While various technologies for high‐throughput genotyping have been developed for ecological studies, simple methods tolerant to low‐quality DNA samples are still limited. In this study, we tested ...the availability of a random PCR‐based genotyping‐by‐sequencing technology, genotyping by random amplicon sequencing, direct (GRAS‐Di). We focused on population genetic analysis of estuarine mangrove fishes, including two resident species, the Amboina cardinalfish (Fibramia amboinensis, Bleeker, 1853) and the Duncker's river garfish (Zenarchopterus dunckeri, Mohr, 1926), and a marine migrant, the blacktail snapper (Lutjanus fulvus, Forster, 1801). Collections were from the Ryukyu Islands, southern Japan. PCR amplicons derived from ~130 individuals were pooled and sequenced in a single lane on a HiSeq2500 platform, and an average of three million reads was obtained per individual. Consensus contigs were assembled for each species and used for genotyping of single nucleotide polymorphisms by mapping trimmed reads onto the contigs. After quality filtering steps, 4,000–9,000 putative single nucleotide polymorphisms were detected for each species. Although DNA fragmentation can diminish genotyping performance when analysed on next‐generation sequencing technology, the effect was small. Genetic differentiation and a clear pattern of isolation‐by‐distance was observed in F. amboinensis and Z. dunckeri by means of principal component analysis, FST and the admixture analysis. By contrast, L. fulvus comprised a genetically homogeneous population with directional recent gene flow. These genetic differentiation patterns reflect patterns of estuary use through life history. These results showed the power of GRAS‐Di for fine‐grained genetic analysis using field samples, including mangrove fishes.
Fish assemblage structures and environmental properties (e.g., water quality, sediment condition and prey abundance) were compared between tidal marshes, dominated by the common reed
Phragmites ...australis
, and bare sandy areas in the brackish-water Lake Hinuma, eastern Japan, by daytime seine net sampling in October 2014, and January, April and July 2015. A total of 4,076 fish individuals from 30 species and 5,431 individuals from 23 species were collected in the tidal marshes and sandy areas, respectively. Higher species richness in the former habitat was due to the restricted occurrence of ten species, including threatened or near threatened, only to that habitat. Species composition and the abundances of several dominant species, such as the commercially important icefish
Salangichthys microdon
and the goby
Acanthogobius lactipes
, also differed between the two habitats, although no interhabitat differences in the mean species and individual numbers per haul were found. Moreover, the individual number of small benthic and epiphytic crustacean feeders, including
A
.
lactipes
, was greater in the tidal marshes than in the sandy areas, whereas zooplankton feeders, including
S
.
microdon
, showed the opposite pattern. Such interhabitat differences in fish assemblage structures may be partly related to food availability, sediment condition and/or the presence or absence of vegetative structures. Because each of the two habitats harbored a unique fish assemblage, conservation efforts for both habitats are important for enhancing overall fish species diversity and sustaining fishery resources in Lake Hinuma.
Hybridization induced by human activities, such as crossbreeding between invasive and native species, can adversely affect the natural biodiversity of an ecosystem. In Japan, the endemic turtle ...species
is known to hybridize with the alien species
, and putative hybrids have been encountered in the wild. If
×
hybrids can readily crossbreed with
, the hybridization with
could lead to the extinction of pure
populations. However, information on the reproductive ability of
×
hybrids is limited. In this study, we collected wild-caught hybrids from across western Japan to assess their reproductive ability. We investigated the nesting season timing, clutch size, embryonic development, hatching success, and sperm viability. The results showed that female hybrids nested during the same months as the parental species and had similar clutch sizes and hatching success. No embryonic development abnormalities were detected, and viable sperm were observed in all hybrid male semen samples. In conclusion, the fertility of
×
hybrids appears to be similar to the fertilities of the parental species, posing a potential challenge for
conservation.
The diets and feeding guild structure of a freshwater reed belt fish assemblage (30 species) were examined in Lake Kitaura, part of the Lake Kasumigaura system, eastern Japan, from June to September ...in 2009 and 2010. Ontogenetic dietary shifts were recognized in 14 species, including several species (e.g.,
Cyprinus carpio
,
Tridentiger brevispinis
and
Hyporhamphus intermedius
) targeted by local fisheries. Juveniles of these species generally fed on zooplankton, later switching to other prey items (e.g., benthic chironomid larvae, gammaridean amphipods, shrimps, juvenile fishes, diatoms and decomposing reeds) with growth. A cluster analysis based on dietary overlaps showed that the reed belt fish assemblage comprised five feeding guilds (plant, zooplankton, benthic invertebrate, terrestrial insect and fish feeders). Of these, zooplankton feeders were the most abundantly represented in terms of species numbers, suggesting that the main food items for the fish assemblage were zooplankton (e.g., cladocerans, and calanoid and cyclopoid copepods). Fish feeders included five species, of which one was an alien species introduced from another region in Japan (
Opsariichthys uncirostris
) and three were from foreign countries (
Micropterus salmoides
,
Lepomis macrochirus macrochirus
and
Ictalurus punctatus
).
A total of 33 fish species, including commercially important and threatened species, were collected in three microhabitats (upper and lower areas of a small creek, and a marsh edge separate from the ...creek) of a salt marsh in Lake Hinuma, eastern Japan, in October 2014, and January, April and July 2015. Five species (
Acanthogobius lactipes
,
Oryzias latipes
,
Mugil cephalus cephalus
,
Tribolodon brandtii
and
Salangichthys microdon
) were dominant and accounted for 90.7% of the total number of individuals. The fish assemblage structures differed remarkably among the microhabitats, tending toward higher species and individual numbers on the marsh edge than in the upper creek. Species compositions also differed between the upper creek and the other microhabitats. Food availability (e.g., mysids, chironomid larvae and detritus) was considered to be a causative factor of the assemblage structure differences. In addition, microhabitat variations in water depth, dissolved oxygen level and bottom sediment, the upper creek being shallower with lower dissolved oxygen and higher sediment silt–clay proportion compared with the marsh edge, were also causative factors that indicated the importance of both biotic and abiotic environmental factors in the determination of fish distribution patterns across salt marsh microhabitats.
This study examined the effects of mangrove structure on fish distribution patterns and predation risks in southern Japan, utilizing field experiments in which artificial units mimicked mangrove root ...structure and canopy shade in a mangrove estuary. Fishes responded strongly to the different levels of root structure complexity but not to canopy shade, fish species richness and abundance being consistently higher in the units with roots than in those without roots, regardless of shade presence/absence. With increasing root density, fish abundance increased considerably, although with decreasing fish body size. A tethering experiment, employing the above units and the most abundant local fish Apogon amboinensis as representative of small fishes, revealed that the predation mortality rates of small fishes decrease with increasing root density. The results suggested that the sheltering effects provided by root structure against predators may be one of the most important factors determining the distribution patterns of mangrove-associated fishes, and at least partly explain the greater abundance of small-sized fishes in microhabitats with greater root densities.
•Fish abundance was higher in artificial unit with roots than in unit without roots.•Fishes did not respond to presence/absence of canopy shade.•Fish abundance increased with increasing root density.•Predation mortality rates of small fishes decreased with increasing root density.•Sheltering effect of root structure may be responsible for small fish distributions.
To clarify the role of salt marsh creeks as fish refuges, predation risks for two small species (the nektonic
Oryzias latipes
and benthic
Acanthogobius lactipes
) were compared among three ...microhabitats (upper and lower areas of a creek, and marsh edge separate from the creek) in a salt marsh in Lake Hinuma, eastern Japan, in July 2016, using daytime tethering experiments. The survival rate of
O. latipes
was highest in the upper creek (96%) and lowest at the marsh edge (62%), whereas no significant differences were found among the microhabitats for
A. lactipes
, with high survival rates (> 90%) in all microhabitats. Individual numbers of larger piscivorous fishes, determined by fyke net sampling, were greatest at the marsh edge, whereas no individuals were recorded in the upper creek, which was characterized by shallower depths and lower dissolved oxygen levels. The results suggested that the upper creek provides potential refugia for
O. latipes
, which occupied the upper and middle layers of the water column and exhibited hypoxia tolerance. The higher survival rate of benthic
A. lactipes
at the marsh edge may be due to their cryptic coloration in relation to bottom sediments, which helps them to avoid predation.
Crab assemblage structures in sandy flat, muddy flat and mangrove forest microhabitats in a mangrove estuary of the Urauchi River, Iriomote Island, southern Japan, differed clearly among the three ...microhabitats, species and individual numbers being greater inside the mangrove forest than on the flats. A similarity index showed distinct differences in species composition among the microhabitat assemblages, primarily due to the differential distributions of dominant species, such as the soldier crab
Mictyris guinotae
, sentinel crab
Macrophthalmus convexus
and sesarmid crab
Perisesarma bidens
. A canonical correspondence analysis indicated that the differences likely arose from among-microhabitat differences in the physical environment, the mangrove forest being characterized mainly by structurally complex mangrove roots, lower soil porewater temperatures and higher relative substrate elevation, the sandy flat by lower organic content of the sediment and higher porewater oxygen amount, and the muddy flat by higher levels of sediment water and organic material. The findings suggested that microhabitat-related physical differences are important factors determining crab distribution patterns in mangrove estuaries.
To determine differences in fish assemblage structures between beach morphodynamic types on an exposed sandy shore, three beach types (reflective, intermediate, and dissipative) were sampled at ...Fukiagehama Beach, Kyushu Island, southern Japan, in May, August, and November 2006 and 2007. Distinct differences in physical conditions and the amount of major prey invertebrates, such as copepods, mysids, and amphipods, were recognized between the three beach types. The reflective beach was characterized mainly by turbulent swashes, coarse sediment, and a low abundance of major prey invertebrates. In contrast, the dissipative beach was characterized mostly by benign swashes, fine sediment, and a high abundance of prey invertebrates. The intermediate beach tended toward an intermediate condition between the reflective and dissipative beaches. The fish assemblage structures also differed clearly between the three beach types, with species and individual numbers being greatest on the dissipative beach and lowest on the reflective beach. A similarity index indicated differences in species composition of the assemblages between the beach types. Such differences arose primarily from the differential distributions of two dominant trophic groups, zooplankton (mostly copepods) and epibenthic crustacean (mainly mysids and amphipods) feeders, between the beach types, both groups tending to increase in species and individual numbers from the reflective beach to the dissipative beach. In addition, the mean standard length of all fish collected in each month tended to decrease toward the dissipative beach. These results suggested that beach types strongly influence sandy beach fish assemblage structures.
The low digestibility of cellulose-rich detritus in primary consumers has been considered to limit its incorporation by higher level consumers. A recent study revealed, however, that the sesarmid ...crab Parasesarma bidens, which is a dominant benthic consumer in East Asian mangrove forests, possesses high cellulase enzyme activity enabling the species to efficiently digest and assimilate refractory detritus. To elucidate whether P. bidens acts as a trophic intermediate facilitating the incorporation of mangrove detritus into the food chain, the food habits of benthivorous fishes within a subtropical mangrove estuary were investigated. Stomach content analyses indicated that crabs, especially P. bidens, made a large contribution to the diets of the fishes examined, including the snapper Lutjanus argentimaculatus and the seabream Acanthopagrus sivicolus, which were both common at the study site. Furthermore, carbon and nitrogen stable isotope analyses revealed that mangrove detritus contributed significantly to all fish species examined, due to their consumption of P. bidens. These findings suggested that the detrital trophic pathway, via crabs with greater ability to digest/assimilate cellulose materials, plays an integral part in maintaining food chain structures in mangrove ecosystems.
