Toshihide Kitakado

Hyper-expansion of large DNA segments in the genome of kuruma shrimp, Marsupenaeus japonicus

BackgroundHigher crustaceans (class Malacostraca) represent the most species-rich and morphologically diverse group of non-insect arthropods and many of its members are commercially important. Although the crustacean DNA sequence information is growing exponentially, little is known about the genome organization of Malacostraca. Here, we constructed a bacterial artificial chromosome (BAC) library and performed BAC-end sequencing to provide genomic information for kuruma shrimp (Marsupenaeus japonicus), one of the most widely cultured species among crustaceans, and found the presence of a redundant sequence in the BAC library. We examined the BAC clone that includes the redundant sequence to further analyze its length, copy number and location in the kuruma shrimp genome.ResultsMj024A04 BAC clone, which includes one redundant sequence, contained 27 putative genes and seemed to display a normal genomic DNA structure. Notably, of the putative genes, 3 genes encode homologous proteins to the inhibitor of apoptosis protein and 7 genes encode homologous proteins to white spot syndrome virus, a virulent pathogen known to affect crustaceans. Colony hybridization and PCR analysis of 381 BAC clones showed that almost half of the BAC clones maintain DNA segments whose sequences are homologous to the representative BAC clone Mj024A04. The Mj024A04 partial sequence was detected multiple times in the kuruma shrimp nuclear genome with a calculated copy number of at least 100. Microsatellites based BAC genotyping clearly showed that Mj024A04 homologous sequences were cloned from at least 48 different chromosomal loci. The absence of micro-syntenic relationships with the available genomic sequences of Daphnia and Drosophila suggests the uniqueness of these fragments in kuruma shrimp from current arthropod genome sequences.ConclusionsOur results demonstrate that hyper-expansion of large DNA segments took place in the kuruma shrimp genome. Although we analyzed only a part of the duplicated DNA segments, our result suggested that it is difficult to analyze the shrimp genome following normal analytical methodology. Hence, it is necessary to avoid repetitive sequence (such as segmental duplications) when studying the other unique structures in the shrimp genome.

Empirical Bayes Inference of Pairwise FST and Its Distribution in the Genome

Populations often have very complex hierarchical structure. Therefore, it is crucial in genetic monitoring and conservation biology to have a reliable estimate of the pattern of population subdivision. FSTs for pairs of sampled localities or subpopulations are crucial statistics for the exploratory analysis of population structures, such as cluster analysis and multidimensional scaling. However, the estimation of FST is not precise enough to reliably estimate the population structure and the extent of heterogeneity. This article proposes an empirical Bayes procedure to estimate locus-specific pairwise FSTs. The posterior mean of the pairwise FST can be interpreted as a shrinkage estimator, which reduces the variance of conventional estimators largely at the expense of a small bias. The global FST of a population generally varies among loci in the genome. Our maximum-likelihood estimates of global FSTs can be used as sufficient statistics to estimate the distribution of FST in the genome. We demonstrate the efficacy and robustness of our model by simulation and by an analysis of the microsatellite allele frequencies of the Pacific herring. The heterogeneity of the global FST in the genome is discussed on the basis of the estimated distribution of the global FST for the herring and examples of human single nucleotide polymorphisms (SNPs).

Abundance estimation of diving animals by the double-platform line transect method

In conventional line transect theory, it is assumed that all animals on the line are detected. This article introduces an extended and generalized hazard probability model without the need for such an assumption. The proposed method needs a survey design with independent observers having the same visual region and assumes an explicit distinction of simultaneous and delayed duplicates. It can take account of random heterogeneity caused by surfacing behavior as well as systematic heterogeneity by covariate effects. Furthermore, it can be easily extended to cases in which data from incompletely independent observers are available. The abundance estimate is based on the Horvitz-Thompson estimator in unequal detectability sampling scheme. Simulation studies suggest that the proposed method has good performance. The method is applied to a real data set on Antarctic minke whales in the illustration.

An Integrated-Likelihood Method for Estimating Genetic Differentiation Between Populations

The aim of this article is to develop an integrated-likelihood (IL) approach to estimate the genetic differentiation between populations. The conventional maximum-likelihood (ML) and pseudolikelihood (PL) methods that use sample counts of alleles may cause severe underestimations of FST, which means overestimations of θ = 4Nm, when the number of sampling localities is small. To reduce such bias in the estimation of genetic differentiation, we propose an IL method in which the mean allele frequencies over populations are regarded as nuisance parameters and are eliminated by integration. To maximize the IL function, we have developed two algorithms, a Monte Carlo EM algorithm and a Laplace approximation. Our simulation studies show that the method proposed here outperforms the conventional ML and PL methods in terms of unbiasedness and precision. The IL method was applied to real data for Pacific herring and African elephants.

Effect of surfacing patterns on abundance estimates of long-diving animals

Population sizes of long-diving marine mammals can be estimated with minimal bias using line transect sampling techniques in conjunction with data on surfacing/diving, even though the detection probability on the trackline is considerably less than 1. Using a simulation, it was investigated whether population sizes can be accurately estimated when only the mean cue production rate, without information on surfacing/diving patterns, is available. In addition, a new model that incorporates information on surfacing/diving patterns into the estimation procedure was developed. The simulation showed that the new model can provide less biased abundance estimates, whereas neglecting surfacing/diving patterns can result in serious underestimates of abundance, in particular for longdiving animals.

Simultaneous Estimation of Mixing Rates and Genetic Drift under Successive Sampling of Genetic Markers with Application to the Mud Crab (Scylla Paramamosain) in Japan

In stock enhancement programs, it is important to assess mixing rates of released individuals in stocks. For this purpose, genetic stock identification has been applied. The allele frequencies in a composite population are expressed as a mixture of the allele frequencies in the natural and released populations. The estimation of mixing rates is possible, under successive sampling from the composite population, on the basis of temporal changes in allele frequencies. The allele frequencies in the natural population may be estimated from those of the composite population in the preceding year. However, it should be noted that these frequencies can vary between generations due to genetic drift. In this article, we develop a new method for simultaneous estimation of mixing rates and genetic drift in a stock enhancement program. Numerical simulation shows that our procedure estimates the mixing rate with little bias. Although the genetic drift is underestimated when the amount of information is small, reduction of the bias is possible by analyzing multiple unlinked loci. The method was applied to real data on mud crab stocking, and the result showed a yearly variation in the mixing rate.

Spatial and temporal migration modeling for stock of Pacific saury Cololabis saira (Brevoort), incorporating effect of sea surface temperature

A model is proposed that expresses the spatial and temporal migration pattern for stock of Pacific saury Cololabis saira (Brevoort), in order to investigate the effect of sea surface temperature (SST) on migration rates. Two factors are considered: (i) Saury emigrate to waters of an optimal SST zone; and (ii) saury immigrate from water zone that is extremely cold for saury. Parameters of migration and initial levels of stock are estimated with a maximum likelihood method based on catch per unit effort (CPUE) data for 1995–2001. The best model was selected using Akaike’s information criteria. The results suggested that the emigration rate to southern adjacent regions is dependent on the coverage proportion of their waters under some threshold temperatures; 20°C to Doutou and Sanriku, 23°C to Joban and Izu.

Modelling the contact probability and size-selectivity of toothed dredges

To estimate fishing gear selectivity of clam dredges from data of paired-gear tests in the SELECT analysis process, this paper presents a statistical model of the probability of a clam coming into contact with the dredge teeth and size-selectivity of the control gear. The net-mouth available selectivity is defined as the product of the probability of a clam contacting the dredge teeth and size-selectivity induced by tooth spacing. The model based on the SELECT analysis was tested by using data generated by virtual paired-gear test in which the control dredge of the smallest tooth spacing is assumed to be size-selective. No clear difference in shell length distribution between dredges of different tooth spacings was found in the simulation when the contact probability was small. The plots of proportion of clams caught in the test dredge to the total catch number of clams were U-shaped, and the model fitted the data well. For each simulation consisting of 500 replications, the sample mean and mean square error of each parameter were obtained to evaluate the performance of estimation by comparing with the true value. Parameters were properly estimated with the model.

A resource selection model for analyzing pseudoreplicated data due to grouping behavior of animals

Quantifying resource selection is of primary interest in animal ecology. Many analyses of resource selection assume spatial and temporal independence of the sampling unit. Autocorrelation between observations, which is a general property of ecological variables, causes difficulties for most standard statistical procedures of resource selection because autocorrelated data violate the assumption of independence. To overcome this problem, we develop a mixed-effects model to estimate resource selection functions from data that are autocorrelated because of unobserved grouping behavior by animals. In the application of the expectation-maximization (EM) algorithm, the computation of the conditional expectation of the complete-data log-likelihood function does not have a closed-form solution requiring numerical integration. A Monte Carlo EM algorithm with Gibbs sampling can be used effectively in such situations to find exact maximum likelihood estimates. We propose a simple automated Monte Carlo EM algorithm with multiple sequences in which the Monte Carlo sample size is increased when the EM step is swamped by Monte Carlo errors.We demonstrate that the model can detect inherent autocorrelation and provide reasonable variance estimates when applied to nocturnal bird migration data. This approach could also be applied to ecological processes with various types of spatially and temporally autocorrelated data, circumventing serious problems caused by dangerous pseudoreplication.

Size at maturity of fluvial white-spotted charr, Salvelinus leucomaenis, around the Lake Biwa water system varies with habitat size

Size at maturity of fluvial white-spotted charr, Salvelinus leucomaenis, was studied in small headwater tributaries of nine rivers around the Lake Biwa water system, Japan. Threshold size at maturity in both sexes showed significant positive relationships with water discharge, indicating that smaller threshold sizes at maturity of fluvial white-spotted charr occurred in smaller habitats. These results provide a link between size at maturity and habitat size and have important implications for the management of both habitats and white-spotted charr populations.