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The amphidromous goby Sicyopterus japonicus is distributed throughout southern Taiwan and Japan. Larvae of this freshwater fish go through a long marine stage. This migratory mode influences population genetic structure. We examined the genetic diversity, population differentiation, and demographic history of S. japonicus based on the mitochondrial...
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... Kuroshio Current is a strong, warm water mass flowing steadily northward along the east coast of Taiwan and beyond, past Okiwana, Japan. Along the west coast, there is also a persistent northward flow through the Taiwan Strait ( Figure 5). Along the coastline of Taiwan (spanning approximately 400 km), the Kuroshio Current flows from south to north at an average rate of 25 cm/s and can carry fish larvae over 3000 km. ...
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... High haplotype diversity and low nucleotide diversity can be attributed to a recent population expansion after a low effective population size caused by bottlenecks or founder events [83]. Large effective population size [84], environmental and habitat heterogeneity [85,86], broader distributional range, and inter-basin connectivity [28,32] have all been proposed as explanations for the maintenance of high diversity within populations. Glossogobius aureus is an amphidromous fish that spends its planktonic larval stage in marine environment and ascends to freshwater habitat to mature and reproduce. ...
The golden flathead goby Glossogobius aureus is a native species in the Philippines, Australia, Japan, Taiwan, and many other countries in Asia. In the Philippines, it is an important food fish as it is commonly caught in major lakes. In this study, a total of 307 specimens morphologically identified as G . aureus were sampled from nine major lakes in the Philippines and were sequenced for their mitochondrial cytochrome b ( cyt b ) gene. Two hundred sixty of the 307 cyt b sequences had sequence similarities of ≥ 99% with G . aureus reference sequence in GenBank, while the remaining 47 (all from Lake Lanao) had sequence similarities of only 95% and were thus designated as Glossogobius cf. aureus and treated as a separate population. The sequences were then analyzed to examine the pattern of genetic diversity, relatedness, divergence, and demographic history among native and translocated populations of the species. Twenty-nine haplotypes were recovered, of which four haplotypes were shared among three to seven populations. Only one haplotype each was found in the native population in Lake Buhi and translocated population in Lake Paoay. Low haplotype and low nucleotide diversities were found for the populations in Laguna de Bay, Lanao, Bato, Buhi, Paoay, and Sebu lakes, which indicate founder event for the introduced populations in Lanao, Paoay, and Sebu lakes and recent genetic bottleneck for the native populations in Laguna de Bay, Bato, and Buhi. In contrast, high haplotype but low nucleotide diversities were found for the native populations of Taal, Naujan, and Buluan lakes, signifying a recent bottleneck followed by population expansion. Pairwise F ST values showed generally large ( F ST = 0.168–0.249) to very large ( F ST = 0.302–1.000) genetic divergence between populations except between Laguna de Bay and Lake Bato, Laguna de Bay and Lake Buhi, and Lake Bato and Lake Buhi populations, which showed nonsignificant genetic differentiation. Lake Buluan and Lake Sebu populations showed moderate genetic differentiation ( F ST = 0.098). Neutrality tests showed significant negative Tajima’s D and Fu’s F S values only for the population from Laguna de Bay, which suggests that the population is undergoing expansion. These results are important for establishing scientifically sound strategies for effective conservation and sustainable exploitation of G . aureus in the Philippines.
... This hypothesis can explain why the genetic migration from Taiwan to Ryukyu was larger than that in the opposite direction. Dispersal between Taiwan and Ryukyu in this region of the Kuroshio Current was previously studied in other widespread marine-dispersed species, such as Sicyopterus japonicus [44]. Based on the AMOVA results, genetic differentiation within populations of M. japonicum from the two geographic regions (Taiwan + Ryukyu) accounted for 90.28% of the total genetic variation, but only 8.87% (F SC = 0.0093, p =0.105) of the variation among groups and 0.85% (F ST = 0.097, p < 0.001) of the variation among populations within groups (Table 2). ...
... Therefore, the pattern of phylogeographic structure observed in M. japonicum may indicate that both the life history of oceanic planktonic larvae and ocean currents are the most important factors facilitating the gene flow. A similar result was encountered in the related species distributed in the same region, Rhinogobius gigas [40] and S. japonicus [44], as well as in amphidromous representatives of goby, the other main family of freshwater fish. M. japonicum does not form a true panmictic population, as the Taiwan and Ryukyu populations are differentiated. ...
Oceanic currents, biological traits, and geological evidence from historical climate change have shaped the distribution of genetic diversity and demographic history in Macrobrachium japonicum. In this study, we investigated the phylogeographic structures and demographic history of M. japonicum in Taiwan and the Ryukyu Islands by the partial mitochondrial COI gene. The topology of the haplotype minimum-spanning network revealed a star-like structure, which suggested a recent range expansion. With the apparent lack of strong dispersal barriers to gene flow between ocean basins, amphidromous prawns, as marine organisms with larvae of high dispersal abilities, are generally expected to show genetic homogeneity. Divergence data suggested that M. japonicum populations diverged 0.462 ± 0.164 myr. Complex patterns of asymmetrical gene flow indicate that variation in dispersal ability is affected by the dominant Kuroshio Current systems of the Pacific Ocean. Analysis of its demographic history revealed that M. japonicum underwent a decline in size following a recent population expansion based on ABC analysis. Bayesian skyline plot analyses of all populations indicated that the expansion of M. japonicum was estimated to have occurred in 175 Kya and that the effective population size rapidly increased by approximately 50 Kya. The results of this study may offer both practical and theoretical value for the further study of conservation genetics, management, and sustainable resource utilization.
... Congruently, Sands et al. (2019) found that Chibanian divergences characterized the Ponto-Caspian neritid snail genus Theodoxus. Such demographic expansions stemming from Pleistocene sea-level oscillations have included fishes (Ludt et al., 2012;Ju et al., 2013), crabs (Pfeiler et al., 2005), mollusks (Kochzius and Nuryanto, 2008), crustaceans (Haig et al., 2010), and seaweeds (Albaina et al., 2012). ...
... The star-like pattern of the haplotype network also indicated a continuous population, which may reflect dispersal during the pelagic post-larval stage by the Deepwater Goby. Relatively high haplotype diversity and low nucleotide diversity were estimated across the entire sampled population area, which may denote environmental heterogeneity and a large population (Ju et al., 2013) that has recently expanded from a smaller population (Ludt et al., 2012). ...
The taxonomic status and phylogenetic relationships of the Deepwater Goby, Ponticola bathybius, an endemic species in the southern Caspian Sea, which were previously unknown, are examined here. Deepwater Goby samples were collected from three southern Caspian Sea localities (southwest, mid-south, and southeast), and phylogenetic analyses were conducted using mitochondrial cytochrome b (cyt b) and S7 nuclear gene sequences with maximum likelihood and Bayesian approaches. Additionally, the Deepwater Goby's population genetic structure and demographic history were evaluated for cyt b. Results were highly congruent, providing strong support for inclusion of the Deepwater Goby in the genus Neogobius (tribe: Neogobiini), from its previous placement in the genus Ponticola (tribe: Ponticolini). AMOVA analyses showed significant differences between western and eastern sampling localities (P < 0.05) of Deepwater Goby, with moderate FST (0.095) divergence. The haplotype network appeared star-like in formation, with no apparent genetic structure, indicating high connectivity and gene flow, and supporting a single continuous population. Since the Deepwater Goby exhibits low mobility after settlement, except for some migration between deeper and shallower waters, gene flow primarily occurs through spread of pre-settlement post-larvae via regional water currents. Mismatch distribution and neutrality tests both indicated that the Deepwater Goby likely underwent a recent demographic expansion in the southern Caspian Sea, estimated at ∼247 kya during the Pleistocene epoch, coinciding with similar expansions of other Caspian Sea taxa.
... DNA was purified by standard phenol:chloroform extraction and ethanol precipitation. DNA was subsequently re-suspended in 50 μL TE buffer (Ju et al., 2013). The forward primer used for PCR amplification was 3NDF (5′-GGCAAGTCTGGTGCCAG-3′) which was designed to amplify the variable V4 region of the 18S rRNA gene, and the reverse primer was V4_euk_R2 (5′-ACGGTATCT(AG)ATC(AG)TCTTCG-3′). ...
Orange-spotted grouper (Epinephelus coioides) is one of the most important aquaculture species in tropical and subtropical Asia. Traditionally, rotifer are fed to the larvae after they hatched. However, larval survival rate has been very low, and prey of suitable size during the first week after hatching is a major constraint. In this study, we raised grouper larvae by using an inorganic fertilization method to produce natural assemblages of phytoplankton and zooplankton, and compared it to a traditional rotifer-fed group. The results showed higher larval survival rate in inorganic fertilization group, albeit not significantly different due to high variation. Using next-generation sequencing to examine the fish stomach content from inorganic fertilization group, we found that copepods and choanoflagellates were actively consumed, whereas rotifers were not. The results imply that the inorganic fertilization method can produce desirable forage species for the grouper larvae, and it can be an alternative way in grouper larviculture worldwide.
... Sicyopterus japonicus Tanaka, 1909 and S. lagocephalus Pallas, 1770, for example, are two small amphidromous gobies with a long pelagic larval duration (PLD) of 133 to 266 days and distributed across ranges of c. 2400 and 18000 km, respectively (Shen and Tzeng 2002;Hoareau et al. 2007;McDowall 2007). The dispersal of the former is documented by genetic homogeneity across the distribution range (Watanabe et al. 2006;Ju et al. 2013), but the later shows high population structure across the Indo-Pacific Barrier (Lord et al. 2012). Narrowly endemic species, such as Sicyopterus aiensis Keith, Watson &Marquet, 2004 andS. ...
Rhinogobius formosanus Oshima, 1919 has long been considered an amphidromous goby. However, a landlocked population recently found in the Jingualiao Creek upstream of the Feitsui Reservoir in Taipei suggests that R. formosanus may complete its life in the river. This study aims to verify the habitat use of the landlocked population of R. formosanus collected from the Feitsui Reservoir and an amphidromous population collected in Malian Creek using otolith Sr:Ca ratio analysis. The hypothesis that early life history varies between the landlocked and migratory gobies was also tested. Genetic analyses show that the Feitsui Reservoir and Malian Creek populations are not genetically different. Rhinogobius formosanus from Malian Creek showed high-to-low otolith Sr:Ca ratios suggesting that these specimens spent a planktonic larval stage in the sea followed by a freshwater life at later stages. In contrast, R. formosanus from the Feitsui Reservoir showed constant lower otolith Sr:Ca ratios, implying a landlocked life history of fish in the creek upstream of the reservoir. In addition, the analysis of growth increments showed a longer pelagic larval duration for the fish in the Malian Creek (58.8 days) than those in the Feitsui Reservoir (38.8). Variation of pelagic larval duration in two genetically homogenous populations implies acclimatization to the reservoir by the landlocked gobies. This study shows that R. formosanus , like some other congeners, is capable of adapting to a freshwater landlocked environment in its early developmental stage and supports the hypothesis that landlocked populations may have a shorter pelagic larval duration.
... results of the population growth of coastal organisms during the late Pleistocene are similar to previous studies in the marginal seas of the Northwestern Pacific and coalescence times are consistent with population expansions associated with the LGM (e.g. Sicyopterus japonicus, see Ju et al. (2013); Lunella granulata, see Chiu et al. (2013); Scoliodon macrorhynchos, see Chen et al. (2018)). ...
To priority areas for conservation in the coast of Zhejiang, this study attempts to map the spatial patterns of the intra-specific genetic diversity of two intertidal species, Septifer virgatus and Tetraclita japonica, using the sequences of mitochondrial DNA cytochrome oxidase subunit I (COI) and large subunit ribosomal RNA (16S rRNA) genes. In total, 129 and 112 specimens were collected from 12 and 11 populations for S. virgatus and T. japonica, respectively. These two species revealed congruent population historical signals, including (1) high levels of haplotype diversity and low values of nucleotide diversity, (2) post-LGM expansion, (3) the lack of population genetic structure, sharing haplotypes over all sampling populations, (4) gene flow connections, and (5) migration directions. Largely, all results supported that all sampling populations could be divided into two main metapopulations, exhibiting a northern and southern distribution. The north metapopulation could be considered as a marine protected area. The genetic patterns of the two species should be considered in the management and conservation in the islands along the Zhejiang, China.
... Sicyopterus japonicus is an algae-grazing sicydiine gobiid found along the Pacific coast of Taiwan to Japan, and this gobiid species has a long oceanic dispersal range (2500-3000 km) due to an amphidromous life history that involves migration between freshwater streams and the ocean (e.g., Akihito et al., 2000;Iguchi et al., 2005;Shen and Tzeng, 2008;Iida et al., 2009Iida et al., , 2010Ju et al., 2013). After growing for several months in the ocean (e.g., approx. ...
An amphidromous sicydiine goby, Sicyopterus japonicus, exhibits rock-climbing behavior during upstream migration along rivers and streams. Using a pelvic sucker formed by fused pelvic fins, S. japonicus generates suction adhesion on the climbing surface. By measuring performance variables that correlate with successful rock-climbing capability, we evaluated scaling relationships of adhesive suction force generated by the pelvic sucker and fatigue during climbing in S. japonicus during ontogeny. In continuous climbing on the experimental 60°-inclined surface, the pelvic sucker of S. japonicus exhibited strong positive allometry in generating suction force for adhesion during ontogeny. In contrast, fatigue time of the pelvic sucker muscles for sustained adhesion scaled non-linearly with body mass during ontogeny. In addition, fatigue time and body mass showed the best fit to a quadratic regression, which predicted intermediate-sized individuals (large juveniles to small adults) to have better performance in adhesive endurance than smaller or larger individuals. Our experimental results indicate that different sizes of waterfall-climbing gobies have different performance capacities for rock climbing perhaps because of physiological differences in their pelvic muscles. In addition, our data from S. japonicus indicates that selection pressures on the locomotor capacities of waterfall-climbing gobiids vary during ontogeny.
... The Kuroshio Current originates in the westward-flowing North Equatorial Current of the central Pacific then deflects towards the northeast offshore of the Philippine Islands (Dou et al., 2012), and producing striking influence on biodiversity and genetic structure of marine species in the Northwestern Pacific (Yasuda et al., 2009;Nakajima et al., 2014). Along the coastline of Taiwan, the Kuroshio Current flows south to north at an average rate of 25 cm/s (Ju et al., 2013) (Zhang et al., 2014(Zhang et al., , 2016. Evidence for the occurrence of population expansion of O. oratoria in the Yellow Sea and East China Sea were confirmed by the mismatch distribution analyses and neutrality tests (Fig.3). ...
The mantis shrimp Oratosquilla oratoria is an ecologically and economically important species in the Western Pacific. In present study, the population genetic structure of Oratosquilla oratoria from the Yellow Sea and East China Sea was examined with mitochondrial DNA control region sequences. In total, 394 samples were collected from 18 locations and 102 haplotypes were obtained. For the Yellow Sea, the overall nucleotide diversity and haplotype diversity were 0.006 9 and 0.946 8, respectively; while across all the East China Sea locations, the overall nucleotide diversity and haplotype diversity were 0.027 94 and 0.979 0, respectively. The results of AMOVA and pairwise FST (0.145 2, P <0.001) revealed moderate differentiation between the Yellow Sea and East China Sea populations of O. oratoria. However, neither the neighbor-joining tree nor haplotype network showed clades with geographic pattern, which indicated considerable gene flow was existed between the Yellow Sea and East China Sea, and supporting the high larval dispersal ability in this species. Mismatch distribution analysis and neutrality tests suggested that O. oratoria has undergone population expansion event, and the Pleistocene glacial cycles might have an impact on the historical demography of O. oratoria. The genetic information obtained in this study can provide useful information for sustainable improvements for capture fisheries management strategies.
... Consistent with the result of cox1, the significant differentiation between the east and west groups was confirmed ( Figure 1(D,E)). Even between the populations on same side as FC and DH, the value of Fst for G. lacustris was obviously higher than that for Large yellow croaker (Larimichthys crocea) collected from the inshore of the same zone, or amphidromous goby (Sicyopterus japonicus) with planktonic eggs or larvae (Ju et al. 2013;Wang et al. 2014). Different from these two species, G. lacustris is a small, benthic fish and its eggs are 'bunched together by the filaments' (Blanco 1947), so its capacity to swim or float far distances may be limited like Round goby (LaRue et al. 2009). ...
In our recent survey, the transparent small Lacustrine goby, Gobiopterus lacustris had reported as the endemic species of Luzon, Philippines, was identified as an abundant species in mangroves of Leizhou Peninsula, China. Here, high diversity and significant differentiation of five sites of samples representing the west and east populations were revealed by mitochondrial DNA sequences. Five haplotypes of 56 cytochrome oxidase subunit I (Cox1) with the lengths of 623 base pairs (bp) have the high pairwise identity (>98.8%). Moreover, a total of 31 haplotypes for 129 partial D-loop regions were clustered into two clades corresponding to the east and west sampling sites. The strong population structure was confirmed (ΦST = 0.43017, p < .0001) with high haplotype diversity (h = 0.880 ± 0.017) and low nucleotide diversity (p=.00484). Moreover, both the mismatch distribution analysis and neutral test of D-loop revealed that the west group might experience a recent demographic expansion. Lastly, the isolation-with-migration analysis supported the expansion and indicated that the east–west split happened at approximately 7.1 kyr ago. Given the distribution and diversity, G. lacustris could be a good model for the study of the sea-level fluctuations and coast evolution of the South China Sea.
... software (Guindon and Gascuel, 2003; Darriba et al., 2012 ) and selected according to Akaike and Bayesian information criteria. The analyses were based on strict molecular clock used for the teleost D-loop region, with a substitution rate of 3.6% per million years (Donaldson and Wilson, 1999; Aboim et al., 2005; Ju et al., 2013). A total of 20 6 generations were run for each dataset to reach effective sample size (ESS) of at least 200. ...
... Therefore , COI sequences deposited in the GenBank database (accession numbers KT367889 and KT367966) will certainly contribute to minimize problems related to species identification, since these sequences became part of the universal identification system proposed by Hebert et al. (2003). Regarding the mtDNA D-loop, results showed moderate to high haplotype diversity (h) and low nucleotide diversity (π) when compared with other marine fishes (Aboim et al., 2005; Damasceno et al., 2015; Ju et al., 2013; Planes et al., 2001; Stepien et al., 2001; Santos et al., 2006). Furthermore, a significant genetic divergence between Tropical and Subtropical groups of C. faber in SW Atlantic was identified, suggesting a restriction to gene flow. ...
... Such severe climatic and sea level fluctuations during the late Pleistocene (Adams et al., 1999) have been suggested as strong influence in shaping patterns of genetic variability and the geographic distribution of marine fauna (Almada et al., 2001; Domingues et al., 2006 Domingues et al., , 2007a Domingues et al., , 2007b Santos et al., 2006; Stefanni et al., 2006 ). Genetic signatures of population expansion produced by environmental changes of the late Pleistocene have been worldwide documented for marine fishes such as Ocyurus chrysurus (25 kyr ago; Silva et al., 2015); Engraulis mordax (61kyr ago; DíazViloria et al., 2012), Sicyopterus japonicus (135 to 25 kyr ago; Ju et al., 2013) and Cephalopholis fulva (148 to 131 kyr ago; Souza et al., 2015). Concerning the Subtropical clade, several demographic analyses indicate that the population has experienced a size increase. ...
