Yuichi Nakajima

Gene Flow and Genetic Diversity of a Broadcast-Spawning Coral in Northern Peripheral Populations

Recently, reef-building coral populations have been decreasing worldwide due to various disturbances. Population genetic studies are helpful for estimating the genetic connectivity among populations of marine sessile organisms with metapopulation structures such as corals. Moreover, the relationship between latitude and genetic diversity is informative when evaluating the fragility of populations. In this study, using highly variable markers, we examined the population genetics of the broadcast-spawning coral Acropora digitifera at 19 sites in seven regions along the 1,000 km long island chain of Nansei Islands, Japan. This area includes both subtropical and temperate habitats. Thus, the coral populations around the Nansei Islands in Japan are northern peripheral populations that would be subjected to environmental stresses different from those in tropical areas. The existence of high genetic connectivity across this large geographic area was suggested for all sites (F ST≤0.033) although small but significant genetic differentiation was detected among populations in geographically close sites and regions. In addition, A. digitifera appears to be distributed throughout the Nansei Islands without losing genetic diversity. Therefore, A. digitifera populations in the Nansei Islands may be able to recover relatively rapidly even when high disturbances of coral communities occur locally if populations on other reefs are properly maintained.

The Kuroshio Current influences genetic diversity and population genetic structure of a tropical seagrass, Enhalus acoroides

Information on genetic diversity and differentiation of seagrass populations is essential for the conservation of coastal ecosystems. However, little is known about the seagrasses in the Indo‐West Pacific Ocean, where the worlds highest diversity of seagrasses occurs. The influence of sea currents on these populations is also unknown. We estimated the genetic diversity and population genetic structure and identified reproductive features in Enhalus acoroides populations from the Yaeyama Islands, Hainan Island and the Philippines. The Philippines are situated at the centre of the E. acoroides range, Yaeyama and Hainan are peripheral populations, and the Yaeyama population is at the northern limit of the species range. The powerful Kuroshio Current flows from the Philippines to Yaeyama. Genetic analyses using nine microsatellite markers indicated that reproduction of E. acoroides is mostly sexual. Clonal diversity does not decrease in northern populations, although genetic diversity does. However, the genetic diversity of the Yaeyama populations is greater than that of the Hainan populations. Significant genetic differentiation among most populations was evident; however, the Yaeyama and north‐east Philippines populations were genetically similar, despite being separated by ~1100 km. An assignment test suggested that recruitment occurs from the north‐east Philippines to Yaeyama. The strong current in this region is probably responsible for the extant genetic diversity and recruitment patterns.

Quantifying dispersal from hydrothermal vent fields in the western Pacific Ocean

Significance Submarine hot springs known as hydrothermal vents host unique ecosystems of endemic animals that do not depend on photosynthesis. Quantifying larval dispersal processes is essential to understanding gene flows and diversity distributions of vent endemic species, as well as to protect vent communities from anthropological disturbances (e.g., deep-sea mining). In this study, we assess the potential frequency of larval exchange between vent fields throughout the entire western Pacific via ocean circulation processes, so that population geneticists can make quantitative comparisons. We show that western Pacific vents in distant basins are potentially connected with strong directionality. This article makes a valuable contribution to a difficult and important area of deep ocean processes. Hydrothermal vent fields in the western Pacific Ocean are mostly distributed along spreading centers in submarine basins behind convergent plate boundaries. Larval dispersal resulting from deep-ocean circulations is one of the major factors influencing gene flow, diversity, and distributions of vent animals. By combining a biophysical model and deep-profiling float experiments, we quantify potential larval dispersal of vent species via ocean circulation in the western Pacific Ocean. We demonstrate that vent fields within back-arc basins could be well connected without particular directionality, whereas basin-to-basin dispersal is expected to occur infrequently, once in tens to hundreds of thousands of years, with clear dispersal barriers and directionality associated with ocean currents. The southwest Pacific vent complex, spanning more than 4,000 km, may be connected by the South Equatorial Current for species with a longer-than-average larval development time. Depending on larval dispersal depth, a strong western boundary current, the Kuroshio Current, could bridge vent fields from the Okinawa Trough to the Izu-Bonin Arc, which are 1,200 km apart. Outcomes of this study should help marine ecologists estimate gene flow among vent populations and design optimal marine conservation plans to protect one of the most unusual ecosystems on Earth.

The population genetic approach delineates the species boundary of reproductively isolated corymbose acroporid corals.

In this study, we used a population genetic approach with microsatellite markers to attempt to clarify the species boundary of Acropora corals. Species in this taxon are usually difficult to distinguish with the usual molecular phylogenetic approach. We used Acropora sp. 1 and Acropora digitifera as the target species to shed light on the species boundary of Acropora at the population level. These species are morphologically and ecologically similar but are reproductively isolated by differences of a few months in their spawning seasons. We could not distinguish these species using a phylogenetic analysis of the mitochondrial control region, as previously reported in other Acropora species. In contrast, a population genetic approach clearly distinguished these species both sympatrically and allopatrically. Our results suggest that recent speciation and shared ancestral polymorphisms could partly explain the para- and polyphyly of several Acropora species.

Genetic diversity and structure of the tropical seagrass Cymodocea serrulata spanning its central diversity hotspot and range edge

Abstract Persistence of populations at their distributional ranges relies on local population dynamics and the fitness of species with low dispersal potential. We analyzed the population genetic diversity and structure of a tropical seagrass species, Cymodocea serrulata, at 34 sites spanning Philippine (diversity hotspot) and Ryukyu Islands (northern limit of distribution) populations using microsatellite (SSR) markers. Seagrass populations in the diversity hotspot are hypothesized to contain higher genetic diversity and clonal richness than those resulting from expansion or geographic range limits. We tested this hypothesis by comparing the genetic diversity, genetic structure and clonal richness of C. serrulata populations in the Philippines and Ryukyu Islands. C. serrulata populations showed decreased genetic diversity and clonal richness at their northern limit. Clonal reproduction predominated at the northern limit, while sexual reproduction prevailed in the diversity hotspot. Decreased genetic diversity and clonal richness at the northern limit may be the consequence of drift resulting from founder effect, reduced habitat, sea surface temperature and low gene flow and/or natural selection across life stages, wherein clonal reproduction confers greater environmental fitness. Analysis of molecular variance (AMOVA) and the fixation index, FST, showed significant genetic differentiation within and among geographic populations. STRUCTURE analysis revealed that the Ryukyu Islands populations were mosaics of genets from the eastern Philippines, likely carried by the Kuroshio Current.

In vitro fertilization efficiency in coral Acropora digitifera

We performed fertilization experiments with Acropora digitifera, which is one of the dominant scleractinian corals in the Ryukyu Archipelago, Japan, to determine optimal conditions for in vitro manipulations. Our result suggests that conspecific fertilization is essentially complete within 30 min under the experimental conditions used in usual fertilization experiments in corals. Previous in vitro experiments (1 x 10(5)-10(6) sperm/ml, 4-8 h) are likely to have overestimated the efficiency of fertilization of Acropora spp. in the field. Therefore, we suggest that incubation periods shorter than those used to date (i.e. complete exclusion of sperm 1 h after their addition) would be more appropriate for the estimation of fertilization rates in corals.

Genetic connectivity in the broadcast-spawning coral Acropora digitifera analyzed by microsatellite markers on the Sekisei Reef, southwestern Japan.

Worldwide decline has been observed in coral populations due to environmental changes at both regional and global levels. Since corals have a typical metapopulation structure, the recovery of severely disturbed local populations depends on larval recruitment from outside the disturbed region. Therefore, the connectivity among local populations may play a key role in the disturbance/ recovery dynamics of coral populations. On the basis of the simulation of surface currents, derived from ocean currents, we hypothesized that the genetic connectivity of coral populations is weak between the northern and southern regions of Sekisei Reef, Japan. To test this hypothesis, the connectivity of the population of the broadcast-spawning coral Acropora digitifera, one of the dominant corals in the Sekisei Reef, was analyzed at six sampling sites that were 5–25 km apart by using six microsatellite markers. The degree of genetic differentiation of A. digitifera was very low among all the sites (FST from -0.006 to 0.015), and no evidence was found in support of our hypothesis. The relative lack of genetic differentiation of A. digitifera among the sites may be attributable to the large effect of wind-driven surface currents, which highly vary on an annual basis, on coral larvae or to the time gap between simulation based on ocean current patterns and accumulation of genetic differences. Considering the pattern of the genetic connectivity of A. digitifera in the Sekisei Reef, the sites that are located within less-disturbed areas may act as larval sources and should, therefore, be preserved.

Development of novel, cross-species microsatellite markers for Acropora corals using next-generation sequencing technology

The genus Acropora (Scleractinia, Acroporidae) is one of the most widespread coral genera, comprising the largest number of extant species among scleractinian (reef-building) corals. Molecular phylogenetic studies have suggested that A. tenuis belongs to the most basal clade (clade I) while A. digitifera belongs to a derived clade (clade IV). In order to develop microsatellite markers that would be useful for most Acropora species, we sequenced the genomic DNA of A. tenuis, using a next generation sequencer (Illumina MiSeq), and designed primer sets that amplify microsatellite loci. Afterward we selected primer pairs with perfectly matched nucleotide sequences from which at least one primer was uniquely mapped to the A. digitifera genome. Fourteen microsatellite markers showed non-significant departure from Hardy–Weinberg equilibrium (HWE) in both A. tenuis and A. digitifera. Thus these markers could be used for wide range of species and may provide powerful tools for population genetics studies and conservation of Acropora corals.

Genetic differentiation and connectivity of morphological types of the broadcast-spawning coral Galaxea fascicularis in the Nansei Islands, Japan.

Abstract Population connectivity resulting from larval dispersal is essential for the maintenance or recovery of populations in marine ecosystems, including coral reefs. Studies of species diversity and genetic connectivity within species are essential for the conservation of corals and coral reef ecosystems. We analyzed mitochondrial DNA sequence types and microsatellite genotypes of the broadcast‐spawning coral, Galaxea fascicularis, from four regions in the subtropical Nansei Islands in the northwestern Pacific Ocean. Two types (soft and hard types) of nematocyst morphology are known in G. fascicularis and are significantly correlated with the length of a mitochondrial DNA noncoding sequence (soft type: mt‐L; hard type: mt‐S type). Using microsatellites, significant genetic differentiation was detected between the mitochondrial DNA sequence types in all regions. We also found a third genetic cluster (mt‐L+), and this unexpected type may be a cryptic species of Galaxea. High clonal diversity was detected in both mt‐L and mt‐S types. Significant genetic differentiation, which was found among regions within a given type (F ST = 0.009–0.024, all Ps ≤ 0.005 in mt‐L; 0.009–0.032, all Ps ≤ 0.01 in mt‐S), may result from the shorter larval development than in other broadcast‐spawning corals, such as the genus Acropora. Nevertheless, intraspecific genetic diversity and connectivity have been maintained, and with both sexual and asexual reproduction, this species appears to have a potential for the recovery of populations after disturbance.

Novel Polymorphic Microsatellite Markers Reveal Genetic Differentiation between Two Sympatric Types of Galaxea fascicularis.

The reef-building, scleractinian coral, Galaxea fascicularis, is classified into soft and hard types, based on nematocyst morphology. This character is correlated with the length of the mitochondrial non-coding region (mt-Long: soft colony type, and nematocysts with wide capsules and long shafts; mt-Short: hard colony type, and nematocysts with thin capsules and short shafts). We isolated and characterized novel polymorphic microsatellite markers for G. fascicularis using next-generation sequencing. Based upon the mitochondrial non-coding region, 53 of the 97 colonies collected were mt-Long (mt-L) and 44 were mt-Short (mt-S). Among the 53 mt-L colonies, 27 loci were identified as amplifiable, polymorphic microsatellite loci, devoid of somatic mutations and free of scoring errors. Eleven of those 27 loci were also amplifiable and polymorphic in the 44 mt-S colonies; these 11 are cross-type microsatellite loci. The other 16 loci were considered useful only for mt-L colonies. These 27 loci identified 10 multilocus lineages (MLLs) among the 53 mt-L colonies (N MLL/N = 0.189), and the 11 cross-type loci identified 7 MLLs in 44 mt-S colonies (N MLL/N = 0.159). Significant genetic differentiation between the two types was detected based on the genetic differentiation index (F ST = 0.080, P = 0.001). Bayesian clustering also indicated that these two types are genetically isolated. While nuclear microsatellite genotypes also showed genetic differentiation between mitochondrial types, the mechanism of divergence is not yet clear. These markers will be useful to estimate genetic diversity, differentiation, and connectivity among populations, and to understand evolutionary processes, including divergence of types in G. fascicularis.