Biology subjects

Akita, T.

Publications and source records attributed to Akita, T..

10 recordsLinked to original sources

bioRxiv2026

Demographic stochasticity can drive population variability even in large populations

Demographic stochasticity is generally expected to contribute little to population variability when census abundance is large, because random demographic events are increasingly averaged across many individuals. This expectation, however, depends on how evenly individuals contribute to reproduction. In many natural populations, reproductive success is highly skewed, so that a large census population can coexist with a much smaller effective number of breeders (Nb). Although Nb is commonly used as a genetic measure of contemporary effective size, it also summarizes variation in reproductive contribution and may therefore contain information about demographic variability. Here, we develop a female-based age-structured theoretical framework linking Nb to temporal variability in mature population abundance, with N denoting the census number of mature females and Nb the effective number of female breeders. Recruitment variability arises from non-Poisson reproductive variation and environmental stochasticity, and its transmission to mature abundance is described by a life-history coefficient, {gamma}, determined by survival, maturation, and the contribution of overlapping cohorts. When the Poisson component of recruitment variance is negligible and Nb/N is sufficiently small, the coefficient of variation in mature abundance, CV[N], can be approximated from Nb, environmental variability, and {gamma}, with little additional information from census abundance. This approximation does not require specification of the functional form of the relationship between adult abundance and recruitment. Stochastic age-structured simulations closely reproduced the analytical prediction, even when additional demographic stochasticity in survival was included. Substantial fluctuations in mature abundance occurred at census sizes on the order of 105 when Nb was small, whereas overlapping cohorts buffered recruitment fluctuations. Because Nb can be estimated genetically from samples of a single cohort, the framework provides a direct link between genetic monitoring and population dynamics. More broadly, these results show that large census abundance alone does not guarantee weak demographic variability and highlight the potential of genetic data to inform expected population fluctuations when detailed demographic information is limited.

ecology↗

bioRxiv2026

Genetic population structure and demographic history of Pacific cod in Japanese waters: Implications for stock identification using SNP markers

Pacific cod is a key species in North Pacific fisheries, and its stock assessment and management units are separated according to biological, geographical, and administrative information. Understanding the fine-scale genetic population structure of this species is crucial for effective management, particularly in regions such as Japan, where complex coastal geography and localised fisheries management prevail. Therefore, in this study, we analysed genome-wide single nucleotide polymorphisms (SNPs; 6,035 loci) in 496 individuals of Pacific cod sampled from 33 sites around the Japanese archipelago via genotyping by random amplicon sequencing-direct (GRAS-Di) analysis. Our analyses revealed three major genetic groups: Japanese Broad Range, Northernmost Honshu-Hokkaido (NHH), and Western Sea of Japan groups. These groups exhibited significant genetic differentiation (global FST = 0.056), distinct levels of nucleotide diversity, and group-specific genome-wide patterns of Tajimas D. Moreover, demographic history reconstruction based on whole-genome sequencing of three representative individuals revealed that each genetic group followed distinct demographic trajectories since the last glacial period. Importantly, the NHH group, related to the Mutsu Bay spawning aggregation and previously shown to exhibit strong natal homing in tagging surveys, was genetically identified for the first time in this study. Isolation-by-distance was observed across Japanese waters and within the Japanese Broad Range group, but not within the NHH group, suggesting that gene flow is generally restricted by geographic distance, except within the NHH group. To evaluate the potential for genetic stock identification, we extended a resampling-based cross-validation framework by incorporating outlier detection to assess marker selection strategies. Over 500 background SNPs were required to achieve >90% assignment accuracy for genetic stock identification, whereas only eight or more outlier SNPs showed comparable performance. These findings suggest that carefully selected SNP panels, particularly those including outlier loci, substantially improve stock discrimination. Overall, our study demonstrates the fine-scale genetic structure and demographic history of Pacific cod in Japanese waters and highlights the utility of practical marker strategies for enhancing the biological realism of fisheries assessment and supporting sustainable fisheries management.

genetics↗

bioRxiv2026

Inferring the number of spawning events from young-of-year genomic samples and otolith-derived birth dates: a richness-estimator perspective

Estimating the number of spawning events per female is key to understanding individual reproductive output in batch-spawning species, yet direct observation of spawning is often infeasible in the wild. Recent advances in genetic kinship inference enable the identification of maternal half siblings from young-of-the-year genomic samples, while otolith-based age determination provides reconstruction of offspring birth dates. Here we develop an offspring-based framework for estimating the number of clutches produced by individual females by integrating sibling structure inferred from genomic data with otolith-derived birth-date information. By recasting clutch identification as a richness estimation problem, we apply the Chao1 estimator to infer the total number of spawning events from incomplete offspring samples. Using simulation experiments, we evaluate how sampling effort and heterogeneity in clutch size influence clutch detection and estimation. Under uniform clutch-size distributions, modest numbers of offspring sampled per maternal family (10-20 offspring) yield accurate estimates of the total number of clutches, substantially outperforming naive counts of observed birth-date classes by recovering information from rare or unobserved spawning events. In contrast, skewed or multimodal clutch-size distributions lead to underestimation at low sample sizes, indicating that uneven reproductive output increases sampling effort required for reliable inference. Overall, our results demonstrate how offspring genomic data and otolith-derived birth dates can be jointly leveraged to reconstruct individual spawning histories under realistic sampling constraints. This perspective provides a framework for inferring within-season reproductive schedules in batch-spawning species, and highlights opportunities for integrating genomic and life-history data in fisheries monitoring and reproductive ecology.

ecology↗

bioRxiv2024

Strong dependence of demographic stochasticity on a small effective number of breeders in iteroparous species

The effective number of breeders (Nb) is widely used as a genetic summary statistic, yet its role in shaping demographic variability has remained underexplored. Here, we present a theoretical framework for iteroparous species that integrates Nb into the stochastic recruitment process of the number of adults (N) by modeling individual-level relationships between adult females and their offspring. We partition recruitment variation into parental, non-parental, and environmental components, and show that demographic stochasticity arising from non-Poisson reproduction, summarized by Nb, can amplify environmental variance. Assuming an equal sex ratio and no sex-specific variation, we derive an approximation linking Nb to this amplification when Nb/N < 0.1. For instance, Nb < 42 can increase recruitment variance by more than 5%. A key advantage of this approach is that Nb can be estimated from genetic data collected from a single cohort, making it applicable in data-limited or conservation-priority systems. Our framework highlights a distinct causal pathway by which increased reproductive variance contributes to demographic variability and extinction risk, especially in species where both Nb and Nb/N are small. These findings provide new theoretical justification for using Nb as a life-history-independent metric to quantify demographic stochasticity and connect genetic monitoring with population viability analysis.

ecology↗

bioRxiv2022

A Novel Bacterial Speciation Process Observed in a Symbiotic Marine Population

Incomplete lineage sorting (ILS), where ancestral polymorphisms persist through rapid speciation, is a hallmark of eukaryotic radiations but undocumented in prokaryotes. We report ILS associated speciation in the globally distributed marine bacterium Sulfitobacter, analyzing 74 strains from 16 oceanic regions and 15 ecosystem types. Genomic analysis resolved over ten genetically monomorphic clades sharing near uniform whole genome divergence (average nucleotide identity {approx}95%). However, individual genes and even adjacent nucleotide sites support conflicting phylogenetic relationships among clades. The median length of nearly identical sequence blocks supporting alternative topologies is less than 50 base pairs, far shorter than typical adaptive cassettes. This within gene, site level discordance provides a diagnostic signature of ancestral polymorphism retention following rapid fragmentation, ruling out adaptive gene sweeps. Demographic inference places this radiation on a timescale of tens of millennia, 100 to 1,000 fold faster than eukaryotic ILS, and traces the clades to a hyper polymorphic, highly recombining ancestor. Neutral simulations show that transient mutation surges or population bottlenecks alone can generate this pattern, without adaptive selection or ecological partitioning. By bridging eukaryotic and prokaryotic speciation paradigms, our findings demonstrate that ILS, previously considered exclusive to sexual eukaryotes, can drive rapid, neutral diversification in bacteria, expanding the mechanisms known to generate prokaryotic biodiversity.

microbiology↗

bioRxiv2022

Estimating contemporary migration numbers of adults based on kinship relationships in iteroparous species

In this paper, we describe the development of estimators for the contemporary migration number and rate of adults between two populations in iteroparous species. The proposed estimators are based on known half-sibling (HS) and/or parent-offspring (PO) relationships observed between the populations across breeding seasons. The rationale is that the HS and PO pairs exhibit information about the occurrence frequency of parental movements during the breeding interval. The proposed method allows for variance in the average number of off-spring per parent both within and between populations. In addition, coupled with the PO pairs found within the population, the estimators can be obtained from only genetic data. Generally, a sample size representing the square root of the population size is required to obtain meaningful information regarding migration. We describe a detailed evaluation of the performance of the estimators by running an individual-based model, and the results provide guidance regarding sample sizes to ensure the required accuracy and precision. Furthermore, given that there are few effective methods to estimate adult movement (especially when populations cannot be genetically distinct), we discuss the usefulness of this proposed kinship assignment method in terms of conservation biology and wildlife management.

ecology↗

bioRxiv2019

Nearly unbiased estimator of Ne/N based on kinship relationships

This study develops a nearly unbiased estimator of the ratio of the contemporary effective mother size to the census size in a population, as a proxy of the ratio of contemporary effective size to census size (Ne/N). The proposed estimator is based on both known mother-offspring (MO) and maternal-sibling (MS) relationships observed within the same cohort, in which sampled individuals in the cohort probably share MO relationships with sampled mothers. The rationale is that the frequency of MO and MS pairs contains information regarding the contemporary effective mother size and the (mature) census size, respectively. Therefore, the estimator can be obtained only from genetic data. Moreover, We also evaluate the performance of the estimator by running an individual-based model. The results of this study provide the following: i) parameter range for satisfying the unbiasedness, and ii) guidance for sample sizes to ensure the required accuracy and precision, especially when the order of the ratio is available. Furthermore, the results demonstrate the usefulness of a sibship assignment method for genetic monitoring, providing insights for interpreting environmental and/or anthropological factors fluctuating Ne/N, especially in the context of conservation biology and wildlife management.

ecology↗

bioRxiv2019

Nearly unbiased estimator of contemporary effective population size using within-cohort sibling pairs incorporating parental and non-parental reproductive variations

In this study, we developed a nearly unbiased estimator of contemporary effective mother size in a population, which is based on a known maternal half-sibling relationship found within the same cohort. Our method allows for variance of the average number of offspring per mother (i.e., parental variation, such as age-specific fecundity) and variance of the number of offspring among mothers with identical reproductive potential (i.e., non-parental variation, such as family-correlated survivorship). We also developed estimators of the variance and coefficient variation of contemporary effective mother size and qualitatively evaluated the performance of the estimators by running an individual-based model. Our results provide guidance for (i) a sample size to ensure the required accuracy and precision when the order of effective mother size is available and (ii) a degree of uncertainty regarding the estimated effective mother size when information about the size is unavailable. To the best of our knowledge, this is the first report to demonstrate the derivation of a nearly unbiased estimator of effective population size; however, its current application is limited to effective mother size and situations in which the sample size is not particularly small and maternal half-sibling relationships can be detected without error. The results of this study demonstrate the usefulness of a sibship assignment method for estimating effective population size; in addition, they have the potential to greatly widen the scope of genetic monitoring.

ecology↗

bioRxiv2018

Nearly unbiased estimator of adult population size based on within-cohort half-sibling pairs incorporating flexible reproductive variation

Close-kin mark-recapture (CKMR) is a kinship-based method for estimating adult abundance. However, the application of CKMR is limited to using a kinship relationship that is not affected by family-correlated survivorship, which leads to a biased estimation. We developed a nearly unbiased estimator of the number of mothers in a population, which is based on the known maternal half-sibling relationship found within the same cohort. Our method allowed for variance of the averaged offspring number per mother (between-age variation) and for variance of the offspring number among mothers with the same reproductive potential (within-age variation). Estimators of its variance and coefficient variation were also provided. The performance of the estimators was quantitatively evaluated by running an individual-based model. Our results provide guidance for (i) a sample size to archive the required accuracy and precision when the order of mother size is available and (ii) a degree of uncertainty regarding the estimated mother size when information about the mother size is not available. Taken together, these findings offer an opportunity to shed light on the usefulness of analysing within-cohort half-sibling pairs and will greatly widen the scope of the CKMR method.

ecology↗

bioRxiv2017

The coalescent for prokaryotes with homologous recombination from external source

The coalescent process for prokaryote species is theoretically considered. Prokaryotes undergo homologous recombination not only with other individuals within the same species (intra-specific recombination) but also with other species (inter-specific recombination). This work particularly focuses the latter because the former has been well incorporated in the framework of the coalescent. We here developed a simulation framework for generating patterns of SNPs (single nucleotide polymorphisms) allowing integration of external DNA out of the focal species, and a simulator named msPro was developed. We found that the joint work of intra- and inter-specific recombination creates a complex pattern of SNPs. The direct effect of inter-specific recombination is to increase the amount of polymorphism. Because inter-specific recombination is very rare in general, it creates a regions with an exceptionally high level of polymorphisms. Following an inter-specific recombination event, intra-specific recombination chop the integrated foreign DNA into small pieces, making a complicated pattern of SNPs that looks as if foreign DNAs were integrated multiple times. This work with the msPro simulator would be useful to understand and evaluate the relative contribution of intra- and inter specific recombination to creating complicated patterns of SNPs in prokaryotes.

evolutionary biology↗