Metacommunity ecology of Symbiodiniaceae hosted by the coral Galaxea fascicularis

Coral−algae symbiosis represents the trophic and structural basis of coral reef ecosystems. However, despite global threats to coral reefs and the dependence of coral health and stress resistance upon such mutualisms, little is known about the community ecology of endosymbiotic Symbiodiniaceae. Concepts and methods from metacommunity ecology may be used to help us understand the assembly and stability of symbiont communities and the mutualisms they comprise. In this study, we sampled colonies of the symbiont-generalist coral Galaxea fascicularis in southwestern Japan and assessed the effects of environmental and host factors on Symbiodinia ceae community composition, while simultaneously exploring residual correlations among symbiont types that may reflect non-random assembly processes such as species interactions. We metabarcoded the Symbiodiniaceae ribosomal internal transcribed spacer 2 (ITS2) region and characterized the endosymbiotic community using 2 different OTU identity cut-offs, and analyzed them with generalized dissimilarity modeling and joint species distribution modeling. We found that Symbiodiniaceae form discrete communities characterized by the dominance of ITS2 types C1, C21a, or D1, that are each associated with a different suite of co-occurring background types and tend to exclude each other in an endosymbiotic community. The communities showed modest responses to temperature, water depth, host genotype, polyp size, and bleaching status, and there was local sequence variation within the ITS2 types. After accounting for the effects of those variables, residual correlations remained in community composition, pointing to the possibility that Symbiodiniaceae community assembly in corals may be structured by interspecific competitive or facilitating interactions rather than only exogenous variables

Microsatellite markers for multiple Pocillopora genetic lineages offer new insights about coral populations

Population genetics of the coral genus Pocillopora have been more intensively studied than those of any other reef-building taxon. However, recent investigations have revealed that the current morphological classification is inadequate to represent genetic lineages. In this study, we isolated and characterized novel microsatellite loci from morphological Pocillopora meandrina (Type 1) and Pocillopora acuta (Type 5). Furthermore, we characterized previously reported microsatellite loci. A total of 27 loci (13 novel loci) proved useful for population genetic analyses at two sites in the Ryukyu Archipelago, in the northwestern Pacific. Clonal diversity differed in each genetic lineage. Genetic structure suggested by microsatellites corresponded to clusters in a phylogenetic tree constructed from a mitochondrial open reading frame (mtORF). In addition, we found an unknown mitochondrial haplotype of this mtORF. These microsatellite loci will be useful for studies of connectivity and genetic diversity of Pocillopora populations, and will also support coral reef conservation

Spatial diversity structure in the coral genus Galaxea (Euphyllidae) and their associated Symbiodinium communities

The evolution and systematics of corals have been difficult to unravel despite being the fundament of one of the world\u27s most charismatic ecosystems. Coral diversity and diversification processes are not well understood due to morphological plasticity, potential hybridization and generally high rates of dispersal. Both geographically and methodologically extensive studies are needed to improve our understanding of coral ecology and evolution, including spatial biodiversity processes involving hosts and their associated symbionts. This dissertation investigates coral evolution in three complementary studies using the genus Galaxea L. as a model. First, I ask whether endosymbiotic community composition differentiate among morphologically cryptic genetic lineages in G. fascicularis. The Symbiodinium ITS2-sequence was metabarcoded using next generation sequencing (NGS) and community assembly was analyzed with joint distribution models. Symbiodinium communities were found to cluster into three regular community types that cannot be explained by environment or host genotype, potentially indicating species interactions between Symbiodinium types. Second, I assessed how spatial connectivity between geographic populations corresponds to neutral differentiation on the subspecies level using population genomic methods. Coral populations from the Ryukyu archipelago, the Daito islands, and the Ogasawara Islands were characterized by restriction site-associated DNA sequencing (RAD) to investigate whether the Daito Islands could be a stepping stone between Ryukyu and Ogasawara. The Ogasawara population was found to be highly differentiated and to have diverged under little amounts of continuous gene flow since the early Pliocene. No stepping stone role of the Daito Islands was found and the Ogasawara population may receive most migrants from the Ryukyu Islands, which was consistent with the dispersal patterns predicted by a oceanographic dispersal model. Lastly, I investigated the evolutionary history in the genus Galaxea taking a phylogeographic approach. I asked whether the genetically well-differentiated and sympatric lineages within G. fascicularis in Okinawa maintain their separation over geographic space and to what extent their spatial distributions overlap in the genus distribution range. Galaxea field collections were gathered from across the Indo-Pacific, and complemented by museum specimens to increase geographical coverage. At the same time the relationship between genetic lineages and taxonomic species was evaluated based on five out of seven currently accepted species (G. fascicularis, G. astreata, G. cryptoramosa, G. paucisepta, G. horrescens). The genus Galaxea clustered into three highly divergent clades; one Indo-Pacific, one Pacific, and one basal small clade found in Chagos. All morphological species were part of the Pacific clade. Overall this study indicates spatial rather than ecological or symbiosis-related processes to drive diversification and that the current taxonomy does not reflect biological species in this genus.Okinawa Institute of Science and Technology Graduate Universit

Spatial diversity structure in the coral genus Galaxea (Euphyllidae) and their associated Symbiodinium communities

The evolution and systematics of corals have been difficult to unravel despite being the fundament of one of the world\u27s most charismatic ecosystems. Coral diversity and diversification processes are not well understood due to morphological plasticity, potential hybridization and generally high rates of dispersal. Both geographically and methodologically extensive studies are needed to improve our understanding of coral ecology and evolution, including spatial biodiversity processes involving hosts and their associated symbionts. This dissertation investigates coral evolution in three complementary studies using the genus Galaxea L. as a model. First, I ask whether endosymbiotic community composition differentiate among morphologically cryptic genetic lineages in G. fascicularis. The Symbiodinium ITS2-sequence was metabarcoded using next generation sequencing (NGS) and community assembly was analyzed with joint distribution models. Symbiodinium communities were found to cluster into three regular community types that cannot be explained by environment or host genotype, potentially indicating species interactions between Symbiodinium types. Second, I assessed how spatial connectivity between geographic populations corresponds to neutral differentiation on the subspecies level using population genomic methods. Coral populations from the Ryukyu archipelago, the Daito islands, and the Ogasawara Islands were characterized by restriction site-associated DNA sequencing (RAD) to investigate whether the Daito Islands could be a stepping stone between Ryukyu and Ogasawara. The Ogasawara population was found to be highly differentiated and to have diverged under little amounts of continuous gene flow since the early Pliocene. No stepping stone role of the Daito Islands was found and the Ogasawara population may receive most migrants from the Ryukyu Islands, which was consistent with the dispersal patterns predicted by a oceanographic dispersal model. Lastly, I investigated the evolutionary history in the genus Galaxea taking a phylogeographic approach. I asked whether the genetically well-differentiated and sympatric lineages within G. fascicularis in Okinawa maintain their separation over geographic space and to what extent their spatial distributions overlap in the genus distribution range. Galaxea field collections were gathered from across the Indo-Pacific, and complemented by museum specimens to increase geographical coverage. At the same time the relationship between genetic lineages and taxonomic species was evaluated based on five out of seven currently accepted species (G. fascicularis, G. astreata, G. cryptoramosa, G. paucisepta, G. horrescens). The genus Galaxea clustered into three highly divergent clades; one Indo-Pacific, one Pacific, and one basal small clade found in Chagos. All morphological species were part of the Pacific clade. Overall this study indicates spatial rather than ecological or symbiosis-related processes to drive diversification and that the current taxonomy does not reflect biological species in this genus.Okinawa Institute of Science and Technology Graduate Universit

Data from: Influences of climate and historical land connectivity on ant beta diversity in East Asia

Aim Biodiversity patterns reflect both ecological and evolutionary processes interacting with geographical variation in climate and the current and historical connectivity between land areas. We sought to disentangle these effects in explaining the organization of ant diversity across geographical areas and islands in East Asia. Location The Japanese Archipelago including the Ryukyu and Ogasawara Islands, Taiwan and coastal continental regions of Korea, China and Russia. Methods We aggregated species occurrence records from published literature, specimen databases and museum records, and compiled climatic variables for islands and politically defined continental areas. Current and historic land connections in the Last Glacial Maximum were determined using bathymetric databases. We analysed factors driving patterns of Simpson composition dissimilarity using multiple regression of distance matrices (MRM). Results Temperature was the largest driver of dissimilarity among areas, with geographical distance and historical land contiguity also being important. Current land contiguity had no detectable effect. Main Conclusions We found climate to be a primary driver of ant diversity patterns on large scales, consistent with previous work on ants and other organisms. Interestingly, land connectivity during historical periods of low sea level was more important than current land connectivity in explaining faunal similarities. This implies that despite the potential overwater dispersal of ants, overland dispersal via transient land connections is a more important driver of regional-scale biogeographical pattern in East Asia

Ant species occurrence records from East Asia

Ant species checklists representing local species pools across 159 islands and areas in East Asia were compiled, including Japan, South Korea, North Korea, China and Russia (Far East). The records represent nominal valid species and are based on 1093 publications from 1874-2014. This .txt file consists of two columns, listing species and area names. The preceding letters before the area names separated by an underscore abbreviate countries or island archipelagoes where the areas belong to (C China, DT Daito Islands, IZ Izu Islands, J Japan, JM Japanese main islands, NK North Korea, OG Ogasawara Islands, R Russia, RC Ryukyu Islands - central, RFE Russia Far East, RN Ryukyu Islands - north, RS Ryukyu Islands south, SK South Korea, SKM South Korea mainland, SN Senkaku Islands)

Evolutionary biogeography of the reef-building coral genus Galaxea across the Indo-Pacific ocean

Stony corals (Scleractinia) form the basis for some of the most diverse ecosytems on Earth, but we have much to learn about their evolutionary history and systematic relationships. In order to improve our understanding of species in corals we here investigated phylogenetic relationships between morphologically defined species and genetic lineages in the genus Galaxea (Euphyllidae) using a combined phylogenomic and phylogeographic approach. Previous studies revealed the nominal species G. fascicularis included three genetically well-differentiated lineages (L, S & L+) in the western Pacific, but their distribution and relationship to other species in the genus was unknown. Based on genomic (RAD-seq) and mitochondrial sequence data (non-coding region between cytb and ND2) we investigated whether the morphological taxa represent genetically coherent entities and what is the phylogenetic relationship and spatial distribution of the three lineages of G. fascicularis throughout the observed species range. Using the RAD-seq data, we find that the genus Galaxea is monophyletic and contains three distinct clades: an Indo-Pacific, a Pacific, and a small clade restricted to the Chagos Archipelago. The three lineages of G. fascicularis were associated with different RAD-seq clades, with the ‘L’ lineage showing some morphological distinction from the other two lineages (larger more asymmetrical polyps). In addition to these, three more genetic lineages in G. fascicularis may be distinguished – a Chagossian, an Ogasawaran, and one from the Indian-Red Sea. Among nominal taxa for which we have multiple samples, G. horrescens was the only monophyletic species. The mitochondrial non-coding region is highly conserved apart of the length polymorphism used to define L, S & L+ lineages and lacks the power to distinguish morphological and genetic groups resolved with genomic RAD-sequencing. The polyphyletic nature of most species warrants a careful examination of the accepted taxonomy of this group with voucher collections and their comparison to type specimens to resolve species boundaries. Further insight to the speciation process in corals will require international cooperation for the sharing of specimens to facilitate scientific discovery