Zi-Min Hu

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

Pleistocene glacial oscillations and associated tectonic processes are believed to have influenced the historical abundances and distribution of organisms in the Asia Northwest Pacific (ANP). Accumulating evidence indicates that factors shaping tempospatial population dynamics and distribution patterns of marine taxa vary with biogeographical latitude, pelagic behaviour and oceanographic regimes. To detect what kinds of historical and contemporary factors affected genetic connectivity, phylogeographic profiles of littoral macroalga Sargassum horneri in the ANP were analysed based on mitochondrial (Cox3) and chloroplast (rbcL) data sets. Five distinct clades were recovered. A strong signature of biogeographical structure was revealed (ΦCT = 0.487, P < 0.0001) derived from remarkable differentiation in clade distribution, as clade I is restricted to Chinese marginal seas (Yellow–Bohai Sea, East China Sea and South China Sea), whereas clades II–V are discontinuously scattered around the main Islands of Japan. Furthermore, two secondary contact regions were identified along the south Japan‐Pacific coastline. This significant differentiation between the two basins may reflect historical glacial isolation in the northwestern Pacific, which is congruent with the estimates of clade divergence and demographic expansion during the late Quaternary low sea levels. Analysis of molecular variance and the population‐pair statistic FST also revealed significant genetic structural differences between Chinese marginal seas and the Japanese basin. This exceptional phylogeographic architecture in S. horneri, initially shaped by historical geographic isolation during the late Pleistocene ice age and physical biogeographical barriers, can be complicated by oceanographic regimes (ocean surface currents) and relocating behaviour such as oceanic drifting.

Distribution, function and evolution characterization of microsatellite in Sargassum thunbergii (Fucales, Phaeophyta) transcriptome and their application in marker development.

Using transcriptome data to mine microsatellite and develop markers has growingly become prevalent. However, characterizing the possible function of microsatellite is relatively rare. In this study, we explored microsatellites in the transcriptome of the brown alga Sargassum thunbergii and characterized the frequencies, distribution, function and evolution, and developed primers to validate these microsatellites. Our results showed that Tri-nucleotide is the most abundant, followed by di- and mono-nucleotide. The length of microsatellite was significantly affected by the repeat motif size. The density of microsatellite in the CDS region is significantly lower than that in the UTR region. The annotation of the transcripts containing microsatellite showed that 573 transcripts have GO terms and can be categorized into 42 groups. Pathways enrichment showed that microsatellites were significantly overrepresented in the genes involved in pathways such as Ubiquitin mediated proteolysis, RNA degradation, Spliceosome, etc. Primers flanking 961 microsatellite loci were designed, and among the 30 pairs of primer selected randomly for availability test, 23 were proved to be efficient. These findings provided new insight into the function and evolution of microsatellite in transcriptome, and the identified microsatellite loci within the annotated gene will be useful for developing functional markers in S. thunbergii.

Adaptation mechanisms and ecological consequences of seaweed invasions: a review case of agarophyte Gracilaria vermiculophylla

To prioritize management, conservation and restoration from seaweed invasions, it is important for policy-makers to elucidate the ecological mechanisms during the three phases of invasion: introduction, establishment, and diffusion. In this review, we synthesize the current knowledge of the invasion mechanisms and ecological impacts of Gracilaria vermiculophylla, a red agarophyte native to Asia Northwest Pacific, which now has become a rapid and successful coastal invader in the Atlantic and Eastern Pacific Oceans. Eco-physiological and chemical studies have revealed that some ecological traits, including survival in dark condition (e.g. the ballast water), tolerance to grazing and extreme salinities and temperatures, insensitive to UVR and light intensity and nutrient levels, adaptation to a wide diversity of habitats, and chemical defense to potential predators, may provide G. vermiculophylla an unmatched advantage during its global invasion. The rapid growth, flexible reproduction through fragmentation, efficient recruitment on hard substratum, seeding success on various vectors, and interaction with local community organisms may also contribute to its rapid increase in abundance and effects on the invaded coastal ecosystems. G. vermiculophylla showed both negative and positive impacts to the marine ecosystems through changing interspecific competition, increasing habitat diversity, altering the community complex, and transforming biogeochemical cycles and estuarine food webs. Future surveys such as marine exotic genomics, transcriptome sequencing and epigenetic variation between native and invasive entities may provide insightful promise on molecular mechanisms of seaweed invasion.

Phylogeography of the Northern Atlantic species Chondrus crispus (Gigartinales, Rhodophyta) inferred from nuclear rDNA internal transcribed spacer sequences

Eighteen isolates of the red algae Chondrus crispus were collected from Northern Atlantic sites, together with C. ocellatus, C. yendoi and C. pinnulatus from the North Pacific. The nuclear rDNA internal transcribed spacer (ITS) was sequenced and compared, spanning both the ITS regions and the 5.8S rRNA gene. Percentage of nucleotide variation for C. crispus ranged from 0.3% to 4.0%. Phylogenetic analyses were performed using maximum parsimony (MP), neighbor-joining (NJ) and minimum evolution methods. They showed that two main clades existed within the C. crispus samples examined and that suggested C. crispus had a single Atlantic origin. The clustering however did not follow the geographic origin. We hypothesized that the current distribution of C. crispus populations might be a result of three main factors: temperature boundaries, paleoclimate and paleoceanography. ITS data exhibited abundant molecular information not only for phylogeographical investigation but also for systematics studies.

Identification of SCAR marker linking to longer frond length of Saccharina japonica (Laminariales, Phaeophyta) using bulked-segregant analysis

To construct a molecular-marker-assisted selection (MAS) system, research was done on identifying molecular markers linking to longer frond length, a crucial selection index in the breeding of the commercially important seaweed Saccharina japonica. An F2-segregant population of 92 individuals was obtained by crossing two prominent S. japonica strains. Genomic DNA from ten individuals with the longest frond and ten individuals with the shortest frond in the F2-segregant population were mixed to create two DNA pools for screening polymorphic markers. In bulked-segregant analysis (BSA), out of 100 random amplified polymorphic DNA (RAPD) primers only two produced three polymorphic RAPD markers between the two DNA pools. In conversion of the three RAPD markers into sequence-characterized amplified region (SCAR) markers, only one was successfully converted into a SCAR marker FL-569 linking to the trait of longer frond. Test of the marker FL-569 showed that 80% of the individuals with longest fronds in a wild population and 87.5% of individuals with the longest fronds in an inbred line “Zhongke No. 2” could be detected by FL-569. Additionally, genetic linkage analysis showed that the SCAR marker could be integrated into the reported genetic map and QTL mapping showed that FL-569 linking to qL1-1. The obtained marker FL-569 will be beneficial to MAS in S. japonica breeding.

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.

NrDNA internal transcribed spacer revealed molecular diversity in strains of red seaweed Porphyra yezoensis and genetic insights for commercial breeding

Unraveling the cryptic genetic diversity and selective breeding network in various Porphyra strains is of significance for conservation and utilization of economically important nori crops, for both current and future needs. Here, we used nuclear ribosomal spacer (ITS1) region to investigate the genetic variation and intra-specific relatedness of 59 Porphyra yezoensis Ueda specimens worldwide using phylogenetic and parsimony genealogical approaches. 23 nrDNA ITS1 genotypes were revealed and clustering analysis grouped them into two distinct clades. High genetic diversity was detected in wild P. yezoensis strains from Miyagi and Hokkaido Prefectures in Japan, while the cultivated strains from China and South Korea exhibited relatively higher genetic diversity likewise, which provided crucial genetic insights for future commercial breeding of P. yezoensis on a global scale. In addition, phylogenetic study has revealed the genetic relationship of strains with unknown parentage to those with known parentage, and also ITS1 sequence pattern could be correlated with the geographic origin of P. yezoensis specimens. All these pedigree information generated from this research can be used to select parents for inter-specific or intra-specific selective breeding and cross breeding to maximize the preservation of stock resource and sustainable development of nori industry.

Intertidal population genetic dynamics at a microgeographic seascape scale

The intertidal community is among the most physically harsh niches on earth, with highly heterogeneous environmental and biological factors that impose strong habitat selection on population abundance, genetic connectivity and ecological adaptation of organisms in nature. However, most genetic studies to date have concentrated on the influence of basin‐wide or regional marine environments (e.g. habitat discontinuities, oceanic currents and fronts, and geographic barriers) on spatiotemporal distribution and composition of intertidal invertebrates having planktonic stages or long‐distance dispersal capability. Little is known about sessile marine organisms (e.g. seaweeds) in the context of topographic tidal gradients and reproductive traits at the microgeographic scale. In this issue of Molecular Ecology, Krueger‐Hadfield et al. ( ) implemented an elaborate sampling strategy with red seaweed (Chondrus crispus) from a 90‐m transect stand near Roscoff and comprehensively detected genome‐scale genetic differentiation and biases in ploidy level. This study not only revealed that tidal height resulted in genetic differentiation between high‐ and low‐shore stands and restricted the genetic exchange within the high‐shore habitat, but also demonstrated that intergametophytic nonrandom fertilization in C. crispus can cause significant deviation from Hardy–Weinberg equilibrium. Such new genetic insights highlight the importance of microgeographic genetic dynamics and life history characteristics for better understanding the evolutionary processes of speciation and diversification of intertidal marine organisms.

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. FST 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.

Survival in Glacial Refugia Versus Postglacial Dispersal in the North Atlantic: The Cases of Red Seaweeds

The past two decades have witnessed the North Atlantic used as a model system to explore how climate changes and environmental conditions shaped the spatiotemporal distributions and biogeographic processes of intertidal seaweed species. The tectonic reconfigurations of the Northwestern and Northeastern Atlantic shores caused by the Quaternary ice ages allow us to examine two evolutionarily contrasting scenarios: survival in local glacial refugia versus postglacial trans-Atlantic dispersal. In this chapter, we collected comparative data from the red algae Chondrus crispus, Mastocarpus stellatus, Palmaria palmata, and Porphyra umbilicalis across the North Atlantic to illustrate the effects of paleoclimatic oscillations on historical demography, lineage divergence, and genetic connectivity. The genetic signals detected in C. crispus and P. palmata are consistent with the hypothesis that they survived in situ on each side of the North Atlantic during the Quaternary glaciations, while the phylogeographic evidence for M. stellatus and P. umbilicalis indicates postglacial trans-Atlantic dispersals. Bayesian coalescent analysis detected signals of demographic expansions in the four algal species, during the late Pliocene to the middle Pleistocene. In addition, the dated genetic splits between lineages were compatible with the expansion times for each species. In summary, our comparative analysis revealed contrasting biogeographic processes in these seaweeds despite their similar contemporary distributional ranges in the North Atlantic. These results also highlight the importance of comparative phylogeographic surveys in exploring dynamic evolutionary patterns and phylogeographic histories of intertidal marine organisms.