Check out our New Publishers' Select for Free Articles

Biochemical Genetics (v.42, #9-10)

Phylogeographic Analysis of the Firefly, Luciola lateralis, in Japan and Korea Based on Mitochondrial Cytochrome Oxidase II Gene Sequences (Coleoptera: Lampyridae) by Hirobumi Suzuki; Yasushi Sato; Nobuyoshi Ohba; Jin-Sik Bae; Byung-Rae Jin; Hung-Dae Sohn; Sam-Eun Kim (pp. 287-300).

Luciola lateralis is widely distributed throughout the Korean Peninsula, northeast China, Sakhalin, and Japan. Two ecological types are recognized in Japan based on flash and hatching time characteristics. The mitochondrial cytochrome oxidase II gene was surveyed by restriction fragment length polymorphism analysis for Japan (46 populations) and Korea (two populations). Eleven haplotypes were detected. Gene trees revealed that haplotypes between Japan and Korea are much more differentiated in nucleotide sequences (8.1%) than those within Japan (0.3–1.4%) and Korea (0.7%). Haplotypes between Honshu and Hokkaido are not separated as clades, and the two ecological types cannot be segregated from each other phylogenetically. We suggest that the Japanese populations of this species may have dispersed within one million years ago and that ecological differences may be the result of physiological adaptation to cold climates.

Keywords: Phylogeography; Lampyridae; Luciola lateralis ; mtDNA; CO II

Phylogenetic Analysis of Mediterranean Mugilids by Allozymes and 16S mt-rRNA Genes Investigation: Are the Mediterranean Species of Liza Monophyletic? by Anna Rita Rossi; Andrea Ungaro; Sabina De Innocentiis; Donatella Crosetti; Luciana Sola (pp. 301-315).

The family Mugilidae (Pisces, Mugiliformes) includes species which are present in all tropical and temperate regions. Six species, Chelon labrosus, Mugil cephalus, Liza aurata, L. ramada, L. saliens, Oedalechilus labeo, are commonly found in the Mediterranean. These species have been widely studied through morphological, biochemical, and molecular markers. However, their phylogenetic relationships, and therefore the assumed monophyly of Liza species, still remain unclear. To further investigate this topic, gene–enzyme systems and sequences of the partial 16S rRNA mitochondrial gene were analyzed in Italian samples of all six Mediterranean species. The phylogenetic reconstructions indicated M. cephalus as being the most divergent species and the existence of a main cluster including all the Mediterranean species of Liza and C. labrosus. The parametric bootstrap approach adopted to test alternative phylogenetic hypotheses indicated that the Mediterranean species of Liza do not form a monophyletic group exclusive of Chelon.

Keywords: Mugilidae; grey mullets; allozymes; mitochondrial DNA; parametric bootstrap

Biochemical Polymorphisms and Genetic Relationships in Rodents of the Genera Oryzomys and Oligoryzomys (Sigmodontinae) from Brazil by Marcos Vinícius Perini; Tania A. Weimer; Sidia M. Callegari-Jacques; Margarete S. Mattevi (pp. 317-329).

An electrophoretic analysis of 12 allozyme systems (14 loci, 40 alleles) was performed in the rodent genera Oryzomys and Oligoryzomys, in order to determine the levels of genetic variability within and among populations and species. One hundred and fifty-five individuals from 16 populations of Oryzomys russatus, Or. angouya, Oligoryzomys flavescens, and Ol. nigripes species were trapped in nine Brazilian localities. Genetic divergence among populations, as well as the interpopulational gene diversity, was higher in Oryzomys than in Oligoryzomys. The dendrogram of the phenetic relationships among the 16 populations of these four species displays three clusters: the first one joins the Ol. flavescens populations with those of Ol. nigripes; the second groups the populations of Or. russatus, and the last assembles the populations of Or. angouya. The genetic parameters analyzed reveal that the species belonging to the genus Oryzomys are genetically more structured than those of Oligoryzomys, the latter presenting lower levels of intrademe genetic differentiation (G _ST′).

Keywords: biochemical polymorphisms; allozymes; Oligoryzomys ; Oryzomys ; Sigmodontinae; population genetics

Phylogenetic Relationships of 12 Penaeoidea Shrimp Species Deduced from Mitochondrial DNA Sequences by Jiexia Quan; Zhimeng Zhuang; Jingyao Deng; Jixun Dai; Ya-ping Zhang (pp. 331-345).

DNA sequences of an 847 bp fragment of mitochondrial cytochrome oxidase subunit I (COI) gene and a 514 bp fragment of 16s rRNA gene were determined to examine the phylogenetic relationships of 12 Penaeoidea shrimp species (Penaeus chinensis, Penaeus japonicus, Penaeus penicillatus, Penaeus vannamei, Penaeus canaliculatus, Trachypenaeus curvirostris, Metapenaeus affinis, Metapenaeus ensis, Metapenaeopsis barbata, Parapenaeus fissuroides, Parapenaeopsis hardiwickii, Solenocera crassicornis). Both fragments of the swimming crab Portunus trituberculaus chosen as the outgroup were also sequenced. Intraspecific sequence divergence of 0.24–1.2% in the COI gene was found in 5 species, while no intraspecific variation was observed in the 16s rRNA gene. Three phylogenetic trees based on the 1361 bp combined sequences of COI and 16s rRNA were concordant in indicating the following suggestions: (1) phylogenetic relationship of the 11 Penaeidae species based on our result support the opinion of Burkenroad (Burkenroad, M. D. (1983). Crustacean Issues 3:279–290) on the basis of morphological features; (2) it seems more reasonable to class Solenocera crassicorni in the family Penaeidae; (3) the fragment of the COI gene chosen here appears to be a good marker for speciation studies and population analysis in Crustaceans, while the 16s rRNA gene fragment here seems suitable for examining phylogenetic relationships at the species or genus levels in Crustaceans. Our time estimates suggest that Penaeus and Metapenaeus might have separated about 6.38 × 10⁶–7.98 × 10⁶ years BP in the post-Miocene, and the species separation within Metapenaeus and Penaeus might occur 0.08 × 10⁶–0.4 × 10⁶ years BP in the late Pleistocene.

Keywords: molecular phylogeny; mtDNA; COI gene; 16s rRNA gene; Penaeoidea

Quantitative Trait Locus Analysis of Plasma Cholesterol and Triglyceride Levels in C57BL/6J × RR F₂ Mice by Jun-ichi Suto; Yuji Takahashi; Kenji Sekikawa (pp. 347-363).

A highly significant cholesterol quantitative trait locus (QTL) (Cq6) was identified on chromosome 1 in C57BL/6J × RR F₂ mice. The Cq6 was located over the gene for apolipoprotein A-II (Apoa2), and the RR allele was associated with increased plasma cholesterol. C57BL/6J has Apoa2 ^a alleles and RR has Apoa2 ^b alleles. Three different Apoa2 alleles are known on the basis of amino acid substitutions at four residues. Analysis with partial Apoa2 congenic strains possessing Apoa2 ^a, Apoa2 ^b, and Apoa2 ^c alleles revealed that the Apoa2 ^b allele is unique in the ability to increase cholesterol among the three Apoa2 alleles, and that the Ala-to-Val substitution at residue 61 may be crucial as far as cholesterol metabolism is concerned. We also investigated the question of whether the Apoa1 gene is responsible for the cholesterol QTLs (Cq4 and Cq5) that had been identified previously on chromosome 9 in C57BL/6J × KK-A^y/a F₂ and in KK × RR F₂, but not in C57BL/6J × RR F₂ mice. Similar to Apoa2 alleles, three different Apoa1 alleles with two successive amino acid substitutions were revealed among the strains. However, we could not correlate Apoa1 polymorphisms with the occurrence of QTLs in these three sets of F₂ mice.

Keywords: quantitative trait locus (QTL); cholesterol; triglyceride; apolipoprotein A-I (Apoa1); apolipoprotein A-II (Apoa2)

Cloning and Sequencing of the Growth Hormone Gene of Large Yellow Croaker and Its Phylogenetic Significance by Yun Chen; Yaping Wang; Shunping He; Zuoyan Zhu (pp. 365-375).

Using conserved primers and the PCR reaction, the growth hormone (GH) gene and the 3'-UTR of the large yellow croaker (Pseudosciaena crocea) were amplified and sequenced. The gene structure was analyzed and compared to the GH genes of 5 other percoid fish downloaded from Genbank. Also the GH gene of the large yellow croaker and the genes from 14 Percoidei and 2 Labroidei species were aligned using Clustal X. A matrix of 564 bp was used to construct the phylogenetic tree using maximum parsimony and neighbor-joining methods. Phylogenetic trees by the two methods are identical in most of the clades with high bootstrap support. The results are also identical to those from morphological data. In general, this analysis does not support the monophyly of the families Centropomidae and Carangidae. But our GH gene tree indicates that the representative species of the families Sparidae and Sciaenidae are a monophyletic group.

Keywords: Sciaenidae; Perciformes; GH gene; phylogenetics

Note: Identification of Three Novel Insertion/Deletion Mutations in Wilson Disease's Gene by Yuxin Fan; Long Yu; Yongzhu Han; Mingshan Ren; Renmin Yang; Shouyuan Zhao (pp. 377-384).

Note: Polymorphisms of the Second Exon of MHC-DRB Gene in Chinese Local Sheep and Goat by Sun Dongxiao; Zhang Yuan (pp. 385-390).

Sections

Personal tools

Biochemical Genetics (v.42, #9-10)

Sections

Personal tools

Local resources

Biochemical Genetics (v.42, #9-10)