Yuichi Kano

GEDIMAP: a database of genetic diversity for Japanese freshwater fishes

Genetic diversity is a key component of biodiversity, and thus represents important information for evolutionary and conservation biology. DNA sequence data are primary sources of information on genetic diversity and are now accumulated and managed in international databases, such as the DNA Data Bank of Japan (DDBJ), the European Molecular Biology Laboratory (EMBL) Nucleotide Sequence Database, and GenBank of the US National Center for Biotechnology Information (NCBI). Such databases provide basic information that is used in most areas of contemporary bioscience (Brunak et al. 2002). MitoFish (Nishida 2009), a DNA database devoted to the mitochondrial DNA (mtDNA) genomes of fish, supports research into fish biology, and contains links to other international DNA databases and general fish databases (e.g., FishBase; Froese and Pauly 2009). Genetic diversity and divergence within and among local populations within a species are primary elements of biodiversity at the genetic level and are of essential conceptual and practical importance (Avise 2004). Genetic data from population genetic and phylogeographic studies based on various genetic markers, especially mtDNA sequences, are increasingly being reported. However, the DNA databases mentioned above do not provide effective functions for accumulating and searching for population genetic data, which are based on allele frequencies in each population with geographical data. Thus, when researchers want to browse or reuse data from previous studies, they typically need to reconstruct such a dataset by combining information described in original papers with that deposited in the DNA databases. Further, probably because of the lack of a platform for accumulating such information, a significant proportion of the papers do not provide fundamental information for reconstructing the population genetic data analyzed in those papers. Thus, it is difficult for anyone to use these valuable data secondarily. This situation impedes evolutionary and biogeographic research and applications in biodiversity conservation based on comprehensive population genetic data, and it leads to a waste of human, monetary, and wildlife resources. To improve this situation, we have constructed a comprehensive database for genetic diversity in Japanese freshwater fish. Freshwater fish are good targets for studying evolution and biogeography because of their restricted dispersal ability and conspicuous intraspecific divergence (Avise 2000; Watanabe et al. 2006). Research in this area will benefit from accumulated population genetic data. Here, we outline and describe the application of the database. ‘‘GEDIMAP’’ (genetic diversity and distribution map) is a public database primarily for mtDNA genetic diversity data within populations of freshwater fish in and around Japan (URL: http://gedimap.zool.kyoto-u.ac.jp/). The beta version was released in January 2008, and the current K. Watanabe (&) R. Kakioka K. Tominaga Department of Zoology, Division of Biological Science, Graduate School of Science, Kyoto University, KitashirakawaOiwakecho, Sakyo-ku, Kyoto 606-8502, Japan e-mail: watanak@terra.zool.kyoto-u.ac.jp

An online database on freshwater fish diversity and distribution in Mainland Southeast Asia

Mainland Southeast Asia, the region that includes Cambodia, Laos, Thailand, Vietnam and Peninsular Malaysia, is known for its high diversity of freshwater fishes (e.g., Myers et al. 2000; Dudgeon 2005; Kang et al. 2009). Recently, however, intensive exploitation pressures have been threatening this biodiversity. While some studies on fish fauna of the region have been made (e.g., Taki 1974; Rainboth 1996; Kottelat 2000; Vidthayanon and Premcharoen 2002), most have been of limited duration and geographical range, and the full extent of the effect of this exploitation on the fish diversity is not fully understood. The main obstacles standing in the way of a proper understanding of the threats to this biodiversity and determining the means to alleviate them have been hindered by several factors: one is a general shortage of trained scientists in the region proficient in fish taxonomy; another is that exchanges of the results of the taxonomical studies done by scientists in the region are few and far between. And finally there is a general lack of awareness of the significance of species diversity in ecosystems. Beginning in 2007, the Nagao Natural Environment Foundation (NEF), from Japan, has been working to improve this situation in the Mekong-Chao Phraya region, the results of which are presented in a new online database, ‘‘Fishes of Mainland Southeast Asia (FiMSEA)’’ (Fig. 1; URL: http://ffish.asia). Since the outset of the project, the NEF has worked in collaboration with a number of counterpart institutions in the region, namely: Can Tho University (Vietnam), The Inland Fisheries Research and Development Institute

Present status and conservation of the markless forms of stream-resident masu salmon Oncorhynchus masou (the so-called 'iwame') in Japanese mountain streams

As a markless form of stream-resident masu salmon (Oncorhynchus masou), the so-called ‘iwame,’ which can be distinguished from the sympatric normal form of the salmon by their plain body pattern, has been previously reported among seven local populations (A–G) in Japanese mountain streams. In the present study, all populations but B (where any information is entirely missing) were surveyed in a snorkeling survey (detection rate: 34.7%) in 2005 to elucidate the recent conditions of the markless forms. The ratios of the markless forms were 13.0% (9/69), 0.0% (0/364), 5.6% (68/1,205), 0.8% (1/132), 0.0% (0/1,181) and 64.6% (155/240) in A, C, D, E, F and G, respectively. Markless forms might indeed be already extinct in C and F where the stocking of non-native hatchery individuals has been carried out extensively. The same survey was repeated in D in 2009: the markless ratio had significantly decreased to 2.4% (19/783), although the reason for this was unknown. In D, the ratio of the markless form was higher in the mainstream as opposed to the tributaries in both 2005 and 2009, which might imply that the habitat of the markless form differs from that of the normal form.

Distribution pattern, threats and conservation of fish biodiversity in the East Tiaoxi, China

East Tiaoxi River is one of the largest inflowing rivers into Taihu Lake, and the fish fauna in the river is poorly understood. In the present study, an extensive survey of fish was conducted in October and November 2009, May and September 2010 and May 2011 covering a total of 55 sites along the whole river. A total of 84 freshwater fish species belonging to 8 orders, 18 families and 52 genera have been recorded. Among these are 35 species endemic to China, and 3 newly recorded exotic species. The fish composition varies greatly from headwaters to downstream. Based on cluster analysis with presence-absence data, the East Tiaoxi River is divided into four regions, specifically, the upper reach, middle-up reach, middle reach and lower reach. It is observed that species richness and the proportion of omnivorous species increased from upstream to downstream while the proportion of invertivorous species decreased consequently. Habitat alteration, overfishing, pollution and inland navigation adversely affect the fish diversity and ecosystem functioning in the East Tiaoxi River. To protect fish diversity more effectively in the area, the conservation of fish biodiversity in the North Tiaoxi River and Middle Tiaoxi River should be considered as a priority. Meanwhile, shallow zones or backwater areas should be created in the middle-lower reaches. Furthermore, river restoration, in terms of habitat creation, should be considered to protect the structure and diversity of fish communities, halt the progressive deterioration of freshwater ecosystems and sustain a valuable ecological resource for humans.

Fluctuation and variation in stream-fish assemblages after a catastrophic flood in the Miyagawa River, Japan

In the autumn of 2004, a typhoon caused a catastrophic flood of the Miyagawa River in Japan. Based upon snorkeling surveys conducted every autumn from 2005 to 2009, we monitored the post flood fluctuation of the local fish assemblages at nine sites of both the main stream and subsidiary streams of the river. Results revealed that species richness significantly increased from 2005 to 2009. In addition, the fish densities of eight species significantly increased over the same period, whereas the density of one species decreased, and that of eight others remained unchanged. Categorization based on Euclidean distance revealed five main clusters from the nine sites. Among these sites, fish assemblages within subsidiary streams were stable as they remained within the same clusters while those in the main stream were dynamically variable through time as they changed cluster membership. In addition, the Euclidean distance between two arbitrary fish assemblages was positively correlated with environmental distance (the Euclidean distance calculated based on river width, depth, velocity and pebble size), time distance, and spatial distance along the river. In conclusion, the fish assemblages were dynamically and regularly altered and varied in the five years after the flood, except for those in the subsidiary streams, and such variation was related to environmental, temporal and spatial variation.

Spatial and temporal variation of fish assemblages and their associations to habitat variables in a mountain stream of north Tiaoxi River, China

The spatial and temporal variations of the fish assemblages in mountain streams of China are poorly understood. The relationships between the fish assemblage and selected habitat features were examined in the North Tiaoxi River, one of headwaters of Taihu Lake. A total of 3,348 individuals belonging to 5 orders, 11 families, 25 genera and 34 species were collected including 33 native species and one invasive species. Among those, about 20 species were endemic to China. Non-metric Multidimensional Scaling (NMDS) was applied to compare fish assemblage structures from upstream to downstream during four seasons. Species assemblages differed along the stream continuum, but there was little apparent change associated with the seasons. Species richness and Shannon-Weaver index (H′) tended to increase along the stream continuum from the upstream to downstream and the proportion of invertivorous fish tended to significantly decrease along the continuum with a parallel significant increase in the percentage of omnivores. Fish assemblages were significantly related to both water quality and habitat structure variables. Canonical Correspondence Analysis ordinations (CCA) revealed that 6 of the 14 selected environmental variables had significant relationships with the fish assemblage such as distance to source, stream width, altitude, pH, water depth, and water velocity and different sampling sites were associated with different environmental variables in different seasons. The main differences in fish assemblage structure and diversity within the whole watercourse are probably related to large-scale factors such distance to source, altitude and stream width. Differences of instream characteristics are likely to be caused by natural variability of the ecosystems but also, in some case, by anthropogenic influence like human settlements, agriculture and river embankment and pollution from small factory.

Waterfalls drive parallel evolution in a freshwater goby

Waterfalls may affect fish distribution and genetic structure within drainage networks even to the extent of leading evolutionary events. Here, parallel evolution was studied by focusing on waterfall and the landlocked freshwater goby Rhinogobius sp. YB (YB), which evolved from amphidromous R. brunneus (BR). The fish fauna was surveyed at 30 sites in 11 rivers on Iriomote Island, Japan, the geography of which was characterized by terraces/tablelands with many waterfalls. We found that all YB individuals were distributed only above waterfalls (height 6.8–58.7 m), whereas BR, and other fishes, were mostly distributed below waterfalls. Mitochondrial DNA analysis showed that every YB local population above the waterfall was independently evolved from BR. In contrast, cluster analysis of nine morphological characters, such as fin color and body pattern, showed that the morphology of YB individuals held a similarity beyond the genetic divergence, suggesting parallel evolution has occurred relating to their morphology. Genetic distance between each YB local population and BR was significantly correlated with waterfall height (r2 = 0.94), suggesting that the waterfalls have been heightened due to the constant geological erosion and that their height represents the isolation period of YB local populations from BR (ca. 11,000–88,000 years). Each local population of BR was once landlocked in upstream by waterfall formation, consequently evolving to YB in each site. Although the morphology of YB had a high degree of similarity among local populations, finer scale analysis showed that the morphology of YB was significantly correlated with the genetic distance from BR. Consequently, there could be simultaneous multiple phases of allopatric/parallel evolution of the goby due to variations in waterfall height on this small island.

Linking mesohabitat selection and ecological traits of a fish assemblage in a small tropical stream (Tinggi River, Pahang Basin) of the Malay Peninsula

Mesohabitat selection in fluvial fishes was studied in a small tropical stream of the Malay Peninsula. A total of 681 individuals representing 24 species were sampled at 45 stations within heterogeneous stream (ca. 1 km in length), in which water depth, water velocity, substrate size, and riparian canopy cover were measured as environmental variables. A canonical correspondence analysis (CCA) yielded a diagram that shows a specific mesohabitat selection of the fish assemblage, in which the species were plotted widely on the CCA1-CCA2 biplot. Generalized linear model also revealed a significant pattern of the mesohabitat selection of several species. Water velocity and substrate size mainly separated on CCA1, indicating variation of pool (deep, slow-flow section) and riffle (shallow, fast-flow section) structures is a primary factor of mesohabitat selection in the fluvial fish assemblage. The mean body weight of species significantly correlated with CCA1; larger species tended to inhabit pools, while small ones occupied riffles. The riparian canopy cover separated on CCA2. The trophic level of species significantly correlated with CCA2; herbivorous species (low trophic level) selected open sites without riparian cover, whereas omnivorous/carnivorous (middle-high trophic level) species preferred highly covered sites. In conclusion, our results suggest that mesohabitat selection is closely related to the species feeding habit, which is consistent with the results of previous studies.

Population genetic structure, diversity and stocking effect of the oriental weatherloach (Misgurnus anguillicaudatus) in an isolated island

Genetic endemism of island organisms and the threat to such organisms provided by artificially introduced genes are aspects of major interest in evolutionary and conservation studies of fishes. In this paper the genetic population structure of the oriental weatherloach, Misgurnus anguillicaudatus, in Sado Island of Japan was elucidated by phylogeographic analysis based on partial mitochondrial control region sequences. The specimens were sampled at 62 sites in Sado Island and 14 sites on the mainland close to the island. We found various haplotypes of different origins, most of which had already been reported from the mainland and other places of Japan. This suggests that the loach has been historically introduced to the island from various regions of Japan. Of the 62 sites on the island, cultured/nonnative individuals were confirmed to have been stocked at eight specific sites for feeding of re-introduced Japanese crested ibis (Nipponia nippon). By a Mantel test, geographical and genetic distances were not significantly correlated among the local populations in Sado Island. However a significant correlation was found when the eight stocked local populations were excluded from the analysis. This implied that the genetic distribution pattern of the loach on the island has been disturbed by the stocking. In addition, the nucleotide diversity values of stocked local populations were significantly higher than those of other local populations, also a likely outcome of the stocking. In conclusion, the loach on the island likely had their origins in multiple historical introductions and colonizations, where more recent stocking for the ibis has caused further genetic disturbance to their local populations.

Ichthyofaunal assessment of the Gelami and Tinggi Rivers, Pahang River System, eastern Malay Peninsula, following construction of an adjacent building complex

The fluvial fish fauna of the Gelami and Tinggi Rivers, before and after the construction of a building complex in the adjacent forest, was compared on the basis of a literature survey (covering the period: 1997–2003) and a field survey in 2010. Forty fish species, representing 14 families and 5 orders, were recorded in total, the field survey including new records for Barbonymus gonionotus , Glyptothorax laosensis and Macrognathus maculatus . On the other hand, twelve species, including Osteochilus microcephalus, Luciosoma setigerum , Cyclocheilichthys apogon , Tor tambroides , Acantopsis choirorhynchos , Homaloptera orthogoniata , Clarias teijsmanni , Clarias macrocephalus , Pseudomystus leiacanthus , Mystus nigriceps , Parambassis siamensis and Trichopodus trichopterus , that had been listed previously, were not recorded by the latter. An analysis of the results using McNemar’s chi-squared test indicated that the fish fauna of the rivers has changed significantly following the construction, continuous quantitative monitoring and habitat evaluation being necessary for conservation of future biodiversity levels.