Phylogeographic heterogeneity of the brown macroalga Sargassum horneri (Fucaceae) in the northwestern Pacific in relation to late Pleistocene glaciation and tectonic configurations

Population genetic patterns across the native and invasive range of a widely distributed seagrass: Phylogeographic structure, invasive history and conservation implications

Aim

The seagrass Zostera japonica is a dramatically declined endemic species in the Northwestern Pacific from the (sub)tropical to temperate areas, however, it is also an introduced species along the Pacific coast of North America from British Columbia to northern California. Understanding the population's genetic patterns can inform the conservation and management of this species.

Location

North Pacific.

Methods

We used sequences of the nuclear rDNA internal transcribed spacer (ITS) and chloroplast trnK intron maturase (matK), and 24 microsatellite loci to survey 34 native and nonnative populations (>1000 individuals) of Z. japonica throughout the entire biogeographic range. We analysed the phylogeographic relationship, population genetic structure and genetic diversity of all populations and inferred possible origins and invasion pathways of the nonnative ones.

Results

All markers revealed a surprising and significant deep divergence between northern and southern populations of Z. japonica in the native region separated by a well-established biogeographical boundary. A secondary contact zone was found along the coasts of South Korea and Japan. Nonnative populations were found to originate from the central Pacific coast of Japan with multiple introductions from at least two different source populations, and secondary spread was likely aided by waterfowl.

Main Conclusions

The divergence of the two distinct clades was likely due to the combined effects of historical isolation, adaptation to distinct environments and a contemporary physical barrier created by the Yangtze River, and the warm northward Kuroshio Current led to secondary contact after glacial separation. Existing exchanges among the nonnative populations indicate the potential for persistence and further expansion. This study not only helps to understand the underlying evolutionary potential of a widespread seagrass species following global climate change but also provides valuable insights for conservation and restoration.

Sargassum sp. extract improve hematological profile of tilapia fish ( Oreochromis niloticus)

Background: Strategies to increase body resistance and prevent disease in aquaculture include using vaccines, antibiotics, and probiotics. Today, the use of antibiotics with natural ingredients is becoming a trend. One of the natural ingredients that contain high antioxidants and antibiotics is Sargassum sp. Methods: This research was conducted from March to May 2022 at the Biotechnology Laboratory, Faculty of Fisheries and Marine, Universitas Riau, in two stages: 1) the sensitivity of extracts of Sargassum sp. and 2) the application of Sargassum sp. extract orally in tilapia ( O. niloticus). The parameters measured were clear zone, minimum inhibitory concentration, LD 50 test of leaf extract of Sargassum sp. in tilapia ( O. niloticus), hemoglobin levels, hematocrit, total leukocytes, total erythrocytes, leukocyte differentiation, and survival rate. Data on hematology parameters were tabulated and analyzed using a One-Way ANOVA followed by a Student Newman Keuls (SNK) test when deemed necessary. Results: The results showed that the extract of Sargassum sp. inhibited the growth of Aeromonas hydrophila bacteria with a clear zone of 6.5-15.0 mm, which is classified as resistant. At doses of 2000, 2500, and 3000 ppm, it did not cause death in fish for 96 hours (LD 50). Hematological parameters can be a sign of the health status of fish. Tilapia given Sargassum sp. in different doses gave an effect between treatments, both after 30 days of rearing and post-test against A. hydrophila bacteria (p<0.05). The results showed that the hematology of fish fed with Sargassum sp. extract was in the normal or healthy range. Healthy tilapia had erythrocyte counts ranging from 1.34-2.11×10 6 cells/mm 3, hematocrit 26.17-33.19%, hemoglobin 6.26-11.2 g/dL and total leukocytes 1.01-1.50×10 4 cells/mm 3 and total erythrocytes 5.88-9.13×10 4 cells/ mm 3. Conclusions: A dose of 3000 ppm provided the highest health improvement against A. hydrophila bacterial infection.

Interannual variations of Sargassum blooms in the Yellow Sea and East China Sea during 2017-2021

Golden tide, caused by Sargassum horneri, is becoming another periodic and trans-regional harmful macroalgal bloom in the Yellow Sea (YS) and East China Sea (ECS) other than the green tide. In this study, we employed high-resolution remote sensing, field validations, and population genetics to investigate the spatiotemporal development pattern of Sargassum blooms during the years 2017 to 2021 and explore the potential environmental factors that influence them. Sporadic floating Sargassum rafts could be detected in the middle or northern YS during autumn and the distribution area then occurred sequentially along the Chinese and/or western Korean coastlines. The floating biomass amplified significantly in early spring, reached its maximum in two to three months with an evident northward expansion, and then declined rapidly in May or June. The scale of the spring bloom was much larger than the winter one in terms of coverage, suggesting an additional local source in ECS. The blooms were mostly confined to waters with a sea surface temperature range of 10-16℃, while the drifting pathways were consistent with the prevailing wind trajectory and surface currents. The floating S. horneri populations exhibited a homogenous and conservative genetic structure among years. Our findings underscore the year-round cycle of golden tides, the impact of physical hydrological environments on the drifting and blooming of pelagic S. horneri, and provide insights for monitoring and forecasting this emerging marine ecological disaster.

Organelle Genome Variation in the Red Algal Genus Ahnfeltia (Florideophyceae)

The agarophyte Ahnfeltia (Ahnfeltiales, Rhodophyta) is a globally widespread genus with 11 accepted species names. Two of the most widespread species in this genus, A. plicata and A. fastigiata, may have diverged genetically due to past geographic changes and subsequent geographic isolation. To investigate this genomic and genetic diversity, we generated new plastid (ptDNAs) and mitochondrial genomes (mtDNAs) of these Ahnfeltia species from four different regions (A. plicata - Chile and UK and A. fastigiata - Korea and Oregon). Two architecture variations were found in the Ahnfeltia genomes: in ptDNA of A. fastigiata Oregon, the hypothetical pseudogene region was translocated, likely due to recombination with palindromic repeats or a gene transfer from a red algal plasmid. In mtDNA of A. fastigiata Korea, the composition of the group II intronic ORFs was distinct from others suggesting different scenarios of gain and loss of group II intronic ORFs. These features resulted in genome size differences between the two species. Overall gene contents of organelle genomes of Ahnfeltia were conserved. Phylogenetic analysis using concatenated genes from ptDNAs and mtDNAs supported the monophyly of the Ahnfeltiophycidae. The most probable individual gene trees showed that the Ahnfeltia populations were genetically diversified. These trees, the cox1 haplotype network, and a dN/dS analysis all supported the theory that these Ahnfeltia populations have diversified genetically in accordance with geographic distribution.

Harmful macroalgal blooms (HMBs) in China's coastal water: Green and golden tides

Harmful macroalgal blooms (HMBs) have been increasing along China's coasts, causing significant social impacts and economic losses. Besides extensive eutrophication sustaining coastal seaweed tides, the stimuli and dynamics of macroalgal blooms in China are quite complex and require comprehensive studies. This review summarizes the distinct genesis, development and drifting patterns of three HMBs that have persistently occurred in China's coastal waters during recent years: transregional green tides of drifting Ulva prolifera in the Yellow Sea (YS), local green tides of multiple suspended seaweeds in the Bohai Sea and large-scale golden tides of pelagic Sargassum horneri in the YS and East China Sea. While specific containment measures have been developed and implemented to effectively suppress large-scale green tides in the YS, the origin and blooming mechanism of golden tides remain unclear due to lack of field research. With the broad occurrence of HMBs and their increased accumulation on beaches and coastal waters, it is necessary to investigate the blooming mechanism and ecological impacts of these HMBs, especially with the growing stresses of climate change and anthropogenic disturbances.

Climate-induced range shifts shaped the present and threaten the future genetic variability of a marine brown alga in the Northwest Pacific

Glaciation-induced environmental changes during the last glacial maximum (LGM) have strongly influenced species' distributions and genetic diversity patterns in the northern high latitudes. However, these effects have seldom been assessed on sessile species in the Northwest Pacific. Herein, we chose the brown alga Sargassum thunbergii to test this hypothesis, by comparing present population genetic variability with inferred geographical range shifts from the LGM to the present, estimated with species distribution modelling (SDM). Projections for contrasting scenarios of future climate change were also developed to anticipate genetic diversity losses at regional scales. Results showed that S. thunbergii harbours strikingly rich genetic diversity and multiple divergent lineages in the centre-northern range of its distribution, in contrast with a poorer genetically distinct lineage in the southern range. SDM hindcasted refugial persistence in the southern range during the LGM as well as post-LGM expansion of 18 degrees of latitude northward. Approximate Bayesian computation (ABC) analysis further suggested that the multiple divergent lineages in the centre-northern range limit stem from post-LGM colonization from the southern survived lineage. This suggests divergence due to demographic bottlenecks during range expansion and massive genetic diversity loss during post-LGM contraction in the south. The projected future range of S. thunbergii highlights the threat to unique gene pools that might be lost under global changes.

Ocean Currents Drove Genetic Structure of Seven Dominant Mangrove Species Along the Coastlines of Southern China

Mangrove forest ecosystems, which provide important ecological services for marine environments and human activities, are being destroyed worldwide at an alarming rate. The objective of our study was to use molecular data and analytical techniques to separate the effects of historical and contemporary processes on the distribution of mangroves and patterns of population genetic differentiation. Seven mangrove species (Acanthus ilicifolius, Aegiceras corniculatum, Avicennia marina, Bruguiera gymnorrhiza, Kandelia obovata, Lumnitzera racemosa, and Rhizophora stylosa), which are predominant along the coastlines of South China, were genotyped at nuclear (nSSR) and chloroplast (cpSSR) microsatellite markers. We estimated historical and contemporary gene flow, the genetic diversity and population structure of seven mangrove species in China. All of these seven species exhibited few haplotypes, low levels of genetic diversity (H E = 0.160-0.361, with the exception of K. obovata) and high levels of inbreeding (F IS = 0.104-0.637), which may be due to their marginal geographical distribution, human-driven and natural stressors on habitat loss and fragmentation. The distribution patterns of haplotypes and population genetic structures of seven mangrove species in China suggest historical connectivity between populations over a large geographic area. In contrast, significant genetic differentiation [F ST = 0.165-0.629 (nSSR); G ST = 0.173-0.923 (cpSSR)] indicates that populations of mangroves are isolated from one another with low levels of contemporary gene flow among populations. Our results suggest that populations of mangroves were historically more widely inter-connected and have recently been isolated, likely through a combination of ocean currents and human activities. In addition, genetic admixture in Beibu Gulf populations and populations surrounding Hainan Island and southern mainland China were attributed to asymmetric gene flow along prevailing oceanic currents in China in historical times. Even ocean currents promote genetic exchanges among mangrove populations, which are still unable to offset the effects of natural and anthropogenic fragmentation. The recent isolation and lack of gene flow among populations of mangroves may affect their long-term survival along the coastlines of South China. Our study enhances the understanding of oceanic currents contributing to population connectivity, and the effects of anthropogenic and natural habitat fragmentation on mangroves, thereby informing future conservation efforts and seascape genetics toward mangroves.

Sargassum blooms in the East China Sea and Yellow Sea: Formation and management

Large-scale Sargassum blooms, known as golden tides, have been occurring along the coast of the Yellow Sea in recent years, resulting in an enormous loss of Pyropia yezoensis production. To locate the source of the blooms, we performed large-scale spatio-temporal sampling in the South Yellow Sea, East China Sea, and Jeju Island, South Korea. Based on morphology and molecular traits, the attached and floating Sargassum samples collected from the three regions were all identified as Sargassum horneri, although slight differences were observed in morphology among samples. Genetic distance and automatic barcode gap discovery analysis revealed very low genetic diversity among the three regions. The 33 samples from 12 sites were divided into six haplotypes, and the samples from the ECS shared more haplotypes than samples from other two regions. Our results suggested that S. horneri in the ECS was responsible for the formation of blooms in the Yellow Sea.

Comparative Analysis of Sequence Polymorphism in Complete Organelle Genomes of the ‘Golden Tide’ Seaweed Sargassum horneri between Korean and Chinese Forms

Drifting and inundating brown seaweed Sargassum horneri biomass is called “golden tide”, as it resembles golden massive algal blooms like green tides. This phenomenon occurs globally and its serious ecological impacts on coastal ecosystems have recently begun to be paid attention to. In the present study, by sequencing whole organelle genomes of Korean indigenous S. horneri, we aimed to develop novel molecular markers that can be used for differentiating indigenous from nonindigenous individuals. To this end, we analyzed sequence polymorphisms in mitochondrial (mt) and chloroplast (cp) genomes of two Korean benthic samples in comparison to Chinese ones as a reference. We mapped mt genomes of 34,620~34,628 bp and cp genomes of 123,982~124,053 bp for the Korean samples. In comparative analyses, mtDNA cytochrome c oxidase subunit II (cox2) gene showed the highest number of single nucleotide polymorphisms (SNPs) between Korean and Chinese individuals. NADH dehydrogenase subunit 7 (Nad7)-proline tRNA (trnP) intergenic spacer (IGS) in the mt genome showed a 14 bp insertion or deletion (indel) mutation. For the cp genome, we found a total of 54 SNPs, but its overall evolution rate was approximately four-fold lower than the mt genome. Interestingly, analysis of Ka/Ks ratio in the cp genome revealed a signature of positive selection on several genes, although only negative selection prevalent in mt genome. The ‘candidate’ genetic markers that we found can be applied to discriminate between Korean indigenous and nonindigenous individuals. This study will assist in developing a molecular-based early detection method for effectively managing nonindigenous S. horneri in Korean waters.

Limited Genetic Connectivity Among Sargassum horneri (Phaeophyceae) Populations in the Chinese Marginal Seas Despite Their high Dispersal Capacity

Sargassum horneri is a habitat-forming species in the Northwest Pacific and an important contributor to seaweed rafts. In this study, 131 benthic samples and 156 floating samples were collected in the Yellow Sea and East China Sea (ECS) to test the effects of seaweed rafts on population structure and connectivity. Our results revealed high levels of genetic diversity in both benthic and floating samples based on concatenated mitochondrial markers (rpl5-rps3, rnl-atp9, and cob-cox2). Phylogenetic analyses consistently supported the existence of two lineages (lineages I and II), with divergence dating to c. 0.692 Mya (95% HPD: 0.255-1.841 Mya), indicating that long-term isolation may have occurred during the mid-Pleistocene (0.126-0.781 Mya). Extended Bayesian skyline plots demonstrated a constant population size over time in lineage I and slight demographic expansion in lineage II. Both lineages were found in each marginal sea (including both benthic and floating samples), but PCoA, FST , and AMOVA analyses consistently revealed deep genetic variation between regions. Highly structured phylogeographic pattern supports limited genetic connectivity between regions. IMA analyses demonstrated that asymmetric gene flow between benthic populations in the North Yellow Sea (NYS) and ECS was extremely low (ECS→NYS, 2Nm = 0.6), implying that high dispersal capacity cannot be assumed to lead to widespread population connectivity, even without dispersal barriers. In addition, there were only a few shared haplotypes between benthic and floating samples, suggesting the existence of hidden donors for the floating masses in the Chinese marginal seas.

Marine Heatwave Drives Cryptic Loss of Genetic Diversity in Underwater Forests

Extreme events have profound ecological impacts on species and ecosystems, including range contractions and collapse of entire ecosystems. Although theory predicts that extreme events cause loss of genetic diversity, empirical demonstrations are rare, obscuring implications for future adaptive capacity of species and populations. Here, we use rare genetic data from before an extreme event to empirically demonstrate massive and cryptic loss of genetic diversity across ∼800 km of underwater forests following the most severe marine heatwave on record. Two forest-forming seaweeds (Sargassum fallax and Scytothalia dorycarpa) lost ∼30%-65% of average genetic diversity within the 800-km footprint of the heatwave and up to 100% of diversity at some sites. Populations became dominated by single haplotypes that were often not dominant or present prior to the heatwave. Strikingly, these impacts were cryptic and not reflected in measures of forest cover used to determine ecological impact of the heatwave. Our results show that marine heatwaves can drive strong loss of genetic diversity, which may compromise adaptability to future climatic change.

Population Dynamics of the ‘Golden Tides’ Seaweed, Sargassum horneri, on the Southwestern Coast of Korea: The Extent and Formation of Golden Tides

Since 2015, troublesome masses of floating Sargassum horneri have been introduced via ocean currents and winds to the southwestern coastline of Korea, including Jeju Island. These massive mats have caused considerable damage to the aquaculture industry, tourism, and the marine ecosystem. Most previous studies of S. horneri have focused on cultivation, the development of gene markers, and photosynthetic activity, but few data on population dynamics are available. We investigated the population dynamics of native S. horneri off the southwestern coast of Korea with the aim of predicting the formation of golden tides. Populations at two sites had obligate annual life cycles. Thalli were recruited during the period September–November, grew during the period December–April, and senesced by July. This pattern reflected seasonal trends in water temperature. Specific growth rates and heights of the thalli at Munseom were significantly higher than those at Jindo. The greatest environmental difference between the two sites is probably the degree of exposure to wave action. Mortality density (thalli lost per unit area) in the Munseom population was highest during the period December–January (i.e., 2–3 months after recruitment) and in March. Most thalli in the Jindo population died off in July when water temperatures increased. The maximum average biomass of S. horneri thalli detaching from the substrata reached 1.6 kg fresh weight m–2 during January and March. Thus, large-scale drifting mats were formed by S. horneri detachment from the substrata. Despite the differences in space and environment between China and Korea, our findings will enable quantitative assessments of the overall floating Sargassum biomass in the East China and Yellow Seas.

An anomalous bi-macroalgal bloom caused by Ulva and Sargassum seaweeds during spring to summer of 2017 in the western Yellow Sea, China

An unprecedented bi-macroalgal bloom caused by Ulva prolifera and Sargassum horneri occurred from spring to summer of 2017 in the western Yellow Sea (YS) of China, where annual large-scale green tides have prevailed for a decade. The distinct genesis and blooming dynamics of the two seaweed species were detected and described. Unlike the consistent raft-origin of the floating Ulva biomass, the massive pelagic S. horneri was derived from multiple sources (residual seaweeds from the previous winter bloom and those drifting from offshore water in the south). The scale of the green tide in 2017 was found smaller than the previous four years. We then discussed a number of hypotheses attributing to this reduction, including reduced epiphytic green algae from aquaculture rafts and the influences of the massive pelagic S. horneri. However, further research is needed to identify the origin of the pelagic S. horneri in the western YS and any affiliations with the benthic populations, and to elucidate the interactions of this species with the annual green tides and the ensuing consequences.

Contrasting patterns of genetic structure and phylogeography in the marine agarophytes Gelidiophycus divaricatus and G. freshwateri (Gelidiales, Rhodophyta) from East Asia

The evolutionary and population demographic history of marine red algae in East Asia is poorly understood. Here, we reconstructed the phylogeographies of two upper intertidal species endemic to East Asia, Gelidiophycus divaricatus and G. freshwateri. Phylogenetic and phylogeographic inferences of 393 mitochondrial cox1, 128 plastid rbcL, and 342 nuclear ITS2 sequences were complemented with ecological niche models. Gelidiophycus divaricatus, a southern species adapted to warm water, is characterized by a high genetic diversity and a strong geographical population structure, characteristic of stable population sizes and sudden reduction to recent expansion. In contrast, G. freshwateri, a northern species adapted to cold temperate conditions, is genetically relatively homogeneous with a shallow population structure resulting from steady population growth and recent equilibrium. The overlap zone of the two species roughly matches summer and winter isotherms, indicating that surface seawater temperature is a key feature influencing species range. Unidirectional genetic introgression was detected at two sites on Jeju Island where G. divaricatus was rare while G. freshwateri was common, suggesting the occurrence of asymmetric natural hybrids, a rarely reported event for rhodophytes. Our results illustrate that Quaternary climate oscillations have left strong imprints on the current day genetic structure and highlight the importance of seawater temperature and sea level change in driving speciation in upper intertidal seaweed species.

Phylogeographic studies on two shore crab species from East Asia: similar but different stories

BACKGROUND

The genetic structure of marine organisms in the East Asian region has long been a subject of interest. Two grapsid crab species, Hemigrapsus penicillatus (De Haan, 1835) and Hemigrapsus sanguineus (De Haan, 1835), are commonly found in the rocky intertidal zones around this region. They are known to spread via larval migration, which makes them an appropriate model species for observing the genetic structure of East Asian intertidal invertebrate animals.

OBJECTIVE

We investigated the genetic structure of the East Asian crabs H. penicillatus and H. sanguineus.

METHODS

We collected specimens of H. penicillatus from seven locations (42 individuals) and of H. sanguineus from ten locations (58 individuals) in Korea, Japan, and Taiwan. We investigated and compared the genetic diversity and structure of populations of these species using mitochondrial cytochrome oxidase subunit I (COI) sequences.

RESULTS

Our results show that both species are genetically structured between South Korea and Japan, and that the Taiwan population forms a cluster that is separate from those of the other countries. Populations of H. penicillatus contain less genetic diversity than those of H. sanguineus.

CONCLUSION

These results suggest that there is a genetic structure between the two species at present in East Asia.

The origin and population genetic structure of the 'golden tide' seaweeds, Sargassum horneri, in Korean waters

In recent years, drifting and inundating brown seaweed (Sargassum horneri) biomass, called 'golden tides', has frequently drifted and accumulated along the southern coastlines of Korea, causing devastating impacts on the local economy and coastal ecosystems. In this study, based on combined analyses of mitochondrial DNA cox3 gene and seven microsatellites, we investigated the genetic makeup of the floating S. horneri populations (N = 14) in comparison to Korean benthic populations (N = 5), and tracked their genetic sources. Given a shared mtDNA haplotype and oceanic circulation systems, the floating populations may have been originated from the southeastern coast of China (e.g. Zhoushan, Zhejiang province). Population structure analyses with microsatellites revealed two distinct genetic clusters, each comprising floating and benthic populations. High levels of inter-population differentiation were detected within Korean benthic samples. The floating populations from the same periods during a 2015-2018 year were genetically more different from one another than those from different periods. These results suggest that the floating populations might be of multiple genetic sources within geographic origin(s). This study will inform management efforts including the development of "S. horneri blooming forecasting system", which will assist in mitigating ecological and economic damages on the Korean coastal ecosystems in the future.

Phylogeographic diversification and postglacial range dynamics shed light on the conservation of the kelp Saccharina japonica

Studies of postglacial range shifts could enhance our understanding of seaweed species' responses to climate change and hence facilitate the conservation of natural resources. However, the distribution dynamics and phylogeographic diversification of the commercially and ecologically important kelp Saccharina japonica in the Northwest Pacific (NWP) are still poorly surveyed. In this study, we analyzed the evolutionary history of S. japonica using two mitochondrial markers and 24 nuclear microsatellites. A STRUCTURE analysis revealed two partially isolated lineages: lineage H, which is scattered along the coast of Japan; and lineage P, which occurs along the west coast of the Japan Sea. Ecological niche modeling projections to the Last Glacial Maximum (LGM) revealed that the southern coasts of the Japan Sea and the Pacific side of the Oshima and Honshu Peninsulas provided the most suitable habitats for S. japonica, implying that these regions served as ancient refugia during the LGM. Ancient isolation in different refugia may explain the observed divergence between lineages P and H. An approximate Bayesian computation analysis indicated that the two lineages experienced post-LGM range expansion and that postglacial secondary contact occurred in Sakhalin. Model projections into the year 2,100 predicted that S. japonica will shift northwards and lose its genetic diversity center on the Oshima Peninsula in Hokkaido and Shimokita Peninsula in Honshu. The range shifts and evolutionary history of S. japonica improve our understanding of how climate change impacted the distribution range and diversity of this species and provide useful information for the conservation of natural resources under ongoing environmental change in the NWP.

Phylogeography and genetic connectivity of the marine macro-alga Sargassum ilicifolium (Phaeophyceae, Ochrophyta) in the northwestern Pacific1

The evolutionary influences of historical and contemporary factors on the population connectivity and phylogeographic structure of a brown seaweed, Sargassum ilicifolium, were elucidated using the nuclear ITS2 and mitochondrial COI markers for the collections newly sampled within its distribution range in the northwestern Pacific (NWP). Significant genetic structure at variable levels was identified between populations (pairwise FST ) and among populations grouped by geographical proximity (ΦCT among regions). The adjacent groups of populations with moderate structure revealed from AMOVA appeared to have high genetic connectivity. However, a lack of genealogical concordance with the geographic distribution was uncovered for S. ilicifolium from the NWP. Such genetic homogeneity is interpreted as a result of the interaction between postglacial recolonization and dynamic oceanic current regimes in the region. Two separated glacial refugia, the South China Sea and the Okinawa Trough, in the marginal seas of east China were recognized based on the presence of endemic haplotypes and high haplotype diversity in the populations at southern China and northeast of Taiwan. Populations persisting in these refugia may have served as the source for recolonization in the NWP with the rise of sea level during the warmer interglacial periods. The role of oceanic currents in maintaining genetic connectivity of S. ilicifolium in the region was further corroborated by the coherence between the direction of oceanic currents and that of gene flow, especially along the eastern coast of Taiwan. This study underlines the interaction between historical postglacial recolonization and contemporary coastal hydrodynamics in contributing to population connectivity and distribution for this tropical seaweed in the NWP.

ddRAD-seq based phylogeographic study of Sargassum thunbergii (Phaeophyceae, Heterokonta) around Japanese coast

Using genome-wide SNP data obtained from high-throughput techniques based on double digest restriction site-associated DNA sequencing (ddRAD-seq), we elucidated the migration history and genetic diversity of the Japanese population of the ecologically important brown seaweed Sargassum thunbergii (Mertens ex Roth) Kuntze. STRUCTURE and NeighborNet analyses showed a clear genetic differentiation among populations of four geographic regions: Kyushu (POP1); Sea of Japan (POP2); Hokkaido and Tohoku (POP3); and Pacific coast from Kyushu to Kanto (POP4). Approximate Bayesian Computation (ABC) analysis indicated that POP4 diverged first, followed by the separation between POP2 (the largest effective population size) and POP3; POP1 was the last to form, shaped by the mixture of POP2 (73%) and POP4 (27%). High genetic diversity was detected in POP1 and POP2, whereas low genetic diversity was detected in POP3 and POP4. These results indicated that S. thunbergii populations of Kyushu and the Sea of Japan might have been maintained as large and stable populations gathered different lineages from China, Korea and/or Japan.

Upwelling and eddies affect connectivity among local populations of the goldeye rockfish, Sebastes thompsoni (Pisces, Scorpaenoidei)

The goldeye rockfish, Sebastes thompsoni, commercial rockfish catch in the Northwest Pacific Ocean, may influence its population structure. To clarify the population genetic structure of Korean S. thompsoni and its degree of hybridization with the most close species, Sebastes joyneri, we analyzed a mitochondrial (mt) DNA control region and eleven polymorphic microsatellite (ms) loci. S. joyneri individuals were clearly distinguished from S. thompsoni by the mtDNA control region and ms loci results, with single interspecific hybridization between two species suggesting no impact on genetic structure of S. thompsoni. Analysis of mtDNA revealed no population structure within S. thompsoni, suggesting the survival of a single population in southern refugia during the glacial period. The ms loci results, in contrast, showed two genetically distinct clusters within S. thompsoni: One was predominant throughout Korean coasts (from the Yellow Sea, via the Korea Strait to the East Sea); the other was predominant at Dokdo Island in the East Sea; and both occurred in similar ratios at Wangdolcho Reef in the East Sea. A possible factor that restricts gene flow between Korean coastal and offshore populations in the East Sea may be related to the complex oceanic current patterns such as eddies and upwelling, which represent impermeable barriers to population connectivity for this species. Our findings highlight that these two populations might be representative of two separate stock within Korean waters and maintain their geographically related genetic structure.

Historical isolation and contemporary gene flow drive population diversity of the brown alga Sargassum thunbergii along the coast of China

BACKGROUND

Long-term survival in isolated marginal seas of the China coast during the late Pleistocene ice ages is widely believed to be an important historical factor contributing to population genetic structure in coastal marine species. Whether or not contemporary factors (e.g. long-distance dispersal via coastal currents) continue to shape diversity gradients in marine organisms with high dispersal capability remains poorly understood. Our aim was to explore how historical and contemporary factors influenced the genetic diversity and distribution of the brown alga Sargassum thunbergii, which can drift on surface water, leading to long-distance dispersal.

RESULTS

We used 11 microsatellites and the plastid RuBisCo spacer to evaluate the genetic diversity of 22 Sargassum thunbergii populations sampled along the China coast. Population structure and differentiation was inferred based on genotype clustering and pairwise F ST and allele-frequency analyses. Integrated genetic analyses revealed two genetic clusters in S. thunbergii that dominated in the Yellow-Bohai Sea (YBS) and East China Sea (ECS) respectively. Higher levels of genetic diversity and variation were detected among populations in the YBS than in the ECS. Bayesian coalescent theory was used to estimate contemporary and historical gene flow. High levels of contemporary gene flow were detected from the YBS (north) to the ECS (south), whereas low levels of historical gene flow occurred between the two regions.

CONCLUSIONS

Our results suggest that the deep genetic divergence in S. thunbergii along the China coast may result from long-term geographic isolation during glacial periods. The dispersal of S. thunbergii driven by coastal currents may facilitate the admixture between southern and northern regimes. Our findings exemplify how both historical and contemporary forces are needed to understand phylogeographical patterns in coastal marine species with long-distance dispersal.

Cryptic diversity in the Japanese mantis shrimp Oratosquilla oratoria (Crustacea: Squillidae): Allopatric diversification, secondary contact and hybridization

Mounting evidence of cryptic species in the marine realm emphasizes the necessity to thoroughly revise our current perceptions of marine biodiversity and species distributions. Here, we used mitochondrial cytochrome oxidase subunit I (mtDNA COI) and nuclear ribosomal internal transcribed spacer (nrDNA ITS) to investigate cryptic diversity and potential hybridization in the Japanese mantis shrimp Oratosquilla oratoria in the Northwestern (NW) Pacific. Both mitochondrial and nuclear gene genealogies revealed two cryptic species in this morphotaxon, which was further confirmed by extensive population-level analyses. One cryptic species is restricted to cold waters with a distribution range corresponding to temperate affinities, while the other dwelled warm waters influenced by the Kuroshio Current. Their divergence was postulated to be attributable to the vicariant event which resulted from the isolation of the Sea of Japan during the middle Pliocene (c. 3.85 Mya, 95% HPD 2.23–6.07 Mya). Allopatric speciation was maintained by limited genetic exchange due to their habitat preferences. Furthermore, the observation of recombinant nrDNA ITS sequence and intra-individual ITS polymorphism suggested recent hybridization event of the two cryptic species occurred in sympatric areas. Our study also illustrated that the Changjiang River outflow might act as an oceanic barrier to gene flow and promoted allopatric diversification in O. oratoria species complex.

Hidden diversity and phylogeographic history provide conservation insights for the edible seaweed Sargassum fusiforme in the Northwest Pacific

Understanding the evolutionary processes that have created diversity and the genetic potential of species to adapt to environmental change is an important premise for biodiversity conservation. Herein, we used mitochondrial trnW‐L and cox3 and plastid rbcL‐S data sets to analyze population genetic variation and phylogeographic history of the brown alga Sargassum fusiforme, whose natural resource has been largely exterminated in the Asia–Northwest Pacific in the past decades. Phylogenetic trees and network analysis consistently revealed three major haplotype groups (A, B, and C) in S. fusiforme, with A and B distributed in the Japan‐Pacific coast. Group C consisted of three subgroups (C1, C2, and C3) which were distributed in the Sea of Japan, the Yellow–Bohai Sea, and East China Sea, respectively. Isolation‐with‐migration (IMa) analysis revealed that the three groups diverged approximately during the mid‐Pleistocene (c. 756–1,224 ka). Extended Bayesian skyline plots (EBSP) showed that groups A and B underwent relatively long‐term stable population size despite a subsequent rapid demographic expansion, while subgroups C2 and C3 underwent a sudden expansion at c. 260 ka. F_ST and AMOVA detected low population‐level genetic variation and high degrees of divergence between groups. The cryptic diversity and phylogeographic patterns found in S. fusiforme not only are essential to understand how environmental shifts and evolutionary processes shaped diversity and distribution of coastal seaweeds but also provide additional insights for conserving and managing seaweed resources and facilitate predictions of their responses to future climate change and habitat loss.

Genetic diversity of the NE Atlantic sea urchin Strongylocentrotus droebachiensis unveils chaotic genetic patchiness possibly linked to local selective pressure

We compared the genetic differentiation in the green sea urchin Strongylocentrotus droebachiensis from discrete populations on the NE Atlantic coast. By using eight recently developed microsatellite markers, genetic structure was compared between populations from the Danish Strait in the south to the Barents Sea in the north (56-79°N). Urchins are spread by pelagic larvae and may be transported long distances by northwards-going ocean currents. Two main superimposed patterns were identified. The first showed a subtle but significant genetic differentiation from the southernmost to the northernmost of the studied populations and could be explained by an isolation by distance model. The second pattern included two coastal populations in mid-Norway (65°N), NH and NS, as well as the northernmost population of continental Norway (71°N) FV. They showed a high degree of differentiation from all other populations. The explanation to the second pattern is most likely chaotic genetic patchiness caused by introgression from another species, S. pallidus, into S. droebachiensis resulting from selective pressure. Ongoing sea urchin collapse and kelp forests recovery are observed in the area of NH, NS and FV populations. High gene flow between populations spanning more than 22° in latitude suggests a high risk of new grazing events to occur rapidly in the future if conditions for sea urchins are favourable. On the other hand, the possibility of hybridization in association with collapsing populations may be used as an early warning indicator for monitoring purposes.

Spatial and seasonal variations in the biofunctional lipid substances (fucoxanthin and fucosterol) of the laboratory-grown edible Japanese seaweed (Sargassum horneri Turner) cultured in the open sea

This work studied the effect of spatial and seasonal differences on the accumulation of functional lipid components in Sargassum horneri (Turner), an edible Japanese seaweed popularly called Akamoku. S. horneri obtained from Samenoura bay area of Japan was laboratory cultured to evaluate the effect of temperature on the accumulation of total lipids (TL), fucoxanthin (Fx) and fucosterol (Fs) by the alga. The laboratory cultured 3 month old S. horneri were cultured in the open sea in two different geographical locations off Usujiri and Matsushima to evaluate the monthly variations, over a year, in their TL, Fx and Fs contents. S. horneri grown off the Usujiri area accumulated the maximum TL close to 193 mg g^-1 dry weight during the coldest part of the year. Fx and Fs contributed 5.6% and 16.2% of the TL in S. horneri harvested off Usujiri in February. Further, in spite of being the same species and parent stock, S. horneri grown off the Matsushima area accumulated less TL, Fx and Fs as compared to their Usujiri counterparts. Our study clearly indicates the role of temperature and light apart from nutritional profile and depth of waters where the seaweed was grown on the accumulation of functional lipid components in S. horneri.

Phylogeographic structure and deep lineage diversification of the red alga Chondrus ocellatus Holmes in the Northwest Pacific

A major goal of phylogeographic analysis using molecular markers is to understand the ecological and historical variables that influence genetic diversity within a species. Here, we used sequences of the mitochondrial Cox1 gene and nuclear internal transcribed spacer to reconstruct its phylogeography and demographic history of the intertidal red seaweed Chondrus ocellatus over most of its geographical range in the Northwest Pacific. We found three deeply separated lineages A, B and C, which diverged from one another in the early Pliocene-late Miocene (c. 4.5-7.7 Ma). The remarkably deep divergences, both within and between lineages, appear to have resulted from ancient isolations, accelerated by random drift and limited genetic exchange between regions. The disjunct distributions of lineages A and C along the coasts of Japan may reflect divergence during isolation in scattered refugia. The distribution of lineage B, from the South China Sea to the Korean Peninsula, appears to reflect postglacial recolonizations of coastal habitats. These three lineages do not coincide with the three documented morphological formae in C. ocellatus, suggesting that additional cryptic species may exist in this taxon. Our study illustrates the interaction of environmental variability and demographic processes in producing lineage diversification in an intertidal seaweed and highlights the importance of phylogeographic approaches for discovering cryptic marine biodiversity.

Phylogeographic data revealed shallow genetic structure in the kelp Saccharina japonica (Laminariales, Phaeophyta)

BACKGROUND

Population structure and genetic diversity of marine organisms in the Northwestern Pacific Ocean exhibited complex patterns. Saccharina japonica is a commercially and ecologically important kelp species widely distributed along the coast of Japan Sea. However, it is still poorly known about population genetics and phylogeographic patterns of wild S. japonica populations on a large geographic scale, which is an important contribution to breeding and conservation of this marine crop.

RESULTS

We collected 612 mitochondrial COI and trnW-trnL sequences. Diversity indices suggested that S. japonica populations along the coast of Hokkaido exhibited the highest genetic diversity. Bayesian Analysis of Population Structure (BAPS) revealed four clusters in the kelp species (cluster 1: Hokkaido and South Korea; cluster 2: northwestern Hokkaido; cluster 3: Far Eastern Russia; cluster 4: China). The network inferred from concatenated data exhibited two shallow genealogies corresponding to two BAPS groups (cluster 2 and cluster 3). We did not detect gene flow between the two shallow genealogies, but populations within genealogy have asymmetric gene exchange. Bayesian skyline plots and neutrality tests suggested that S. japonica experienced postglacial expansion around 10.45 ka.

CONCLUSIONS

The coast of Hokkaido might be the origin and diversification center of S. japonica. Gene exchange among S. japonica populations could be caused by anthropogenic interference and oceanographic regimes. Postglacial expansions and gene exchange apparently led to more shared haplotypes and less differentiation that in turn led to the present shallow phylogeographical patterns in S. japonica.

Causations of phylogeographic barrier of some rocky shore species along the Chinese coastline

BACKGROUND

Substrate, ocean current and freshwater discharge are recognized as important factors that control the larval dispersal and recruitment of intertidal species. Life history traits of individual species will determine the differential responses to these physical factors, and hence resulting in contrasting phylogeography across the same biogeographic barrier. To determine how these factors affect genetic structure of rocky shore species along the China coast, a comparative phylogeographic study of four intertidal and subtidal species was conducted using mitochondrial and nuclear DNA by combining new sequences from Siphonaria japonica with previously published sequences from three species (Cellana toreuma, Sargassum horneri and Atrina pectinata).

RESULTS

Analysis of molecular variance and pairwise ΦST revealed significant genetic differences between the Yellow Sea (YS) and the other two marginal seas (East China Sea, ECS and South China Sea, SCS) for rocky-shore species (S. japonica, C. toreuma, S. horneri), but not for muddy-shore species Atrina pectinata. Demographic history analysis proved that the population size of all these four species were persistent though the Last Glacial Maximum (LGM, ~20 ka BP). Migration analysis revealed that gene flow differentiated northward and southward migration for these four species. However, the inferred direction of gene flow using alternatively mitochondrial or nuclear markers was contradictory in S. japonica.

CONCLUSIONS

It is concluded that there is a phylogeographical break at the Yangtze River estuary for the rocky shore species and the causation of the barrier is mainly due to the unsuitable substratum and freshwater discharge. All four intertidal and subtidal species appear to have persisted through the LGM in China, indicating the lower impact of LGM on intertidal and subtidal species than generally anticipated. The imbalanced gene flow between YS and ESCS groups for these four species could be explained by historical refugia. The discordance between mitochondrial and nuclear markers in the MIGRATE analysis of S. japonica prove the importance of employing multi-locus data in biogeographic study. Climate change, land reclamation and dam construction, which are changing substrate and hydrological conditions around Yangtze River estuary, will consequently affect the biogeographic pattern of intertidal species.

Possible change in distribution of seaweed, Sargassum horneri, in northeast Asia under A2 scenario of global warming and consequent effect on some fish

Global warming effects on seaweed beds are already perceptible. Their geographical distributions greatly depend on water temperatures. To predict future geographical distributions of brown alga, Sargassum horneri, forming large beds in the northwestern Pacific, we referred to future monthly surface water temperatures at about 1.1° of longitude and 0.6° of latitude in February and August in 2050 and 2100 simulated by 12 organizations under an A2 scenario of global warming. The southern limit of S. horneri distribution is expected to keep moving northward such that it may broadly disappear from Honshu Island, the Chinese coast, and Korean Peninsula in 2100, when tropical Sargassum species such as Sargassum tenuifolium may not completely replace S. horneri. Thus, their forests in 2100 do not substitute those of S. horneri in 2000. Fishes using the beds and seaweed rafts consisting of S. horneri in East China Sea suffer these disappearances.

Unusual distribution of floating seaweeds in the East China Sea in the early spring of 2012

Floating seaweeds play important ecological roles in offshore waters. Recently, large amounts of rafting seaweed have been observed in the East China Sea. In early spring, juveniles of commercially important fish such as yellowtail accompany these seaweed rafts. Because the spatial distributions of seaweed rafts in the spring are poorly understood, research cruises were undertaken to investigate them in 2010, 2011, and 2012. Floating seaweed samples collected from the East China Sea during the three surveys contained only Sargassum horneri. In 2010 and 2011, seaweed rafts were distributed only in the continental shelf and the Kuroshio Front because they had become trapped in the convergence zone of the Kuroshio Front. However, in 2012, seaweed was also distributed in the Kuroshio Current and its outer waters, and massive strandings of seaweed rafts were observed on the northern coast of Taiwan and on Tarama Island in the Ryukyu Archipelago. Environmental data (wind, currents, and sea surface height) were compared among the surveys of 2010, 2011, and 2012. Two factors are speculated to have caused the unusual distribution in 2012. First, a continuous strong north wind produced an Ekman drift current that transported seaweed southwestward to the continental shelf and eventually stranded seaweed rafts on the coast of Taiwan. Second, an anticyclonic eddy covering northeast Taiwan and the Kuroshio Current west of Taiwan generated a geostrophic current that crossed the Kuroshio Current and transported the rafts to the Kuroshio Current and its outer waters. Such unusual seaweed distributions may influence the distribution of fauna accompanying the rafts.

Homogeneous population of the brown alga Sargassum polycystum in Southeast Asia: possible role of recent expansion and asexual propagation

Southeast Asia has been known as one of the biodiversity hotspots in the world. Repeated glacial cycles during Pleistocene were believed to cause isolation of marine taxa in refugia, resulting in diversification among lineages. Recently, ocean current was also found to be another factor affecting gene flow by restricting larval dispersal in animals. Macroalgae are unique in having mode of reproduction that differs from that of animals. Our study on the phylogeographical pattern of the brown macroalga Sargassum polycystum using nuclear Internal Transcribed Spacer 2 (ITS2), plastidal RuBisCO spacer (Rub spacer) and mitochondrial cytochrome oxidase subunit-III (Cox3) as molecular markers revealed genetic homogeneity across 27 sites in Southeast Asia and western Pacific, in sharp contrast to that revealed from most animal studies. Our data suggested that S. polycystum persisted in single refugium during Pleistocene in a panmixia pattern. Expansion occurred more recently after the Last Glacial Maximum and recolonization of the newly flooded Sunda Shelf could have involved asexual propagation of the species. High dispersal ability through floating fronds carrying developing germlings may also contribute to the low genetic diversity of the species.

Population genetic structure and larval dispersal strategy of portunid crab Charybdis bimaculata in Yellow sea and East China sea

Larval dispersal may have an important effect on genetic structure of benthic species. However, different species may choose different larval dispersal strategy. To examine the population genetic structure and larval dispersal strategy of portunid crab Charybdis bimaculata, a 658 base pair (bp) fragment of mtDNA COI gene was sequenced in this species. In total, 67 individuals were collected from 5 locations in Yellow Sea and East China, and 24 haplotypes were obtained. Mean haplotype diversity and nucleotide diversity for the five populations ranged from 0.2000 ± 0.1541 (Zhoushan) to 0.8333 ± 0.1265 (Nanji island), and from 0.0003 ± 0.0005 (Zhoushan) to 0.0026 ± 0.0019 (Nanji island). Analysis of molecular variance and pairwise FST revealed no significant differentiation between the Yellow Sea and the East China Sea in C. bimaculata, supporting high larval dispersal ability in this species, rejecting larval retention. Mismatch distribution revealed that C. bimaculata had undergone population expansion. Larval drift in the ocean currents, and recent range expansion could be the reasons for little genetic structure in the studied area.

The impact of Yangtze River discharge, ocean currents and historical events on the biogeographic pattern of Cellana toreuma along the China coast

AIM

Genetic data were used to measure the phylogeographic distribution of the limpet, Cellana toreuma along the China coast in order to acsertain impacts of historic events, ocean currents and especially freshwater discharge from the Yangtze River on the connectivity of intertidal species with limited larval dispersal capability.

METHODOLOGY/PRINCIPAL FINDINGS

Genetic variation in 15 populations of C. toreuma (n = 418), ranging from the Yellow Sea (YS), East China Sea (ECS) and South China Sea (SCS), were determined from partial mitochondrial cytochrome c oxidase subunit I gene. Genetic diversity and divergence based on haplotype frequencies were analyzed using CONTRIB, and AMOVA was used to examine genetic population structure. Historic demographic expansions were evaluated from both neutrality tests and mismatch distribution tests. Among the 30 haplotypes identified, a dominant haplotype No. 1 (H1) existed in all the populations, and a relatively abundant private haplotype (H2) in YS. Pairwise F(ST) values between YS and the other two groups were relatively high and the percentage of variation among groups was 10.9%.

CONCLUSIONS

The high nucleotide and gene diversity in the YS, with large pairwise genetic distances and relatively high percentages of variation among groups, suggests that this group was relatively isolated from ECS and SCS. This is likely driven by historic events, ocean currents, and demographic expansion. We propose that freshwater discharge from the Yangtze River, which may act as physical barrier limiting the southward dispersal of larvae from northern populations, is especially important in determining the separation of the YS group from the rest of the Chinese populations of C. toreuma.