Nian-Hong Jang-Liaw

Molecular phylogeny of 48 species of damselfishes (Perciformes: Pomacentridae) using 12S mtDNA sequences

Phylogenetic relastionships within the family pomacentridae teleostei: Perciformes) were inferred by analyzing a portion of the 12S mitochondrial ribosomal DNA gene. Thirty-four pomacentrid species were sequenced for this study and the resulting data were combined with previously published pomacentrid sequence data to form a combined matrix of 53 pomacentrids representing 48 different species in 18 genera. Four outgroup species were also drawn from published data; these taxa were taken from the other three putative families of the suborder Labroidei, as well as a single representative of the family Moronidae. The data set contained 1053 data columns after alignment according to ribosomal secondary structure and the removal of all ambiguously aligned positions. The resulting strict consensus tree topology generally agreed with the previous molecular hypothesis, and recovers a monophyletic Pomacentridae and subfamily Amphiprioninae. The two other subfamilies included, Chrominae and Pomacentrinae, were found to be polyphyletic. A monophyletic group consisting of the Amphiprioninae, Pomacentrus, Acanthochromis, Amblyglyphidodon, Neoglyphidodon, Chrysiptera, Neopomacentrus, and Teixeirichthys was found. This group was recovered as the sister group to a clade consisting of a paraphyletic Chromis and a monophyletic Dascyllus. A sister-group relationship between the genus Pomacentrus and the subfamily Amphiprioninae was observed.

Complete mitochondrial genome of the megamouth shark Megachasma pelagios (Chondrichthyes, Megachasmidae)

Abstract Here we describe the complete mitochondrial genome sequence of the megamouth shark, Megachasma pelagios, which is an extremely rare species of deepwater shark. The circle genome (16,694 bp) consists of 13 protein coding, 22 tRNA, 2 rRNA genes and 1 control region. It has the typical vertebrate mitochondrial gene arrangement.

Complete mitochondrial genome of the Kikuchi's minnow Aphyocypris kikuchii (Teleostei, Cyprinidae)

We have sequenced the complete mitochondrial genome of the Kikuchis minnow, Aphyocypris kikuchii (Oshima 1919), which is an endemic species to Taiwan. The complete mitochondrial genome is 16,601 bp in size, containing 37 genes coding for 13 proteins, 2 rRNAs, 22 tRNAs, and 1 control region. It has the typical vertebrate mitochondrial gene arrangement. The sequence information could play an important role in resolving the conflict on its current taxonomic position and preservation of genetic resources for helping conservation of the endangered species.

Comparative phylogeography of bagrid catfishes in Taiwan

A phylogeographic analysis of two bagrid catfishes in Taiwan was conducted using sequence data from a portion of the mitochondrial DNA (mtDNA) control region. For Pseudobagrus brevianalis, which is most probably endemic to Taiwan, a total of eight haplotypes were detected in 189 specimens from nine river systems covering its entire distribution range, from northern to central western areas of the island. Obvious genetic differentiation was observed among its populations (average FST = 0.753); in particular, the northernmost Tamsui River population was fixed for a single endemic haplotype. Nested clade phylogeographic analysis (NCPA) indicated that the dispersal center of mtDNA was the area around the Touchien River and Holong River, north to the Miaoli Plateau, in northwestern Taiwan, suggesting both northward and southward dispersal in this species. There was no evidence for the validity of P. taiwanensis, the nominal species described from Taiwan, morphologically similar to P. brevianalis. We confirmed that P. adiposalis was distributed discontinuously in three river systems; analysis of 42 specimens from the rivers indicated a total of four haplotypes and population differentiation (average FST = 0.876). Fixation into a largely differentiated haplotype in the northernmost Tamsui River population was also found in this species, but different processes for this phylogeographic pattern were implied for the two species. Comparison with P. ussuriensis, a widespread continental species morphologically similar to P. adiposalis, suggested the possibility that P. adiposalis is a group of local populations of P. ussuriensis in Taiwan. Two migration routes vs. random fixation scenarios for the population structure of P. adiposalis are discussed with information on other fishes and the geological history of the island.

Intraspecific relationships of populations of the brown frog Rana sauteri (Ranidae) on Taiwan, inferred from mitochondrial cytochrome b sequences.

We studied the phylogenetic relationships among populations of Rana sauteri using partial sequences of the mitochondrial cytochrome b gene from 244 samples from 29 localities in Taiwan. We detected 77 haplotypes among these sequences. The phylogenetic trees contained five distinct lineages: the northern (NL), eastern (EL), southern hill (SHL), northern mountain (NML), and southern mountain (SML) lineages, defined by geographical distribution. The lineage phylogeny did not support the two-species hypothesis inferred from larval morphology. To describe the possible colonization history of R. sauteri in Taiwan, we propose hypotheses of within-island differentiation and a multiple-invasion model. Using a molecular clock, we estimated the order of divergence times between lineages in order to test the migration hypothesis. The multiple-invasion model was well supported by the phylogeny and a nested clade network.

Phylogeography of the fanged dicroglossine frog, Limnonectes fujianensis (Anura, Ranidae), in Taiwan

A phylogenetic analysis of Taiwanese fanged dicroglossine frog, Limnonectes fujianensis (Anura, Ranidae), was conducted to examine its genetic diversification using sequence data from a portion of the mitochondrial DNA (mtDNA) cytochrome b sequences. We collected genetic data from 200 individuals at 23 localities in Taiwan and three localities in China. A neighbor-joining tree of 39 haplotypes revealed two clades in Taiwan and a clade in China, each showing restricted geographical distribution. The pattern of geographical divergence suggests a single invasion into Taiwan. Divergence times between clades were inferred using molecular clock tests. The population relationship of L. fujianensis between Taiwan and mainland China, and the phylogenetic relationships with its congeners, e.g., L. bannaensis, L. fragilis and L. kuhlii, were obtained and discussed.

Complete mitochondrial genome of the Moltrecht's minnow, Aphyocypris moltrechti (Teleostei, Cyprinidae), in comparison with A. kikuchii

We sequenced the complete mitochondrial genome of the Moltrechts minnow, Aphyocypris moltrechti, which is known as an endemic species to Taiwan. The complete mitochondrial genome is 16,617 bp in size, consisting of 37 genes coding for 13 proteins, 2 rRNAs, 22 tRNAs, and 1 control region. Its gene arrangement pattern was identical with most vertebrates. We compared the mitochondrial genome of A. moltrechti with that of the Kikuchis minnow, Aphyocypris kikuchii, which had been considered closely related to A. moltrechti within a same genus. Nucleotide sequence divergence (K2P distance) between the two whole mitochondrial genomes was 11.62%. The detailed comparison between the mitochondrial genomes of two species was done.

Complete mitochondrial genome of the Chinese rasbora Rasbora steineri (Teleostei, Cyprinidae)

We describe the complete mitochondrial genome sequence of the Chinese rasbora, Rasbora steineri, which is a small cyprinid distributed in southeastern Asia. The circle genome (16,530 bp) consists of 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes and 1 control region. It has the typical vertebrate mitochondrial gene arrangement.

The complete mitochondrial genome of the tiger tail seahorse, Hippocampus comes (Teleostei, Syngnathidae)

The complete mitochondrial genome of the tiger tail seahorse was sequenced using a polymerase chain reaction-based method. The total length of mitochondrial DNA is 16,525 bp and includes 13 protein-coding genes, 2 ribosomal RNA, 22 transfer RNA genes, and a control region. The mitochondrial gene arrangement of the tiger tail seahorse is also matching the one observed in the most vertebrate creatures. Base composition of the genome is A (32.8%), T (29.8%), C (23.0%), and G (14.4%) with an A+T-rich hallmark as that of other vertebrate mitochondrial genomes.

The complete mitochondrial genome of the salmon shark, Lamna ditropis (Chondrichthyes, Lamnidae).

Abstract The complete mitochondrial genome of the salmon shark consists of 16,699 bp and includes 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes, 1 replication origin region and 1 control region. The mitochondrial gene arrangement of the salmon shark is the same as that of most vertebrates. Base composition of the genome is A (29.6%), T (28.6%), C (27.1%), and G (14.8%).