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.

Comparing family functionality perception between non-Aymara and indigenous Aymara families in northern Chile

We compared perception of family functioning in a sample (N = 1,496) of Aymara and non-Aymara parents and children living in Arica, Chile. The children were aged from 9 to 15 years and were recruited from the 5th to 8th grades of 9 elementary schools (4 public, 5 government-subsidized private schools) serving lower socioeconomic areas. Participants completed the Family Functioning Test (FF-SIL), which consists of 14 events or characteristics that may occur in a family. The results showed that parents and children from the Aymara group recorded lower scores for their perception of family functioning than did the non-Aymara group. Addressing this issue may be important in the prevention of psychological problems in these families.

Poor adoption of ley-pastures in south-west Queensland: biophysical, economic and social constraints.

The present review identifies various constraints relating to poor adoption of ley-pastures in south-west Queensland, and suggests changes in research, development and extension efforts for improved adoption. The constraints include biophysical, economic and social constraints. In terms of biophysical constraints, first, shallower soil profiles with subsoil constraints (salt and sodicity), unpredictable rainfall, drier conditions with higher soil temperature and evaporative demand in summer, and frost and subzero temperature in winter, frequently result in a failure of established, or establishing, pastures. Second, there are limited options for legumes in a ley-pasture, with the legumes currently being mostly winter-active legumes such as lucerne and medics. Winter-active legumes are ineffective in improving soil conditions in a region with summer-dominant rainfall. Third, most grain growers are reluctant to include grasses in their ley-pasture mix, which can be uneconomical for various reasons, including nitrogen immobilisation, carryover of cereal diseases and depressed yields of the following cereal crops. Fourth, a severe depletion of soil water following perennial ley-pastures (grass + legumes or lucerne) can reduce the yields of subsequent crops for several seasons, and the practice of longer fallows to increase soil water storage may be uneconomical and damaging to the environment. Economic assessments of integrating medium- to long-term ley-pastures into cropping regions are generally less attractive because of reduced capital flow, increased capital investment, economic loss associated with establishment and termination phases of ley-pastures, and lost opportunities for cropping in a favourable season. Income from livestock on ley-pastures and soil productivity gains to subsequent crops in rotation may not be comparable to cropping when grain prices are high. However, the economic benefits of ley-pastures may be underestimated, because of unaccounted environmental benefits such as enhanced water use, and reduced soil erosion from summer-dominant rainfall, and therefore, this requires further investigation. In terms of social constraints, the risk of poor and unreliable establishment and persistence, uncertainties in economic and environmental benefits, the complicated process of changing from crop to ley-pastures and vice versa, and the additional labour and management requirements of livestock, present growers socially unattractive and complex decision-making processes for considering adoption of an existing medium- to long-term ley-pasture technology. It is essential that research, development and extension efforts should consider that new ley-pasture options, such as incorporation of a short-term summer forage legume, need to be less risky in establishment, productive in a region with prevailing biophysical constraints, economically viable, less complex and highly flexible in the change-over processes, and socially attractive to growers for adoption in south-west Queensland.

Ongoing poor management of medicines in the older-aged living independently in a rental retirement village

Background In a low socioeconomic status, small, rental retirement village, we have shown the older-aged managed their medicines poorly [1]. Objective As the number of participants was only 25, and the population in the rental retirement village turns over regularly; our objective was to determine whether the findings were consistent and ongoing. Methods We returned to the rental retirement villages after one and two years, and reassessed the management of medicines, using the same semi-structured interview method. Main outcome measure The main outcome measure was the perception of present and ongoing adherence. Results Although similar numbers (23-25) participated in the studies in 2011-2013, the actual participants changed with only 3 being interviewed on 3 occasions. Nevertheless, the findings over the 3 years were similar: less than 50% of the participants were adherent at the time of the study and unlikely to have problems in the next 6-12 months; only 50% had a good knowledge of their illnesses. Conclusions The management of medicines by the older-aged living in a low socioeconomic, rental retirement village is poor, and this finding is ongoing and consistent. This supports the need for extra assistance and resources for the older-aged, living in rental retirement villages, to manage their medicines.

Portrait of Molling and Sanger (Loewy) families on vacation; Marienbad Portraits Family

Therese Molling (1890-1981) is in back row in white dress, to her left is her mother Henny Molling nee Meyerhof (1864-1934), her husband (and Therese's father) Adolf Molling (1865-1921) is posing on the grass in front.

Family portrait at double wedding ceremony of the Heimann and Rosenfelder families Portraits; Family

Double Wedding Ceremony Heimann-Rosenfelder August 17, 1909

A genome wide linkage scan for dizygotic twinning in 525 families of mothers of dizygotic twins

BACKGROUND: The tendency to conceive dizygotic (DZ) twins is a complex trait influenced by genetic and environmental factors. To search for new candidate loci for twinning, we conducted a genome-wide linkage scan in 525 families using microsatellite and single nucleotide polymorphism marker panels. METHODS AND RESULTS: Non-parametric linkage analyses, including 523 families containing a total of 1115 mothers of DZ twins (MODZT) from Australia and New Zealand (ANZ) and The Netherlands (NL), produced four linkage peaks above the threshold for suggestive linkage, including a highly suggestive peak at the extreme telomeric end of chromosome 6 with an exponential logarithm of odds \[(exp)LOD] score of 2.813 (P = 0.0002). Since the DZ twinning rate increases steeply with maternal age independent of genetic effects, we also investigated linkage including only families where at least one MODZT gave birth to her first set of twins before the age of 30. These analyses produced a maximum expLOD score of 2.718 (P = 0.0002), largely due to linkage signal from the ANZ cohort, however, ordered subset analyses indicated this result is most likely a chance finding in the combined dataset. Linkage analyses were also performed for two large DZ twinning families from the USA, one of which produced a peak on chromosome 2 in the region of two potential candidate genes. Sequencing of FSHR and FIGLA, along with INHBB in MODZTs from two large NL families with family specific linkage peaks directly over this gene, revealed a potentially functional variant in the 5' untranslated region of FSHR that segregated with the DZ twinning phenotype in the Utah family. CONCLUSION: Our data provide further evidence for complex inheritance of familial DZ twinning.

Genetic influences on handedness: data from 25,732 Australian and Dutch twin families

Handedness refers to a consistent asymmetry in skill or preferential use between the hands and is related to lateralization within the brain of other functions such as language. Previous twin studies of handedness have yielded inconsistent results resulting from a general lack of statistical power to find significant effects. Here we present analyses from a large international collaborative study of handedness (assessed by writing/drawing or self report) in Australian and Dutch twins and their siblings (54,270 individuals from 25,732 families). Maximum likelihood analyses incorporating the effects of known covariates (sex, year of birth and birth weight) revealed no evidence of hormonal transfer, mirror imaging or twin specific effects. There were also no differences in prevalence between zygosity groups or between twins and their singleton siblings. Consistent with previous meta-analyses, additive genetic effects accounted for about a quarter (23.64%) of the variance (95%CI 20.17, 27.09%) with the remainder accounted for by non-shared environmental influences. The implications of these findings for handedness both as a primary phenotype and as a covariate in linkage and association analyses are discussed.

Portrait of Molling and Sanger (Loewy) families on vacation; Marienbad Portraits Family

Therese Molling (1890-1981) is in back row in white dress, to her left is her mother Henny Molling nee Meyerhof (1864-1934), her husband (and Therese's father) Adolf Molling (1865-1921) is posing on the grass in front.

Personality, health and lifestyle in a questionnaire family study: A comparison between highly cooperative and less cooperative families

The effect of nonresponse on health and lifestyle measures has received extensive study, showing at most relatively modest effects. Nonresponse bias with respect to personality has been less thoroughly investigated. The present study uses data from responding individuals as a proxy for the missing data of their nonresponding family members to examine the presence of nonresponse bias for personality traits and disorders as well as health and lifestyle traits. We looked at the Big Five personality traits, borderline personality disorder (BPD) features, attention-deficit/hyperactivity disorder, Anger, and several measures of health (Body Mass Index, migraine) and lifestyle (smoking, alcohol use). In general, outcomes tend to be slightly more favorable for individuals from highly cooperative families compared to individuals from less cooperative families. The only significant difference was found for BPD features (p = .001). However, the absolute difference in mean scores is very small, less than 1 point for a scale ranging from 0 to 72. In conclusion, survey data on personality, health and lifestyle are relatively unbiased with respect to nonresponse.

Genomewide linkage study in 1,176 affected sister pair families identifies a significant susceptibility locus for endometriosis on chromosome 10q26

Endometriosis is a common gynecological disease that affects up to 10% of women in their reproductive years. It causes pelvic pain, severe dysmenorrhea, and subfertility. The disease is defined as the presence of tissue resembling endometrium in sites outside the uterus. Its cause remains uncertain despite >50 years of hypothesis-driven research, and thus the therapeutic options are limited. Disease predisposition is inherited as a complex genetic trait, which provides an alternative route to understanding the disease. We seek to identify susceptibility loci, using a positional-cloning approach that starts with linkage analysis to identify genomic regions likely to harbor these genes. We conducted a linkage study of 1,176 families (931 from an Australian group and 245 from a U.K. group), each with at least two members--mainly affected sister pairs--with surgically diagnosed disease. We have identified a region of significant linkage on chromosome 10q26 (maximum LOD score [MLS] of 3.09; genomewide P = .047) and another region of suggestive linkage on chromosome 20p13 (MLS = 2.09). Minor peaks (with MLS > 1.0) were found on chromosomes 2, 6, 7, 8, 12, 14, 15, and 17. This is the first report of linkage to a major locus for endometriosis. The findings will facilitate discovery of novel positional genetic variants that influence the risk of developing this debilitating disease. Greater understanding of the aberrant cellular and molecular mechanisms involved in the etiology and pathophysiology of endometriosis should lead to better diagnostic methods and targeted treatments.

Dominant negative ATM mutations in breast cancer families

BACKGROUND: The ATM gene encoding a putative protein kinase is mutated in ataxia-telangiectasia (A-T), an autosomal recessive disorder with a predisposition for cancer. Studies of A-T families suggest that female heterozygotes have an increased risk of breast cancer compared with noncarriers. However, neither linkage analyses nor mutation studies have provided supporting evidence for a role of ATM in breast cancer predisposition. Nevertheless, two recurrent ATM mutations, T7271G and IVS10-6T-->G, reportedly increase the risk of breast cancer. We examined these two ATM mutations in a population-based, case-control series of breast cancer families and multiple-case breast cancer families. METHODS: Five hundred twenty-five or 262 case patients with breast cancer and 381 or 68 control subjects, respectively, were genotyped for the T7271G and IVS10-6T-->G ATM mutations, as were index patients from 76 non-BRCA1/2 multiple-case breast cancer families. Linkage and penetrance were analyzed. ATM protein expression and kinase activity were analyzed in lymphoblastoid cell lines from mutation carriers. All statistical tests were two-sided. RESULTS: In case and control subjects unselected for family history of breast cancer, one case patient had the T7271G mutation, and none had the IVS10-6T-->G mutation. In three multiple-case families, one of these two mutations segregated with breast cancer. The estimated average penetrance of the mutations was 60% (95% confidence interval [CI] = 32% to 90%) to age 70 years, equivalent to a 15.7-fold (95% CI = 6.4-fold to 38.0-fold) increased relative risk compared with that of the general population. Expression and activity analyses of ATM in heterozygous cell lines indicated that both mutations are dominant negative. CONCLUSION: At least two ATM mutations are associated with a sufficiently high risk of breast cancer to be found in multiple-case breast cancer families. Full mutation analysis of the ATM gene in such families could help clarify the role of ATM in breast cancer susceptibility.

Choosing a fishery's governance structure using data poor methods

Multi-species fisheries are complex to manage and the ability to develop an appropriate governance structure is often seriously impeded because trading between sustainability objectives at the species level, economic objectives at the fleet level, and social objectives at the community scale, is complex. Many of these fisheries also tend to have a mix of information, with stock assessments available for some species and almost no information on other species. The fleets themselves comprise fishers from small family enterprises to large vertically integrated businesses. The Queensland trawl fishery in Australia is used as a case study for this kind of fishery. It has the added complexity that a large part of the fishery is within a World Heritage Area, the Great Barrier Reef Marine Park, which is managed by an agency of the Australian Commonwealth Government whereas the fishery itself is managed by the Queensland State Government. A stakeholder elicitation process was used to develop social, governance, economic and ecological objectives, and then weight the relative importance of these. An expert group was used to develop different governance strawmen (or management strategies) and these were assessed by a group of industry stakeholders and experts using multi-criteria decision analysis techniques against the different objectives. One strawman clearly provided the best overall set of outcomes given the multiple objectives, but was not optimal in terms of every objective, demonstrating that even the "best" strawman may be less than perfect. © 2012.