S. corniculatus complex of three morphospecies is a single, morphologically variable species across the Central Indo-Pacific. Resolving the taxonomy of S. corniculatus presents novel opportunities to utilize this tentative bio-indicator species for monitoring reef health.6 page(s

Comparative phylogeography of the Coral Triangle and implications for marine management

Extreme concentration of marine biodiversity and exploitation of marine resources in the Coral Triangle pose challenges to biogeographers and resource managers. Comparative phylogeography provides a powerful tool to test biogeographic hypotheses evoked to explain species richness in the Coral Triangle. It can also be used to delineate management units for marine resources. After about a decade of phylogeographical studies, patterns for the Coral Triangle are emerging. Broad connectivity in some species support the notion that larvae have maintained gene flow among distant populations for long periods. Other phylogeographic patterns suggest vicariant events resulting from Pleistocene sea level fluctuations, which have, at least occasionally, resulted in speciation. Divergence dates ranging back to the Miocene suggest that changing land configurations may have precipitated an explosion of species diversification. A synthesis of the marine phylogeographic studies reveals repeated patterns that corroborate hypothesized biogeographic processes and suggest improved management schemes for marine resources. © Copyright 2011 Kent E. Carpenter et al

Advancing biodiversity research in developing countries: The need for changing paradigms

The world is in the midst of a biodiversity crisis, threatening essential goods and services on which humanity depends. While there is an urgent need globally for biodiversity research, growing obstacles are severely limiting biodiversity research throughout the developing world, particularly in Southeast Asia. Facilities, funding, and expertise are often limited throughout this region, reducing the capacity for local biodiversity research. Although western scientists generally have more expertise and capacity, international research has sometimes been exploitative parachute science, creating a culture of suspicion and mistrust. These issues, combined with misplaced fears of biopiracy, have resulted in severe roadblocks to biodiversity research in the very countries that need it the most. Here, we present an overview of challenges to biodiversity research and case studies that provide productive models for advancing biodiversity research in developing countries. Key to success is integration of research and education, a model that fosters sustained collaboration by focusing on the process of conducting biodiversity research as well as research results. This model simultaneously expands biodiversity research capacity while building trust across national borders. It is critical that developing countries enact policies that protect their biodiversity capital without shutting down international and local biodiversity research that is essential to achieve the long-term sustainability of biodiversity, promoting food security and economic development.© 2014 Rosenstiel School of Marine and Atmospheric Science of the University of Miami