Phylogeny of the Southeast Asian freshwater fish genus Pangio (Cypriniformes; Cobitidae)

Phylogenetic analysis and osteological comparison of the cave-dwelling spined loach, Bibarba parvoculus (Cypriniformes: Cobitidae), and its surface congener

Bibarba parvoculus, a depigmented and small-eyed, spined loach, is endemic to a karst cave in southern China. Both mitochondrial Cytb and nuclear RAG1 gene analyses indicate that B. parvoculus and its only surface congener, B. bibarba, form the basal-most lineage in the so-called Northern Clade of Cobitidae. Genetic divergence for Cytb is 10.3 % between B. parvoculus and B. bibarba. A duplication of the lamina circularis on the second and third pectoral rays occurs in male Bibarba species. The osteology of the two species is illustrated and compared using X-ray microtomography. Bibarba parvoculus has higher vertebral counts, a broader anterior part of the frontal bone at the orbital region and decreased sexual dimorphism when compared with B. bibarba. The coracoid, mesocoracoid and scapula are stouter in males of both species, but the three bones are autogenous in B. parvoculus, while fused with the cleithrum in B. bibarba. Specific differentiation of B. parvoculus is corroborated by both molecular and morphological evidence. The split between the two species is estimated to have occurred in the Early Miocene.

One northward, one southward: Contrasting biogeographical history in two benthic freshwater fish genera across Southeast Asia (Teleostei: Cobitoidea: Nemacheilus, Pangio)

Southeast Asia is one of the world's biodiversity hotspots, and the high level of diversity and endemism was reached by colonisation events as well as internal diversification. We investigate the phylogenetic relationships and biogeographic history of the loach genus Nemacheilus, which is widely distributed and common across freshwaters of Southeast Asia. In addition we present the ancestral range reconstruction of the related loach genus Pangio that commonly occurs in the same region as Nemacheilus. Our results reveal that the species currently classified as Nemacheilus in fact are a polyphyletic assemblage; most species are now retaining in a monophyletic Nemacheilus sensu stricto and five species belong to different lineages. We further indicate the existence of hidden diversity within Nemacheilus in the form of several undescribed species. Three major clades (Selangoricus, Masyae and Ornatus) are found within the genus Nemacheilus sensu stricto. These clades generally correspond to the species groups formerly defined on the basis of their pigmentation pattern. The biogeographic analyses show that Nemacheilus most likely originated in mainland Southeast Asia and subsequently expanded in a southward direction to Borneo, Sumatra and Java and the southern Malay Peninsula. In contrast, the genus Pangio originated in Sundaland, from where it extended several times northwards into Indochina and to northern India. Our results demonstrate that small freshwater fishes with restricted dispersal ability are very helpful for the reconstruction of biogeographic history. The contrasting biogeographic history of these two groups of small, benthic and related fish show how complex and case-specific the processes that lead to the biodiversity richness of Southeast Asia are.

Comparative mitogenome analyses uncover mitogenome features and phylogenetic implications of the subfamily Cobitinae

BACKGROUND

Loaches of Cobitinae, widely distributed in Eurasian continent, have high economic, ornamental and scientific value. However, the phylogeny of Cobitinae fishes within genera or family level remains complex and controversial. Up to now, about 60 Cobitinae mitogenomes had been deposited in GenBank, but their integrated characteristics were not elaborated.

RESULTS

In this study, we sequenced and analyzed the complete mitogenomes of a female Cobits macrostigma. Then we conducted a comparative mitogenome analysis and revealed the conserved and unique characteristics of 58 Cobitinae mitogenomes, including C. macrostigma. Cobitinae mitogenomes display highly conserved tRNA secondary structure, overlaps and non-coding intergenic spacers. In addition, distinct base compositions were observed among different genus and significantly negative linear correlation between AT% and AT-skew were found among Cobitinae, genus Cobitis and Pangio mitogenomes, respectively. A specific 3 bp insertion (GCA) in the atp8-atp6 overlap was identified as a unique feature of loaches, compared to other Cypriniformes fish. Additionally, all protein coding genes underwent a strong purifying selection. Phylogenetic analysis strongly supported the paraphyly of Cobitis and polyphyly of Misgurnus. The strict molecular clock predicted that Cobitinae might have split into northern and southern lineages in the late Eocene (42.11 Ma), furthermore, mtDNA introgression might occur (14.40 Ma) between ancestral species of Cobitis and ancestral species of Misgurnus.

CONCLUSIONS

The current study represents the first comparative mitogenomic and phylogenetic analyses within Cobitinae and provides new insights into the mitogenome features and evolution of fishes belonging to the cobitinae family.

Plio-Pleistocene phylogeography of the Southeast Asian Blue Panchax killifish, Aplocheilus panchax

The complex climatic and geological history of Southeast Asia has shaped this region’s high biodiversity. In particular, sea level fluctuations associated with repeated glacial cycles during the Pleistocene both facilitated, and limited, connectivity between populations. In this study, we used data from two mitochondrial and three anonymous nuclear markers to determine whether a fresh/brackish water killifish, Aplocheilus panchax, Hamilton, 1822, could be used to further understand how climatic oscillations and associated sea level fluctuations have shaped the distribution of biota within this region, and whether such patterns show evidence of isolation within palaeodrainage basins. Our analyses revealed three major mitochondrial clades within A. panchax. The basal divergence of A. panchax mitochondrial lineages was approximately 3.5 Ma, whilst the subsequent divergence timings of these clades occurred early Pleistocene (~2.6 Ma), proceeding through the Pleistocene. Continuous phylogeographic analysis showed a clear west-east dispersal followed by rapid radiation across Southeast Asia. Individuals from Krabi, just north of the Isthmus of Kra, were more closely related to the Indian lineages, providing further evidence for a freshwater faunal disjunction at the Isthmus of Kra biogeographic barrier. Our results suggest that Sulawesi, across the Wallace Line, was colonised relatively recently (~30 ka). Nuclear DNA is less geographically structured, although Mantel tests indicated that nuclear genetic distances were correlated with geographic proximity. Overall, these results imply that recent gene flow, as opposed to historical isolation, has been the key factor determining patterns of nuclear genetic variation in A. panchax, however, some evidence of historical isolation is retained within the mitochondrial genome. Our study further validates the existence of a major biogeographic boundary at the Kra Isthmus, and also demonstrates the use of widely distributed fresh/brackishwater species in phylogeographic studies, and their ability to disperse across major marine barriers in relatively recent time periods.

A DNA Barcode-Based Evaluation of the Southeast Asian Catfish Genus Hemibagrus Bleeker, 1862 (Teleostei: Siluriformes; Bagridae)

Species of the genus Hemibagrus are large river catfishes found throughout South-east Asia. The complexity of the region’s biogeographical history and the lack of well-defined morphological characters render the taxonomy and phylogenetic reconstruction of Hemibagrus problematical. Early molecular studies of the H. nemurus species group revealed extensive genetic subdivisions, the taxonomic status of which remained unclear. A recent, morphologically-based, revision of the genus provides an opportunity to clarify the taxonomic status of these lineages. We employ a DNA barcode derived from the mitochondrial cytochrome b gene to expand our genetic analyses of the genus and to test the congruence of morphologically and genetically based taxonomies. Secondly, we evaluate phylogenetic relationships among taxa. Thirdly, we describe the phylogeography of Hemibagrus in South-east Asia. The species groups and nominal species proposed in the morphology-based revision generally reflect a hierarchy of monophyletic groups based on phenetic and maximum likelihood reconstructions of mtDNA phylogenies. The most notable exception involves the definition of a morphologically cryptic group from North Borneo. H. nemurus from West Java appears to be a regional population of H. capitulum. The phylogeography of the genus has been principally influenced by the formation of North Borneo and the emergence of the Sunda Islands.

DNA Barcoding Indonesian freshwater fishes: challenges and prospects

With 1172 native species, the Indonesian ichthyofauna is among the world’s most speciose. Despite that the inventory of the Indonesian ichthyofauna started during the eighteen century, the numerous species descriptions during the last decades highlight that the taxonomic knowledge is still fragmentary. Meanwhile, the fast increase of anthropogenic perturbations during the last decades is posing serious threats to Indonesian biodiversity. Indonesia, however, is one of the major sources of export for the international ornamental trade and home of several species of high value in aquaculture. The development of new tools for species identification is urgently needed to improve the sustainability of the exploitation of the Indonesian ichthyofauna. With the aim to build comprehensive DNA barcode libraries, the co-authors have started a collective effort to DNA barcode all Indonesian freshwater fishes. The aims of this review are: (1) to produce an overview of the ichthyological researches conducted so far in Indonesia, (2) to present an updated checklist of the freshwater fishes reported to date from Indonesia’s inland waters, (3) to highlight the challenges associated with its conservation and management, (4) to present the benefits of developing comprehensive DNA barcode reference libraries for the conservation of the Indonesian ichthyofauna.