A new data source for fisheries resource assessment: genetic estimates of the effective number of spawners. Final Report to the Fisheries Research and Development Corporation.

The development of innovative methods of stock assessment is a priority for State and Commonwealth fisheries agencies. It is driven by the need to facilitate sustainable exploitation of naturally occurring fisheries resources for the current and future economic, social and environmental well being of Australia. This project was initiated in this context and took advantage of considerable recent achievements in genomics that are shaping our comprehension of the DNA of humans and animals. The basic idea behind this project was that genetic estimates of effective population size, which can be made from empirical measurements of genetic drift, were equivalent to estimates of the successful number of spawners that is an important parameter in process of fisheries stock assessment. The broad objectives of this study were to 1. Critically evaluate a variety of mathematical methods of calculating effective spawner numbers (Ne) by a. conducting comprehensive computer simulations, and by b. analysis of empirical data collected from the Moreton Bay population of tiger prawns (P. esculentus). 2. Lay the groundwork for the application of the technology in the northern prawn fishery (NPF). 3. Produce software for the calculation of Ne, and to make it widely available. The project pulled together a range of mathematical models for estimating current effective population size from diverse sources. Some of them had been recently implemented with the latest statistical methods (eg. Bayesian framework Berthier, Beaumont et al. 2002), while others had lower profiles (eg. Pudovkin, Zaykin et al. 1996; Rousset and Raymond 1995). Computer code and later software with a user-friendly interface (NeEstimator) was produced to implement the methods. This was used as a basis for simulation experiments to evaluate the performance of the methods with an individual-based model of a prawn population. Following the guidelines suggested by computer simulations, the tiger prawn population in Moreton Bay (south-east Queensland) was sampled for genetic analysis with eight microsatellite loci in three successive spring spawning seasons in 2001, 2002 and 2003. As predicted by the simulations, the estimates had non-infinite upper confidence limits, which is a major achievement for the application of the method to a naturally-occurring, short generation, highly fecund invertebrate species. The genetic estimate of the number of successful spawners was around 1000 individuals in two consecutive years. This contrasts with about 500,000 prawns participating in spawning. It is not possible to distinguish successful from non-successful spawners so we suggest a high level of protection for the entire spawning population. We interpret the difference in numbers between successful and non-successful spawners as a large variation in the number of offspring per family that survive – a large number of families have no surviving offspring, while a few have a large number. We explored various ways in which Ne can be useful in fisheries management. It can be a surrogate for spawning population size, assuming the ratio between Ne and spawning population size has been previously calculated for that species. Alternatively, it can be a surrogate for recruitment, again assuming that the ratio between Ne and recruitment has been previously determined. The number of species that can be analysed in this way, however, is likely to be small because of species-specific life history requirements that need to be satisfied for accuracy. The most universal approach would be to integrate Ne with spawning stock-recruitment models, so that these models are more accurate when applied to fisheries populations. A pathway to achieve this was established in this project, which we predict will significantly improve fisheries sustainability in the future. Regardless of the success of integrating Ne into spawning stock-recruitment models, Ne could be used as a fisheries monitoring tool. Declines in spawning stock size or increases in natural or harvest mortality would be reflected by a decline in Ne. This would be good for data-poor fisheries and provides fishery independent information, however, we suggest a species-by-species approach. Some species may be too numerous or experiencing too much migration for the method to work. During the project two important theoretical studies of the simultaneous estimation of effective population size and migration were published (Vitalis and Couvet 2001b; Wang and Whitlock 2003). These methods, combined with collection of preliminary genetic data from the tiger prawn population in southern Gulf of Carpentaria population and a computer simulation study that evaluated the effect of differing reproductive strategies on genetic estimates, suggest that this technology could make an important contribution to the stock assessment process in the northern prawn fishery (NPF). Advances in the genomics world are rapid and already a cheaper, more reliable substitute for microsatellite loci in this technology is available. Digital data from single nucleotide polymorphisms (SNPs) are likely to super cede ‘analogue’ microsatellite data, making it cheaper and easier to apply the method to species with large population sizes.

Influence of effective number of pulses on the morphological structure of teeth and bovine femur after femtosecond laser ablation

Femtosecond lasers have been widely used in laser surgery as an instrument for contact-free tissue removal of hard dental, restorative materials, and osseous tissues, complementing conventional drilling or cutting tools. In order to obtain a laser system that provides an ablation efficiency comparable to mechanical instruments, the laser pulse rate must be maximal without causing thermal damage. The aim of this study was to compare the different morphological characteristics of the hard tissue after exposure to lasers operating in the femtosecond pulse regime. Two different kinds of samples were irradiated: dentin from human extracted teeth and bovine femur samples. Different procedures were applied, while paying special care to preserving the structures. The incubation factor S was calculated to be 0.788 +/- 0.004 for the bovine femur bone. These results indicate that the incubation effect is still substantial during the femtosecond laser ablation of hard tissues. The plasma-induced ablation has reduced side effects, i.e., we observe less thermal and mechanical damage when using a superficial femtosecond laser irradiation close to the threshold conditions. In the femtosecond regime, the morphology characteristics of the cavity were strongly influenced by the change of the effective number of pulses. (C) 2012 Society of Photo-Optical Instrumentation Engineers (SPIE). [DOI: 10.1117/1.JBO.17.4.048001]

Effective number of accessed nodes in complex networks

The measurement called accessibility has been proposed as a means to quantify the efficiency of the communication between nodes in complex networks. This article reports results regarding the properties of accessibility, including its relationship with the average minimal time to visit all nodes reachable after h steps along a random walk starting from a source, as well as the number of nodes that are visited after a finite period of time. We characterize the relationship between accessibility and the average number of walks required in order to visit all reachable nodes (the exploration time), conjecture that the maximum accessibility implies the minimal exploration time, and confirm the relationship between the accessibility values and the number of nodes visited after a basic time unit. The latter relationship is investigated with respect to three types of dynamics: traditional random walks, self-avoiding random walks, and preferential random walks.

Robust Parametric Estimation of Branching Processes with a Random Number of Ancestors

2000 Mathematics Subject Classification: 60J80.

Parametric Estimation in Branching Processes with an Increasing Random Number of Ancestors

2000 Mathematics Subject Classification: 60J80, 62M05

Population structure and inbreeding effects on growth traits of Santa Ines sheep in Brazil

The aim of this study was to describe the population structure, inbreeding and to quantify their effect for different weights, of Santa Ines sheep. For this reason, 6490 data of production and 17,097 animals in the pedigree data set were utilized to evaluate birth weight (BW), weight at 60 days (W60) and weight at 180 days (W180). The genetic structure analysis of the population was realized by the software ENDOG (v.4.6.), resulting in some level of inbreeding for 21.72% of the animals in the pedigree data, being 41.02% the maximum value, and average of 10.74% for the inbred individuals. The population average inbreeding was 2.33% and the average relatedness was 0.73%. The effective number of ancestors was 156 animals and the effective number of founders was 211 individuals. A significant depressive effect of the inbreeding can be verified for all traits. The monitored parameters related with the genetic variability on this population must be constant in order to prevent the decrease in the genetic progress. The utilization of a program for directed mating in the present flock is an appropriate alternative to keep the level of inbreeding under control. (C) 2010 Elsevier B.V. All rights reserved.

Electoral institutions,cleavage structures,and the number of parties

Theory: A classic question in political science concems ",hat deteImines the number of parties that compete in a given polity. Broadly speaking, there are two approaches to answering this question, one that emphasizes the role of electorallaws in structuring coalitional incentives, another that emphasizes the importance of pre-existing social cleavages. In tbis paper, we view the number of parties as a product of the interaction between these two forces, following Powell (1982) and Ordeshook and Shvetsova (1994). Hypotheses: The effective number of parties in a polity should be a multiplicative rather than an additive function ofthe peImissiveness ofthe electoral system and the heterogeneity ofthe society. Methods: Multiple regression on cross-sectional aggregate electoral statistics. Unlike previous studies, we (1) do not confine attention to developed democracies; (2) explicitly control for the influence of presidential elections, taking account of whether they are concurrent or nonconcurrent, and ofthe effective number ofpresidential candidates; and (3) also control for the presence and operation of upper tiers in legislative elections. Results: The hypothesis is confiImed, both as regards the number of legislative and the number of presidential parties .

Population structure and genetic variability in the Murrah dairy breed of water buffalo in Brazil accessed via pedigree analysis

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

History, structure, and genetic diversity of Brazilian Gir cattle

The Gir cattle breed (Bos indicus) is an important genetic resource for milk production throughout the tropics. The small number of Gir animals introduced in Brazil, rapid dissemination of this breed recently, and the intensification of selection practices could contribute to increase of inbreeding level and reduce genetic diversity in this population. The population was analyzed in terms of pedigree completeness level, inbreeding coefficient, coancestry, generation interval, effective population size, effective number of founders and ancestors, among others. Despite the low mean inbreeding (around 2%), minor problems were identified in the population structure of the Brazilian Gir cattle, e.g., trend of narrower bottlenecks in the pedigree in recent years. The effective population sizes based on inbreeding (94) or coancestry (165.9) as well as the effective number of ancestors (76) and founders (143) were relativity high. The major subdivision of the Gir breed was observed between 1993 and 2002 (dairy and dual-purpose herds, wide use of within-herd matings). In this period the level of inbreeding remained at a higher level, there was a small increase in coancestry and the number of equivalent subpopulations was approximately 6. After 2002, there was genetic exchange between subpopulations, reduction in the average inbreeding, pronounced increase in the average coancestry, and the number of equivalent subpopulations was about 2. Furthermore, it was found that the mean generation interval of the population tended to increase in recent years (around 9 years). About 23% of genetic diversity has been lost since the first generation of founders. Based on the effective population size, number of equivalent subpopulations, inbreeding, coancestry, and loss of genetic diversity, the Gir population is still highly structured, but there is ample room for artificial selection. The results regarding the effective number of founders and ancestors in the present population demonstrate the existence of bottlenecks in the pedigree and indicate the need for population structure monitoring. Nevertheless, the Brazilian Gir breed can perfectly face a breeding program with high selection intensity. (C) 2014 Elsevier B.V. All rights reserved.

Variabilidade genética da raça Brahman no Brasil detectada por meio de análise de pedigree

O objetivo deste trabalho foi analisar a variabilidade genética da raça Brahman no Brasil, por meio da análise de 15.851 pedigrees. O arquivo de dados foi dividido em dois períodos: 1998-2001 e 2002-2005. A variabilidade genética foi avaliada por parâmetros baseados na probabilidade de origem do gene: número efetivo de ancestrais, número efetivo de fundadores, número efetivo de genomas remanescentes e coeficientes de parentesco e de endogamia. Os valores encontrados quanto ao número de fundadores mostraram que a população está em expansão, embora o número efetivo de fundadores tenha diminuído de um período para outro. Os resultados foram diferentes em relação ao número de ancestrais e genomas remanescentes, que apresentaram crescimento de 23% nos períodos avaliados. O coeficiente de endogamia diminuiu nos períodos estudados, porém o coeficiente de parentesco inter se cresceu. Poucos ancestrais apresentaram grande contribuição genética para a população, o que evidencia a utilização de poucos indivíduos na reprodução. A raça Brahman, no Brasil, encontra-se em expansão, caracterizada pela diminuição do coeficiente de endogamia e aumento nos números efetivos de fundadores e de genótipos remanescentes. Entretanto, a variabilidade genética da raça mostra aumento do parentesco inter se e grande concentração do patrimônio genético de poucos indivíduos na população.

Genetic variability in Mediterranean buffalos evaluated by pedigree analysis

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Análises quantitativas aplicadas à seleção e acasalamento de búfalos na Amazônia Oriental

O trabalho aplica estudos de genética quantitativa aos registros de búfalos do Estado do Pará, gerando respostas auxiliares aos criadores para a seleção e acasalamento dos animais. A análise de pedigree para estudo da variabilidade genética nos rebanhos participantes do Programa de Melhoramento Genético foi estimada por meio dos cálculos dos parâmetros baseados na probabilidade de origem de gene, coeficiente de endogamia, parentesco e intervalo médio entre gerações, pelo software PEDIG®; do número efetivo de fundadores (Nfun), número efetivo de ancestrais (Na) e intervalo de gerações pelo software PROB_ORIG.exe presente no pacote PEDIG®; do número efetivo de genomas remanescentes (Ng), calculado pelo software SEGREG.exe. Foram calculadas as estatísticas descritivas, a análise de variância e realizado o teste de Normalidade de Shapiro-Wilk por meio do pacote estatístico Statistical Analisys System. As estimativas de herdabilidade para a característica Peso ao Nascer (PN) foram obtidas por meio de inferência Bayesiana pelo programa GIBBS2F90.exe. Os valores genéticos foram obtidos por meio do programa BLUPF90.exe e a regressão das Diferenças Esperadas na Progênie sobre o ano de nascimento foi realizada pelo Excel for Windows para obtenção da tendência genética do PN. O Nfun foi igual a 28,6, o Na igual a 22,8, o Ng igual a 11,2, a razão Nfun/Na foi 1,25, indicando a diminuição do número de reprodutores ao longo dos períodos e a razão Ng/Nfun foi de 0,39. Apesar do intervalo de gerações de 12,5 anos, o número efetivo de gerações foi próximo a cinco. O número total de animais estudados considerados endogâmicos foi 33,4%, sendo a máxima encontrada de 40,8%, a média da endogamia entre os animais endogâmicos foi 10,4%, e o valor médio da endogamia no arquivo total foi 3,5%. O PN de bezerros bubalinos apresentou média e desvio padrão de 36,6 ± 4,7 kg. A característica PN não apresentou distribuição Normal, com valor de W=0,976271 e P

Análise de pedigree aplicada a búfalos (Bubalu bubalis kerebao) em conservação na Amazônia Oriental

O trabalho analisa a genética de bubalinos da raça Carabao em conservação, provenientes dos rebanhos das fazendas Campo Experimental do Baixo Amazonas (CEBA) e do Banco de Germoplasma Animal do Marajó (BAGAM). O arquivo contou com 445 informações de parentesco (215 machos e 230 fêmeas) com nascimentos entre maio de 1976 e setembro de 2008. Para estudo de pedigree e determinação dos parâmetros genéticos, a média de filhos/mãe foi de 2,7, sendo 131 mães e cinco pais diferentes. O número de fundadores foi igual a 32 animais, o número efetivo de fundadores (Nfun) igual a 5,3 indivíduos; número efetivo de ancestrais (Na) igual a 4,73 animais; o número efetivo de genomas remanescentes (Ng) igual a 3,79 indivíduos; a razão Nfun/Na foi de 1,12 e o indicativo do processo de deriva genética (Ng/Nfun) foi 0,66. Constatou- se que 11 animais, nascidos entre 1987 e 2000, responderam por 84% da contribuição genética do rebanho, sendo que apenas um reprodutor responsável por 42% da contribuição genética. O intervalo de geração médio ficou próximo a oito anos. O número de animais endogâmicos, os coeficientes médios de endogamia (F) da população e entre os endogâmicos, por geração foram 69, 1,85% e 11,95%, respectivamente, sendo os animais endogâmicos agrupados, em sua maioria, na classe de 10 a 15% de coeficiente individual de endogamia. Estes resultados apontam provável efeito gargalo e deriva genética dessa população por perda de alelos pelo pequeno número de indivíduos usados nos acasalamentos, e aumento da endogamia. A adoção de nova estratégia de acasalamento e a busca de possíveis reprodutores 2n = 48, para serem utilizados no rebanho, possibilitaria a redução da perda de variabilidade genética do rebanho Carabao.

Análise de pedigree e estimativas de parâmetros genéticos para características reprodutivas em bovinos da raça Brahman

Pós-graduação em Ciência e Tecnologia Animal - FEIS