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

Verification of hotspots of genetic diversity in Korean population of Grateloupia asiatica and G. jejuensis (Rhodophyta) show low genetic diversity and similar geographic distribution

BACKGROUND

Understanding the genetic diversity and distribution patterns of seaweeds species is crucial for evaluating key regions of high genetic diversity. Identifying hotspots of high intraspecific diversity is an important step for developing conservation strategies. Grateloupia is a diverse genus of Rhodophyta, many of which are resource of numerous useful bioactive compounds; therefore, the genus is valuable target for conservation.

OBJECTIVE

The aim of this study is to examine the genetic diversity and population structure of two Grateloupia species, Grateloupia asiatica and Grateloupia jejuensis, with the understanding of the phylogeography of the Korean genetic diversity hotspot for two species.

METHODS

Plastid rbcL gene sequences of 134 specimens of G. asiatica and 112 specimens of G. jejuensis collected from the Korean coast were analyzed. We evaluated the number of haplotypes, genetic diversity (haplotype and nucleotide diversity), and haplotype networks of two species. Historical demographic was inferred by calculating neutrality tests and genetic differentiation was estimated using the fixation index, F_ST.

RESULTS

Our results show that both species are generally similar in geographical distribution patterns, that is, relatively homogeneous with few haplotypes derived from the most frequent haplotype. The east coast of Korea is identified as a 'hotspot' with the highest genetic diversity for both species, whereas Jeju Island is identified as a 'cold spot' with the lowest genetic diversity for G. jejuensis. Analyses across most distribution ranges of the two species in Korea reveal low genetic and haplotype diversities, which could indicate that these two Grateloupia species have either experienced a historical lack of diversity or a recent reduction in diversity due to high gene flow.

CONCLUSIONS

The low genetic diversity values found in the present study raise considerable concern about the conservation status of these two Grateloupia species and highlight the need to locate further hotspots of genetic diversity to strengthen their resilience against further decline.

Ecological, physiological, and biomechanical differences between gametophytes and sporophytes of Chondrus ocellatus (Gigartinales, Rhodophyta)1

Although variation among habitats in the ratio of gametophytes to sporophytes has been reported in various gigartinacean species, factors controlling the phase ratio remain poorly understood. Over 18 months, we examined the phase ratio of Chondrus ocellatus at three sites: a sheltered intertidal site, Hiruga A; an exposed intertidal site, Hiruga B; and a subtidal site, Shikimi. The mean proportion of gametophytes at Hiruga A (73.1%) was significantly higher than that at Shikimi (51.2%) and Hiruga B (44.7%). Due to a significantly higher water retention ability of the gametophytes, it was expected that the gametophytes would exhibit higher desiccation tolerance. After dehydration treatments, however, neither the photosynthetic rate of vegetative blades nor the survival rate of spores was significantly different between the phases. Measurements of blade strength indicated that the sporophytic blades were less stiff and more flexible, and a culture experiment revealed that the sporophytic germlings showed a significantly higher growth rate. Flexible blades and fast-growing germlings are considered advantageous for colonizing wave-swept intertidal habitats, so these properties may have caused the different fluctuation pattern of phase ratio among the sites. The present data demonstrate that biomechanical and physiological differences between the two phases of C. ocellatus make one phase advantageous in certain environmental conditions, and that these differences likely cause an unequal ratio of isomorphic phases.

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.

Nuclear microsatellites reveal population genetic structuring and fine-scale pattern of hybridization in the Japanese mantis shrimp Oratosquilla oratoria

The interplay between historical and contemporary processes can produce complex patterns of genetic differentiation in the marine realm. Recent mitochondrial and nuclear sequence analyses revealed cryptic speciation in the Japanese mantis shrimp Oratosquilla oratoria. Herein, we applied nuclear microsatellite markers to examine patterns and causes of genetic differentiation in this morphotaxon. Population structure analyses revealed two genetically divergent and geographically structured clades in O. oratoria, one dominating the temperate zone of the Northwestern (NW) Pacific and the other occurring in the subtropical and tropical waters where are influenced by the Kuroshio Current. Two sympatric zones, one around the Changjiang Estuary in China coast and the other in the northern Japan Sea, were demonstrated to be hybrid zones where introgressive hybridization occurred asymmetrically. The interaction between historical climate shifts and contemporary factors (e.g., freshwater discharge, temperature gradient and isolation by distance) may contribute to the present-day genetic architecture in the Japanese mantis shrimp. Range shift induced by climate changes and oceanographic factors may promote hybridization and gene flow between the O. oratoria complex. Our results provide insights into the interacting mechanisms that give rise to diversification and speciation of coastal species in the NW Pacific.

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.

Distribution and genetic diversity of the toxic benthic dinoflagellate genus Ostreopsis in Korea

Species belonging to the toxic dinoflagellate genus Ostreopsis are widespread, occurring from tropical to temperate waters. As mainly benthic/epiphytic species, they would be expected to show distinct geographical patterns. In this study, ribosomal DNA (rDNA) sequences from partial nuclear LSU D8-D10, 5.8S, and ITS regions were determined for 169 isolates of Ostreopsis species collected from three coastal sites (i.e., Jeju Island, Chuja Island, and Pohang) within Korea. The phylogenetic tree inferred from the LSU rDNA D8-D10 sequences showed that Korean Ostreopsis species corresponded to either Ostreopsis sp. 1 or sp. 6, with Ostreopsis sp. 1 being relatively predominant regarding their distribution. While Ostreopsis sp. 1 occurred throughout all the three sampling sites within Korea, Ostreopsis sp. 6 was confined to the northern part of Jeju Island. When further investigated, the genetic diversity of Ostreopsis sp. 1 in Korea based on ITS sequences showed a total of 21 haplotypes. The presumed ancestral haplotype H3, was also present in the Japanese and Russian populations of Ostreopsis sp. 1. Although the overall demographic history of all the Korean populations of Ostreopsis sp. 1 could not be clearly identified, probably due to a mixture of different regional demographic patterns within Korea, each Ostreopsis sp. 1 population showed a characteristic demographic pattern at a regional scale. While the Jeju Island Ostreopsis sp. 1 population showed a signal in agreement with population equilibrium, the Chuja Island and Pohang Ostreopsis sp. 1 populations showed distribution patterns that are expected in a sudden population expansion model. The results from this study provide a basis for a better understanding of the distribution and genetic structure of the Asian Ostreopsis sp. 1 populations.

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.

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.

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.

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.