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.     

Dissecting the forces that shape crops: an interview with Ryohei Terauchi

Ryohei Terauchi is a Professor at Kyoto University and a Group Leader at the Iwate Biotechnology Research Center, Japan, studying the evolution of crops and their pathogens. In this interview, Ryohei describes his research interests, how the revolution in sequencing technology helped improve our understanding of orphan crops, and who are the scientists that inspire him.     

Purification and some properties of the isomaltodextranase of Actinomadura strain r10 and comparison with that of Arthrobacter globiformis t6

A newly isolated soil-actinomycete, Actinomadura strain R10 (NRRL B-11411), produces an extracellular isomaltodextranase (optinal pH, 5.0) that was purified to homogeneity. It exolytically releases isomaltose and a minor trisaccharide product,α-d-Glcp-(1→3)-α-d-Glcp, from dextran B-512 and, in addition, forms transient transisomaltosylation products. This pattern of products is qualitatively similar to that previously reported for the isomaltodextranase (EC 3.2.1.94, optimal pH, 4-0) of Arthrobacter globiformis T6 (NRRL B-4425). The Arthrobacter isomaltodextranase is most active on the (1→6)-α-d-glucopyranosidic linkage, but the relative activity increases with the degrees of polymerization of isomalto-oligosaccharide substrates. In contrast, the relative activity of Actinomadura isomaltodextranase is almost constant throughout the same series of substrates, and is much higher on 3 O- and 4-O-α-isomaltosyl-oligosaccharides than that exhibited by the Arthrobacter enzyme; the activity of Actinomadura isomaltodextranase on the α-(1→4) linkage is 3-4 times greater than on the α-(1→6). These results indicate that, generically, the bacterial isomaltodextranase is a glycanase, whereas the actinomycetal enzyme is a glycosidase. This difference is reflected in the hydrolysis of dextrans, especially of dextran B-1355 (fraction S), which has a high content of unbranched α-(1→3) linked residues. In the digest of this dextran with Arthrobacter isomaltodextranse, short-chain fragments accumulated that were absent when the Actinomadura enzyme was employed.