Development of Genomic Resources for Pacific Herring through Targeted Transcriptome Pyrosequencing

Pacific herring (Clupea pallasii) support commercially and culturally important fisheries but have experienced significant additional pressure from a variety of anthropogenic and environmental sources. In order to provide genomic resources to facilitate organismal and population level research, high-throughput pyrosequencing (Roche 454) was carried out on transcriptome libraries from liver and testes samples taken in Prince William Sound, the Bering Sea, and the Gulf of Alaska. Over 40,000 contigs were identified with an average length of 728 bp. We describe an annotated transcriptome as well as a workflow for single nucleotide polymorphism (SNP) discovery and validation. A subset of 96 candidate SNPs chosen from 10,933 potential SNPs, were tested using a combination of Sanger sequencing and high-resolution melt-curve analysis. Five SNPs supported between-ocean-basin differentiation, while one SNP associated with immune function provided high differentiation between Prince William Sound and Kodiak Island within the Gulf of Alaska. These genomic resources provide a basis for environmental physiology studies and opportunities for marker development and subsequent population structure analysis

Richards growth model and viability indicators for populations subject to interventions

In this work we study the problem of modeling identification of a population employing a discrete dynamic model based on the Richards growth model. The population is subjected to interventions due to consumption, such as hunting or farming animals. The model identification allows us to estimate the probability or the average time for a population number to reach a certain level. The parameter inference for these models are obtained with the use of the likelihood profile technique as developed in this paper. The identification method here developed can be applied to evaluate the productivity of animal husbandry or to evaluate the risk of extinction of autochthon populations. It is applied to data of the Brazilian beef cattle herd population, and the the population number to reach a certain goal level is investigated.<br>Neste trabalho estudamos o problema de identificação do modelo de uma população utilizando um modelo dinâmico discreto baseado no modelo de crescimento de Richards. A população é submetida a intervenções devido ao consumo, como no caso de caça ou na criação de animais. A identificação do modelo permite-nos estimar a probabilidade ou o tempo médio de ocorrência para que se atinja um certo número populacional. A inferência paramétrica dos modelos é obtida através da técnica de perfil de máxima verossimilhança como desenvolvida neste trabalho. O método de identificação desenvolvido pode ser aplicado para avaliar a produtividade de criação animal ou o risco de extinção de uma população autóctone. Ele foi aplicado aos dados da população global de gado de corte bovino brasileiro, e é utilizado na investigação de a população atingir um certo número desejado de cabeças