Molecular Evolution, Systematics, and Zoogeography of the Rockfish SubgenusSebastomus(Sebastes,Scorpaenidae) Based on Mitochondrial Cytochromeband Control Region Sequences

Rocha‐Olivares, Axayácatl; Rosenblatt, Richard H.; Vetter, Russell D.

doi:10.1006/mpev.1998.0585

Cited by 84 publications

(51 citation statements)

References 40 publications

(58 reference statements)

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“…This remarkable level of crossspecies microsatellite conservation is a clear indication of the close molecular relatedness of species of Sebastes that has surfaced in other microsatellite studies (e.g. Miller et al, 2000;Roques et al, 1999;Wimberger et al, 1999) as well as other molecular investigations (Rocha-Olivares et al, 1999a;RochaOlivares et al, 2000;Rocha-Olivares et al, 1999b;Rocha-Olivares et al, 1999c). Most loci analysed were polymorphic, except for one.…”

Section: Genetic Diversitysupporting

confidence: 53%

Microsatellite variation in the Mexican rockfish <i>Sebastes macdonaldi</i>

Rocha‐Olivares¹,

Leal-Navarro²,

Kimbrell³

et al. 2003

Sci. Mar.

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SUMMARY: The Mexican rockfish Sebastes macdonaldi is the Northeast Pacific rockfish with the southernmost distribution, featuring isolated populations in the Gulf of California. We analysed seven microsatellite loci in 111 organisms collected throughout most of its geographical range to test long-standing hypotheses regarding its disjunct distribution. One locus was fixed and the number of alleles in polymorphic loci ranged from 2 to 24 (average 13.5). We found very high levels of polymorphism (overall He = 0.75) comparable to other congeneric species but no significant differences in genetic diversity among localities or between Pacific and Gulf of California populations (p > 0.1). Significant shifts in allelic and genotypic frequencies were detected at three loci, which resulted in a small but significant partitioning of genetic variance among California, Baja California and Gulf of California populations (F ST = 0.007, p = 0.03) and between Gulf and Pacific populations (F ST = 0.01, p = 0.004). The latter but not the former result was corroborated by analyses of molecular variance (AMOVA) using the number of distinct alleles (F ST ) and the sum of square differences of allele sizes (R ST ) as Euclidean distances. The evidence argues against contemporary gene flow between the gulf and the Pacific ocean and against an ancient invasion of the gulf with a founder effect. The small level of divergence favours a recent dispersal but a larger data set including DNA sequences amenable to phylogenetic analyses will help to test alternative hypotheses of dispersal versus vicariance.Key words: Mexican rockfish, disjunct distribution, microsatellites, genetic structure, Baja California, México. RESUMEN: VARIACIÓN DE MICROSATÉLITES EN EL ROCKOT MEXICANO SEBASTES MACDONALDI. -El rockot mexicanoSebastes macdonaldi es la especie de Sebastes del Pacífico nororiental con la distribución geográfica más sureña e incluye poblaciones aisladas dentro del Golfo de California. Analizamos siete loci microsatelitales en 111 organismos que se colectaron a lo largo de gran parte de su distribución geográfica para probar hipótesis acerca de su distribución discontinua. Un locus se encontró fijado y el número de alelos en loci polimórficos varió entre 2 y 24 (media 13.5). Encontramos altos niveles de polimorfismo (en general He = 0.75) comparables con otras especies congenéricas, sin embargo no se encontraron diferencias en los niveles de diversidad entre las localidades ni entre las poblaciones del Pacífico y del Golfo de California (p > 0.1). Se detectaron cambios significativos en las frecuencias alélicas y genotípicas en tres loci, que resultaron en una división pequeña pero significativa de la variancia genética entre California, Baja California y el Golfo de California (F ST = 0.007, p = 0.03) y entre las poblaciones del golfo y del Pacífico (F ST = 0.01, p = 0.004). Solamente esta última diferenciación fue corroborada por un análisis de variancia molecular (AMOVA) en el que se utilizaron el número de alelos distintos (F ST ) y la su...

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Section: Genetic Diversitysupporting

confidence: 53%

Microsatellite variation in the Mexican rockfish <i>Sebastes macdonaldi</i>

Rocha‐Olivares¹,

Leal-Navarro²,

Kimbrell³

et al. 2003

Sci. Mar.

Self Cite

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“…DNA was extracted using a DNeasy extraction kit (Qiagen) according to manufacturer's protocol. The mitochondrial cytochrome b gene was amplified via PCR using primers Gludg-L (5'TGA CTT GAA RAA CCA YCG TTG 3') (Palumbi et al 1991) and revThrRF (5'TCC GAC ATC TGG ATT ACA A 3') (Rocha-Olivares et al 1999). Briefly, 50 µl reaction volumes containing (67 mM Tris-HCl pH 8.8, 16.6 mM (NH 4 ) 2 SO 4 , 10 mM β-mercaptoethanol, 2 mM MgCl 2 , 800 µM dNTPs, 0.4 µM each primer, 2.5 units Taq DNA polymerase (New England Biolabs), and 100 ng of DNA template) were amplified using the following temperature profile in a 9600 GeneAmp PCR System (PerkinElmer); 94°C (2:00 min), 35 cycles of [94°C (0:45 min), 53°C (1:30 min), 72°C (1:30 min)], followed by 5 min at 72°C.…”

Section: Methodsmentioning

confidence: 99%

Shipboard identification of fish eggs and larvae by multiplex PCR, and description of fertilized eggs of blue marlin, shortbill spearfish, and wahoo

Hyde¹,

Lynn²,

Humphreys³

et al. 2005

Mar. Ecol. Prog. Ser.

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The study of the early life history of large, open-ocean pelagic fishes such as tunas and billfish, and the identification of spawning and nursery habitats, has been extremely difficult as these animals are intrinsically rare, highly migratory, and difficult to study in captivity. Traditional methods such as the assembling of a developmental series of life stages, or the culturing of unknown eggs and larvae to a point where they can be identified, has not been easy or fruitful for many pelagic species. The discovery of a putative spawning 'hot spot' off the Kona coast of Hawaii, coupled with the development of shipboard approaches to real time identification and adaptive sampling of eggs, may provide new approaches and insights into the spawning ecology and reproductive biology of these highly valuable but poorly known species. Here we report the use of a shipboard PCR based assay to differentiate species of istiophorid billfish larvae and identify eggs of istiophorid and xiphiid billfish, coryphaenid dolphinfish, and wahoo. A species-specific multiplex PCR assay was designed to amplify a single, unique size fragment of the mitochondrial cytochrome b gene for all 6 species of Indo-Pacific billfish, both dolphinfish, and the monospecific wahoo. A boiling technique used to extract DNA from larval eye tissue or an individual egg, combined with a single-step PCR assay and agarose electrophoresis, allowed species identification within 3 h of sample acquisition. This nearly real-time identification method for morphologically indistinguishable eggs and larvae provides an opportunity to employ adaptive sampling methods to increase sampling efficiency and will help in determining the spatial and temporal dimensions of spawning and nursery habitats offshore. This study describes the occurrence of blue marlin, dolphinfish, shortbill spearfish, swordfish and wahoo off the Kona coast by molecular approaches, and it provides the first description of the eggs of blue marlin, shortbill spearfish and wahoo.

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“…In this paper we describe for the first time sequences of the mitochondrial cytochrome b gene of 54 Sebastes and use them to evaluate the monophyly of the subgenus Sebastomus. In an accompanying paper (Rocha-Olivares et al, 1999) we specifically address the phylogenetic relationships among the species of Sebastomus using fewer species outside the subgenus and an expanded molecular data set.…”

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confidence: 99%