National Fisheries University

Background Biotic diversification in ancient lakes is shaped by complex geological histories and genetic exchange among populations. The Malili Lake system on Sulawesi Island represents a classic natural laboratory for studying freshwater fish evolution and harbors multiple endemic Oryzias species that diversified under repeated hydrological reorganizations. Previous genomic analyses inferred that two sympatric species in Lake Towuti (O. profundicola and O. loxolepis) experienced a single ancient introgression event from a "ghost lineage" derived from O. marmoratus inhabiting another lake. However, recent taxonomic re-evaluation has revealed the presence of an extant O. marmoratus population within Lake Towuti itself. This finding suggests that the putative ghost lineage may in fact represent a living population co-occurring in the lake, calling for a re-examination of the introgression history and speciation mode in Lake Towuti. Results By incorporating newly generated ddRAD-seq data from the true O. marmoratus in Lake Towuti, we reanalyzed phylogenetic relationships and population genetic structure among Malili Lake Oryzias. Previously reported major phylogenetic relationships and inter-lake introgression patterns were largely reproduced. In contrast, TreeMix and f(4)-statistic analyses revealed that introgression signals previously attributed to a "ghost lineage" into O. profundicola and O. loxolepis instead originated from the extant O. marmoratus population coexisting within Lake Towuti. Demographic model comparisons explicitly incorporating within-lake gene flow further supported a scenario in which O. profundicola and O. loxolepis diverged in allopatry, subsequently came into secondary contact within Lake Towuti, and later experienced additional gene flow following secondary contact with O. marmoratus that entered the lake. Conclusion Our results demonstrate that introgression from the O. marmoratus lineage into O. profundicola and O. loxolepis was not a single ancient event, but rather a more sustained process.This finding highlights the critical importance of taxonomic resolution for accurately inferring introgression and divergence history. Comparative studies across other ancient lakes on Sulawesi will be valuable for understanding how the timing and nature of gene flow from third lineages influence patterns of population divergence and the strength of reproductive isolation.

Size-dependent survival is a well-known phenomenon in fishes, typically positive but with exceptions. I investigated survival of chum salmon, Oncorhynchus keta, smolts in coastal waters of the Shiretoko Peninsula, northern Japan, using tethering experiments. Of 111 smolts, only 11 survived. Survival was explained solely by body size and was negatively correlated with it. These results suggest that predator foraging strategy and hatchery-wild differences may underlie the observed pattern, with implications for salmon management strategies.

Homeostasis is a fundamental property of life, intricately regulated by genetic information in extant organisms. However, a central mystery in the origin of life is how primordial life, before the establishment of a genetic system, could have adapted to fluctuating environments and acquired homeostatic capabilities. To address this question, this paper proposes an abstract, proof-of-concept mathematical model to explore how homeostasis could emerge through self-organization from a simple chemical reaction network, without reliance on genetic information or externally defined setpoints. Crucially, the system does not require direct sensory information of either the target value (Topt) or its current state (Tcell); it only evaluates the resulting global performance metric (replication rate). The model utilizes an internal Lotka-Volterra chemical oscillator within a protocell as a “search engine” to periodically vary the system’s phenotype (cell pigmentation). The system then adjusts its internal state by evaluating only the temporal correlation between these internal fluctuations and a single, global performance metric—the cell’s self-replication rate. This simple loop of “exploration by oscillation and optimization by correlation” is realized through a chemically implementable mechanism termed “antagonistic memory molecules.” Numerical simulations demonstrate that the model can autonomously converge to and maintain the optimal temperature for its self-replication, even amid significant fluctuations in the external environment (e.g., solar luminosity and water temperature). These results present the model as a constructive proof-of-concept, demonstrating how a core process of active inference under the free energy principle—minimizing prediction error through action—can emerge from a simple physicochemical system. This research provides a concrete scenario for the acquisition of adaptive capabilities at the origin of life and offers new guiding principles for the design of self-adaptive systems.

Some deep-sea crustaceans produce larger eggs, which are hypothesised to be an adaptation to the food-scarce deep-sea environment, promoting development of larger offspring with enhanced starvation resistance. Larger offspring also adhere more strongly to benthic substrates, reducing the risk of being advected by currents. Limited dispersal likely increases genetic differentiation among regional populations. Pandalus coccinatus and its putative sister species, Pandalus spinosior, are cold-water pandalid shrimps that live at depths of 400-500 m along the Pacific and Okhotsk coasts of Japan, respectively. Unlike other marine species, P. coccinatus and P. spinosior develop directly without a pelagic larval stage and produce a small number of large eggs, making them ideal models for investigating the relationship between reproductive strategy and genetic patterns in deep-sea crustaceans. In this study, we collected 24-30 specimens from each of three locations across the species range and investigated genetic differentiation among populations. We used mitochondrial DNA (mtDNA) cytochrome c oxidase subunit I (COI) gene sequences and multiplexed inter-simple sequence repeat genotyping, employing MIG-seq, which provides genome-wide single-nucleotide polymorphisms (SNPs). We also examined diagnostic morphological traits and assessed congruence between morphological taxonomy and genetic patterns revealed by molecular markers. Our findings present a conceptual framework in which deep-sea adaptations lead to reduced larval dispersal, increased genetic differentiation, and allopatric speciation, accompanied by morphological divergence. This study suggests that benthic deep-sea animals may undergo significant diversification as a result of both adaptive traits and environmental barriers, potentially explaining the unexpectedly high levels of biodiversity in deep-sea benthic communities.

Microalgae of the genus Nannochloropsis are one of the diets suited for mass production of rotifers used in marine finfish larviculture. Manipulation of the cellulose synthase gene in Nannochloropsis can facilitate degradation of the cell-wall structure and potentially enhance nutritional accessibility to rotifers. We aimed to evaluate growth potentials of rotifers Brachionus rotundiformis and B. plicatilis fed the cellulose synthase gene-knockout strain (Delta CESA) of Nannochloropsis oceanica (NO). Just-hatched individuals of two rotifer species were reared until death under feeding treatments with Chlorella vulgaris (control), NO-wild type (WT), or NO-Delta CESA. For the rotifer B. rotundiformis, both the WT- and Delta CESA-fed groups had higher total offspring production than the control diet group. The B. rotundiformis fed Delta CESA had shorter reproductive periods than those fed WT, despite total offspring production being comparable between the two treatments. This resulted in higher daily offspring production earlier in the culture period and an acceleration of population growth for B. rotundiformis. As in B. rotundiformis, B. plicatilis also exhibited longer lifespan and enhanced total offspring production when fed the WT strain of Nannochloropsis. However, there were no differences between those fed the control diet and those fed the Delta CESA strain. In vitro microalgae digestion tests revealed that cell nutrients were released from Delta CESA at 10 times the amount released from WT when exposed to crude enzymes from B. plicatilis, possibly implying a high risk of adiposis in B. plicatilis. Delta CESA should enhance rotifer growth when used properly as a species-specific diet.