The Mekong giant catfish
Pangasianodon gigas
is endemic to the Mekong River and is one of the largest freshwater fish. This critically endangered species is a popular food for local people and a ...commercially essential fishery resource. Ecological knowledge of this catfish is required to conserve it. However, its ecology has not yet been well studied. We monitored the food intake of the Mekong giant catfish in a stable aquarium for over 13 years. We analyzed their feeding rhythms and fasting periods. The feeding rhythm (circannual rhythm) of the Mekong giant catfish over 13 years and its temporal variations were revealed. Four of the six catfish showed feeding cycles that extended more than one year (395.7 days). Five of the six catfish showed prolonged fasting periods over 30 consecutive days. These patterns coincide with the wet/dry seasons in Thailand, corresponding to the abundance of catfish food resources (
Cladophora
spp.). Furthermore, it is suggested that the Mekong catfish has acquired the physiological ability to tolerate a fasting state for about 1 year, possibly because this species may have survived many critical situations in the Mekong River in the past, such as food insufficiency. At the same time, however, this also indicates that the fish is highly dependent on
Cladophora
spp. as a food item and may not be able to substitute other food items. From these, reductions in food items or feeding habitats for catfish after damming in many places of the Mekong River basin may decrease the population size of this species.
Biodiversity is an important parameter for the evaluation of the extant environmental conditions. Here, we used environmental DNA (eDNA) metabarcoding to investigate fish biodiversity in five ...different estuaries in Japan. Water samples for eDNA were collected from river mouths and adjacent coastal areas of two estuaries with high degrees of development (the Tama and Miya Rivers) and three estuaries with relatively low degrees of development (the Aka, Takatsu, and Sendai Rivers). A total of 182 fish species across 67 families were detected. Among them, 11 species occurred in all the rivers studied. Rare fishes including endangered species were successfully detected in rich natural rivers. Biodiversity was the highest in the Sendai River and lowest in the Tama River, reflecting the degree of human development along each river. Even though nutrient concentration was low in both the Aka and Sendai Rivers, the latter exhibited greater diversity, including many tropical or subtropical species, owing to its more southern location. Species composition detected by eDNA varied among rivers, reflecting the distribution and migration of fishes. Our results are in accordance with the ecology of each fish species and environmental conditions of each river.
Colonization of new ecological niches has triggered large adaptive radiations. Although some lineages have made use of such opportunities, not all do so. The factors causing this variation among ...lineages are largely unknown. Here, we show that deficiency in docosahexaenoic acid (DHA), an essential ω-3 fatty acid, can constrain freshwater colonization by marine fishes. Our genomic analyses revealed multiple independent duplications of the fatty acid desaturase gene
in stickleback lineages that subsequently colonized and radiated in freshwater habitats, but not in close relatives that failed to colonize. Transgenic manipulation of
in marine stickleback increased their ability to synthesize DHA and survive on DHA-deficient diets. Multiple freshwater ray-finned fishes also show a convergent increase in
copies, indicating its key role in freshwater colonization.
Japanese eels (
Anguilla japonica
) utilize a broad range of habitats along the marine-freshwater ecotone during their growth phase in inland waters. This study aimed to analyze the foraging behavior ...of yellow-phase Japanese eels in connected fresh- and brackish water habitats and to connect foraging behavior and habitat use through the analysis of carbon (
δ
13
C) and nitrogen (
δ
15
N) stable isotopes. Stomach contents of eels collected in fresh- and brackish waters were analyzed to identify food sources. Values of
δ
13
C and
δ
15
N were analyzed in eels and their potential food sources, and used to predict the recent foraging patterns of eels in the Matsukawa-ura, a brackish water lagoon, and in three freshwater tributaries. Eels preyed on the benthic river community and the mudflat community of the lagoon. Gobiid fishes were found to be an important food source for eels in fresh- and brackish water habitats, while Japanese mitten crabs (
Eriocheir japonica
) and shore crabs (
Hemigrapsus
spp.) were major prey in fresh- and brackish waters respectively.
δ
13
C values of potential eel prey differed significantly between fresh- and brackish waters and were used to classify three recent patterns of foraging by the 73 eels included in this study: 1) freshwater foraging, 2) brackish water foraging, and 3) multiple-habitat foraging. The data suggested that some eels recently or frequently moved between fresh- and brackish water habitats while others demonstrated a higher fidelity to either fresh- or brackish waters. Isotopic characteristics of prey in the respective foraging habitats revealed the plasticity of habitat use of yellow eels in the study area. This study demonstrates an integrated approach to study habitat use and foraging behavior of eels. Furthermore, the study underlines the need to consider freshwater and estuarine habitats and the connectivity between them for eel management and conservation.
Japanese eel (
Anguilla japonica
) is a commercially important species; however, its population has declined in recent years. Appropriate conservation management, including habitat protection, is ...required to reverse this decline. However, their habitat use pattern during the riverine life stage is poorly understood. In this study, we investigated the longitudinal distribution and microhabitat of small-sized (<200 mm total length) and large-sized (≥200 mm total length) Japanese eels observed in 83 and 124 quadrats (1 m × 1 m), respectively, placed at seven stations in the Nikkeshi River in Fukushima Prefecture, Japan. Analysis using generalized linear models revealed that the eel density of both size classes decreased with increasing distance from the river mouth. In addition, the density of small-sized eels, but not large-sized ones, decreased as weir numbers increased. Moreover, analysis using generalized additive models showed that microhabitat uses differed between the size classes. The small-sized eels used near-shore habitats which had low current velocities. Their preferred habitats contained both complex substrates with smaller particle sizes and simple substrates with relatively large particle sizes. In contrast, the large-sized eels used both near-shore habitats with lower current velocities and the center of the river which had high current velocities. They preferred simple riverbed habitats with large particle-sized substrates and no underwater vegetation. These results suggest that there is a size-dependent change in the longitudinal distribution and microhabitat use of Japanese eels during their river life stage. These findings provide valuable information for the conservation and management of Japanese eels in rivers.
Sexual antagonism, or conflict between the sexes, has been proposed as a driving force in both sex-chromosome turnover and speciation. Although closely related species often have different ...sex-chromosome systems, it is unknown whether sex-chromosome turnover contributes to the evolution of reproductive isolation between species. Here we show that a newly evolved sex chromosome contains genes that contribute to speciation in threespine stickleback fish (Gasterosteus aculeatus). We first identified a neo-sex chromosome system found only in one member of a sympatric species pair in Japan. We then performed genetic linkage mapping of male-specific traits important for reproductive isolation between the Japanese species pair. The neo-X chromosome contains loci for male courtship display traits that contribute to behavioural isolation, whereas the ancestral X chromosome contains loci for both behavioural isolation and hybrid male sterility. Our work not only provides strong evidence for a large X-effect on reproductive isolation in a vertebrate system, but also provides direct evidence that a young neo-X chromosome contributes to reproductive isolation between closely related species. Our data indicate that sex-chromosome turnover might have a greater role in speciation than was previously appreciated.
Yellow-phase Japanese eel
Anguilla japonica
(Temminck & Schlegel, 1846) utilize a variety of anthropogenically impacted habitats. An extensive understanding of the trophic ecology and habitat use is ...necessary for the conservation of this endangered species. In this study, we analysed the trophic ecology and feeding habitat of Japanese eels in two small rivers, the Akugawa River and Takase River in Wakayama Prefecture, Japan, dominated by an urban landscape and agricultural land use, respectively. The main goals were to assess the dietary diversity and trophic niche width for eels of two size classes (small eels: ≤ 240 mm total length, large eels: > 240 mm total length) in both habitats. The suitability of both rivers as a feeding habitat for eels was also evaluated. The trophic ecology of eels was inferred based on analysis of carbon and nitrogen stable isotopes, as well as stomach contents. Our results indicated that both rivers are suitable habitats to accommodate this eel, but to varying degrees. The dietary diversity of small eels and trophic niche width differed between rivers, indicating limiting factors, such as insufficient food sources and unfavourable abiotic habitat requirements for small eels in urban rivers. Also, the body condition of eels was found to be lower in the urban Akugawa River than in the Takase River.
Divergent selection and adaptive divergence can increase phenotypic diversification amongst populations and lineages. Yet adaptive divergence between different environments, habitats or niches does ...not occur in all lineages. For example, the colonization of freshwater environments by ancestral marine species has triggered adaptive radiation and phenotypic diversification in some taxa but not in others. Studying closely related lineages differing in their ability to diversify is an excellent means of understanding the factors promoting and constraining adaptive evolution. A well-known example of the evolution of increased phenotypic diversification following freshwater colonization is the three-spined stickleback. Two closely related stickleback lineages, the Pacific Ocean and the Japan Sea occur in Japan. However, Japanese freshwater stickleback populations are derived from the Pacific Ocean lineage only, suggesting the Japan Sea lineage is unable to colonize freshwater. Using stable isotope data and trophic morphology, we first show higher rates of phenotypic and ecological diversification between marine and freshwater populations within the Pacific Ocean lineage, confirming adaptive divergence has occurred between the two lineages and within the Pacific Ocean lineage but not in the Japan Sea lineage. We further identified consistent divergence in diet and foraging behaviour between marine forms from each lineage, confirming Pacific Ocean marine sticklebacks, from which all Japanese freshwater populations are derived, are better adapted to freshwater environments than Japan Sea sticklebacks. We suggest adaptive divergence between ancestral marine populations may have played a role in constraining phenotypic diversification and adaptive evolution in Japanese sticklebacks.
Sex chromosomes turn over rapidly in some taxonomic groups, where closely related species have different sex chromosomes. Although there are many examples of sex chromosome turnover, we know little ...about the functional roles of sex chromosome turnover in phenotypic diversification and genomic evolution. The sympatric pair of Japanese threespine stickleback (Gasterosteus aculeatus) provides an excellent system to address these questions: the Japan Sea species has a neo-sex chromosome system resulting from a fusion between an ancestral Y chromosome and an autosome, while the sympatric Pacific Ocean species has a simple XY sex chromosome system. Furthermore, previous quantitative trait locus (QTL) mapping demonstrated that the Japan Sea neo-X chromosome contributes to phenotypic divergence and reproductive isolation between these sympatric species. To investigate the genomic basis for the accumulation of genes important for speciation on the neo-X chromosome, we conducted whole genome sequencing of males and females of both the Japan Sea and the Pacific Ocean species. No substantial degeneration has yet occurred on the neo-Y chromosome, but the nucleotide sequence of the neo-X and the neo-Y has started to diverge, particularly at regions near the fusion. The neo-sex chromosomes also harbor an excess of genes with sex-biased expression. Furthermore, genes on the neo-X chromosome showed higher non-synonymous substitution rates than autosomal genes in the Japan Sea lineage. Genomic regions of higher sequence divergence between species, genes with divergent expression between species, and QTL for inter-species phenotypic differences were found not only at the regions near the fusion site, but also at other regions along the neo-X chromosome. Neo-sex chromosomes can therefore accumulate substitutions causing species differences even in the absence of substantial neo-Y degeneration.
•Environmental DNA metabarcoding detects rare, endangered, and alien species in estuarine and coastal fish communities.•Latitudinal effect is found in estuarine and coastal fish communities across ...Japan.•Bank artificialisation negatively impacts estuarine and coastal fish community structures.•Ocean currents weakly affect estuarine and coastal fish community structures.•Environmental DNA metabarcoding is useful for large-scale assessing fish communities in estuaries and coasts.
Estuarine and coastal ecosystems are important habitats for many fish species. Large-scale patterns of estuarine and coastal fish communities can be affected by geographical factors, such as water temperature and latitude, that limit or allow fish dispersal, and/or by environmental factors that select locally adapted species. Furthermore, increased human activity has also altered fish diversity by modifying estuarine/coastal environments. Here, we used environmental DNA metabarcoding to study a large-scale pattern of estuarine/coastal fish communities across 25 watersheds in the Japanese Archipelago, and we assessed the effects of geographical, environmental, and anthropogenic factors in structuring these communities. Of the 290 fish species detected, 47 species were red-listed by the Japanese Ministry of Environment, and nine were alien. Non-metric multidimensional scaling showed that latitude and water temperature affected both river-mouth and coastal-sea fish communities. Although other anthropogenic factors did not affect these communities, bank artificialisation rates influenced both. The relationship between each fish community and ocean currents was weak. The number of red-listed fish affected both fish community structures, whereas that of alien species did not. The numbers of red-listed fish in coastal points and of all fish species were negatively influenced to the human population density. These findings provide useful information that may be used to conserve estuarine and coastal ecosystems.
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