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Genetic diversity and population structure of Nibea albiflora in the China Sea revealed by mitochondrial COI sequences
Biochemical Systematics and Ecology 45 (2012) 158–165
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Genetic diversity and population structure of Nibea albiflora in the China Sea revealed by mitochondrial COI sequences Dongdong Xu*, Bao Lou*, Huilai Shi, Zhi Geng, Sanlei Li, Yurong Zhang Marine Fishery Institute of Zhejiang Province, Key Lab of Mariculture and Enhancement of Zhejiang Province, Zhoushan 316100, Zhejiang Province, PR China
a r t i c l e i n f o
a b s t r a c t
Article history: Received 20 January 2012 Accepted 14 July 2012 Available online 24 August 2012
The genetic diversity and population genetic structure of Nibea albiflora were investigated using mitochondrial cytochrome c oxidase subunit I (COI) gene sequences. A total of 108 individuals from four localities around the China Sea were included in the analysis. Overall, 21 polymorphic sites were observed and 19 haplotypes were defined. The N. albiflora populations were characterized by medium/high haplotype diversity (0.580–0.815) and low nucleotide diversity (0.00125–0.00219). Analysis of neutral evolution and mismatch distribution implied that N. albiflora might have experienced a recent population expansion. Pairwise fixation index (Fst) analysis indicated significant genetic differentiation among populations from different localities. The hierarchical analysis of molecular variance (AMOVA) analysis also showed significant genetic divergence (4st ¼ 0.0233, P < 0.01) among these populations. The present results suggest that N. albiflora populations around the China Sea have developed significantly divergent genetic structures. This study provides new information for genetic assessment and will be crucial for establishing fisheries management and strategies for this species. Ó 2012 Elsevier Ltd. All rights reserved.
Keywords: Nibea albiflora Cytochrome c oxidase subunit I Genetic diversity Population structure
1. Introduction Nibea albiflora (family Sciaenidae) is a coastal fish species mainly distributed from the South China Sea to the coastal waters of Japan and Korea (Zhu et al., 1963; Takita, 1974). This species inhabits coastal waters with mud or sandy mud bottoms, and lays pelagic eggs in estuaries and coastal waters, with a spawning season occurs in the China Seas from early-April to late-May (Takita, 1974; Lei et al., 1981). N. albiflora is an economically important fisheries and aquaculture species in China. However, in recent years the wild resource of N. albiflora has sharply decreased because of overfishing and water pollution. The fishing grounds and season for N. albiflora have almost disappeared in many regions of the China Sea (Yu et al., 2010). The rational exploitation and proper resource management of fish species could be greatly enhanced by understanding the population structure of wild populations. The determination of fish populations is an important step towards establishing effective conservation strategies that can protect locally-adapted populations. The genetic variation in three wild populations of N. albiflora in the Yellow Sea and East China Sea has been examined previously using mitochondrial DNA (mtDNA) control region sequencing data. Results indicated no significant genetic differentiation among the three geographical populations (Han et al., 2008). However, the sample size and geographical diversity of the populations were limited. A much larger and more intensive survey is needed to clarify the population structure of N. albiflora around the China Sea. In addition to protein and nuclear DNA markers, mtDNA markers are extensively used to evaluate genetic diversity and population structure in marine organisms (Liu and Cordes, 2004; Avise, 2004). The high rate of mtDNA evolution, coupled
* Corresponding authors. Tel.: þ86 580 3080985; fax: þ86 580 3080417. E-mail addresses: [email protected] (D. Xu), [email protected] (B. Lou). 0305-1978/$ – see front matter Ó 2012 Elsevier Ltd. All rights reserved. http://dx.doi.org/10.1016/j.bse.2012.07.028
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with maternal inheritance, have made mtDNA an extremely useful genetic system for studying gene flow, hybrid zones, population structure, and other population-related questions (Avise et al., 1984). Among the most frequently used mitochondrial genes in detecting genetic analysis, the cytochrome c oxidase subunit I (COI) gene is easily amplified using polymerase chain reaction (PCR) method and conserved primers (Folmer et al., 1994). Variation in mtDNA COI gene sequence has been used for population studies in marine species such as shrimp (Croos and Palsson, 2010), crab (Azuma et al., 2008; Liu et al., 2009a) and fish (Yu et al., 2005; Habib et al., 2011; Sun et al., 2012). In the present study, we employed partial mtDNA COI gene sequences to assess the genetic diversity and intraspecific population differentiation of N. albiflora populations in the China Sea. This baseline information is critical for resource conversation and fisheries management for this species. 2. Materials and methods 2.1. Sample collection A total of 108 specimens of N. albiflora were collected from four locations in the coastal waters of the China Sea: Qingdao (QD), Zhoushan (ZS), Ningde (ND), and Zhuhai (ZH). Geographic locations and sample size are given in Fig. 1 and Table 1. All individuals were identified based on morphological characteristics, and muscle tissues samples were preserved in 95% ethanol and stored at 20 C until DNA extraction. 2.2. DNA extraction, PCR amplification and sequencing Genomic DNA was isolated from muscle tissue using DNA extraction kits (Tiangen, Beijing, China). The COI gene was PCR amplified using two primers COI-F (50 -CCTGCAGGAGGAGGAGAYCC-30 ) and COI-R (50 -AGTATAAGCGTCTGGGTAGTC-30 ) (Vrijenhoek, 1994; Sun et al., 2012). PCR amplification was performed in a reaction volume of 50 mL containing 29.6 mL highperformance liquid chromatography (HPLC) water, 1 PCR buffer, 0.2 mM dNTPs, 2 mM MgCl2, 0.2 mM of each primer, 2 units of Taq DNA polymerase, and 400 ng diluted DNA. The PCR reaction was performed as follows: an initial incubation at 94 C for 2 min, followed by 35 cycles of PCR denaturing at 94 C for 45 s, annealing at 52 C for 1 min, and extension at 72 C for 1 min, and a final extension at 72 C for 7 min. PCR products were gel-purified using an agarose gel DNA purification Kit (Tiangen) following with the manufacturer’s introductions. The purified fragments were sequenced on an ABI Prism 3730 automatic sequencer (Applied Biosystems, Foster City, CA, USA) using both forward and reverse primers. 2.3. Data analysis The COI gene sequences were edited and aligned by ClustalX 1.83 (Thompson et al., 1997). Nucleotide composition and variable sites were analyzed in MEGA 4.0 (Tamura et al., 2007). The genetic diversity indices of mtDNA such as the nucleotide diversity (p) (Lynch and Crease, 1990) and haplotype diversity (Hd) (Nei, 1987), were calculated using DnaSP 4.0 (Rozas et al., 2003). Genetic relationships among haplotypes were reconstructed using the neighbor-joining method implemented in MEGA 4.0 (Tamura et al., 2007). A bootstrap analysis with 1000 replicates was used to evaluate phylogenetic relationships. To depict phylogenetic and geographical relationships of the haplotypic sequences, a haplotype network was created with the median-joining method using Network 4.1 (Rohl, 2003). A hierarchical analysis of molecular variance (AMOVA) was performed to reveal the geographical structure of genetic variation using Arlequin 3.1 (Excoffier et al., 2005). The significance of the fixation index was tested by 1000 permutations of the data set. Demographic history of N. albiflora was examined by neutrality statistics of Tajima’s D test (Tajima, 1989), Fu’s Fs test (Fu, 1997), and mismatch distribution analysis implemented in Arlequin 3.1 (Excoffier et al., 2005). Tajima’s D and Fu’s Fs tests were carried out to examine deviations from neutrality, which would be expected with population expansion. Large negative D and Fs values were characteristic of population expansion. Mismatch distribution analysis was used to evaluate the frequency distribution of pairwise differences between sequences. A unimodal approximately Poisson-like distribution is expected for populations that have experienced demographic expansion in the recent past, while multimodal frequency distribution may be interpreted as evidence for populations at equilibrium (Stopar et al., 2010). The population expansion was further assessed by examining the fitness between the observed and expected frequency distribution with the Harpending raggedness index (Harpending, 1994) and sum of squared difference (SSD) statistics (Rogers and Harpending, 1992) implemented in Arlequin 3.1 (Excoffier et al., 2005). Significance was assessed with permutation tests under the null hypothesis that sudden population expansion cannot be rejected. 3. Results 3.1. Genetic diversity A 601 bp fragment of the 30 -end of the mitochondrial COI gene was amplified and sequenced from all the collected samples. The average base composition was as follows: T ¼ 22.1%, C ¼ 20.1%, A ¼ 29.9%, and G ¼ 27.8%. Amongst the 108 individuals there were 21 polymorphic sites, including 11 singleton variable sites and 10 parsimony-informative sites, and no
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Fig. 1. Map of sampling locations of N. albiflora along the coasts of the China Sea. The four sampling localities were Qingdao (QD), Zhoushan (ZS), Ningde (ND), Zhuhai (ZH).
insertions or deletions were observed in the examined sequences. Nineteen haplotypes were identified in the 108 samples. The number of haplotypes ranged from 6 to 11 for each sampled population. Genetic diversity indices (average standard deviation), haplotype diversity (Hd), and nucleotide diversity (p) are presented in Table 1. The mean haplotype diversity and nucleotide sequence diversity in the four populations were 0.697 0.00225 and 0.00172 0.000210, respectively. The Table 1 Sample localities, size and genetic diversity of N. albiflora populations based on COI sequence. Sample locality
Abbreviation
N
np
nh
Hd
Qingdao (120 380 N, 36 090 E) Zhoushan (122 300 N, 30 080 E) Ningde (120 600 N, 27 450 E) Zhuhai (22 270 N, 114 190 E) Total
QD ZS ND ZH
25 29 25 29 108
5 11 10 8 21
6 11 8 9 19
0.580 0.815 0.673 0.677 0.697
p (0.0115) (0.00426) (0.00927) (0.00733) (0.00225)
0.00125 0.00219 0.00187 0.00140 0.00172
(0.000310) (0.000350) (0.000580) (0.000260) (0.000210)
N, Sample size; nh, haplotype number; np, number of polymorphic sites; Hd, haplotype diversity; p, nucleotide diversity; and standard deviation (SD).
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haplotype diversity ranged from 0.580 0.0115 (QD) to 0.815 0.00426 (ZS), and nucleotide diversity ranged from 0.00125 0.000310 to 0.00219 0.000350. 3.2. Phylogenetic and network analyses The neighbor-joining (NJ) tree based on Kimura 2-Parameter distances was divided into two clusters. One cluster contained most of the individuals, while the second cluster contained eight individuals, none of which were from the QD populations (Fig. 2). To further depict the phylogenetic and geographical relationships among the identified sequences, haplotype networks were constructed using the median-joining method in Network 4.1 software (Fig. 3). The resultant network exhibited a star-like pattern surrounding haplotype H_1, which was the most common haplotype (53.7%) in all of the four sample regions. Haplotype H_2 was also shared by all the four sample regions, and accounted for 7.41% of all individuals. Four haplotypes (H_3, H_9, H_11, and H_13) were shared by three populations, while nine haplotypes were only found once and were restricted to a single population (Fig. 3). 3.3. Population structure analysis The AMOVA analysis based on haplotype frequencies revealed that 97.67% of the genetic variation occurred within populations, whereas 2.33% of the genetic variation occurred among populations (Table 2). The average 4st value was 0.0233 (P < 0.01), suggesting significant genetic variation among the four populations. Further evidence of population genetic structuring within the four localities was revealed by Fst analysis, which identified genetic structure between the sampled regions, especially between the QD and the ND populations (Fst ¼ 0.0509, P < 0.01), as well as between the QD and ZH populations (Fst ¼ 0.0403, P < 0.05) (Table 3). 3.4. Tests of neutrality and estimates of population expansion Tests for neutral evolution (Tajima’s D and Fu’s Fs tests) were performed to identify the presence of selective sweep or balancing selection in N. albiflora populations. Tajima’s D and Fu’s Fs tests resulted in negative values for all populations (Table 4), which indicated deviation from neutrality for the populations (P < 0.05). This finding is consistent with the scenario that fish from these locations have experienced population selection or expansion. The mismatch analysis yielded a unimodal distribution of pairwise differences for each samples and for the pooled samples (Fig. 4), further elucidating the demographic history of N. albiflora. The observed mismatch distributions did not deviate from the expected values based on the sudden expansion model. Values for raggedness statistic ranged from 0.103 to 0.184 and were not statistically significant (P > 0.05) (Table 4). These results suggested a significant fitness between the observed and expected distributions, and thereby also provided evidence for a recent expansion of N. albiflora populations.
Fig. 2. Neighbor-joining phylogenetic tree of the 108 individuals collected from four sampling localities.
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Fig. 3. Median-joining networks constructed for the COI haplotypes of N. albiflora populations in the China Sea. Each circle represents one unique haplotype, with the area being proportional to the frequency of the haplotype in the four populations.
4. Discussion We analyzed 601 bp of mtDNA COI gene in 108 N. albiflora individuals from four localities in the China Sea. The mtDNA COI sequence is polymorphic and 21 polymorphic sites and 19 haplotypes were detected amongst the 108 sequences. Overall, the mean haplotype diversity of the N. albiflora populations was medium/high (0.697 0.00225), while nucleotide diversity was low (0.00172 0.00021). This result is consistent with previous findings, which also reported high haplotypic diversity and low nucleotide diversity (h ¼ 0.9678 0.0102; p ¼ 0.0081 0.0046) among the N. albiflora populations in the Yellow Sea and East China Sea by mtDNA control region sequence analysis (Han et al., 2008). The extensive haplotype diversity could be attributable to the complex and variable nature of N. albiflora population distribution in China (Nei, 1987; Avise, 2004). The nucleotide diversity (p) is a sensitive index of the genetic diversity of a population (Nei and Li, 1979). The p values for N. albiflora in this study were lower than that reported for many other marine fishes. For example, Yu et al. (2005) found an average nucleotide diversity of p ¼ 0.0064 for Japanese anchovy (Engraulis japonicus) in the Yellow Sea and East China Sea, and Lynch et al. (2010) reported an average p of 0.0274 for Atlantic menhaden (Brevoortia tyrannus) along the U.S. Atlantic coast. Genetic diversity is influenced by many factors, including historical factors, anthropogenic activity, habitation and a low rate of mitochondrial evolution (Avise, 2004; Grant et al., 2006). Historical factors may play an important role in determining the patterns of genetic variability (Yamaguchi et al., 2010; Xiao et al., 2009). Populations of fishes that experienced rapid expansion following a period of low effective population size often display high haplotype but medium to low nucleotide diversities (Grant and Bowen, 1998). In this study, we performed Tajima’s D test, Fu’s Fs analysis for neutral evolution, and mismatch distribution analysis to examine the historical demographic expansions of N. albiflora. The resulting significantly negative values for Tajima’ D and Fu’s Fs tests and unimodal distribution of mismatched nucleotide frequency support the occurrence of a recent population expansion in N. albiflora (Haney et al., 2010). Moreover, the haplotype network was
Table 2 Analysis of molecular variance (AMOVA) for the COI sequences of N. albiflora. Source of variation
df
Sum of squares
Variance components
Percentage variation
4st
P
Among populations Within populations Total
3 104 107
2.504 52.801 55.306
0.0165 0.495 0.520
2.330 97.670
0.0233
0.005
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Table 3 Pairwise Fst values for COI sequences of N. albiflora.
QD ZS ND ZH a b
QD
ZS
ND
0.00272 0.0509b 0.0403a
0.0160 0.0138
0.0286
ZH
Significant at the 5% level. Significant at the 1% level.
Table 4 Statistical tests for neutrality, mismatch analysis and the estimate of demographic parameters for N. albiflora based on mitochondrial COI sequence data. Test
QD
ZS
ND
ZH
Total
Tajima’s D (P-value) Fu’s Fs (P-value)
1.23496 (0.082) 2.79794 (0.010) 0.844 0.00569 (0.450) 0.103 (0.445)
1.86942 (0.027) 6.89489 (0.001) 1.461 0.0127 (0.162) 0.119 (0.108)
1.89804 (0.009) 3.87596 (0.005) 0.986 0.0208 (0.105) 0.154 (0.101)
1.79585 (0.017) 6.39369 (0.001) 1.060 0.0225 (0.049) 0.184 (0.033)
2.18849 (0.001) 16.87900 (0.001) 1.088 0.0155 (0.192) 0.147 (0.160)
s SSD (P-value) Raggedness (P-value)
s, units of mutational time; SSD, sum of squared deviations; Raggedness, Harpending (1994) raggedness index.
characterized by a star-like phylogeny, a typical signature of a past recent population expansion following a population bottleneck (Avise, 2004). Another factor likely to be responsible for the low genetic diversity in N. albiflora is overexploitation, which is known to be one of the main causes of extinction of marine species (Rodrigues et al., 2008; Yu et al., 2010). Long-term overfishing has resulted in habitat degradation, which has a deleterious effect on N. albiflora by decreasing population levels and genetic diversity. Therefore, fisheries management strategies should be undertaken to protect this species and prevent the loss of genetic variation.
Fig. 4. Mismatch distribution of COI haplotypes in N. albiflora populations along the coasts of the China Sea. (a) Qingdao population; (b) Zhoushan population; (c) Ningde population; (d) Zhuhai population.
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N. albiflora has a long planktonic larval stage of more than a month. The pelagic larval stage may be susceptible to dispersal by water currents and can be expected to increase gene flow (Zhu et al., 1963; Takita, 1974; Lei et al., 1981). This may explain the genetic similarities among the sampled locations (Nei, 1987; Han et al., 2008). However, we detected significant genetic differentiation between QD and ND, and QD and ZH populations. Several causes, including geographic segregation, habitat differences, migration, and human activities, can be involved in determining a genetic population structure (Grant and Bowen, 1998). We hypothesized that the large distance between the sampled regions, physical barriers, and reproductive differences restricted the gene flow in these regions (Zhu et al., 1963; Ma et al., 2010). Unexpectedly, the pairwise Fst values between QD and ND were larger than those between QD and ZH. The ND sample was collected at the inner edge of the Gulf of Ningde (Fig. 1). The Gulf and islands around the region of Ningde seem to act as barriers to gene flow, which could result in high genetic divergence between the two populations. Nevertheless, the exact dispersal potential of N. albiflora in the waters of the Gulf of Ningde is unknown. This potential should be studied further to understand population structure of N. albiflora. A number of studies have focused on the population structure of fishes around the China Sea and adjacent ocean. The lack of significant population structure has been reported for Japanese anchovy (Yu et al., 2005), redlip mullet (Chelon haematocheilus) (Liu et al., 2007), and Japanese Spanish mackerel (Scomberomorus niphonius) (Shui et al., 2009), amongst others. In contrast, some marine fishes exhibit significant genetic structure, often attributed to the presence of geographic barriers or temporal reproductive isolation. These include Coilia ectenes (Ma et al., 2010) and Mugil cephalus (Liu et al., 2009b; Sun et al., 2012) around the China Sea. Zhao et al. (2011) also identified significant genetic differentiation in silver pomfret (Pampus argenteus) in the Southern Yellow and East China Seas. The data present here using mtDNA COI gene sequences identified low genetic diversity and significant genetic differentiation in N. albiflora from Chinese coastal waters. The low genetic diversity raised concerns over the conservation status of N. albiflora. The population structure implied that subdivisions exist in N. albiflora populations around the China Sea, and should be considered as different management units for further effective conservation and management purposes (Grant and Bowen, 1998; Liu et al., 2007). However, we examined only a portion of the entire genome in this study. The use of multiple genetic marker systems could increase the resolving power of genetic studies (Gruenthal et al., 2007). Further studies including nuclear markers are needed to extend and corroborate the present population structure findings to understand the comprehensive population structure in N. albiflora.
Acknowledgements This work was supported by grants from the Project of Zhejiang Province of China (Nos. 2009C12081 and 2010F20006).
References Avise, J.C., Neigel, J.E., Arnold, J., 1984. Demographic influences on mitochondrial DNA lineage survivorship in animal populations. Mol. Evol. 20, 99–105. Avise, J.C., 2004. Molecular Markers, Natural History, and Evolution, second ed. Sinauer Associates, Sunderland (Massachusetts), p. 684. Azuma, N., Kunihiro, Y., Sasaki, J., Mihara, E., Abe, Y.S., 2008. Genetic variation and population structure of hair crab (Erimacrus isenbeckii) in Japan inferred from mitochondrial DNA sequence analysis. Mar. Biotechnol. 10, 39–48. Croos, D.M., Palsson, S., 2010. Mitochondrial DNA variation and population genetic structure of white shrimp Fenneropenaeus indicus along the coastal belt of Sri Lanka. Aquat. Living Resour. 23, 315–323. Excoffier, L., Laval, G., Schneider, S., 2005. ARLEQUIN, version 3.0: an integrated software package for population genetics data analysis. Evol. Bioinform. 1, 47–50. Folmer, O., Black, M., Hoeh, W., Lutz, R., Vrijenhoek, R., 1994. DNA primers for amplification of mitochondrial cytochrome coxidase subunit I from diverse metazoan invertebrates. Mol. Mar. Biol. Biotechnol. 3, 294–299. Fu, Y.X., 1997. Statistical tests of neutrality of mutations against population growth, hitchhiking and background selection. Genetics 147, 915–925. Grant, W.S., Bowen, B.W., 1998. Shallow population histories in deep evolutionary lineages of marine fishes: insights from sardines and anchovies and lessons for conservation. J. Hered. 89, 415–426. Grant, W.S., Spies, I.B., Canino, M.F., 2006. Biogeographic evidence for selection on mitochondrial DNA in North Pacific Walleye Pollock Theragra chalcogramma. J. Hered. 97, 571–580. Gruenthal, K.M., Acheson, L.K., Burton, R.S., 2007. Genetic structure of natural populations of California red abalone (Haliotis rufescens) using multiple genetic markers. Mar. Biol. 152, 1237–1248. Habib, K.A., Jeong, D., Myoung, J.G., Kim, M.S., Jang, Y.S., Shim, J.S., Lee, Y.H., 2011. Population genetic structure and demographic history of the fat greenling Hexagrammos otakii. Genes Genom. 33, 413–423. Han, Z.Q., Gao, T.X., Yanagimoto, T., Sakurai, Y., 2008. Genetic population structure of Nibea albiflora in Yellow Sea and East China Sea. Fish. Sci. 74, 544–552. Haney, R.A., Silliman, B.R., Rand, D.M., 2010. Effects of selection and mutation on mitochondrial variation and inferences of historical population expansion in a Caribbean reef fish. Mol. Phylogenet. Evol. 57, 821–828. Harpending, H.C., 1994. Signature of ancient population growth in a low-resolution mitochondrial DNA mismatch distribution. Hum. Biol. 66, 591–600. Lei, J.L., Fan, N.C., Zheng, C.W., 1981. A preliminary observation on the morphological characteristics of embryos, larvae and juveniles of Nibea albiflora (Richardson). Mar. Fish. Res. 1, 77–84 (in Chinese with English abstract). Liu, Z.J., Cordes, J.F., 2004. DNA marker technologies and their applications in aquaculture genetics. Aquaculture 238, 1–37. Liu, J.X., Gao, T.X., Wu, S.F., Zhang, Y.P., 2007. Pleistocene isolation in the Northwestern Pacific marginal seas and limited dispersal in a marine fish, Chelon haematocheilus (Temminck & Schlegel, 1845). Mol. Ecol. 16, 275–288. Liu, Y., Liu, R.L., Ye, L.C., Liang, J., Xuan, F.J., Xu, Q.H., 2009a. Genetic differentiation between populations of swimming crab Portunus trituberculatus along the coastal waters of the East China Sea. Hydrobiologia 618, 125–137. Liu, J.Y., Brown, C.L., Yang, T.B., 2009b. Population genetic structure and historical demography of grey mullet, Mugil cephalus, along the coast of China, inferred by analysis of the mitochondrial control region. Biochem. Syst. Ecol. 12, 556–566. Lynch, M., Crease, T.J., 1990. The analysis of population survey data on DNA sequence variation. Mol. Biol. Evol. 7, 377–394. Lynch, A., Mcdowell, J., Graves, J., 2010. A molecular genetic investigation of the population structure of Atlantic rnenhaden (Brevoortia tyrannus). Fish. Bull. 108, 87–97.
D. Xu et al. / Biochemical Systematics and Ecology 45 (2012) 158–165
165
Ma, C.Q., Cheng, Q., Zhang, P., Zhuang, P., Zhao, Y., 2010. Genetic variation of Coilia ectenes (Clupeiformes: Engraulidae) revealed by the complete cytochrome b sequences of mitochondrial DNA. J. Exp. Mar Biol. Ecol. 385, 14–19. Nei, M., Li, W.H., 1979. Mathematical model for studying genetic variation in terms of restriction endonucleases. PNAS 76, 5269–5273. Nei, M., 1987. Molecular Evolutionary Genetics. Columbia University Press, New York, USA, pp. 10–88. Rodrigues, R., Schneider, H., Santos, S., Vallinoto, M., Sain-Paul, U., Sampaio, I., 2008. Low levels of genetic diversity depicted from mitochondrial DNA sequences in a heavily exploited marine fish (Cynoscion acoupa, Sciaenidae) from the Northern coast of Brazil. Genet. Mol. Biol. 31, 487–492. Rogers, A.R., Harpending, H., 1992. Population growth makes waves in the distribution of pairwise genetic differences. Mol. Biol. Evol. 9, 552–569. Rohl, A., 2003. Network: A Program Package for Calculating Phylogenetic Networks, Version 4.6. Fluxus Technology Ltd., Hamburg (Germany). Rozas, J., Sanchez-Delbarrio, J.C., Messeguer, X., Rozas, R., 2003. DnaSP, DNA polymorphism analyses by coalescent and other methods. Bioinformatics 19, 2496–2497. Shui, B.N., Han, Z.Q., Gao, T.X., Miao, Z.Q., Yanagimoto, T., 2009. Mitochondrial DNA variation in East China Sea and Yellow Sea populations of Japanese Spanish mackerel Scomberomorus nipbonius. Fish. Sci. 75, 593–600. Stopar, K., Ramsak, A., Trontelj, P., Malej, A., 2010. Lack of genetic structure in the jellyfish Pelagia noctiluca (Cnidaria: Scyphozoa: Semaeostomeae) across European seas. Mol. Phylogenet. Evol. 57, 417–428. Sun, P., Shi, Z.H., Yin, F., Peng, S.M., 2012. Genetic variation analysis of Mugil cephalus in China sea based on mitochondrial COⅠ gene sequences. Biochem. Genet. 50, 180–191. Tajima, F., 1989. Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123, 585–595. Takita, T., 1974. Studies on the early life history of Nibea albiflora (Richardson) in Ariake Sound. Bull. Fac. Fish. Nagasaki Univ. 38, 1–55. Tamura, K., Dudley, J., Nei, M., Kumar, S., 2007. MEGA4: molecular evolutionary genetics analysis (MEGA) software version 4.0. Mol. Boil. Evol. 24, 1596–1599. Thompson, J.D., Gibson, T.J., Plewniak, F., Jeanmougin, F., Higgins, D.G., 1997. The CLUSTAL-X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucl. Acids Res. 25, 4876–4882. Vrijenhoek, R., 1994. DNA primers for amplification of mitochondrial cytochrome c oxidase subunit I from diverse metazoan invertebrates. Mol. Biotechnol. 3, 294–299. Xiao, Y.S., Zhang, Y., Gao, T.X., Yanagimoto, T., Yabe, M., Sakurai, Y., 2009. Genetic diversity in the mitochondrial DNA control region and population structure in the small yellow croaker Larimichthys polyactis. Environ. Biol. Fish. 85, 303–314. Yamaguchi, K., Nakajima, M., Taniguchi, N., 2010. Loss of genetic variation and increased population differentiation in geographically peripheral populations of Japanese char Salvelinus leucomaenis. Aquaculture 308, S20–S27. Yu, Z.N., Kong, X.Y., Guo, T.H., Jiang, Y.Y., Zhuang, Z.M., Jin, X.S., 2005. Mitochondrial DNA sequence variation of Japanese anchovy Engraulis japonicus from the Yellow Sea and East China Sea. Fish. Sci. 71, 299–307. Yu, C., Chen, Q., Chen, X., Ning, P., Zheng, J., 2010. Species composition and quantitative distribution of fish in the Zhoushan fishing ground and its adjacent waters. Oceanol. Limnol. Sin. 41, 410–417 (In Chinese with English abstract). Zhao, F., Dong, Y., Zhuang, P., Zhang, T., Zhang, L., Shi, Z., 2011. Genetic diversity of silver pomfret (Pampus argenteus) in the Southern Yellow and East China Seas. Biochem. Syst. Ecol. 39, 145–150. Zhu, Y.D., Luo, Y.L., Wu, H.L., 1963. A Study on the Classification of the Sciaenoid Fishes of China, with Description of New Genera and Species. Shanghai Scientific and Technical Press, China.
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Genetic diversity and population structure of Nibea albiflora in the China Sea revealed by mitochondrial COI sequences Dongdong Xu*, Bao Lou*, Huilai Shi, Zhi Geng, Sanlei Li, Yurong Zhang Marine Fishery Institute of Zhejiang Province, Key Lab of Mariculture and Enhancement of Zhejiang Province, Zhoushan 316100, Zhejiang Province, PR China
a r t i c l e i n f o
a b s t r a c t
Article history: Received 20 January 2012 Accepted 14 July 2012 Available online 24 August 2012
The genetic diversity and population genetic structure of Nibea albiflora were investigated using mitochondrial cytochrome c oxidase subunit I (COI) gene sequences. A total of 108 individuals from four localities around the China Sea were included in the analysis. Overall, 21 polymorphic sites were observed and 19 haplotypes were defined. The N. albiflora populations were characterized by medium/high haplotype diversity (0.580–0.815) and low nucleotide diversity (0.00125–0.00219). Analysis of neutral evolution and mismatch distribution implied that N. albiflora might have experienced a recent population expansion. Pairwise fixation index (Fst) analysis indicated significant genetic differentiation among populations from different localities. The hierarchical analysis of molecular variance (AMOVA) analysis also showed significant genetic divergence (4st ¼ 0.0233, P < 0.01) among these populations. The present results suggest that N. albiflora populations around the China Sea have developed significantly divergent genetic structures. This study provides new information for genetic assessment and will be crucial for establishing fisheries management and strategies for this species. Ó 2012 Elsevier Ltd. All rights reserved.
Keywords: Nibea albiflora Cytochrome c oxidase subunit I Genetic diversity Population structure
1. Introduction Nibea albiflora (family Sciaenidae) is a coastal fish species mainly distributed from the South China Sea to the coastal waters of Japan and Korea (Zhu et al., 1963; Takita, 1974). This species inhabits coastal waters with mud or sandy mud bottoms, and lays pelagic eggs in estuaries and coastal waters, with a spawning season occurs in the China Seas from early-April to late-May (Takita, 1974; Lei et al., 1981). N. albiflora is an economically important fisheries and aquaculture species in China. However, in recent years the wild resource of N. albiflora has sharply decreased because of overfishing and water pollution. The fishing grounds and season for N. albiflora have almost disappeared in many regions of the China Sea (Yu et al., 2010). The rational exploitation and proper resource management of fish species could be greatly enhanced by understanding the population structure of wild populations. The determination of fish populations is an important step towards establishing effective conservation strategies that can protect locally-adapted populations. The genetic variation in three wild populations of N. albiflora in the Yellow Sea and East China Sea has been examined previously using mitochondrial DNA (mtDNA) control region sequencing data. Results indicated no significant genetic differentiation among the three geographical populations (Han et al., 2008). However, the sample size and geographical diversity of the populations were limited. A much larger and more intensive survey is needed to clarify the population structure of N. albiflora around the China Sea. In addition to protein and nuclear DNA markers, mtDNA markers are extensively used to evaluate genetic diversity and population structure in marine organisms (Liu and Cordes, 2004; Avise, 2004). The high rate of mtDNA evolution, coupled
* Corresponding authors. Tel.: þ86 580 3080985; fax: þ86 580 3080417. E-mail addresses: [email protected] (D. Xu), [email protected] (B. Lou). 0305-1978/$ – see front matter Ó 2012 Elsevier Ltd. All rights reserved. http://dx.doi.org/10.1016/j.bse.2012.07.028
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with maternal inheritance, have made mtDNA an extremely useful genetic system for studying gene flow, hybrid zones, population structure, and other population-related questions (Avise et al., 1984). Among the most frequently used mitochondrial genes in detecting genetic analysis, the cytochrome c oxidase subunit I (COI) gene is easily amplified using polymerase chain reaction (PCR) method and conserved primers (Folmer et al., 1994). Variation in mtDNA COI gene sequence has been used for population studies in marine species such as shrimp (Croos and Palsson, 2010), crab (Azuma et al., 2008; Liu et al., 2009a) and fish (Yu et al., 2005; Habib et al., 2011; Sun et al., 2012). In the present study, we employed partial mtDNA COI gene sequences to assess the genetic diversity and intraspecific population differentiation of N. albiflora populations in the China Sea. This baseline information is critical for resource conversation and fisheries management for this species. 2. Materials and methods 2.1. Sample collection A total of 108 specimens of N. albiflora were collected from four locations in the coastal waters of the China Sea: Qingdao (QD), Zhoushan (ZS), Ningde (ND), and Zhuhai (ZH). Geographic locations and sample size are given in Fig. 1 and Table 1. All individuals were identified based on morphological characteristics, and muscle tissues samples were preserved in 95% ethanol and stored at 20 C until DNA extraction. 2.2. DNA extraction, PCR amplification and sequencing Genomic DNA was isolated from muscle tissue using DNA extraction kits (Tiangen, Beijing, China). The COI gene was PCR amplified using two primers COI-F (50 -CCTGCAGGAGGAGGAGAYCC-30 ) and COI-R (50 -AGTATAAGCGTCTGGGTAGTC-30 ) (Vrijenhoek, 1994; Sun et al., 2012). PCR amplification was performed in a reaction volume of 50 mL containing 29.6 mL highperformance liquid chromatography (HPLC) water, 1 PCR buffer, 0.2 mM dNTPs, 2 mM MgCl2, 0.2 mM of each primer, 2 units of Taq DNA polymerase, and 400 ng diluted DNA. The PCR reaction was performed as follows: an initial incubation at 94 C for 2 min, followed by 35 cycles of PCR denaturing at 94 C for 45 s, annealing at 52 C for 1 min, and extension at 72 C for 1 min, and a final extension at 72 C for 7 min. PCR products were gel-purified using an agarose gel DNA purification Kit (Tiangen) following with the manufacturer’s introductions. The purified fragments were sequenced on an ABI Prism 3730 automatic sequencer (Applied Biosystems, Foster City, CA, USA) using both forward and reverse primers. 2.3. Data analysis The COI gene sequences were edited and aligned by ClustalX 1.83 (Thompson et al., 1997). Nucleotide composition and variable sites were analyzed in MEGA 4.0 (Tamura et al., 2007). The genetic diversity indices of mtDNA such as the nucleotide diversity (p) (Lynch and Crease, 1990) and haplotype diversity (Hd) (Nei, 1987), were calculated using DnaSP 4.0 (Rozas et al., 2003). Genetic relationships among haplotypes were reconstructed using the neighbor-joining method implemented in MEGA 4.0 (Tamura et al., 2007). A bootstrap analysis with 1000 replicates was used to evaluate phylogenetic relationships. To depict phylogenetic and geographical relationships of the haplotypic sequences, a haplotype network was created with the median-joining method using Network 4.1 (Rohl, 2003). A hierarchical analysis of molecular variance (AMOVA) was performed to reveal the geographical structure of genetic variation using Arlequin 3.1 (Excoffier et al., 2005). The significance of the fixation index was tested by 1000 permutations of the data set. Demographic history of N. albiflora was examined by neutrality statistics of Tajima’s D test (Tajima, 1989), Fu’s Fs test (Fu, 1997), and mismatch distribution analysis implemented in Arlequin 3.1 (Excoffier et al., 2005). Tajima’s D and Fu’s Fs tests were carried out to examine deviations from neutrality, which would be expected with population expansion. Large negative D and Fs values were characteristic of population expansion. Mismatch distribution analysis was used to evaluate the frequency distribution of pairwise differences between sequences. A unimodal approximately Poisson-like distribution is expected for populations that have experienced demographic expansion in the recent past, while multimodal frequency distribution may be interpreted as evidence for populations at equilibrium (Stopar et al., 2010). The population expansion was further assessed by examining the fitness between the observed and expected frequency distribution with the Harpending raggedness index (Harpending, 1994) and sum of squared difference (SSD) statistics (Rogers and Harpending, 1992) implemented in Arlequin 3.1 (Excoffier et al., 2005). Significance was assessed with permutation tests under the null hypothesis that sudden population expansion cannot be rejected. 3. Results 3.1. Genetic diversity A 601 bp fragment of the 30 -end of the mitochondrial COI gene was amplified and sequenced from all the collected samples. The average base composition was as follows: T ¼ 22.1%, C ¼ 20.1%, A ¼ 29.9%, and G ¼ 27.8%. Amongst the 108 individuals there were 21 polymorphic sites, including 11 singleton variable sites and 10 parsimony-informative sites, and no
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Fig. 1. Map of sampling locations of N. albiflora along the coasts of the China Sea. The four sampling localities were Qingdao (QD), Zhoushan (ZS), Ningde (ND), Zhuhai (ZH).
insertions or deletions were observed in the examined sequences. Nineteen haplotypes were identified in the 108 samples. The number of haplotypes ranged from 6 to 11 for each sampled population. Genetic diversity indices (average standard deviation), haplotype diversity (Hd), and nucleotide diversity (p) are presented in Table 1. The mean haplotype diversity and nucleotide sequence diversity in the four populations were 0.697 0.00225 and 0.00172 0.000210, respectively. The Table 1 Sample localities, size and genetic diversity of N. albiflora populations based on COI sequence. Sample locality
Abbreviation
N
np
nh
Hd
Qingdao (120 380 N, 36 090 E) Zhoushan (122 300 N, 30 080 E) Ningde (120 600 N, 27 450 E) Zhuhai (22 270 N, 114 190 E) Total
QD ZS ND ZH
25 29 25 29 108
5 11 10 8 21
6 11 8 9 19
0.580 0.815 0.673 0.677 0.697
p (0.0115) (0.00426) (0.00927) (0.00733) (0.00225)
0.00125 0.00219 0.00187 0.00140 0.00172
(0.000310) (0.000350) (0.000580) (0.000260) (0.000210)
N, Sample size; nh, haplotype number; np, number of polymorphic sites; Hd, haplotype diversity; p, nucleotide diversity; and standard deviation (SD).
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haplotype diversity ranged from 0.580 0.0115 (QD) to 0.815 0.00426 (ZS), and nucleotide diversity ranged from 0.00125 0.000310 to 0.00219 0.000350. 3.2. Phylogenetic and network analyses The neighbor-joining (NJ) tree based on Kimura 2-Parameter distances was divided into two clusters. One cluster contained most of the individuals, while the second cluster contained eight individuals, none of which were from the QD populations (Fig. 2). To further depict the phylogenetic and geographical relationships among the identified sequences, haplotype networks were constructed using the median-joining method in Network 4.1 software (Fig. 3). The resultant network exhibited a star-like pattern surrounding haplotype H_1, which was the most common haplotype (53.7%) in all of the four sample regions. Haplotype H_2 was also shared by all the four sample regions, and accounted for 7.41% of all individuals. Four haplotypes (H_3, H_9, H_11, and H_13) were shared by three populations, while nine haplotypes were only found once and were restricted to a single population (Fig. 3). 3.3. Population structure analysis The AMOVA analysis based on haplotype frequencies revealed that 97.67% of the genetic variation occurred within populations, whereas 2.33% of the genetic variation occurred among populations (Table 2). The average 4st value was 0.0233 (P < 0.01), suggesting significant genetic variation among the four populations. Further evidence of population genetic structuring within the four localities was revealed by Fst analysis, which identified genetic structure between the sampled regions, especially between the QD and the ND populations (Fst ¼ 0.0509, P < 0.01), as well as between the QD and ZH populations (Fst ¼ 0.0403, P < 0.05) (Table 3). 3.4. Tests of neutrality and estimates of population expansion Tests for neutral evolution (Tajima’s D and Fu’s Fs tests) were performed to identify the presence of selective sweep or balancing selection in N. albiflora populations. Tajima’s D and Fu’s Fs tests resulted in negative values for all populations (Table 4), which indicated deviation from neutrality for the populations (P < 0.05). This finding is consistent with the scenario that fish from these locations have experienced population selection or expansion. The mismatch analysis yielded a unimodal distribution of pairwise differences for each samples and for the pooled samples (Fig. 4), further elucidating the demographic history of N. albiflora. The observed mismatch distributions did not deviate from the expected values based on the sudden expansion model. Values for raggedness statistic ranged from 0.103 to 0.184 and were not statistically significant (P > 0.05) (Table 4). These results suggested a significant fitness between the observed and expected distributions, and thereby also provided evidence for a recent expansion of N. albiflora populations.
Fig. 2. Neighbor-joining phylogenetic tree of the 108 individuals collected from four sampling localities.
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Fig. 3. Median-joining networks constructed for the COI haplotypes of N. albiflora populations in the China Sea. Each circle represents one unique haplotype, with the area being proportional to the frequency of the haplotype in the four populations.
4. Discussion We analyzed 601 bp of mtDNA COI gene in 108 N. albiflora individuals from four localities in the China Sea. The mtDNA COI sequence is polymorphic and 21 polymorphic sites and 19 haplotypes were detected amongst the 108 sequences. Overall, the mean haplotype diversity of the N. albiflora populations was medium/high (0.697 0.00225), while nucleotide diversity was low (0.00172 0.00021). This result is consistent with previous findings, which also reported high haplotypic diversity and low nucleotide diversity (h ¼ 0.9678 0.0102; p ¼ 0.0081 0.0046) among the N. albiflora populations in the Yellow Sea and East China Sea by mtDNA control region sequence analysis (Han et al., 2008). The extensive haplotype diversity could be attributable to the complex and variable nature of N. albiflora population distribution in China (Nei, 1987; Avise, 2004). The nucleotide diversity (p) is a sensitive index of the genetic diversity of a population (Nei and Li, 1979). The p values for N. albiflora in this study were lower than that reported for many other marine fishes. For example, Yu et al. (2005) found an average nucleotide diversity of p ¼ 0.0064 for Japanese anchovy (Engraulis japonicus) in the Yellow Sea and East China Sea, and Lynch et al. (2010) reported an average p of 0.0274 for Atlantic menhaden (Brevoortia tyrannus) along the U.S. Atlantic coast. Genetic diversity is influenced by many factors, including historical factors, anthropogenic activity, habitation and a low rate of mitochondrial evolution (Avise, 2004; Grant et al., 2006). Historical factors may play an important role in determining the patterns of genetic variability (Yamaguchi et al., 2010; Xiao et al., 2009). Populations of fishes that experienced rapid expansion following a period of low effective population size often display high haplotype but medium to low nucleotide diversities (Grant and Bowen, 1998). In this study, we performed Tajima’s D test, Fu’s Fs analysis for neutral evolution, and mismatch distribution analysis to examine the historical demographic expansions of N. albiflora. The resulting significantly negative values for Tajima’ D and Fu’s Fs tests and unimodal distribution of mismatched nucleotide frequency support the occurrence of a recent population expansion in N. albiflora (Haney et al., 2010). Moreover, the haplotype network was
Table 2 Analysis of molecular variance (AMOVA) for the COI sequences of N. albiflora. Source of variation
df
Sum of squares
Variance components
Percentage variation
4st
P
Among populations Within populations Total
3 104 107
2.504 52.801 55.306
0.0165 0.495 0.520
2.330 97.670
0.0233
0.005
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Table 3 Pairwise Fst values for COI sequences of N. albiflora.
QD ZS ND ZH a b
QD
ZS
ND
0.00272 0.0509b 0.0403a
0.0160 0.0138
0.0286
ZH
Significant at the 5% level. Significant at the 1% level.
Table 4 Statistical tests for neutrality, mismatch analysis and the estimate of demographic parameters for N. albiflora based on mitochondrial COI sequence data. Test
QD
ZS
ND
ZH
Total
Tajima’s D (P-value) Fu’s Fs (P-value)
1.23496 (0.082) 2.79794 (0.010) 0.844 0.00569 (0.450) 0.103 (0.445)
1.86942 (0.027) 6.89489 (0.001) 1.461 0.0127 (0.162) 0.119 (0.108)
1.89804 (0.009) 3.87596 (0.005) 0.986 0.0208 (0.105) 0.154 (0.101)
1.79585 (0.017) 6.39369 (0.001) 1.060 0.0225 (0.049) 0.184 (0.033)
2.18849 (0.001) 16.87900 (0.001) 1.088 0.0155 (0.192) 0.147 (0.160)
s SSD (P-value) Raggedness (P-value)
s, units of mutational time; SSD, sum of squared deviations; Raggedness, Harpending (1994) raggedness index.
characterized by a star-like phylogeny, a typical signature of a past recent population expansion following a population bottleneck (Avise, 2004). Another factor likely to be responsible for the low genetic diversity in N. albiflora is overexploitation, which is known to be one of the main causes of extinction of marine species (Rodrigues et al., 2008; Yu et al., 2010). Long-term overfishing has resulted in habitat degradation, which has a deleterious effect on N. albiflora by decreasing population levels and genetic diversity. Therefore, fisheries management strategies should be undertaken to protect this species and prevent the loss of genetic variation.
Fig. 4. Mismatch distribution of COI haplotypes in N. albiflora populations along the coasts of the China Sea. (a) Qingdao population; (b) Zhoushan population; (c) Ningde population; (d) Zhuhai population.
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N. albiflora has a long planktonic larval stage of more than a month. The pelagic larval stage may be susceptible to dispersal by water currents and can be expected to increase gene flow (Zhu et al., 1963; Takita, 1974; Lei et al., 1981). This may explain the genetic similarities among the sampled locations (Nei, 1987; Han et al., 2008). However, we detected significant genetic differentiation between QD and ND, and QD and ZH populations. Several causes, including geographic segregation, habitat differences, migration, and human activities, can be involved in determining a genetic population structure (Grant and Bowen, 1998). We hypothesized that the large distance between the sampled regions, physical barriers, and reproductive differences restricted the gene flow in these regions (Zhu et al., 1963; Ma et al., 2010). Unexpectedly, the pairwise Fst values between QD and ND were larger than those between QD and ZH. The ND sample was collected at the inner edge of the Gulf of Ningde (Fig. 1). The Gulf and islands around the region of Ningde seem to act as barriers to gene flow, which could result in high genetic divergence between the two populations. Nevertheless, the exact dispersal potential of N. albiflora in the waters of the Gulf of Ningde is unknown. This potential should be studied further to understand population structure of N. albiflora. A number of studies have focused on the population structure of fishes around the China Sea and adjacent ocean. The lack of significant population structure has been reported for Japanese anchovy (Yu et al., 2005), redlip mullet (Chelon haematocheilus) (Liu et al., 2007), and Japanese Spanish mackerel (Scomberomorus niphonius) (Shui et al., 2009), amongst others. In contrast, some marine fishes exhibit significant genetic structure, often attributed to the presence of geographic barriers or temporal reproductive isolation. These include Coilia ectenes (Ma et al., 2010) and Mugil cephalus (Liu et al., 2009b; Sun et al., 2012) around the China Sea. Zhao et al. (2011) also identified significant genetic differentiation in silver pomfret (Pampus argenteus) in the Southern Yellow and East China Seas. The data present here using mtDNA COI gene sequences identified low genetic diversity and significant genetic differentiation in N. albiflora from Chinese coastal waters. The low genetic diversity raised concerns over the conservation status of N. albiflora. The population structure implied that subdivisions exist in N. albiflora populations around the China Sea, and should be considered as different management units for further effective conservation and management purposes (Grant and Bowen, 1998; Liu et al., 2007). However, we examined only a portion of the entire genome in this study. The use of multiple genetic marker systems could increase the resolving power of genetic studies (Gruenthal et al., 2007). Further studies including nuclear markers are needed to extend and corroborate the present population structure findings to understand the comprehensive population structure in N. albiflora.
Acknowledgements This work was supported by grants from the Project of Zhejiang Province of China (Nos. 2009C12081 and 2010F20006).
References Avise, J.C., Neigel, J.E., Arnold, J., 1984. Demographic influences on mitochondrial DNA lineage survivorship in animal populations. Mol. Evol. 20, 99–105. Avise, J.C., 2004. Molecular Markers, Natural History, and Evolution, second ed. Sinauer Associates, Sunderland (Massachusetts), p. 684. Azuma, N., Kunihiro, Y., Sasaki, J., Mihara, E., Abe, Y.S., 2008. Genetic variation and population structure of hair crab (Erimacrus isenbeckii) in Japan inferred from mitochondrial DNA sequence analysis. Mar. Biotechnol. 10, 39–48. Croos, D.M., Palsson, S., 2010. Mitochondrial DNA variation and population genetic structure of white shrimp Fenneropenaeus indicus along the coastal belt of Sri Lanka. Aquat. Living Resour. 23, 315–323. Excoffier, L., Laval, G., Schneider, S., 2005. ARLEQUIN, version 3.0: an integrated software package for population genetics data analysis. Evol. Bioinform. 1, 47–50. Folmer, O., Black, M., Hoeh, W., Lutz, R., Vrijenhoek, R., 1994. DNA primers for amplification of mitochondrial cytochrome coxidase subunit I from diverse metazoan invertebrates. Mol. Mar. Biol. Biotechnol. 3, 294–299. Fu, Y.X., 1997. Statistical tests of neutrality of mutations against population growth, hitchhiking and background selection. Genetics 147, 915–925. Grant, W.S., Bowen, B.W., 1998. Shallow population histories in deep evolutionary lineages of marine fishes: insights from sardines and anchovies and lessons for conservation. J. Hered. 89, 415–426. Grant, W.S., Spies, I.B., Canino, M.F., 2006. Biogeographic evidence for selection on mitochondrial DNA in North Pacific Walleye Pollock Theragra chalcogramma. J. Hered. 97, 571–580. Gruenthal, K.M., Acheson, L.K., Burton, R.S., 2007. Genetic structure of natural populations of California red abalone (Haliotis rufescens) using multiple genetic markers. Mar. Biol. 152, 1237–1248. Habib, K.A., Jeong, D., Myoung, J.G., Kim, M.S., Jang, Y.S., Shim, J.S., Lee, Y.H., 2011. Population genetic structure and demographic history of the fat greenling Hexagrammos otakii. Genes Genom. 33, 413–423. Han, Z.Q., Gao, T.X., Yanagimoto, T., Sakurai, Y., 2008. Genetic population structure of Nibea albiflora in Yellow Sea and East China Sea. Fish. Sci. 74, 544–552. Haney, R.A., Silliman, B.R., Rand, D.M., 2010. Effects of selection and mutation on mitochondrial variation and inferences of historical population expansion in a Caribbean reef fish. Mol. Phylogenet. Evol. 57, 821–828. Harpending, H.C., 1994. Signature of ancient population growth in a low-resolution mitochondrial DNA mismatch distribution. Hum. Biol. 66, 591–600. Lei, J.L., Fan, N.C., Zheng, C.W., 1981. A preliminary observation on the morphological characteristics of embryos, larvae and juveniles of Nibea albiflora (Richardson). Mar. Fish. Res. 1, 77–84 (in Chinese with English abstract). Liu, Z.J., Cordes, J.F., 2004. DNA marker technologies and their applications in aquaculture genetics. Aquaculture 238, 1–37. Liu, J.X., Gao, T.X., Wu, S.F., Zhang, Y.P., 2007. Pleistocene isolation in the Northwestern Pacific marginal seas and limited dispersal in a marine fish, Chelon haematocheilus (Temminck & Schlegel, 1845). Mol. Ecol. 16, 275–288. Liu, Y., Liu, R.L., Ye, L.C., Liang, J., Xuan, F.J., Xu, Q.H., 2009a. Genetic differentiation between populations of swimming crab Portunus trituberculatus along the coastal waters of the East China Sea. Hydrobiologia 618, 125–137. Liu, J.Y., Brown, C.L., Yang, T.B., 2009b. Population genetic structure and historical demography of grey mullet, Mugil cephalus, along the coast of China, inferred by analysis of the mitochondrial control region. Biochem. Syst. Ecol. 12, 556–566. Lynch, M., Crease, T.J., 1990. The analysis of population survey data on DNA sequence variation. Mol. Biol. Evol. 7, 377–394. Lynch, A., Mcdowell, J., Graves, J., 2010. A molecular genetic investigation of the population structure of Atlantic rnenhaden (Brevoortia tyrannus). Fish. Bull. 108, 87–97.
D. Xu et al. / Biochemical Systematics and Ecology 45 (2012) 158–165
165
Ma, C.Q., Cheng, Q., Zhang, P., Zhuang, P., Zhao, Y., 2010. Genetic variation of Coilia ectenes (Clupeiformes: Engraulidae) revealed by the complete cytochrome b sequences of mitochondrial DNA. J. Exp. Mar Biol. Ecol. 385, 14–19. Nei, M., Li, W.H., 1979. Mathematical model for studying genetic variation in terms of restriction endonucleases. PNAS 76, 5269–5273. Nei, M., 1987. Molecular Evolutionary Genetics. Columbia University Press, New York, USA, pp. 10–88. Rodrigues, R., Schneider, H., Santos, S., Vallinoto, M., Sain-Paul, U., Sampaio, I., 2008. Low levels of genetic diversity depicted from mitochondrial DNA sequences in a heavily exploited marine fish (Cynoscion acoupa, Sciaenidae) from the Northern coast of Brazil. Genet. Mol. Biol. 31, 487–492. Rogers, A.R., Harpending, H., 1992. Population growth makes waves in the distribution of pairwise genetic differences. Mol. Biol. Evol. 9, 552–569. Rohl, A., 2003. Network: A Program Package for Calculating Phylogenetic Networks, Version 4.6. Fluxus Technology Ltd., Hamburg (Germany). Rozas, J., Sanchez-Delbarrio, J.C., Messeguer, X., Rozas, R., 2003. DnaSP, DNA polymorphism analyses by coalescent and other methods. Bioinformatics 19, 2496–2497. Shui, B.N., Han, Z.Q., Gao, T.X., Miao, Z.Q., Yanagimoto, T., 2009. Mitochondrial DNA variation in East China Sea and Yellow Sea populations of Japanese Spanish mackerel Scomberomorus nipbonius. Fish. Sci. 75, 593–600. Stopar, K., Ramsak, A., Trontelj, P., Malej, A., 2010. Lack of genetic structure in the jellyfish Pelagia noctiluca (Cnidaria: Scyphozoa: Semaeostomeae) across European seas. Mol. Phylogenet. Evol. 57, 417–428. Sun, P., Shi, Z.H., Yin, F., Peng, S.M., 2012. Genetic variation analysis of Mugil cephalus in China sea based on mitochondrial COⅠ gene sequences. Biochem. Genet. 50, 180–191. Tajima, F., 1989. Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123, 585–595. Takita, T., 1974. Studies on the early life history of Nibea albiflora (Richardson) in Ariake Sound. Bull. Fac. Fish. Nagasaki Univ. 38, 1–55. Tamura, K., Dudley, J., Nei, M., Kumar, S., 2007. MEGA4: molecular evolutionary genetics analysis (MEGA) software version 4.0. Mol. Boil. Evol. 24, 1596–1599. Thompson, J.D., Gibson, T.J., Plewniak, F., Jeanmougin, F., Higgins, D.G., 1997. The CLUSTAL-X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucl. Acids Res. 25, 4876–4882. Vrijenhoek, R., 1994. DNA primers for amplification of mitochondrial cytochrome c oxidase subunit I from diverse metazoan invertebrates. Mol. Biotechnol. 3, 294–299. Xiao, Y.S., Zhang, Y., Gao, T.X., Yanagimoto, T., Yabe, M., Sakurai, Y., 2009. Genetic diversity in the mitochondrial DNA control region and population structure in the small yellow croaker Larimichthys polyactis. Environ. Biol. Fish. 85, 303–314. Yamaguchi, K., Nakajima, M., Taniguchi, N., 2010. Loss of genetic variation and increased population differentiation in geographically peripheral populations of Japanese char Salvelinus leucomaenis. Aquaculture 308, S20–S27. Yu, Z.N., Kong, X.Y., Guo, T.H., Jiang, Y.Y., Zhuang, Z.M., Jin, X.S., 2005. Mitochondrial DNA sequence variation of Japanese anchovy Engraulis japonicus from the Yellow Sea and East China Sea. Fish. Sci. 71, 299–307. Yu, C., Chen, Q., Chen, X., Ning, P., Zheng, J., 2010. Species composition and quantitative distribution of fish in the Zhoushan fishing ground and its adjacent waters. Oceanol. Limnol. Sin. 41, 410–417 (In Chinese with English abstract). Zhao, F., Dong, Y., Zhuang, P., Zhang, T., Zhang, L., Shi, Z., 2011. Genetic diversity of silver pomfret (Pampus argenteus) in the Southern Yellow and East China Seas. Biochem. Syst. Ecol. 39, 145–150. Zhu, Y.D., Luo, Y.L., Wu, H.L., 1963. A Study on the Classification of the Sciaenoid Fishes of China, with Description of New Genera and Species. Shanghai Scientific and Technical Press, China.