Population Genetic Structure of Stellate Sturgeon (Acipenser stellatus Pallas, 1771) in the South Caspian Sea Using Microsatellite Markers
In this study, 197 samples of adult stellate sturgeon from four fishery regions were collected. DNA was extracted using 15 pairs of microsatellite primers, Polymerase Chain Reaction (PCR) was conducted. DNA bands were analyzed using Biocapt and GenAlex software package. Out of 15 microsatellite primers, 11 loci were produced, in which 10 of them were polymorphic and 1 monomorph. Analyses revealed that average of 13 alleles per locus (range 8 to 18 alleles per locus). Average observed and expected heterozygosity were 0.650 and 0.855 and significant genetic differences between 4 regions were observed (p≤0.01). Deviations from Hardy-Weinberg equilibrium were in most cases. Maximum genetic difference were observed between regions 2 and 4 (FST = 0.063, Nm = 3.728). These results indicate that at least, 3 populations of stellate sturgeon exist in the South Caspian Sea. Population of stellate sturgeon in region 2 where Sefidrud drainage is located was consider as independent population, therefore management of this unique stocks for restocking and conservation of gene pools is highly recommended.
Stellate sturgeon (Acipenser stellatus) is one of the shard stock of the Caspian states that also distributed in the Black and Azov Seas (Keyvan, 2003). Stellate sturgeon populations play an important role in biodiversity and commercial harvest of the Caspian Sea and they were listed as a endangered species IUCN Red list assessment (Pourkazemi, 2006) and since April, 1998 its trade regulated by the Convention on International Trade in Endangered Species Founa and Flora (CITES). Overfishing and increasing illegal unaccounted catches are the main causes to decrease the stocks and adult spawners (Pourkazemi, 2006). The stocks of A. stellatus in the Caspian Sea are maintained through natural spawning as well as artificial breeding, which necessitates the conservation of genetic diversity of this species. Therefore identification of population and races can be considered the first measures for management and conservation of sturgeon species in the Caspian Sea (Pourkazemi, 1996). Two different ecological from of stellate sturgeon in the North (Acipenser stellatus stellatus) and the South (Acipenser stellatus cynensis) were reported in the Caspian Sea regions (Keyvan, 2003). They are identical on spawning time, growth rate and immunological characters (Keyvan, 2003). Pourkazemi (1996) investigated genetic variation of stellate sturgeon (Acipenser stellatus) population in the south Caspian Sea with allozyme electrophoresis and mtDNA using RFLP methods. Shabani (2005) studied mtDNA variation of stellate sturgeon (Acipenser stellatus) population in South Caspian Sea using RFLP analysis of PCR Amplified ND 5/6 gene regions and they found low genetic variation and non-significant difference in haplotype frequency. It has been concluded that mitochondrial DNA technique was not powerful techniques to detect genetic variability sufficiently population-differentiation in order to help management units of stellate sturgeon.
In population genetic studies, more genetic variability would provide a better means by which to compare sturgeon collection from different localities differentiation (McQuown et al., 2003). Microsatellites are hyper variable, co dominant nuclear DNA markers in which variation is partitioned in one to five base pair repeat motifs (Zajc et al., 1997).
In recent years, microsatellite markers as a reliable methods, have been applied for many population as well as phylogenetic studies, this is because microsatellites typically have a higher level polymorphism than traditional nuclear loci. In addition, DNA for microsatellites analysis can be easily extracted from tissues obtained by non-lethal sampling (fins, hair, faces), which is essential when working with threatened or endangered species (McQuown et al., 2003). Several studies have been investigated on population genetic structure of variance Acipenseriformes species: on Acipenser, Huso and Scaphirhynchus (Ludwig et al., 2001); A. transmontanus (Smith et al., 2002); A. sinensis (Zhu et al., 2002); A. oxyrinchus oxyrinchus, A. oxyrinchus desotoi, A. brevirostrum (Waldman et al., 2002); A. oxyrinchus (Wirgin et al., 2002); A. fulvescens (McQuown et al., 2003); A. transmontanus (Rodzen et al., 2004); A. medirostris (Israel et al., 2004); A. sinensis Gray (Zhao et al., 2005); and in Caspian Sea Sturgeon species. On stellate sturgeon (Pourkazemi, 1996; Shabani, 2005); on Russian Sturgeon (Pourkazemi, 1996; Pourkazemi et al., 1999; Rezvani, 1997; Khoshkholgh, 2007); on Beluga (Rezvani, 1997) and on Ship sturgeon (Qasemi et al., 2006; Safari, 2006).
The development of management plans and implementation of actions to restore stellate sturgeon within its native stocks can useful from an understanding of the genetic diversity of its populations. This information is helpful in choosing donor populations to use as sources of reintroduction and in formulating restoration goals regarding population structure. Therefore in this study, the population structure of stellate sturgeon from four regions in Iranian coastline of the South Caspian Sea was investigated. The objective of the present study were to analysis the population genetic structure genetic diversity and identify individual populations of stellate sturgeon using microsatellite method.
MATERIALS AND METHODS
Totally 197 samples (2-3 g dorsal fin tissues) of adult stellate sturgeon
were collected from four regions including 52 samples from region 1(Astara-Anzali),
43 samples, from region 2 (Kiyashahr-Ramsar), 50 samples from region 3 (Nowshahr-Babolsar),
52 samples from region 4 (Miyankale-Gomishan) in 2006 by the International Sturgeon
Research Institute from South Caspian Sea in Iran (Fig. 1).
Genomic DNA was extracted from fin tissue following the method described
by Hillis and Moritz (1990) with some modifications (Pourkazemi, 1996). Approximately
100 mg of fin tissue from the dorsal fin was cut into small pieces. These pieces
were then placed in 1 mL STE buffer (10 mM Tris/HCl, pH 8.0; 50 mM EDTA, 200
mM NaCl and 0.5% SDS) and digested with 0.5 mg mL-1 proteinase K
at 55°C overnight. The resulting solution was centrifuged and the DNA in
supernatant that was precipitated with ethanol and dissolved in TE buffer. DNA
was purified using the phenol-chloroform extraction.
||Map shows the sampling sites of stellate sturgeon where 1,
2, 3 and 4 represent each region and shows sturgeon fishing station
||Loci, repeat motif, primers sequence, gene bank number and
primer sources used at present study in four stellate sturgeon collections
The quality and concentration of DNA were assessed by agarose gel electrophoresis
and spectrophotometry (model CECIL CE2040) stored at -20°C until use.
PCR Profiles and Primer Sequences
Nuclear DNA was amplified using 15 microsatellites primers designed for
Acipenser and Scaphirhynchus (May et al., 1997; McQuown
et al., 2000, Table 1). Polymerases Chain Reaction
(PCR) condition for each primer set were optimized for stellate sturgeon. Experimental
condition tested included varying the annealing temperature (49-61.2°C),
MgCl2 concentration (1-2.5 mM), dinucleotide triphosphate concentration
(200 μM), 1 U Taq DNA polymerase and primer concentration (0.5-1
pμ) and approximately 100 ng of template DNA. All reactions were performed
in 20 μL.
PCR products were separated on 6% polyacrylamid gels (29:1 acrylamid:bis-acrylamid; 1X TBE buffer) and followed by silver-staining. Gels were run at 170 V for 2 h and 30 min. Alleles were sized using BioCapt software and each gel contained an allelic ladder (50 bp) to assist in consistent scoring of alleles.
Allelic frequencies, observed and expected heterozygosities, genetic distance
(Nei, 1978), genetic identity (Nei, 1978) were computed in GeanAlex 6.0 software
(Peakall and Smouse, 2005). This package was also used to calculate FST
and RST, Nm, Hardy-Weinberg (HW) tests of equilibrium, AMOVA (Analysis
of Molecular Variance). The dendrograms of genetic distance (Nei, 1972, 1978)
UPGMA computed in TFPGA (version 1.3).
Amplification and Banding Patterns
Out of 15 sets of microsatellite primers, four sets (LS-69, LS-57, LS-62
and Spl-168) have not shown any flanking sites on stellate sturgeon genome.
Eleven sets of primers were successfully amplified where one sets (Spl-113;
Table 2) produce 2 loci and one set (LS-39) showed monomorphic
pattern. Therefore totally 11 loci were investigated at present study. All microsatellite
primers where able to produce DNA bands displayed a characteristic disomic banding
pattern, where heterozygous individuals showed two bands of equal intensity
on the gels and some times with one band darker than the others. These banding
patterns may be a result of the presence of a homologous locus that is detected
under certain PCR conditions.
Genetic Variation Within Sampling Sites (Region)
The average number of alleles found at each locus was 13 and ranged from
8 (Spl-105) to 18 (Spl-113b) alleles (Table 3). The total
number of alleles found in each population ranged from 122 (region two) to 154
Out of 202 observed alleles, 128 occurred at frequencies of <0.05 in all
samples. Spl-170 showed the highest allele number (30 allele) of which 24 alleles
at frequencies of <0.05 and LS-34 showed the maximum variability ranging
|| PCR condition and reaction, locus and allele size (bp) on
|| Absolute numbers of alleles observed within 4 sampling sites
(region) using 12 sets of microsatellite primers
|N = Mean number of alleles observed per locus. *Loci = Loci
in accordance with H-W equilibrium (p≤0.01)
|| Observed (Ho) and expected (He) heterozygosities at 11 loci
in four sampling regions
||UPGMA dendrogram based on the genetic distance computed by
Neis (1972) between A. stellatus population, according to microsatellite
Average heterozygosity over the loci was 0.650 and ranged from 0.624 region
one to 0.662 in Region four (Table 4).
Deviation from Hardy-Weinberg equilibrium were in all cases (p≤0.01) expect Spl-170 in region one and LS-68 in region two and Spl-173 in region three (Table 3).
Genetic Variation Among Sampling Regions
Genetic distance calculated between each pair of collections ranged from
0.337 (between Regions one and four) to 0.606 (between Regions two and four,
Table 5). In general, similarities in more geographically
close areas were higher than more distance one (Fig. 1, Table
5). Results of analysis of molecular variance of genetic variation, among
regions was 0.0127, among population/regions was 0.035 and individual within
groups was 0.047 (p≤0.01).
||Pairwise population of genetic distance (below diagonal) and
genetic identity (above diagonal) (Nei, 1972) detected at 11 loci in stellate
||Pairwise estimates of genetic differentiation detected at
11 loci in stellate sturgeon samples, using unbiased RST (below
diagonal) and FST values (above diagonal)
|Probabilities of RST or FST determined
by AMOVA tests, p≤0.01
The highest range of genetic difference were observed between regions 2 and
4 (FST = 0.063, RST = 0.287, p≤0.01) and the lowest
between regions 3 and 4 (FST = 0.033, RST = 0.301, p≤0.01).
However, FST and RST estimates often differ in a pronounced
manner (Balloux and Lugon-Moulin, 2002).Values of pairwise RST among
samples were consistently much higher (as much as an order of magnitude) than
equivalent FST values (Table 6).
The dendrogram based on genetic distance Nei (1972, 1978) revealed three
major cluster. One cluster consists of Region two alone, a second consists of
Region three, while the third consists of Region one and four together (Fig.
Out of 15 pairs of studied primers, 4 pairs was not amplified in the PCR reaction,
which may be because of the lack of flanking sites in these primers due to high
genetic distance of primers source species and the stellate sturgeon. One primer
pair was monomorphic and the rest of them were polymorph. One pairs of polymorphic
primers amplificated two loci. Few samples showed few additional bands in some
loci, which may related to non-exclusive primers of this species. The long-term
persistence of an endangered fish species can be investigated by allelic diversity,
gene diversity, effective population size and population structure (Yue et
al., 2004). At present study, comparison of the Ho values of A. stellatus
(0.650, Table 4) it was slight lower than anadromus species
(Ho = 0.68, Dewoody and Avise, 2000) and the mean number of alleles in this
study (13.6) was higher than anadromus species (11.3) for microsatellites. The
high genetic variability of the stellate sturgeon from region two, may reflect
different population colonization origins. Region two populations not only presented
the least similar genetically to other regions, but also showed the lowest number
of alleles (122 alleles) due to bottleneck population such as over fishing and
deterioration in the breeding environment resulting in less recruitment, dams,
pollution. Many alleles with low frequency (<0.05) confirm that. The number
of alleles for a given locus is more sensitive to demographic fluctuations (Nei
et al., 1975; Maruyama and Fuerst, 1985) and is therefore more appropriate
for testing whether a bottleneck has occurred in a population (Luikart and Cornuet,
1998). Therefore it needs immediate attention for its genetic conservation and
overall variability (Table 3). AMOVA test revealed the populations
of each region differ gather presenting a significant difference (p≤0.01)
among the samples of the various regions in the Iranian coast line South Caspian
These results stand in stark contrast to previous studies used mtDNA. Low levels
of variation were detected and little differentiation among sampling site was
detected over a comparable geographic range (Pourkazemi, 1996; Shabani, 2005).
This may result from the more rapid rate of mutational change at microsatellite
loci compared with that at even the most rapidly evolving area of the mitochondrial
genome (Wirgin et al., 2002). At present study deviation from the Hardy-Weinberg
equilibrium observed in most loci. Maybe, it is due to presence of null alleles.
Similar results have been reported the null alleles in inheritance of microsatellite
loci in lake and white sturgeons (Rodzen et al., 2004; Zhao et al.,
2005; McQuown et al., 2003; Pyatskowit et al., 2001; Welsh et
al., 2003) and it also may be related to not using species specific primers
and the most important reason sampling from mixtures of migrating population
and sampling methodology. To detect such a population structure, samples must
be collected from spawning sites. Samples from non-spawning adults may reflect
mixtures of migrating population (McQuown et al., 2003). At present study
FST in all sampling site was low but significant (p<0.001). So
in each river in the South Caspian sea have different population. The lowest
of FST on AMOVA was between region 4 and 3 with the high gene flow.
But the highest of genetic distance and lower genetic identity was between region
2 and 4 (Table 5). Regarding the fishery returning, it is
possible that the caught samples are a combination of the various generation
and different birth places which have formed a gathering to feed.
Phylogenetic tree of stellate sturgeon using 12 microsatellites loci in four regions of south of Caspian Sea showed three clarified clusters included cluster of region two, three, one and four. As it shown in Fig. 2, the samples of the region two is in a separate cluster, which is possibly the samples that have caught before entering spawning sturgeon into the Sefidrude river and suggested the existence of a separate population in Sefidrud. The obtained results of the phylogeny show that 3 populations of stellate sturgeon exist on South of Caspian Sea originated from Sefidrud, one of population is in Sefidrud and other populations are derived from it. However, it should be mentioned that usually phylogeny sanders has not recommended distinguishing different population for a species. Stellate sturgeon is an anadromus species which immigrates to river for spawning and returns to the sea for feeding and growth, but the comprehensive study has not been performed up yet. In comparison with other molecular methods performed in the stellate sturgeon species, microsatellites studies showed the higher genetic variation and heterozygosity than mtDNA. Although this fish has the various allelic number in each of the under-studied regions in the Iranian cost line south Caspian Sea varies greatly. As microsatellites method has higher capacity to show the genetic variation, using above primers compared to other methods and with regard to the severe reduction of these fishes reserves before performing the artificial reproduction, identify the caught sample, then take the required actions for artificial reproduction and transfer among the various workshops. The present study showed that the genetic variation in the stellate sturgeon compared to the other sturgeons is in acceptable level, but the effect of over fishing have caused the reduction stocks in this species. Over fishing and ecologic changes in the Caspian Sea have altered the population structure of this species effectively. With population differentiation in region two especially Sefidrud drainage, we suggest special consideration on conservation policy and restocking program of this species in Sefidrud area.
We are grateful to all support provided by Iranian Fishery Research Organization (Project Cod 82-0710441000-53), Islamic Azad University, Science and Research Branch, Tehran. This research was performed in the Molecular Genetic Lab of the Dr. Dadman International Sturgeon Research Institute-Rasht. The honorable persons in charge and those who are involved in the institute and the export of the genetic lab. We would like to extended our appreciation to, Mr. Nuruzfashkhami head of genetic department, special thanks to Mr. Qasemi, Mr. Chakmeduz, for their great operation.
Balloux, F. and N. Lugon-Moulin, 2002.
The estimation of population differentiation with microsatellite markers. Mol. Ecol., 11: 155-165.CrossRef | Direct Link |
DeWoody, J.A. and J.C. Avise, 2000.
Microsatellite variation in marine, freshwater and anadromous fishes compared with other animals. J. Fish Biol., 56: 461-473.CrossRef | Direct Link |
Hillis, D. and M.C. Moritz, 1990.
Molecular Taxonomic. Sinauer Associate, Inc. Publishers, Massachusetts
Israel, J.A., J.F. Crdes, M.A. Blumberg and B. May, 2004.
Geographic patterns of genetic differentiation among collections of green sturgeon. N. Am. J. Fish. Manage., 24: 922-931.Direct Link |
Keyvan, A., 2003.
Iranian Sturgeons in the Caspian Sea. Iranian Sisheries Company, Iran, pp: 400
Khoshkholgh, M., 2007.
Genetic population structure of Persian sturgeon (Acipenser persicus
) and Russian sturgeon (Acipenser guldenstadti
) in South of Caspian Sea using microsatellite markers. Ph.D. Thesis. Gorgan University of Agricultural Sciences and Natural Resources. pp: 145.
Ludwig, A., M. Belfiore, P. Christian, V. Svirsky and I. Jenneckenes, 2001.
Genom duplication events and functional reduction of ploidy levels in sturgeon (Acipenser, Huso and Scaphirhinchus). Genetics, 158: 1203-1215.Direct Link |
Luikart, G. and J.M. Cornuet, 1998.
Empirical evaluation of a test for identifying recently bottlenecked populations from allele frequency data. Conserv. Biol., 12: 228-237.Direct Link |
Maruyama, T. and P.A. Fuerst, 1985.
Population bottlenecks and nonequilibrium models in population genetics. Genetics, 111: 675-689.
May, B., C. Charles, C. Krueger and L. Kincaid, 1997.
Genetic variation at Microsatellite loci in sturgeon primer sequence homology in Acipenser and Scaphirhenchus. Can. J. Fish. Aquat. Sci., 54: 1542-1547.
McQuown, E.C., B.L. Sloor, R.J. Sheehen and B. May, 2000.
Microsatellite analysis of genetic variation in sturgeon: New primer sequences for Scaphyrhinchus and Acipenser. Am. Fish. Soc., 129: 1380-1388.Direct Link |
McQuown, E., C.C. Krueger, H.L. Kincaid, A.E. Gall and B. May, 2003.
Genetic comparison of Lake Sturgeon population: Differentiation based on allelic frequencies at seven microsatellite loci. J. Great Lake Res., 29: 3-13.Direct Link |
Nei, M., 1972.
Genetic distance between populations. Am. Naturalist, 106: 283-292.Direct Link |
Nei, M., T. Maruyama and R. Chakraborty, 1975.
The bottleneck effect and genetic variability in populations. Evolution, 29: 1-10.Direct Link |
Nei, M., 1978.
Estimation of average heterozygosity and genetic distance from a small number of individuals. Genetics, 89: 583-590.PubMed | Direct Link |
Peakall, R. and P.E. Smouse, 2005.
GenAlEx 6: Genetic analysis in excel. Population genetic software for teaching and research. The Australian National University, Canberra, Australia. http://www.anu.edu.au/BoZo/GenAlEx/.
Pourkazemi, M., 1996.
Molcular and biochemical genetc analysis of sturgeon stocks from the South Caspian Sea. Ph.D. Thesis. School of Biological sciences, University of Wales, Swansea.
Pourkazemi, M., D.O.F. Skibinski and A. Beardmore, 1999.
Application of mtDNA d-loop region for the study of Russian sturgeon population structure from Iranian Coastline of the Caspian Sea. Iranian J. Fish. Sci., 15: 23-28.Direct Link |
Pyatskowit, J.D., C.C. Krueger, H.L. Kincaid and B. May, 2001.
Inheritance of microsatellite loci in the polyploidy lake Sturgeon (Acipenser fluvescens
). Genome, 44: 185-191.Direct Link |
Qasemi, A., M. Pourkazemi and M.R. Kalbassi, 2006.
Comparison of genetic variation of Ship sturgeon (Acipenser nudivrntris
) in the Southern Caspian Sea and Ural River using PCR-RFLP. Iran. Sci. Fish. J., 14: 151-164.CrossRef |
Rezvani, S., 1997.
Molecular population genetic studies of sturgeon species in the South Caspian Sea. Ph.D. Thesis. School of Biological Sciences, University of Wales, Swan Sea. UK.
Rodzen, J.A., T.R. Famula and B. May, 2004.
Estimation of parentage and relatedness in the polyploid white sturgeon (Acipenser transmontanus
) using a dominant marker approach for duplicated microsatellite loci. Aquaculture, 232: 165-182.Direct Link |
Safari, R., 2006.
Genetic population structure of Ship sturgeon (Acipenser nudivrntris
) in South of Caspian Sea and Ural River using microsatellite markers. M.S. Thesis. Gorgan University of Agricultural Sciences and Natural Resources.
Shabani, A., 2005.
Study of mtDNA variation of stellate sturgeon (Acipenser stellatus
) population from the North (Volga River) and South (Sefidrud River) Caspian Sea using RFLP analysis of PCR Amplified ND 5/6 gene reglons. Ph.D. Thesis. Gorgan University of Agricultural Sciences and Natural Resources.
Smith, T., J. Nelson, S. Polard, E. Rubidge and S.J. Mckay et al
Population genetic analysis of sturgeon (Acipenser transmontanus
)in the Fraser river. J. Applied Ichthyol., 18: 307-312.Direct Link |
Waldman, J., C. Grunwald, J. Stabile and I. Wirigin, 2002.
Impacts of the life history and biogeography on the genetic stock structure of Atlantic sturgeon Acipenser oxyrinchus
, Gulf sturgeon A. oxyrinchus desotoi
, shortnose sturgeon A. brevirostrum
. J. Applied Ichthyol., 18: 509-518.Direct Link |
Welsh, A.B., M. Blumberg and B. May, 2003.
Identification of microsatellite loci in lake sturgeon, Acipenser fluvescens and their variability in green sturgeon, Acipenser medirostris
. Mol. Ecol. Primer Note, 3: 47-55.Direct Link |
Wirgin, I., J. Waldman, J. Stabile, B. Lubinski and T. King, 2002.
Comparison of mitochondrial DNA control region sequence and microsatellite DNA analysis in estimating population structure and gene flow rates in Atlanic sturgeon (Acipenser oxyrinchus
). J. Applied Ichthyol., 18: 313-319.Direct Link |
Yue, G.H., Y. Li, L.C. Lim and L. Orban, 2004.
Monitoring the genetic diversity of three Asian arowana (Scleropages formosus
)captive stocks using AFLP and microsatellites. Aquaculture, 237: 89-102.Direct Link |
Zajc, I., C.S. Mellersh and J. Sampson, 1997.
Variability of canine microsatellites within and between different dog breeds. Mammalian Genome, 8: 182-185.CrossRef |
Zhao, N., W. Ai, Z. Shao, B. Zhu, S. Brosse and J. Chang, 2005.
Microsatellites assessment of Chinese sturgeon (Acipenser sinensis
Gray) genetic variability. J. Applied Ichthyol., 21: 7-13.Direct Link |
Zhu, B., F. Zhou, H. Cao, Z. Shao, N. Zhao, B. May and J. Chang, 2002.
Analysis of genetic variation in the Chines sturgeon, Acipenser sinensis
: Estimating the contribution of artificially produced larvae in a wild population. J. Applied Ichthyol., 18: 301-306.Direct Link |