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Novel Polymorphic Microsatellite Markers Reveal Genetic Differentiation between Two Sympatric Types of Galaxea fascicularis.

Nakajima Y, Shinzato C, Satoh N, Mitarai S - PLoS ONE (2015)

Bottom Line: Bayesian clustering also indicated that these two types are genetically isolated.While nuclear microsatellite genotypes also showed genetic differentiation between mitochondrial types, the mechanism of divergence is not yet clear.These markers will be useful to estimate genetic diversity, differentiation, and connectivity among populations, and to understand evolutionary processes, including divergence of types in G. fascicularis.

View Article: PubMed Central - PubMed

Affiliation: Marine Biophysics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, Japan.

ABSTRACT
The reef-building, scleractinian coral, Galaxea fascicularis, is classified into soft and hard types, based on nematocyst morphology. This character is correlated with the length of the mitochondrial non-coding region (mt-Long: soft colony type, and nematocysts with wide capsules and long shafts; mt-Short: hard colony type, and nematocysts with thin capsules and short shafts). We isolated and characterized novel polymorphic microsatellite markers for G. fascicularis using next-generation sequencing. Based upon the mitochondrial non-coding region, 53 of the 97 colonies collected were mt-Long (mt-L) and 44 were mt-Short (mt-S). Among the 53 mt-L colonies, 27 loci were identified as amplifiable, polymorphic microsatellite loci, devoid of somatic mutations and free of scoring errors. Eleven of those 27 loci were also amplifiable and polymorphic in the 44 mt-S colonies; these 11 are cross-type microsatellite loci. The other 16 loci were considered useful only for mt-L colonies. These 27 loci identified 10 multilocus lineages (MLLs) among the 53 mt-L colonies (NMLL/N = 0.189), and the 11 cross-type loci identified 7 MLLs in 44 mt-S colonies (NMLL/N = 0.159). Significant genetic differentiation between the two types was detected based on the genetic differentiation index (FST = 0.080, P = 0.001). Bayesian clustering also indicated that these two types are genetically isolated. While nuclear microsatellite genotypes also showed genetic differentiation between mitochondrial types, the mechanism of divergence is not yet clear. These markers will be useful to estimate genetic diversity, differentiation, and connectivity among populations, and to understand evolutionary processes, including divergence of types in G. fascicularis.

No MeSH data available.


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Genetic differentiation between mt-L and mt-S colonies by discriminant analysis of principal components (DAPC).Five PCs were retained.
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pone.0130176.g003: Genetic differentiation between mt-L and mt-S colonies by discriminant analysis of principal components (DAPC).Five PCs were retained.

Mentions: Significant genetic differentiation between types was detected based on the genetic differentiation index (FST = 0.076, P = 0.001). Furthermore, the results of Bayesian clustering using STRUCTURE also indicated that these two types are genetically isolated (Fig 2). When the number of genetic clusters was assumed to be two (K = 2), ∆K as ad hoc quantity for predicting of K and mean Ln P(D) as posterior probability of the data given K, suggested the largest value (∆K = 475.17, mean Ln P(D) = -945.52), which were indicators of most probable K value. DAPC also indicated obvious differentiation between the mt-L and mt-S clusters (Fig 3). This result showed that the most probable number of genetically clustered populations was two. It is also evident that there is genetic differentiation at the population level between these two sympatric types; therefore they appear to represent legitimate species. These markers provide evidence of significant differentiation between mt-L and mt-S; however, they may underestimate differentiation of the two G. fascicularis types, because the 11 cross-type loci are relatively well conserved between types.


Novel Polymorphic Microsatellite Markers Reveal Genetic Differentiation between Two Sympatric Types of Galaxea fascicularis.

Nakajima Y, Shinzato C, Satoh N, Mitarai S - PLoS ONE (2015)

Genetic differentiation between mt-L and mt-S colonies by discriminant analysis of principal components (DAPC).Five PCs were retained.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4492964&req=5

pone.0130176.g003: Genetic differentiation between mt-L and mt-S colonies by discriminant analysis of principal components (DAPC).Five PCs were retained.
Mentions: Significant genetic differentiation between types was detected based on the genetic differentiation index (FST = 0.076, P = 0.001). Furthermore, the results of Bayesian clustering using STRUCTURE also indicated that these two types are genetically isolated (Fig 2). When the number of genetic clusters was assumed to be two (K = 2), ∆K as ad hoc quantity for predicting of K and mean Ln P(D) as posterior probability of the data given K, suggested the largest value (∆K = 475.17, mean Ln P(D) = -945.52), which were indicators of most probable K value. DAPC also indicated obvious differentiation between the mt-L and mt-S clusters (Fig 3). This result showed that the most probable number of genetically clustered populations was two. It is also evident that there is genetic differentiation at the population level between these two sympatric types; therefore they appear to represent legitimate species. These markers provide evidence of significant differentiation between mt-L and mt-S; however, they may underestimate differentiation of the two G. fascicularis types, because the 11 cross-type loci are relatively well conserved between types.

Bottom Line: Bayesian clustering also indicated that these two types are genetically isolated.While nuclear microsatellite genotypes also showed genetic differentiation between mitochondrial types, the mechanism of divergence is not yet clear.These markers will be useful to estimate genetic diversity, differentiation, and connectivity among populations, and to understand evolutionary processes, including divergence of types in G. fascicularis.

View Article: PubMed Central - PubMed

Affiliation: Marine Biophysics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, Japan.

ABSTRACT
The reef-building, scleractinian coral, Galaxea fascicularis, is classified into soft and hard types, based on nematocyst morphology. This character is correlated with the length of the mitochondrial non-coding region (mt-Long: soft colony type, and nematocysts with wide capsules and long shafts; mt-Short: hard colony type, and nematocysts with thin capsules and short shafts). We isolated and characterized novel polymorphic microsatellite markers for G. fascicularis using next-generation sequencing. Based upon the mitochondrial non-coding region, 53 of the 97 colonies collected were mt-Long (mt-L) and 44 were mt-Short (mt-S). Among the 53 mt-L colonies, 27 loci were identified as amplifiable, polymorphic microsatellite loci, devoid of somatic mutations and free of scoring errors. Eleven of those 27 loci were also amplifiable and polymorphic in the 44 mt-S colonies; these 11 are cross-type microsatellite loci. The other 16 loci were considered useful only for mt-L colonies. These 27 loci identified 10 multilocus lineages (MLLs) among the 53 mt-L colonies (NMLL/N = 0.189), and the 11 cross-type loci identified 7 MLLs in 44 mt-S colonies (NMLL/N = 0.159). Significant genetic differentiation between the two types was detected based on the genetic differentiation index (FST = 0.080, P = 0.001). Bayesian clustering also indicated that these two types are genetically isolated. While nuclear microsatellite genotypes also showed genetic differentiation between mitochondrial types, the mechanism of divergence is not yet clear. These markers will be useful to estimate genetic diversity, differentiation, and connectivity among populations, and to understand evolutionary processes, including divergence of types in G. fascicularis.

No MeSH data available.


Related in: MedlinePlus