Takeshi Kikko’s research while affiliated with Kindai University and other places

Honmoroko ( Gnathopogon caerulescens ), an endangered species endemic to Lake Biwa, is adversely affected by the desiccation of eggs caused by the water level management and deterioration of spawning habitats (lakeshore vegetation zone). Despite a recent study of foreshore spawning of the species having suggested that some local environmental conditions may be related to foreshore spawning habitats selection by the species, no quantitative studies have examined the conditions that determine the suitability of such habitats. The present survey of Honmoroko eggs around emergent vegetation zones along the foreshore in two study areas indicated that Honmoroko selectively spawn at shallow sites with greater water velocity, utilizing emergent plants, such as Salix spp. . The findings confirmed the importance of protecting the spawning habitats around the Lake Biwa shoreline and have important implications for the controlled management of Lake Biwa water levels with regard to Honmoroko spawning.

Near the southern limit of its Japanese distribution range, the white-spotted charr Salvelinus leucomaenis inhabits headwater tributaries of inlet rivers to Lake Biwa, Shiga Prefecture, although failing to migrate to the lake from those tributaries. Even though lower depths (>30 m) of the north basin of the lake are cold throughout the year, the only salmonid inhabiting the lake is the Biwa salmon Oncorhynchus sp. However, between 2018 and 2021, five white-spotted charr were caught in Lake Biwa, their phenotype being characterized by large whitish spots, reminiscent of the anadromous form off northern Japan. Mitochondrial DNA Cyt b haplotype analysis data supported their origin as hatchery-reared specimens from Samegai Trout Farm (Shiga Prefecture), the latter having sourced white-spotted charr from several Japanese populations, including northern Japan (descending anadromous exists). Such white-spotted charr, upon release from the hatchery, may have migrated to the lake during winter, due to a retained migration instinct.

With a view towards effective fisheries management, catch features, including catch per unit effort (CPUE; number of fish caught per angler per hour), sex ratio and maturity status of Honmoroko Gnathopogon caerulescens caught by recreational anglers using long dip nets in the Shinyamaji River inlet to Ibanaiko Lagoon, adjacent to Laka Biwa, were examined. Mature individuals caught from April to June 2020 and 2021 were characterized by the CPUE ranging from 10 to 50, and high gonadosomatic index, the sex ratio tending to be more female biased during the periods of higher CPUE. The higher catches achieved by using long dip nets may be related to the spawning behavior of Honmoroko in the inlet to the lagoon, indicating the importance of evaluating the recreational catches for the management of Honmoroko in Lake Biwa.

Migratory freshwater fish species are particularly susceptible to population decline because they rely on multiple habitats and open passages to complete their life cycle. Understanding the migratory patterns of cyprinids is thus essential for their management and conservation. Gnathopogon caerelescens, a small cyprinid species endemic to Lake Biwa (Japan), is one of the most important targets of inland fisheries. However, their abundance has dramatically decreased. By using an extensive alizarin complexone-mark-and-recapture program for of G. caerelescens juveniles, together with the collaboration of commercial fishermen, this cyprinid fish was demonstrated as: (1) migrating from a nursery lagoon toward the main lake and moving along the near-shore from spring to autumn; (2) migrating from the near-shore shallow habitats to off-shore deep habitats from autumn to winter; and (3) migrating to a nursery lagoon from off-shore deep habitats from winter to spring. These results highlighted the importance of protecting individual spawning/nursery habitats, and maintaining connectivity between each spawning/nursery habitat and the lake system.

Isaza Gymnogobius isaza, a small freshwater goby endemic to Lake Biwa, Japan, is categorized as “Endangered” in the International Union for Conservation of Nature Red List of Threatened Species; nevertheless, it remains subject to fishing without any specific management strategies. The sex ratio, and gonadosomatic and hepatosomatic indices of Isaza caught by commercial bottom trawl and set net while migrating to and from an offshore pelagic area and nearshore spawning area were investigated in Lake Biwa from winter to early summer. Male spawning migrations preceded those of females. In addition, mortality during spawning was male-biased. Both findings suggested a possible impact of the commercial set net fishery on Isaza reproduction. Future conservation and fisheries management of the species need to be considered.

For stock enhancement of the pond smelt Hypomesus nipponensis in Japan, eyed eggs have been transplanted into numerous lakes, ponds, and reservoirs throughout the country from a number of major lake populations. For consistent effective stock enhancement, propagation skills in the recipient lakes, including conservation of spawning habitats and construction of artificial spawning sites, are necessary, independent of eyed-egg transplantation from other lakes. The physical characteristics of the spawning habitats selected by pond smelt in 6 rivers feeding Lake Yogo were surveyed, focusing on water velocity, depth, and substrate. The analysis using Jacobs’ selective index shows that pond smelt selectively spawn at sites in shallow depth (5–30 cm), with moderate water velocity (10–50 cm/s), utilizing gravel, pebbles, and sand in riffles, as opposed to mud and silt near the river mouths. The biological information gained in this study is useful background for the conservation of spawning habitats and construction of artificial spawning sites in other regions of Japan.

Gnathopogon caerulescens , an endemic fish of Lake Biwa, Japan, is one of the most important fishes for lake fisheries. It has been listed as an endangered species following its population decline in the 1990s and thus needs conservation. An increasing number of studies have recently stressed on the importance of incorporating genetic diversity for conservation purposes. In this study, we aimed to evaluate the mitochondrial DNA haplotype composition of G. caerulescens using environmental DNA (eDNA) to determine the genetic diversity of this species. We developed an eDNA‐based haplotyping approach using high‐throughput sequencing (HTS), which can accurately detect and eliminate erroneous HTS reads, even when the target sequences are differentiated by a single or a few mismatches. Field surveys using the developed method successfully revealed the genetic structure of local G. caerulescens populations. We found star‐shaped haplotype networks with two major haplotypes accompanied by several rare haplotypes for all local populations except one, which suggested that the G. caerulescens population had undergone a historical expansion, and its population size did not shrink to the extent that rare haplotypes were eliminated during the population decline in the 1990s. We also observed that the genetic diversity was lower in the northern populations in terms of haplotype number and haplotype diversity ( h ), suggesting that the decline in population was more severe in the north than in the south. We demonstrated the practical use of eDNA analysis in population genetics of endangered species. Continuous monitoring using this approach would facilitate the conservation and management of fish resources.

The stock of the Isaza goby Gymnogobius isaza is known to fluctuate greatly. Because initial recruitment is considered to have a high impact on stock fluctuations, it is important to understand the spatial distribution patterns of Isaza larvae. We conducted towing net surveys at variable depths to clarify the vertical distribution of the larvae. Preflexion Isaza larvae were distributed in the lower water temperature range (10-15℃) regardless of depth, whereas flexion larvae thereafter were distributed under the thermocline. Polyarthra spp. were confirmed as the initial food source of the larvae, in addition to copepod nauplii (previously reported). Flexion (and thereafter) larvae preyed mainly on Eodiaptomus japonicus. The study suggested that Isaza larvae change their feeding preference, associated with habitat change and ontogenetic development in feeding functions.

The possible recovery of a white-spotted charr population in a small tributary of a river to Lake Biwa, following removal of previously stocked red-spotted masu salmon, was investigated by electrofishing. We captured 30 red-spotted masu salmon and two hybrids of these two species in 2014. Prior to the stocking of red-spotted masu salmon, the estimated number of white-spotted charr ≥ 100 mm standard length (SL) in the tributary was more than 200 individuals in 2005, which had reduced to fewer than 30 individuals by 2014 when 30 red-spotted masu salmon plus two charr/masu salmon hybrids were captured. However, no red-spotted masu salmon were captured from 2015 to 2017, indicating the success of a red-spotted masu salmon removal program. The estimated number of white-spotted charr ≥ 100 mm SL ranged from 25 to 91 individuals between 2015 and 2017, implying a great reduction of red-spotted masu. The estimated population size of the former increased further to 171–221 individuals in 2021, comparable to 2005. These results suggest that the white-spotted charr population declined due to stocking of red-spotted masu salmon, and recovered following removal of the latter.

Habitat fragmentation is a pervasive threat to biodiversity. Linearly arranged habitats such as stream networks are particularly vulnerable to fragmentation. As the landscape becomes increasingly human dominated, conservation values of fragmented habitat patches cannot be overlooked. It is critical to understand the demographic mechanisms of population persistence or extirpation in fragmented patches. We studied dynamics of spatially structured populations of two Japanese landlocked salmonids persisting for >30 years in a headwater stream network that is highly fragmented due to low‐head dams in the mainstem. We parameterised and analysed spatial matrix population models using 9‐year mark–recapture data. Tributaries supported higher survival rates in some life stages, and movement was asymmetrical from the tributaries to the mainstem. Accordingly, population growth rates were higher in the tributary patches than the mainstem in both species despite the tributaries occupying only 12% or 18% of the study stream network by surface area. The tributaries harboured more physically and hydraulically complex instream habitats (i.e. higher wood density and flow refugia), indicating that habitat patch quality was more important than habitat patch size in determining the dynamics of these spatially structured populations. Tributary locations in the stream network were important in the trajectory of these populations. The upstream‐dwelling charr persisted in the highly fragmented mainstem patch (i.e. six impassable infrastructures in a <500 m patch) due to immigration of fish from upstream including the tributary. However, the downstream‐dwelling salmon has been gradually extirpated from the uppermost section of the fragmented mainstem patch because they could not maintain a positive population growth rate after loss of emigrants was accounted for and immigration was prevented due to fragmentation. Synthesis and applications. We conclude that small tributaries have rescued the spatially structured populations from extirpation (charr) or at least slowed down extirpation (salmon). Legal protection of headwaters as aquatic habitats is weak globally. Our results suggest that stream management plans underestimating the demographic value of small tributaries will likely fail to conserve populations of headwater inhabitants and therefore endanger aquatic biodiversity. We discuss conservation implications of this study related to habitat connectivity and fisheries management.