Environmental DNA phylogeography: Successful reconstruction of phylogeographic patterns of multiple fish species from cups of water

Phylogeography is an integrative field of science linking micro- and macro-evolutionary processes, contributing to the inference of vicariance, dispersal, speciation, and other population-level processes. Phylogeographic surveys usually require considerable effort and time to obtain numerous samples from many geographical sites covering the distribution range of target species; this associated high cost limits their application. Recently, environmental DNA (eDNA) analysis has been useful not only for detecting species but also for assessing genetic diversity; hence, there has been growing interest in its application to phylogeography. As the first step of eDNA-based phylogeography, we examined (1) data screening procedures suitable for phylogeography and (2) whether the results obtained from eDNA analysis accurately reflect known phylogeographic patterns. For these purposes, we performed quantitative eDNA metabarcoding using group-specific primer sets in five freshwater fish species belonging to two taxonomic groups from a total of 94 water samples collected from western Japan. As a result, three-step data screening based on the DNA copy number of each haplotype detected successfully eliminated suspected false positive haplotypes. Furthermore, eDNA analysis could almost perfectly reconstruct the phylogenetic and phylogeographic patterns obtained for all target species with the conventional method. Despite existing limitations and future challenges, eDNA-based phylogeography can significantly reduce survey time and effort and is applicable for simultaneous analysis of multiple species in single water samples. eDNA-based phylogeography has the potential to revolutionize phylogeography.     

Phylogeography of the Chinese false gudgeon,Abbottina rivularis,in East Asia,with special reference to the origin and artificial disturbance of Japanese populations

Ichthyological Research - The Chinese false gudgeon, Abbottina rivularis, is a common cyprinid fish that is widely distributed throughout continental East Asia, but exhibits a restricted,...     

Annandale’s collection of freshwater fishes from Inle Lake,Myanmar, housed in the Kyoto University Museum

Ichthyological Research -     

Effects of culture conditions on molecular weights of poly(3-hydroxyalkanoates) produced byPseudomonas putida from octanoate

Summary Time-dependent changes in the molecular weights of poly(3-hydroxyalkanoates) (P(3HA)) produced byPseudomonas putida from octanoate were investigated. The mole ratio of carbon to nitrogen sources (C/N), incubation temperature, concentration of octanoate, and pH of culture solution were varied to study the effects of culture conditions on the yield and molecular weights of P(3HA). The molecular weights of P(3HA) decreased with time to reach a constant value during incubation. When the incubation temperature and the concentration of octanoate were low, P(3HA) polymers of high molecular weights were produced.     

Formation of the branching pattern of blood vessels in the wall of the avian yolk sac studied by a computer simulation

The present study was performed to provide data to support the notion previously believed but not proved experimentally or theoretically, that blood vessels are formed by the selection of capillaries in the network. In an attempt to understand the mechanism of formation of blood vessel branching structures, the transformation of a capillary network to a branching system in the wall of quail yolk sac was successively recorded by a series of photographs, and a computer simulation was carried out for the process of in vivo vascularization based on the photographs. The simulation demonstrated that a positive feedback system participated in the formation of a branching structure. That is, vessels which had been much used were enlarged, whereas less used vessels were reduced in their size and finally extinguished. The enlarged vessels became major components of the branching system. As the body of an embryo grew, it was observed that polygonal capillary networks enlarged, which led each polygon of the network to divide into a few finer polygons. Then, some of the capillary vessels were again selected and formed a branching system. This process repeated during the body growth, indicating that the vascular system developed adaptively to the body growth. A region where the growth was fast, received much blood flow and produced finer networks of capillaries. Thus, it was experimentally demonstrated for the first time that capillaries in the network are successively selected by a positive feedback mechanism and form blood vessels.