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Phylogeography study of Ammodytes personatus in Northwestern Pacific: Pleistocene isolation, temperature and current conducted secondary contact.

Han Z, Yanagimoto T, Zhang Y, Gao T - PLoS ONE (2012)

Bottom Line: However, significant genetic structure is also detected in the Sea of Japan, contracting expected homogenization hypothesis in Tsushima Current.The haplotype frequency of lineages in both sides of Japanese Island and significant genetic structure between north and south groups revealed that the distribution of lineage B and north group were highly limited by the annual sea temperature.Lack of genetic structure in the south group and north group populations indicated that ocean currents within groups facilitated the dispersal of A. personatus.

View Article: PubMed Central - PubMed

Affiliation: Fishery College, Zhejiang Ocean University, Zhoushan, Zhejiang, China.

ABSTRACT
To assess the role of historical process and contemporary factors in shaping population structures in Northwestern Pacific, mitochondrial control region sequences were analyzed to characterize the phylogeography and population structure of the Japanese sand lance Ammodytes personatus. A total of 429 individuals sampled from 17 populations through the species' range are sequenced. Two distinct lineages are detected, which might have been divergent in the Sea of Japan and Pacific costal waters of Japanese Island, during the low sea level. Significant genetic structure is revealed between the Kuroshio and Oyashio Currents. However, significant genetic structure is also detected in the Sea of Japan, contracting expected homogenization hypothesis in Tsushima Current. The haplotype frequency of lineages in both sides of Japanese Island and significant genetic structure between north and south groups revealed that the distribution of lineage B and north group were highly limited by the annual sea temperature. The lack of lineage B in Qingdao population with low sea temperature reflects the sea temperature barrier. Lack of genetic structure in the south group and north group populations indicated that ocean currents within groups facilitated the dispersal of A. personatus.

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The study area depicting sample locations, schematic map of currents and the annual sea temperature.
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pone-0037425-g006: The study area depicting sample locations, schematic map of currents and the annual sea temperature.

Mentions: The sample size consists of 429 individuals from 17 samples across its natural distribution, from the southern extreme of its range off the coast of Kyushu and its northern limit Cape Soya. Sampling information and sampling locations are listed in Table 2 and Fig 6, respectively. The south group and north group were identified by the descriptions of Okamoto et al. [23], [28] and Hashimoto and Kawasaki [22]. Two samples (SS, SN), which belong to north and south groups, were collected in the same location in Sendai Bay. Oceanographic features including currents, annual sea surface temperatures (Because of no long migration in adults and vertical migration in night, the annual surface temperature was chosen.) at the sampled localities are also indicated in Fig 6 and Table 2. The annual sea temperature was available in JOC (http: www.jodc.go.jp). Muscle was obtained and preserved in 95% ethanol or frozen for DNA extraction. Genomic DNA was isolated from muscle tissue by proteinase K digestion followed by a standard phenol–chloroform method. DNA was subsequently resuspended in 100 μL of TE buffer. PCR primers specific to A. personatus were designed from the universal primers to amplify the first hypervariable segment of the mtDNA control region [35]. The primer sequences are DL-S, 5′-CCC ACC ACT AAC TCC CAA AGC-3′ (forward) and DL-R, 5′-CTG GAA AGA ACG CCC GGC ATG-3′ (reverse). PCR was carried out in 50 μL volumes containing 1.25 U Taq DNA polymerase (Takara Co., China), 20 ng template DNA, 200 nmol/L forward and reverse primers, 200 μmolL/L of each dNTPs, 10 mmol/L Tris, pH 8.3, 50 mmol/L KCl, 1.5 mmol/L MgCl2. The PCR amplification was carried out in a Biometra thermal cycler under the following conditions: 3 min initial denaturation at 94°C, and 40 cycles of 45 s at 94°C for denaturation, 45 s at 50°C for annealing, and 45 s at 72°C for extension, and a final extension at 72°C for 10 min. All sets of PCR included a negative control reaction tube in which all reagents were included, except template DNA. PCR product was purified with Gel Extraction Mini Kit (Watson BioTechnologies Inc., Shanghai). The purified product was used as the template DNA for cycle sequencing reactions performed using BigDye Terminator Cycle Sequencing Kit (ver. 2.0, PE Biosystems, Foster City, California), and sequencing was conducted on an ABI Prism 3730 (Applied Biosystems) automatic sequencer with both forward and reverse primers. The primers used for sequencing were the same as those for PCR amplification.


Phylogeography study of Ammodytes personatus in Northwestern Pacific: Pleistocene isolation, temperature and current conducted secondary contact.

Han Z, Yanagimoto T, Zhang Y, Gao T - PLoS ONE (2012)

The study area depicting sample locations, schematic map of currents and the annual sea temperature.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3368699&req=5

pone-0037425-g006: The study area depicting sample locations, schematic map of currents and the annual sea temperature.
Mentions: The sample size consists of 429 individuals from 17 samples across its natural distribution, from the southern extreme of its range off the coast of Kyushu and its northern limit Cape Soya. Sampling information and sampling locations are listed in Table 2 and Fig 6, respectively. The south group and north group were identified by the descriptions of Okamoto et al. [23], [28] and Hashimoto and Kawasaki [22]. Two samples (SS, SN), which belong to north and south groups, were collected in the same location in Sendai Bay. Oceanographic features including currents, annual sea surface temperatures (Because of no long migration in adults and vertical migration in night, the annual surface temperature was chosen.) at the sampled localities are also indicated in Fig 6 and Table 2. The annual sea temperature was available in JOC (http: www.jodc.go.jp). Muscle was obtained and preserved in 95% ethanol or frozen for DNA extraction. Genomic DNA was isolated from muscle tissue by proteinase K digestion followed by a standard phenol–chloroform method. DNA was subsequently resuspended in 100 μL of TE buffer. PCR primers specific to A. personatus were designed from the universal primers to amplify the first hypervariable segment of the mtDNA control region [35]. The primer sequences are DL-S, 5′-CCC ACC ACT AAC TCC CAA AGC-3′ (forward) and DL-R, 5′-CTG GAA AGA ACG CCC GGC ATG-3′ (reverse). PCR was carried out in 50 μL volumes containing 1.25 U Taq DNA polymerase (Takara Co., China), 20 ng template DNA, 200 nmol/L forward and reverse primers, 200 μmolL/L of each dNTPs, 10 mmol/L Tris, pH 8.3, 50 mmol/L KCl, 1.5 mmol/L MgCl2. The PCR amplification was carried out in a Biometra thermal cycler under the following conditions: 3 min initial denaturation at 94°C, and 40 cycles of 45 s at 94°C for denaturation, 45 s at 50°C for annealing, and 45 s at 72°C for extension, and a final extension at 72°C for 10 min. All sets of PCR included a negative control reaction tube in which all reagents were included, except template DNA. PCR product was purified with Gel Extraction Mini Kit (Watson BioTechnologies Inc., Shanghai). The purified product was used as the template DNA for cycle sequencing reactions performed using BigDye Terminator Cycle Sequencing Kit (ver. 2.0, PE Biosystems, Foster City, California), and sequencing was conducted on an ABI Prism 3730 (Applied Biosystems) automatic sequencer with both forward and reverse primers. The primers used for sequencing were the same as those for PCR amplification.

Bottom Line: However, significant genetic structure is also detected in the Sea of Japan, contracting expected homogenization hypothesis in Tsushima Current.The haplotype frequency of lineages in both sides of Japanese Island and significant genetic structure between north and south groups revealed that the distribution of lineage B and north group were highly limited by the annual sea temperature.Lack of genetic structure in the south group and north group populations indicated that ocean currents within groups facilitated the dispersal of A. personatus.

View Article: PubMed Central - PubMed

Affiliation: Fishery College, Zhejiang Ocean University, Zhoushan, Zhejiang, China.

ABSTRACT
To assess the role of historical process and contemporary factors in shaping population structures in Northwestern Pacific, mitochondrial control region sequences were analyzed to characterize the phylogeography and population structure of the Japanese sand lance Ammodytes personatus. A total of 429 individuals sampled from 17 populations through the species' range are sequenced. Two distinct lineages are detected, which might have been divergent in the Sea of Japan and Pacific costal waters of Japanese Island, during the low sea level. Significant genetic structure is revealed between the Kuroshio and Oyashio Currents. However, significant genetic structure is also detected in the Sea of Japan, contracting expected homogenization hypothesis in Tsushima Current. The haplotype frequency of lineages in both sides of Japanese Island and significant genetic structure between north and south groups revealed that the distribution of lineage B and north group were highly limited by the annual sea temperature. The lack of lineage B in Qingdao population with low sea temperature reflects the sea temperature barrier. Lack of genetic structure in the south group and north group populations indicated that ocean currents within groups facilitated the dispersal of A. personatus.

Show MeSH