Further progress on application of ADAPT-VPA to Antarctic minke whales

The ADAPT-VPA assessment methodology originally developed by Butterworth et al. (1999) has been appreciably advanced by taking into account various comments made during a series of IWC-SC meetings and is applied here to abundance estimates (from both IDCR/SOWER and JARPA surveys) as well as catch at age data (both commercial and scientific) for the I and P-stocks of Antarctic minke whales. The improvements to the methodology allow account to be taken of various further aspects, primarily: 1) inter-annual differences in the distribution of the population between different management Areas, 2) a stock-recruitment relationship, 3) the effects of possible ageing-error, and 4) the effects of possible change in age-at-sexual maturity over time as indicated by analyses of readings of transition phases in ear plugs. Furthermore sensitivities to various functional forms for selectivity and natural mortality with age are explored. The general pattern shown by analysis for both stocks is of a minke whale abundance trend that increased over the middle decades of the 20th Century to peak at about 1970, and then stabilized or declined somewhat for the next three decades. The recruitment trend is similar, though with its peak slightly earlier. The annual natural mortality rate, M, is estimated to be 0.056 with a CV of 0.16 for the I-stock, and 0.069 with a CV of 0.15 for the P-stock for the “Reference case” assessments. When only the JARPA abundance estimates are used for tuning, M is estimated as 0.037 and 0.060 for the I- and P-stocks, respectively. The estimation of M is fairly robust to the various assumptions of the model. This analysis is considered preliminary, as conclusions relating to estimates of M and trends in abundance and recruitment obtained using this approach await further revisions of 1) abundance estimates obtained from IDCR and JARPA surveys, and 2) error-models for the catch-at-age data, particularly those obtained from the commercial harvests

An estmation of seabird abundance and biomass in the Ross Sea based on ecological functions

第3回極域科学シンポジウム/第34回極域生物シンポジウム 11月26日（月） 統計数理研究所 ３階セミナー

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

<p>Abstract</p> <p>Background</p> <p>Higher 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 (<it>Marsupenaeus japonicus</it>), 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.</p> <p>Results</p> <p>Mj024A04 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 <it>Daphnia </it>and <it>Drosophila </it>suggests the uniqueness of these fragments in kuruma shrimp from current arthropod genome sequences.</p> <p>Conclusions</p> <p>Our 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.</p

A cookbook for using model diagnostics in integrated stock assessments

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Review of potential line-transect methodologies for estimating abundance of dolphin stocks in the eastern tropical Pacific

A twelve-year hiatus in fishery-independent marine mammal surveys in the eastern tropical Pacific Ocean (ETP), combined with a mandate to monitor dolphin stock status under international agreements and the need for reliable stock status information to set dolphin bycatch limits in the tuna purse-seine fishery, has renewed debate about how best to assess and monitor ETP dolphin stock status. The high cost of replicating previous ship-based surveys has intensified this debate. In this review, transect methods for estimating animal abundance from dedicated research surveys are considered, with a focus on both contemporary and potential methods suitable for surveying large areas for dolphin species that can form large, multi-species aggregations. Covered in this review are potential improvements to the previous ship-based survey methodology, other ship-based methods, alternative approaches based on high-resolution imagery and passive acoustics, and combinations of ship-based and alternative approaches. It is concluded that for immediate management needs, ship-based surveys, with some suggested modifications to improve precision, are the only reliable option despite their high cost. However, it is recommended that a top research priority should be development of composite methods. Pilot studies on the use of high-resolution imagery and passive acoustics for development of indices of relative abundance to be used in composite methods should be part of any future ship-based survey efforts

Application of ADAPT-VPA to Antarctic minke whales in the JARPA research area

The ADAPT-VPA assessment methodology originally developed by Butterworth et al. (1999) has been greatly improved by taking into account various comments made during a series of IWC-SC meetings and is applied here to abundance estimates (from both IDCR/SOWER and JARPA surveys) as well as catch at age data (both commercial and scientific) for the I and P-stocks of Antarctic minke whales. The improvements to the methodology allow account to be taken of various further aspects, primarily: 1) inter-annual differences in the distribution of the population between different management Areas, 2) a stock-recruitment relationship, and 3) the effects of possible ageing-error. Furthermore sensitivities to various functional forms for selectivity and natural mortality with age are explored. The general pattern shown by the results for both stocks is of a minke whale abundance trend that increased over the middle decades of the 20th Century to peak at about 1970, and then stabilized or declined somewhat for the next three decades. The recruitment trend is similar, though with its peak slightly earlier. The annual natural mortality rate, M, is estimated to be 0.056 with a CV of 0.16 for the I-stock, and 0.069 with a CV of 0.15 for the P-stock for the “Reference case” assessments. When only the JARPA abundance estimates are used for tuning, M is estimated as 0.038 and 0.060 for the I- and P-stocks, respectively. The estimation of M is fairly robust to the various assumptions of the model. The CVs of these M estimates for the “Reference case” assessments, when compared with those of typically 0.35 for the Areaspecific assessments of Butterworth et al. (1999) which were based on fewer data, indicate an improvement in the precision of these estimates due to the accumulation of data over the long-term of the JARPA surveys. The fits of the stock-recruitment model generally require a carrying capacity for minke whales that first increased and then stabilized or declined somewhat during the last century, and suggest MSYR(1+) values in the 4-6% range. The improved precision in the estimation of M may contribute in the improvement of management and assessment of this species on a stock-specific basis, since it can reduce the uncertainty concerning the value of M and can provide an improved prior distribution for MSYR. The latter in particular, in the context of providing a measure of the productivity of which the species is capable, is essential information for effective RMP implementation through reduction of the range of plausible scenarios which need to be considered in Implementation Simulation Trials.http://www.mth.uct.ac.za/maram/pub/2006/SC_D06_J14.pd

拡張されたConsecutive-k-out-of-n:Fシステムの寿命分布

要旨なし原著論

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. FST's 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 FST's. 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 FST's 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)